Read UCSC Xena Variant Format Data as MAF Object

read_xena_variants(path)

Arguments

path

a path to variant file.

Value

a MAF object.

Examples

# \donttest{
if (requireNamespace("UCSCXenaTools")) {
  library(UCSCXenaTools)
  options(use_hiplot = TRUE)
  example_file <- XenaGenerate(subset = XenaDatasets == "mc3/ACC_mc3.txt") %>%
    XenaQuery() %>%
    XenaDownload()
  x <- read_xena_variants(example_file$destfiles)
  x@data
  y <- sig_tally(x)
  y
}
#> Loading required namespace: UCSCXenaTools
#> =========================================================================================
#> UCSCXenaTools version 1.4.8
#> Project URL: https://github.com/ropensci/UCSCXenaTools
#> Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
#> 
#> If you use it in published research, please cite:
#> Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
#>   from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
#>   Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
#> =========================================================================================
#>                               --Enjoy it--
#> 
#> Attaching package: ‘UCSCXenaTools’
#> The following object is masked from ‘package:Biobase’:
#> 
#>     samples
#> The hiplot server may down, we will not use it for now.
#> This will check url status, please be patient.
#> All downloaded files will under directory /tmp/RtmpT86DiN.
#> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
#> Creating directories for datasets...
#> Downloading mc3/ACC_mc3.txt.gz
#>  [2024-03-13 10:46:50.128063]: Started.
#> Warning: replacing previous import ‘S4Arrays::makeNindexFromArrayViewport’ by ‘DelayedArray::makeNindexFromArrayViewport’ when loading ‘SummarizedExperiment’
#>  [2024-03-13 10:46:59.437203]: We would assume you marked all variants' position in + strand.
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:NMF’:
#> 
#>     nrun
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> 
#> Attaching package: ‘IRanges’
#> The following object is masked from ‘package:R.oo’:
#> 
#>     trim
#> The following object is masked from ‘package:purrr’:
#> 
#>     reduce
#> 
#> Attaching package: ‘XVector’
#> The following object is masked from ‘package:purrr’:
#> 
#>     compact
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> 
#> Attaching package: ‘rtracklayer’
#> The following object is masked from ‘package:BiocIO’:
#> 
#>     FileForFormat
#>  [2024-03-13 10:46:59.558154]: Reference genome loaded.
#>  [2024-03-13 10:46:59.568908]: Variants from MAF object queried.
#>  [2024-03-13 10:46:59.575953]: Chromosome names checked.
#>  [2024-03-13 10:46:59.587384]: Sex chromosomes properly handled.
#>  [2024-03-13 10:46:59.590183]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept.
#>  [2024-03-13 10:46:59.613479]: Variant start and end position checked.
#>  [2024-03-13 10:46:59.619054]: Variant data for matrix generation preprocessed.
#>  [2024-03-13 10:46:59.621973]: SBS matrix generation - start.
#>  [2024-03-13 10:46:59.625231]: Extracting 5' and 3' adjacent bases.
#>  [2024-03-13 10:47:00.208662]: Extracting +/- 20bp around mutated bases for background C>T estimation.
#>  [2024-03-13 10:47:00.693055]: Estimating APOBEC enrichment scores.
#>  [2024-03-13 10:47:00.695056]: Performing one-way Fisher's test for APOBEC enrichment.
#>  [2024-03-13 10:47:00.747178]: APOBEC related mutations are enriched in 19.565% of samples (APOBEC enrichment score > 2; 18 of 92 samples)
#>  [2024-03-13 10:47:00.750856]: Creating SBS sample-by-component matrices.
#>  [2024-03-13 10:47:00.756007]: SBS-6 matrix created.
#>  [2024-03-13 10:47:00.761486]: SBS-96 matrix created.
#>  [2024-03-13 10:47:00.776806]: SBS-1536 matrix created.
#>  [2024-03-13 10:47:00.778538]: Return SBS-96 as major matrix.
#>  [2024-03-13 10:47:00.780903]: Done.
#>  [2024-03-13 10:47:00.782426]: 10.654 secs elapsed.
#> $nmf_matrix
#>                 A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       1       1       0       1
#> TCGA-OR-A5J2-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       2       2       0       4       1       1       0       1
#> TCGA-OR-A5J5-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5J6-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5J7-01       1       0       0       0       1       1       0       0
#> TCGA-OR-A5J8-01       4       1       1       1       0       2       2       0
#> TCGA-OR-A5J9-01       0       0       0       1       0       2       0       0
#> TCGA-OR-A5JA-01      12       8       0       6       0       0       0       1
#> TCGA-OR-A5JB-01      10       9       4       6       3       2       2       2
#> TCGA-OR-A5JC-01       0       0       1       1       0       0       0       1
#> TCGA-OR-A5JD-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JE-01       0       1       0       0       1       1       1       0
#> TCGA-OR-A5JF-01       2       2       0       2       1       1       0       0
#> TCGA-OR-A5JG-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       1       1       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5JM-01       0       0       1       0       2       0       1       0
#> TCGA-OR-A5JO-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       1       0       1       0       1       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5JS-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5JT-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       0       0       0       2       0       0
#> TCGA-OR-A5JV-01       0       0       1       0       1       3       0       1
#> TCGA-OR-A5JW-01       1       0       0       2       0       0       0       0
#> TCGA-OR-A5JX-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5JY-01       0       2       0       0       0       0       0       1
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       3       1       1       0       0       0       1       0
#> TCGA-OR-A5K1-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5K2-01       1       0       1       1       0       0       1       1
#> TCGA-OR-A5K3-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5K4-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5K5-01       5       1       2       1       0       0       0       1
#> TCGA-OR-A5K6-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K8-01       1       1       0       1       2       0       0       0
#> TCGA-OR-A5K9-01       1       4       2       1       0       1       2       1
#> TCGA-OR-A5KB-01      69      64      56      59      24      13       9      10
#> TCGA-OR-A5KO-01       0       0       0       1       2       0       0       0
#> TCGA-OR-A5KP-01       2       1       1       0       0       0       1       0
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5KT-01       0       0       1       0       0       2       0       1
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       0       0       0       0       0       0       1       2
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       1       1
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KZ-01       0       0       0       1       0       0       0       1
#> TCGA-OR-A5L1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L2-01       2       1       1       1       1       0       0       3
#> TCGA-OR-A5L3-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5L4-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       1       1       1       0       0       1       0
#> TCGA-OR-A5L8-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5L9-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       2       1       0       0       0       0       1       0
#> TCGA-OR-A5LC-01       2       1       0       1       0       0       0       1
#> TCGA-OR-A5LD-01       0       1       0       1       0       1       0       3
#> TCGA-OR-A5LE-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LG-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       1       0       0       0       0       1       1       0
#> TCGA-OR-A5LJ-01       4       0       0       1       2       0       0       2
#> TCGA-OR-A5LK-01       2       2       0       2       1       0       0       0
#> TCGA-OR-A5LL-01       1       0       0       0       1       0       0       0
#> TCGA-OR-A5LM-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5LN-01       1       1       0       0       1       0       0       0
#> TCGA-OR-A5LO-01       0       3       1       0       1       2       1       0
#> TCGA-OR-A5LP-01       0       1       0       0       0       0       0       2
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       0       1       0       0       1       0
#> TCGA-OU-A5PI-01       0       0       1       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       1       0       0       0       0       0       0
#> TCGA-P6-A5OG-01       5       9       6       4       2       0       1       0
#> TCGA-P6-A5OH-01       0       1       0       1       1       3       1       2
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       2       1       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       3       0       0       0       1       1       0       1
#> TCGA-PK-A5HB-01      10       6       1       6       1       5       1      11
#> TCGA-PK-A5HC-01       1       0       0       0       0       0       0       0
#>                 A[C>T]A A[C>T]C A[C>T]G A[C>T]T A[T>A]A A[T>A]C A[T>A]G A[T>A]T
#> TCGA-OR-A5J1-01       0       1       6       1       0       0       0       0
#> TCGA-OR-A5J2-01       1       1       5       0       1       0       0       0
#> TCGA-OR-A5J3-01       0       0       3       1       0       0       0       0
#> TCGA-OR-A5J4-01       3       2       3       2       0       0       1       0
#> TCGA-OR-A5J5-01       3       0     143       1       1       1       0       0
#> TCGA-OR-A5J6-01       0       0       0       0       0       0       2       0
#> TCGA-OR-A5J7-01       0       1       6       0       0       0       1       0
#> TCGA-OR-A5J8-01       2       0       2       1       1       0       0       0
#> TCGA-OR-A5J9-01       1       0       6       0       0       1       1       0
#> TCGA-OR-A5JA-01       0       1       1       0       0       0       1       0
#> TCGA-OR-A5JB-01       3       1       5       3       4       1       6       1
#> TCGA-OR-A5JC-01       0       0       4       0       0       0       0       1
#> TCGA-OR-A5JD-01       2       3       1       0       0       1       0       0
#> TCGA-OR-A5JE-01       2       0       5       2       0       0       1       0
#> TCGA-OR-A5JF-01       2       2       4       0       0       0       0       0
#> TCGA-OR-A5JG-01       1       1       2       0       0       0       0       1
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       1       0       0       1       1       0
#> TCGA-OR-A5JJ-01       1       1       0       1       0       0       0       0
#> TCGA-OR-A5JK-01       0       2       1       0       0       0       0       0
#> TCGA-OR-A5JL-01       1       0       1       0       0       0       1       0
#> TCGA-OR-A5JM-01       1       1       3       0       0       1       0       0
#> TCGA-OR-A5JO-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       6       0       0       0       0       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       1       5       0       0       0       0       0
#> TCGA-OR-A5JT-01       3       1       3       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       2       1       0       0       1       0
#> TCGA-OR-A5JV-01       0       1       1       2       0       0       1       0
#> TCGA-OR-A5JW-01       1       3       4       0       1       0       0       0
#> TCGA-OR-A5JX-01       1       0       1       1       0       0       1       0
#> TCGA-OR-A5JY-01       0       0       3       0       0       0       1       0
#> TCGA-OR-A5JZ-01       1       0       0       0       1       0       0       0
#> TCGA-OR-A5K0-01       3       0       0       1       0       0       1       0
#> TCGA-OR-A5K1-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5K2-01       0       1       2       0       0       0       0       0
#> TCGA-OR-A5K3-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       3      78       1       2       1       0       1
#> TCGA-OR-A5K5-01       3       2       6       1       0       1       0       1
#> TCGA-OR-A5K6-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5K8-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5K9-01       1       0       9       1       0       1       0       0
#> TCGA-OR-A5KB-01      25      20      17      15       7      10      17       3
#> TCGA-OR-A5KO-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KP-01       2       0       1       1       0       0       0       0
#> TCGA-OR-A5KQ-01       1       0       3       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5KT-01       0       1       0       0       1       1       0       0
#> TCGA-OR-A5KU-01       0       0       5       1       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5KW-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KZ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5L2-01       3       2      15       4       1       1       0       2
#> TCGA-OR-A5L3-01       0       1       1       0       1       0       0       0
#> TCGA-OR-A5L4-01       0       1       1       0       0       0       0       1
#> TCGA-OR-A5L5-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       0       3       1       0       0       0       1
#> TCGA-OR-A5L8-01       0       0       3       1       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5LB-01       2       3      41       2       0       1       1       2
#> TCGA-OR-A5LC-01       0       0       4       1       1       0       0       1
#> TCGA-OR-A5LD-01       2       0       3       1       0       0       0       0
#> TCGA-OR-A5LE-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5LF-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5LG-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LI-01       2       1       2       1       0       0       0       0
#> TCGA-OR-A5LJ-01       6       1     124       4       1       0       0       0
#> TCGA-OR-A5LK-01       0       0       9       0       0       1       0       0
#> TCGA-OR-A5LL-01       3       0       0       1       0       0       1       0
#> TCGA-OR-A5LM-01       0       1       3       0       1       0       0       0
#> TCGA-OR-A5LN-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5LO-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5LP-01       0       0       2       0       0       0       1       1
#> TCGA-OR-A5LR-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LS-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LT-01       1       1       3       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       0       2       0       0       0       0       0
#> TCGA-P6-A5OF-01       2       0       2       0       0       0       2       0
#> TCGA-P6-A5OG-01       3       5       5       3       0       1       1       0
#> TCGA-P6-A5OH-01       3       2       7       2       0       1       0       2
#> TCGA-PA-A5YG-01       0       0       1       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       0       0       9       1       0       2       1       0
#> TCGA-PK-A5HB-01      16      28      31      15      29      28       8       4
#> TCGA-PK-A5HC-01       0       0       2       1       0       0       0       0
#>                 A[T>C]A A[T>C]C A[T>C]G A[T>C]T A[T>G]A A[T>G]C A[T>G]G A[T>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J2-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       1       2       1       2       0       0       0       1
#> TCGA-OR-A5J5-01       1       1       3       0       0       0       0       0
#> TCGA-OR-A5J6-01       3       0       2       4       0       0       0       0
#> TCGA-OR-A5J7-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5J8-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5J9-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5JA-01       1       1       2       1       0       0       0       0
#> TCGA-OR-A5JB-01       2       2       6       1       1       0       0       0
#> TCGA-OR-A5JC-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JD-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5JE-01       0       2       0       0       0       0       0       1
#> TCGA-OR-A5JF-01       0       0       0       1       0       2       0       0
#> TCGA-OR-A5JG-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JK-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5JL-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JM-01       2       0       1       2       0       0       0       0
#> TCGA-OR-A5JO-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       2       0       1       2       0       1       0       0
#> TCGA-OR-A5JQ-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       1       3       1       0       0       0
#> TCGA-OR-A5JT-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JX-01       2       2       2       0       1       0       1       0
#> TCGA-OR-A5JY-01       1       0       2       0       0       0       0       0
#> TCGA-OR-A5JZ-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5K0-01       2       2       1       0       0       0       0       0
#> TCGA-OR-A5K1-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       1       0       0       1       0       0       1       0
#> TCGA-OR-A5K3-01       0       0       1       1       0       0       0       1
#> TCGA-OR-A5K4-01       1       0       3       0       0       0       0       1
#> TCGA-OR-A5K5-01       3       0       3       5       0       1       1       0
#> TCGA-OR-A5K6-01       1       0       3       1       0       0       0       0
#> TCGA-OR-A5K8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       0       0       2       2       1       0       0       1
#> TCGA-OR-A5KB-01      10       3      12       3       1       0       6       3
#> TCGA-OR-A5KO-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5KP-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KT-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       1       0       0       2       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KZ-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5L1-01       1       1       1       1       0       0       0       1
#> TCGA-OR-A5L2-01       2       3       0       2       0       0       0       1
#> TCGA-OR-A5L3-01       0       0       0       2       0       0       1       0
#> TCGA-OR-A5L4-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       2       2       0       0       0       0       1       0
#> TCGA-OR-A5L8-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LB-01       1       0       1       2       0       0       1       0
#> TCGA-OR-A5LC-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LD-01       1       0       1       1       1       0       0       0
#> TCGA-OR-A5LE-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5LF-01       0       1       1       2       0       0       0       0
#> TCGA-OR-A5LG-01       1       0       1       1       0       0       0       1
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       2       1       1       2       1       0       0       0
#> TCGA-OR-A5LJ-01       4       2       0       2       0       1       1       1
#> TCGA-OR-A5LK-01       0       0       3       0       0       2       0       0
#> TCGA-OR-A5LL-01       0       1       0       1       0       0       0       2
#> TCGA-OR-A5LM-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5LP-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5LS-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5LT-01       1       0       0       0       0       0       0       0
#> TCGA-OU-A5PI-01       1       0       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       0       1       0       0       0       0       0
#> TCGA-P6-A5OG-01       2       0       3       2       0       1       0       0
#> TCGA-P6-A5OH-01       1       2       2       2       0       2       0       0
#> TCGA-PA-A5YG-01       0       0       1       0       0       0       0       0
#> TCGA-PK-A5H8-01       2       0       0       1       0       0       1       0
#> TCGA-PK-A5H9-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       2       0       0       3       0       0       0       0
#> TCGA-PK-A5HB-01      20      13      18      12       2       2       0       4
#> TCGA-PK-A5HC-01       2       1       0       1       0       0       0       0
#>                 C[C>A]A C[C>A]C C[C>A]G C[C>A]T C[C>G]A C[C>G]C C[C>G]G C[C>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J2-01       0       2       0       1       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5J4-01       1       4       0       6       2       2       0       2
#> TCGA-OR-A5J5-01       1       6       2       4       0       0       0       0
#> TCGA-OR-A5J6-01       0       1       0       1       1       0       0       0
#> TCGA-OR-A5J7-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J8-01       4       2       3       8       1       0       0       0
#> TCGA-OR-A5J9-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5JA-01      57      16      10      29       0       0       0       3
#> TCGA-OR-A5JB-01      21      24      14      19       0       2       2       4
#> TCGA-OR-A5JC-01       1       1       1       1       0       1       0       1
#> TCGA-OR-A5JD-01       1       0       1       1       1       0       0       1
#> TCGA-OR-A5JE-01       1       1       0       0       0       0       0       1
#> TCGA-OR-A5JF-01       2       2       0       1       3       2       1       3
#> TCGA-OR-A5JG-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JJ-01       0       2       0       0       0       0       1       1
#> TCGA-OR-A5JK-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JL-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       0       0       1       0       1       1
#> TCGA-OR-A5JO-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5JP-01       3       2       0       1       0       2       0       2
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5JR-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JS-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5JT-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JV-01       1       2       0       0       1       1       0       0
#> TCGA-OR-A5JW-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       1       0       1       0       2
#> TCGA-OR-A5JY-01       1       0       1       3       0       5       0       2
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       1       1       3       1       0       0       1       2
#> TCGA-OR-A5K1-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5K2-01       3       1       0       3       2       0       2       1
#> TCGA-OR-A5K3-01       3       0       1       0       0       0       1       2
#> TCGA-OR-A5K4-01       0       1       0       3       0       0       0       1
#> TCGA-OR-A5K5-01       1       3       1       0       0       2       0       2
#> TCGA-OR-A5K6-01       2       0       0       0       0       1       0       0
#> TCGA-OR-A5K8-01       1       1       1       0       0       0       0       1
#> TCGA-OR-A5K9-01       3       2       1       1       3       4       0       1
#> TCGA-OR-A5KB-01     177     172     109     165      38      31      26      34
#> TCGA-OR-A5KO-01       2       0       1       0       0       0       1       1
#> TCGA-OR-A5KP-01       2       0       0       0       0       0       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KT-01       1       0       0       2       0       1       0       3
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KW-01       1       1       0       2       0       0       0       1
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       0       1
#> TCGA-OR-A5KY-01       1       0       0       3       1       1       0       0
#> TCGA-OR-A5KZ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5L1-01       0       0       0       1       0       1       0       0
#> TCGA-OR-A5L2-01       1       2       0       4       0       3       0       4
#> TCGA-OR-A5L3-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5L4-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5L5-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       1       1       1       1       0       0       0
#> TCGA-OR-A5L8-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       2       0       2       7       0       0       0       1
#> TCGA-OR-A5LC-01       2       4       0       4       1       0       0       0
#> TCGA-OR-A5LD-01       1       0       2       0       2       2       1       1
#> TCGA-OR-A5LE-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LF-01       1       0       0       1       0       0       0       1
#> TCGA-OR-A5LG-01       1       0       0       0       1       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       0       1       0       0       3       1       0       2
#> TCGA-OR-A5LJ-01       2       7       1       8       0       0       1       0
#> TCGA-OR-A5LK-01       2       0       1       1       1       1       0       0
#> TCGA-OR-A5LL-01       2       1       0       0       0       1       0       4
#> TCGA-OR-A5LM-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5LO-01       1       3       0       1       1       2       1       0
#> TCGA-OR-A5LP-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LR-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5LT-01       0       1       0       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       0       0       0       0       0       1       2
#> TCGA-P6-A5OF-01       1       1       1       1       0       1       1       0
#> TCGA-P6-A5OG-01      25       9      12       6       1       1       1       3
#> TCGA-P6-A5OH-01       4       2       1       1       2       2       1       2
#> TCGA-PA-A5YG-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       0       2       0       0       0       0
#> TCGA-PK-A5H9-01       0       1       1       0       0       0       0       0
#> TCGA-PK-A5HA-01       2       2       0       1       1       0       0       1
#> TCGA-PK-A5HB-01       7      16       3      19       5       4       1       3
#> TCGA-PK-A5HC-01       1       1       1       2       2       0       0       1
#>                 C[C>T]A C[C>T]C C[C>T]G C[C>T]T C[T>A]A C[T>A]C C[T>A]G C[T>A]T
#> TCGA-OR-A5J1-01       1       0       1       1       0       0       1       0
#> TCGA-OR-A5J2-01       2       0       2       0       0       1       1       0
#> TCGA-OR-A5J3-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5J4-01       0       1       1       3       1       1       0       3
#> TCGA-OR-A5J5-01       0       6      93       1       0       0       0       0
#> TCGA-OR-A5J6-01       0       2       2       0       0       0       1       0
#> TCGA-OR-A5J7-01       2       0       2       2       0       0       0       1
#> TCGA-OR-A5J8-01       2       2       3       2       0       0       0       1
#> TCGA-OR-A5J9-01       0       1       4       0       0       0       0       1
#> TCGA-OR-A5JA-01       1       0       1       2       0       2       2       0
#> TCGA-OR-A5JB-01       8       3       6       9       2       4       7       2
#> TCGA-OR-A5JC-01       1       0       2       0       0       3       1       0
#> TCGA-OR-A5JD-01       1       0       3       1       0       0       0       0
#> TCGA-OR-A5JE-01       1       3       6       2       0       0       1       0
#> TCGA-OR-A5JF-01       1       2       1       2       1       1       0       1
#> TCGA-OR-A5JG-01       0       0       4       2       0       0       1       0
#> TCGA-OR-A5JH-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5JK-01       1       1       2       2       1       0       0       0
#> TCGA-OR-A5JL-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JM-01       2       1       4       2       0       1       0       1
#> TCGA-OR-A5JO-01       2       1       1       0       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       4       2       1       2       0       0
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       1       1       2       0       1       0       0
#> TCGA-OR-A5JT-01       0       2       2       1       0       0       0       0
#> TCGA-OR-A5JU-01       0       2       4       0       0       0       0       0
#> TCGA-OR-A5JV-01       0       1       2       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       2       0       0       1       0       0
#> TCGA-OR-A5JX-01       0       1       1       0       0       0       2       0
#> TCGA-OR-A5JY-01       1       0       4       2       0       2       1       1
#> TCGA-OR-A5JZ-01       0       0       2       1       0       0       1       0
#> TCGA-OR-A5K0-01       4       2       2       4       2       0       1       0
#> TCGA-OR-A5K1-01       0       0       1       2       0       0       1       1
#> TCGA-OR-A5K2-01       0       3       7       2       0       0       2       1
#> TCGA-OR-A5K3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       2       1      71       3       0       0       0       1
#> TCGA-OR-A5K5-01       6       2       6       1       0       2       0       1
#> TCGA-OR-A5K6-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5K8-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5K9-01       4       4       2       2       0       3       0       1
#> TCGA-OR-A5KB-01      46      43      29      48      18      27      63      22
#> TCGA-OR-A5KO-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5KP-01       4       2       4       1       0       0       1       0
#> TCGA-OR-A5KQ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KS-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5KT-01       1       1       2       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       3       0       0       1       0       0
#> TCGA-OR-A5KV-01       2       1       4       1       0       0       0       0
#> TCGA-OR-A5KW-01       0       0       4       2       1       0       0       0
#> TCGA-OR-A5KX-01       3       2       6       2       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       1       1
#> TCGA-OR-A5KZ-01       2       0       1       0       0       1       0       0
#> TCGA-OR-A5L1-01       0       0       0       1       0       2       0       0
#> TCGA-OR-A5L2-01       3       0       8       3       0       1       1       0
#> TCGA-OR-A5L3-01       1       0       2       1       1       1       1       0
#> TCGA-OR-A5L4-01       1       2       0       1       0       0       1       0
#> TCGA-OR-A5L5-01       0       0       1       0       0       1       0       1
#> TCGA-OR-A5L6-01       1       1       4       3       0       0       2       0
#> TCGA-OR-A5L8-01       0       0       3       1       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LB-01       2       2      24       1       1       0       0       1
#> TCGA-OR-A5LC-01       3       0       4       0       0       0       1       0
#> TCGA-OR-A5LD-01       0       2       5       2       0       2       2       0
#> TCGA-OR-A5LE-01       2       1       1       0       0       0       1       0
#> TCGA-OR-A5LF-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LG-01       1       0       1       0       0       0       0       1
#> TCGA-OR-A5LH-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5LI-01       3       2       9       2       0       1       0       0
#> TCGA-OR-A5LJ-01       3       2      74       4       0       1       1       1
#> TCGA-OR-A5LK-01       0       2       3       0       0       0       1       0
#> TCGA-OR-A5LL-01       0       4       7       0       0       0       1       0
#> TCGA-OR-A5LM-01       1       1       1       2       0       1       0       0
#> TCGA-OR-A5LN-01       0       0       0       1       0       0       0       1
#> TCGA-OR-A5LO-01       2       1       3       2       0       0       1       0
#> TCGA-OR-A5LP-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5LS-01       0       0       1       1       0       0       0       1
#> TCGA-OR-A5LT-01       0       0       0       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       1       1       1       0       0       1       0
#> TCGA-P6-A5OF-01       2       0       1       1       0       1       0       0
#> TCGA-P6-A5OG-01       5       8      13       2       0       0       9       4
#> TCGA-P6-A5OH-01       2       2       6       1       0       1       2       2
#> TCGA-PA-A5YG-01       2       0       1       0       0       0       0       0
#> TCGA-PK-A5H8-01       1       0       0       0       0       0       0       1
#> TCGA-PK-A5H9-01       1       0       1       0       0       0       0       0
#> TCGA-PK-A5HA-01       0       1       5       0       0       0       1       0
#> TCGA-PK-A5HB-01      18      23      34      17       2       9      12       3
#> TCGA-PK-A5HC-01       0       3       1       2       0       2       1       0
#>                 C[T>C]A C[T>C]C C[T>C]G C[T>C]T C[T>G]A C[T>G]C C[T>G]G C[T>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       1       1       0
#> TCGA-OR-A5J2-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J3-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       0       2       2       1       0       0       0       0
#> TCGA-OR-A5J5-01       2       1       2       0       0       0       0       1
#> TCGA-OR-A5J6-01       1       0       2       1       0       0       0       0
#> TCGA-OR-A5J7-01       0       0       0       1       0       1       0       0
#> TCGA-OR-A5J8-01       1       0       1       1       0       0       0       1
#> TCGA-OR-A5J9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JA-01       0       1       0       1       0       0       1       0
#> TCGA-OR-A5JB-01       3       0       4       4       0       0       0       0
#> TCGA-OR-A5JC-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5JD-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JE-01       0       0       3       0       0       1       0       0
#> TCGA-OR-A5JF-01       2       1       1       1       0       0       1       0
#> TCGA-OR-A5JG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JK-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       0       0       0       1       1       1
#> TCGA-OR-A5JO-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       0       0       0       0       1       1
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5JT-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5JV-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JY-01       0       3       0       1       2       0       2       0
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       0       2       4       0       0       0       0       0
#> TCGA-OR-A5K3-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       2       0       2       1       0       0       1       1
#> TCGA-OR-A5K5-01       0       1       1       3       0       1       2       0
#> TCGA-OR-A5K6-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5K8-01       0       0       1       2       0       1       0       0
#> TCGA-OR-A5K9-01       0       1       2       0       0       0       2       1
#> TCGA-OR-A5KB-01      10       4      18       9       1       2      13       3
#> TCGA-OR-A5KO-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KP-01       2       0       1       1       0       0       0       0
#> TCGA-OR-A5KQ-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KT-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L1-01       1       0       0       1       0       0       1       0
#> TCGA-OR-A5L2-01       0       3       2       4       0       0       1       1
#> TCGA-OR-A5L3-01       0       1       3       0       0       0       0       0
#> TCGA-OR-A5L4-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5L8-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5LA-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5LB-01       2       2       2       0       0       2       1       1
#> TCGA-OR-A5LC-01       0       0       2       0       0       0       1       0
#> TCGA-OR-A5LD-01       0       1       1       0       0       0       3       1
#> TCGA-OR-A5LE-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       1       1       1       0       0       0       1
#> TCGA-OR-A5LG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       0       0       1       0       0       0       2       0
#> TCGA-OR-A5LJ-01       1       0       5       0       0       1       0       2
#> TCGA-OR-A5LK-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5LL-01       0       0       1       1       1       1       0       2
#> TCGA-OR-A5LM-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       2       1       0       0       0       1       1
#> TCGA-OR-A5LP-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       2       0       0       0       0       0
#> TCGA-OU-A5PI-01       0       4       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       1       1       0       0       0       0       0
#> TCGA-P6-A5OG-01       0       4       2       0       0       0       2       0
#> TCGA-P6-A5OH-01       0       3       1       1       0       2       0       0
#> TCGA-PA-A5YG-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       1       2       0       0       0       0
#> TCGA-PK-A5H9-01       0       1       0       0       0       0       1       0
#> TCGA-PK-A5HA-01       0       0       0       0       1       1       0       0
#> TCGA-PK-A5HB-01      16      13      17      11       5       1       6       2
#> TCGA-PK-A5HC-01       0       0       0       0       0       0       0       1
#>                 G[C>A]A G[C>A]C G[C>A]G G[C>A]T G[C>G]A G[C>G]C G[C>G]G G[C>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J2-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5J3-01       2       0       0       1       1       0       0       0
#> TCGA-OR-A5J4-01       2       2       0       3       0       3       0       1
#> TCGA-OR-A5J5-01       1       0       0       1       0       2       0       0
#> TCGA-OR-A5J6-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5J7-01       1       0       0       1       0       2       0       0
#> TCGA-OR-A5J8-01       7       3       2       4       1       3       0       1
#> TCGA-OR-A5J9-01       0       0       0       0       0       1       0       1
#> TCGA-OR-A5JA-01      80      19       5      56       1       2       0       0
#> TCGA-OR-A5JB-01       8       7      13       3       3       0       3       0
#> TCGA-OR-A5JC-01       1       1       0       0       1       1       0       0
#> TCGA-OR-A5JD-01       0       0       0       1       0       1       0       1
#> TCGA-OR-A5JE-01       3       0       2       0       0       0       1       2
#> TCGA-OR-A5JF-01       0       1       1       0       3       1       0       2
#> TCGA-OR-A5JG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       1       1       0       0       1
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5JM-01       1       1       2       2       0       3       0       1
#> TCGA-OR-A5JO-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       1       1       3       1       0       1       0       3
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JT-01       0       2       1       2       0       0       0       0
#> TCGA-OR-A5JU-01       0       1       1       1       0       0       0       0
#> TCGA-OR-A5JV-01       0       3       0       0       0       1       0       1
#> TCGA-OR-A5JW-01       1       1       0       2       1       1       0       0
#> TCGA-OR-A5JX-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5JY-01       2       1       0       4       2       1       0       0
#> TCGA-OR-A5JZ-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       2       1       1       0       0       0       0       1
#> TCGA-OR-A5K1-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5K3-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K5-01       1       1       0       2       0       1       2       2
#> TCGA-OR-A5K6-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5K8-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       1       3       2       0       1       3       2       2
#> TCGA-OR-A5KB-01      83     102      62      66      21      29      22      12
#> TCGA-OR-A5KO-01       1       0       0       2       1       0       0       1
#> TCGA-OR-A5KP-01       0       1       1       0       1       0       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KT-01       1       0       0       0       0       2       1       0
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5KW-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5KY-01       4       1       2       0       1       2       0       0
#> TCGA-OR-A5KZ-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5L1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L2-01       3       0       1       3       2       3       1       2
#> TCGA-OR-A5L3-01       0       2       1       0       0       1       0       0
#> TCGA-OR-A5L4-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       2       0       0       0       1
#> TCGA-OR-A5L6-01       0       2       0       0       0       0       1       0
#> TCGA-OR-A5L8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       2
#> TCGA-OR-A5LA-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LB-01       5       2       2       3       0       0       1       0
#> TCGA-OR-A5LC-01       1       2       2       1       0       0       0       0
#> TCGA-OR-A5LD-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LE-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       1       0       0       0       0       1       1       0
#> TCGA-OR-A5LG-01       1       1       1       2       0       1       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LJ-01       4       3       1       2       1       2       0       2
#> TCGA-OR-A5LK-01       0       1       0       2       0       1       0       1
#> TCGA-OR-A5LL-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5LM-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       6       0       0       2       1       0       0       0
#> TCGA-OR-A5LP-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LT-01       0       1       1       0       0       0       0       0
#> TCGA-OU-A5PI-01       1       2       1       0       1       0       1       1
#> TCGA-P6-A5OF-01       0       0       1       0       0       0       0       0
#> TCGA-P6-A5OG-01       6       8       8       7       1       2       2       1
#> TCGA-P6-A5OH-01       3       1       2       0       0       3       0       2
#> TCGA-PA-A5YG-01       0       0       0       1       0       0       0       0
#> TCGA-PK-A5H8-01       2       1       1       0       0       0       0       0
#> TCGA-PK-A5H9-01       2       1       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       1       1       0       2       0       0       0       0
#> TCGA-PK-A5HB-01       6      12       3      11       0      10       1       1
#> TCGA-PK-A5HC-01       1       1       1       2       0       1       0       2
#>                 G[C>T]A G[C>T]C G[C>T]G G[C>T]T G[T>A]A G[T>A]C G[T>A]G G[T>A]T
#> TCGA-OR-A5J1-01       3       4       1       1       0       0       0       0
#> TCGA-OR-A5J2-01       1       1       2       0       0       1       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5J4-01       3       6       5       4       0       1       0       1
#> TCGA-OR-A5J5-01      12       5     116       3       0       0       0       1
#> TCGA-OR-A5J6-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5J7-01       1       0       1       2       0       1       0       0
#> TCGA-OR-A5J8-01       3       2       7       0       0       1       0       0
#> TCGA-OR-A5J9-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5JA-01       1       1       6       1       0       0       0       0
#> TCGA-OR-A5JB-01       2       2       2       2       1       2       4       0
#> TCGA-OR-A5JC-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5JD-01       2       1       2       0       0       0       0       0
#> TCGA-OR-A5JE-01       1       0       0       1       0       0       1       0
#> TCGA-OR-A5JF-01       0       0       1       0       0       1       1       0
#> TCGA-OR-A5JG-01       2       2       3       0       0       0       0       0
#> TCGA-OR-A5JH-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       2       2       4       0       0       0       0       0
#> TCGA-OR-A5JO-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JP-01       1       0       3       1       0       2       0       0
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       1       1       4       1       0       0       0       0
#> TCGA-OR-A5JT-01       1       0       1       0       1       0       0       0
#> TCGA-OR-A5JU-01       0       0       4       0       0       0       0       0
#> TCGA-OR-A5JV-01       0       1       4       0       0       0       0       0
#> TCGA-OR-A5JW-01       1       0       1       0       1       0       0       0
#> TCGA-OR-A5JX-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5JY-01       3       2       4       0       0       1       1       0
#> TCGA-OR-A5JZ-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5K0-01       0       0       2       0       0       0       0       1
#> TCGA-OR-A5K1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       1       0       3       2       0       0       0       0
#> TCGA-OR-A5K3-01       0       0       3       0       0       0       1       0
#> TCGA-OR-A5K4-01       5       5      78       4       0       0       0       0
#> TCGA-OR-A5K5-01       1       1       3       4       0       1       1       0
#> TCGA-OR-A5K6-01       1       0       2       2       0       0       0       0
#> TCGA-OR-A5K8-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       1       3       9       1       0       0       1       0
#> TCGA-OR-A5KB-01      19      17      16      22      12       6      19       9
#> TCGA-OR-A5KO-01       1       1       2       0       0       0       0       0
#> TCGA-OR-A5KP-01       1       4       3       2       0       1       0       0
#> TCGA-OR-A5KQ-01       0       1       2       1       0       0       0       0
#> TCGA-OR-A5KS-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5KT-01       1       0       0       2       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       4       0       0       0       0       0
#> TCGA-OR-A5KV-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5KW-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5KX-01       2       2       8       0       2       0       0       0
#> TCGA-OR-A5KY-01       4       0       1       0       0       0       0       0
#> TCGA-OR-A5KZ-01       0       0       2       1       1       0       0       0
#> TCGA-OR-A5L1-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5L2-01       4       3       8       3       1       3       0       0
#> TCGA-OR-A5L3-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5L4-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       0       2       2       0       0       1       0
#> TCGA-OR-A5L8-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       2       0       0       0       1       0
#> TCGA-OR-A5LB-01      12      10      47      12       1       1       0       1
#> TCGA-OR-A5LC-01       2       3       5       0       0       0       0       0
#> TCGA-OR-A5LD-01       3       2       5       0       0       1       0       0
#> TCGA-OR-A5LE-01       0       0       2       0       0       0       0       1
#> TCGA-OR-A5LF-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LG-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5LI-01       1       2       4       2       0       0       0       1
#> TCGA-OR-A5LJ-01      16      14     114       8       0       1       1       0
#> TCGA-OR-A5LK-01       1       0       5       1       0       1       0       1
#> TCGA-OR-A5LL-01       4       2       6       2       0       1       0       0
#> TCGA-OR-A5LM-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       1       2       0       0       1       0       0
#> TCGA-OR-A5LP-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5LR-01       0       2       0       1       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LT-01       0       0       2       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       1       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       2       1       1       2       0       0       0       0
#> TCGA-P6-A5OG-01       5       3       4       3       0       3       3       0
#> TCGA-P6-A5OH-01       2       6       2       2       0       0       1       0
#> TCGA-PA-A5YG-01       0       0       2       1       0       0       0       0
#> TCGA-PK-A5H8-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       0       0       1       1       0       0       0       0
#> TCGA-PK-A5HA-01       1       3       2       0       0       1       0       0
#> TCGA-PK-A5HB-01      75     111     113      79      11      10       8       6
#> TCGA-PK-A5HC-01       2       1       1       0       0       0       0       0
#>                 G[T>C]A G[T>C]C G[T>C]G G[T>C]T G[T>G]A G[T>G]C G[T>G]G G[T>G]T
#> TCGA-OR-A5J1-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5J2-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       2       3       0       1       1       1       1       1
#> TCGA-OR-A5J5-01       7       0       0       2       0       0       0       0
#> TCGA-OR-A5J6-01       2       0       2       1       0       0       0       0
#> TCGA-OR-A5J7-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5J8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J9-01       1       1       0       1       0       0       0       1
#> TCGA-OR-A5JA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JB-01       3       0       0       0       1       0       1       0
#> TCGA-OR-A5JC-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JD-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JE-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5JF-01       0       1       2       0       0       0       3       0
#> TCGA-OR-A5JG-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JO-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JP-01       1       0       0       1       0       1       2       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JT-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JU-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5JV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5JY-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5JZ-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5K0-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5K1-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5K2-01       0       0       0       2       0       0       0       1
#> TCGA-OR-A5K3-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5K4-01       2       2       0       3       0       0       1       0
#> TCGA-OR-A5K5-01       2       2       4       2       0       1       1       1
#> TCGA-OR-A5K6-01       0       0       0       1       0       1       0       0
#> TCGA-OR-A5K8-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5K9-01       4       2       3       1       1       1       1       0
#> TCGA-OR-A5KB-01       7       5      12       5       1       0       3       3
#> TCGA-OR-A5KO-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5KP-01       0       2       1       0       0       0       1       2
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5KT-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5KU-01       3       0       0       2       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KZ-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L2-01       1       3       1       1       0       1       1       1
#> TCGA-OR-A5L3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L4-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L8-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       3       3       3       1       0       1       0       0
#> TCGA-OR-A5LC-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LD-01       0       3       1       0       0       0       0       0
#> TCGA-OR-A5LE-01       2       1       1       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LI-01       0       1       2       0       0       1       0       1
#> TCGA-OR-A5LJ-01       1       2       1       1       0       0       1       0
#> TCGA-OR-A5LK-01       0       1       0       2       0       0       0       0
#> TCGA-OR-A5LL-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5LM-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LN-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5LO-01       2       1       0       0       0       0       0       0
#> TCGA-OR-A5LP-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LT-01       0       1       0       0       0       0       0       0
#> TCGA-OU-A5PI-01       0       1       0       0       0       0       1       0
#> TCGA-P6-A5OF-01       0       0       0       0       0       0       0       0
#> TCGA-P6-A5OG-01       2       0       2       1       0       0       3       0
#> TCGA-P6-A5OH-01       4       1       0       0       0       1       0       0
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       1       1       0       0       0       0       0       1
#> TCGA-PK-A5H9-01       0       0       0       0       1       0       0       0
#> TCGA-PK-A5HA-01       1       0       0       0       0       0       0       0
#> TCGA-PK-A5HB-01      38      32      29      11       2       2       1       1
#> TCGA-PK-A5HC-01       1       0       0       1       0       0       0       0
#>                 T[C>A]A T[C>A]C T[C>A]G T[C>A]T T[C>G]A T[C>G]C T[C>G]G T[C>G]T
#> TCGA-OR-A5J1-01       1       0       0       0       0       1       0       1
#> TCGA-OR-A5J2-01       3       1       0       1       0       0       0       1
#> TCGA-OR-A5J3-01       1       0       0       1       0       1       0       0
#> TCGA-OR-A5J4-01       6       4       0       3       9       4       4      10
#> TCGA-OR-A5J5-01       2       0       0       2       0       0       0       1
#> TCGA-OR-A5J6-01       0       0       1       0       0       1       1       2
#> TCGA-OR-A5J7-01       0       2       0       3       2       6       0       4
#> TCGA-OR-A5J8-01      12       8       2       9       1       2       0       0
#> TCGA-OR-A5J9-01       0       0       1       0       1       1       0       3
#> TCGA-OR-A5JA-01     114      66      16     120       1       1       0       1
#> TCGA-OR-A5JB-01       8      17       5       7      15       5       3      19
#> TCGA-OR-A5JC-01       0       0       0       0       1       1       0       2
#> TCGA-OR-A5JD-01       0       1       0       1       0       0       0       1
#> TCGA-OR-A5JE-01       1       3       0       0       5       2       0       0
#> TCGA-OR-A5JF-01       2       0       0       2       0       3       0       5
#> TCGA-OR-A5JG-01       0       0       0       0       0       2       0       3
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5JK-01       1       0       0       1       2       0       0       2
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       3       1       2       2       2       1       0       3
#> TCGA-OR-A5JO-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5JP-01       3       3       0       2       5       3       1       4
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       3       0       0       0       0       1       0       1
#> TCGA-OR-A5JT-01       0       1       0       0       0       1       0       2
#> TCGA-OR-A5JU-01       2       0       0       1       0       0       0       0
#> TCGA-OR-A5JV-01       0       0       0       3       0       0       0       0
#> TCGA-OR-A5JW-01       1       1       0       0       1       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       0       2       1       0       2
#> TCGA-OR-A5JY-01       1       2       0       1       2       1       0       4
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       2       0       1       0       1       0       1       3
#> TCGA-OR-A5K1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       0       1       0       1       1       1       1       2
#> TCGA-OR-A5K3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       1       0       1       1       1       0       1
#> TCGA-OR-A5K5-01       2       6       0       4       4       2       0       9
#> TCGA-OR-A5K6-01       2       2       0       0       2       1       2       0
#> TCGA-OR-A5K8-01       1       0       0       0       3       0       0       2
#> TCGA-OR-A5K9-01       4       3       0       4       1       4       1       9
#> TCGA-OR-A5KB-01      73     146      50      82      44      35      19      41
#> TCGA-OR-A5KO-01       0       2       1       1       0       2       0       0
#> TCGA-OR-A5KP-01       0       2       1       1       2       3       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       0       2
#> TCGA-OR-A5KT-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       1       0       1       1       0       0
#> TCGA-OR-A5KV-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5KW-01       1       0       2       0       1       0       1       0
#> TCGA-OR-A5KX-01       0       0       0       0       1       2       0       4
#> TCGA-OR-A5KY-01       1       2       0       1       2       0       0       2
#> TCGA-OR-A5KZ-01       2       0       1       2       0       3       0       1
#> TCGA-OR-A5L1-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5L2-01       1       7       1       4      11       5       0       5
#> TCGA-OR-A5L3-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5L4-01       1       2       1       1       0       1       0       1
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       0       0       1       0       3       0       1
#> TCGA-OR-A5L8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       1       1       1       1       0       0       0       1
#> TCGA-OR-A5LC-01       0       0       0       1       1       0       0       2
#> TCGA-OR-A5LD-01       0       2       1       0       0       0       0       4
#> TCGA-OR-A5LE-01       0       0       0       0       1       0       1       2
#> TCGA-OR-A5LF-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5LG-01       0       1       0       1       1       0       0       2
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       1       1       0       1       1       2       0       2
#> TCGA-OR-A5LJ-01       1       2       1       2       1       0       1       4
#> TCGA-OR-A5LK-01       0       0       1       2       1       2       0       0
#> TCGA-OR-A5LL-01       0       0       0       1       0       1       0       2
#> TCGA-OR-A5LM-01       0       0       1       0       0       1       0       1
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       1       1
#> TCGA-OR-A5LO-01       2       1       1       1       9       4       0       8
#> TCGA-OR-A5LP-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       1       0       0       1       0       0       1
#> TCGA-OR-A5LT-01       0       0       0       0       0       1       0       1
#> TCGA-OU-A5PI-01       0       0       0       1       0       1       0       1
#> TCGA-P6-A5OF-01       1       1       0       1       0       0       0       0
#> TCGA-P6-A5OG-01       6       9       1       3       3       2       4       1
#> TCGA-P6-A5OH-01       2       2       0       3       6       6       2       5
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       2       0       0       0       0       0       1       2
#> TCGA-PK-A5H9-01       1       1       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       1       1       0       2       4       0       0       3
#> TCGA-PK-A5HB-01       6      10       2      10       5      12       0      12
#> TCGA-PK-A5HC-01       4       2       0       5       7       2       1       7
#>                 T[C>T]A T[C>T]C T[C>T]G T[C>T]T T[T>A]A T[T>A]C T[T>A]G T[T>A]T
#> TCGA-OR-A5J1-01       0       1       4       0       0       0       0       0
#> TCGA-OR-A5J2-01       2       2       2       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5J4-01       3       3       3       2       0       0       2       0
#> TCGA-OR-A5J5-01       0       1      53       0       0       1       0       0
#> TCGA-OR-A5J6-01       0       1       1       1       0       0       0       0
#> TCGA-OR-A5J7-01       1       1       4       1       0       1       0       0
#> TCGA-OR-A5J8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J9-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JA-01       5       3       1       0       0       0       0       0
#> TCGA-OR-A5JB-01      28      11      10      16       0       1       2       1
#> TCGA-OR-A5JC-01       1       1       0       1       0       0       0       0
#> TCGA-OR-A5JD-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JE-01       2       3       0       0       0       0       0       0
#> TCGA-OR-A5JF-01       3       5       2       2       0       0       1       0
#> TCGA-OR-A5JG-01       2       0       1       0       0       0       1       0
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5JK-01       1       0       2       2       0       0       2       0
#> TCGA-OR-A5JL-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JM-01       3       2       0       6       0       0       0       0
#> TCGA-OR-A5JO-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JP-01       2       1       2       3       0       0       0       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JS-01       7       0       2       2       0       0       0       0
#> TCGA-OR-A5JT-01       0       3       1       0       1       0       0       0
#> TCGA-OR-A5JU-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JV-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5JW-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JX-01       3       1       2       1       0       0       0       1
#> TCGA-OR-A5JY-01       6       6       4       2       0       0       0       0
#> TCGA-OR-A5JZ-01       0       1       2       1       0       0       0       0
#> TCGA-OR-A5K0-01       1       2       2       2       0       2       1       1
#> TCGA-OR-A5K1-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5K2-01       0       4       0       2       1       0       0       1
#> TCGA-OR-A5K3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       2      35       4       0       0       0       0
#> TCGA-OR-A5K5-01       3       2       2       5       0       2       1       0
#> TCGA-OR-A5K6-01       3       0       1       0       0       0       0       0
#> TCGA-OR-A5K8-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       6       6       4       6       2       0       1       1
#> TCGA-OR-A5KB-01      50      37      18      39       4       9      12       5
#> TCGA-OR-A5KO-01       2       1       0       3       0       0       0       0
#> TCGA-OR-A5KP-01       1       3       3       2       0       0       0       0
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       1       3       1       1       0       0       0       0
#> TCGA-OR-A5KT-01       4       1       0       1       0       0       0       0
#> TCGA-OR-A5KU-01       1       0       3       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       1       1       2       0       0       0       2
#> TCGA-OR-A5KW-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KX-01       2       4       0       0       1       0       0       0
#> TCGA-OR-A5KY-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5KZ-01       1       2       1       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       1       3       0       0       0       0       0
#> TCGA-OR-A5L2-01       5       5       6       2       0       2       0       3
#> TCGA-OR-A5L3-01       1       0       2       0       0       0       0       0
#> TCGA-OR-A5L4-01       4       0       1       1       0       0       0       0
#> TCGA-OR-A5L5-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5L8-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5LB-01       1       3      14       2       0       0       1       0
#> TCGA-OR-A5LC-01       0       5       0       3       0       0       0       0
#> TCGA-OR-A5LD-01       2       1       5       1       0       2       0       0
#> TCGA-OR-A5LE-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5LF-01       0       2       0       1       0       0       0       0
#> TCGA-OR-A5LG-01       1       1       0       2       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       2       3       6       3       0       0       0       0
#> TCGA-OR-A5LJ-01       4       7      39       4       0       0       0       1
#> TCGA-OR-A5LK-01       1       2       3       1       0       0       0       0
#> TCGA-OR-A5LL-01       3       2       3       1       0       0       0       0
#> TCGA-OR-A5LM-01       1       0       4       0       0       1       0       0
#> TCGA-OR-A5LN-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LO-01       5       3       4       3       0       0       0       1
#> TCGA-OR-A5LP-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       3       0       0       0       0       0
#> TCGA-OU-A5PI-01       2       1       1       1       0       0       1       0
#> TCGA-P6-A5OF-01       1       0       5       1       0       1       0       0
#> TCGA-P6-A5OG-01      22       7       6      17       0       0       2       1
#> TCGA-P6-A5OH-01       4       6       6       3       3       2       0       3
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       1       0       2       0       0       0       0       0
#> TCGA-PK-A5H9-01       1       1       0       1       0       0       1       0
#> TCGA-PK-A5HA-01       3       3       1       1       0       0       0       0
#> TCGA-PK-A5HB-01      52      61      35      53       9      12       3       6
#> TCGA-PK-A5HC-01       2       4       1       7       0       1       0       0
#>                 T[T>C]A T[T>C]C T[T>C]G T[T>C]T T[T>G]A T[T>G]C T[T>G]G T[T>G]T
#> TCGA-OR-A5J1-01       0       0       2       0       1       1       0       0
#> TCGA-OR-A5J2-01       0       0       0       0       1       0       0       1
#> TCGA-OR-A5J3-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       1       0       2       0       1       1       0       1
#> TCGA-OR-A5J5-01       3       1       3       1       1       1       0       1
#> TCGA-OR-A5J6-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J7-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5J8-01       1       0       1       0       0       0       1       1
#> TCGA-OR-A5J9-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5JA-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5JB-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5JC-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5JD-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JE-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5JF-01       0       2       0       0       1       0       1       0
#> TCGA-OR-A5JG-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JL-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       2       1       0       0       1       0
#> TCGA-OR-A5JO-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JP-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JT-01       0       1       0       0       0       0       1       0
#> TCGA-OR-A5JU-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5JV-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JY-01       0       2       1       1       0       0       0       0
#> TCGA-OR-A5JZ-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5K1-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5K2-01       0       0       0       0       0       1       1       0
#> TCGA-OR-A5K3-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       4       0       4       1       0       0       1       0
#> TCGA-OR-A5K5-01       0       2       2       2       0       0       0       2
#> TCGA-OR-A5K6-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5K8-01       0       1       0       0       0       1       0       0
#> TCGA-OR-A5K9-01       1       4       1       1       0       0       0       0
#> TCGA-OR-A5KB-01       5       3       5       3       1       3       5       1
#> TCGA-OR-A5KO-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5KP-01       0       1       1       2       0       1       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KS-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5KT-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       1       1       0       1       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       1       0       0       0       2       1
#> TCGA-OR-A5KY-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KZ-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5L2-01       0       0       2       0       0       1       0       0
#> TCGA-OR-A5L3-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L4-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L5-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       2       1       0       0       0       0       0       0
#> TCGA-OR-A5L8-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       1       2       0       1       1       0       0       0
#> TCGA-OR-A5LC-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LD-01       0       0       0       1       0       0       0       3
#> TCGA-OR-A5LE-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LG-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       1       0       1       0
#> TCGA-OR-A5LI-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LJ-01       7       2       5       4       0       0       0       1
#> TCGA-OR-A5LK-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LL-01       2       1       0       0       0       0       0       0
#> TCGA-OR-A5LM-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5LP-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       0       0       0       0       0       1
#> TCGA-OU-A5PI-01       1       1       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       0       0       0       0       1       0       0
#> TCGA-P6-A5OG-01       0       1       1       2       0       0       0       1
#> TCGA-P6-A5OH-01       0       1       1       0       0       0       0       0
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       0       0       0       0       1       0       0       0
#> TCGA-PK-A5HB-01      19      18      12      15       2       3       3       5
#> TCGA-PK-A5HC-01       0       0       0       1       0       0       0       1
#> 
#> $all_matrices
#> $all_matrices$SBS_6
#>                  C>A C>G C>T T>A T>C T>G
#> TCGA-OR-A5J1-01    1   5  25   1   3   4
#> TCGA-OR-A5J2-01   10   2  21   4   2   2
#> TCGA-OR-A5J3-01    5   3   6   2   3   0
#> TCGA-OR-A5J4-01   39  40  44  10  20   8
#> TCGA-OR-A5J5-01   21   3 437   4  27   4
#> TCGA-OR-A5J6-01    5   6   8   4  18   0
#> TCGA-OR-A5J7-01    8  16  24   4   4   2
#> TCGA-OR-A5J8-01   71  13  26   3   8   3
#> TCGA-OR-A5J9-01    3  10  18   3   5   2
#> TCGA-OR-A5JA-01  614  10  24   5   9   1
#> TCGA-OR-A5JB-01  175  65 111  38  26   4
#> TCGA-OR-A5JC-01    8   9  13   5   5   1
#> TCGA-OR-A5JD-01    7   5  16   2   5   0
#> TCGA-OR-A5JE-01   12  14  28   3   7   4
#> TCGA-OR-A5JF-01   17  25  27   6  11   8
#> TCGA-OR-A5JG-01    3   6  20   3   5   0
#> TCGA-OR-A5JH-01    5   0   3   1   0   1
#> TCGA-OR-A5JI-01    2   1   4   2   4   0
#> TCGA-OR-A5JJ-01    4   4  11   0   1   1
#> TCGA-OR-A5JK-01    3   7  14   4   6   1
#> TCGA-OR-A5JL-01    2   2   5   1   2   0
#> TCGA-OR-A5JM-01   16  16  33   3  11   4
#> TCGA-OR-A5JO-01    4   2   7   0   5   0
#> TCGA-OR-A5JP-01   22  23  27   5  10   6
#> TCGA-OR-A5JQ-01    2   2   2   2   1   0
#> TCGA-OR-A5JR-01    1   2   3   0   1   0
#> TCGA-OR-A5JS-01    8   3  28   1   8   1
#> TCGA-OR-A5JT-01    9   3  18   2   6   1
#> TCGA-OR-A5JU-01    7   2  13   2   5   2
#> TCGA-OR-A5JV-01   10   9  14   1   2   0
#> TCGA-OR-A5JW-01   12   3  14   3   3   0
#> TCGA-OR-A5JX-01    5   8  14   4   8   2
#> TCGA-OR-A5JY-01   18  18  37   7  14   4
#> TCGA-OR-A5JZ-01    1   0  11   2   6   0
#> TCGA-OR-A5K0-01   18  10  25   9   8   0
#> TCGA-OR-A5K1-01    2   2   6   3   3   0
#> TCGA-OR-A5K2-01   14  13  27   5  10   4
#> TCGA-OR-A5K3-01    5   4   4   1   5   1
#> TCGA-OR-A5K4-01    7   5 292   5  25   5
#> TCGA-OR-A5K5-01   30  25  48  10  32  10
#> TCGA-OR-A5K6-01    7   7  12   0   7   3
#> TCGA-OR-A5K8-01    9   8   8   1   6   2
#> TCGA-OR-A5K9-01   32  35  59  10  24   8
#> TCGA-OR-A5KB-01 1535 408 461 243 114  46
#> TCGA-OR-A5KO-01   11   8  14   0   5   1
#> TCGA-OR-A5KP-01   12  10  34   2  13   5
#> TCGA-OR-A5KQ-01    0   1   9   0   2   1
#> TCGA-OR-A5KS-01    1   3  11   1   3   2
#> TCGA-OR-A5KT-01    6  10  14   2   5   0
#> TCGA-OR-A5KU-01    1   2  17   1   9   0
#> TCGA-OR-A5KV-01    4   3  16   3   0   0
#> TCGA-OR-A5KW-01    8   6  13   1   7   0
#> TCGA-OR-A5KX-01    3  11  33   3   2   3
#> TCGA-OR-A5KY-01   15  10   9   2   1   1
#> TCGA-OR-A5KZ-01    8   6  11   2   4   0
#> TCGA-OR-A5L1-01    3   1  10   2   9   2
#> TCGA-OR-A5L2-01   32  40  74  15  24   7
#> TCGA-OR-A5L3-01    4   4  12   4   7   1
#> TCGA-OR-A5L4-01    8   3  12   2   5   0
#> TCGA-OR-A5L5-01    3   1   3   2   2   0
#> TCGA-OR-A5L6-01   11   7  20   4   9   1
#> TCGA-OR-A5L8-01    3   0  13   0   4   2
#> TCGA-OR-A5L9-01    1   2   4   0   2   2
#> TCGA-OR-A5LA-01    2   0   8   1   2   1
#> TCGA-OR-A5LB-01   30   4 178  10  24   7
#> TCGA-OR-A5LC-01   21   5  30   3   6   1
#> TCGA-OR-A5LD-01   10  14  34   7  10   8
#> TCGA-OR-A5LE-01    2   4  10   3   6   1
#> TCGA-OR-A5LF-01    4   4  10   0   7   1
#> TCGA-OR-A5LG-01    9   5   9   1   5   1
#> TCGA-OR-A5LH-01    0   0   4   1   1   2
#> TCGA-OR-A5LI-01    6  14  45   2  11   5
#> TCGA-OR-A5LJ-01   39  16 424   7  37   8
#> TCGA-OR-A5LK-01   16   8  28   4   9   2
#> TCGA-OR-A5LL-01    8   9  38   3   7   7
#> TCGA-OR-A5LM-01    5   4  17   3   3   0
#> TCGA-OR-A5LN-01    3   4   6   1   3   0
#> TCGA-OR-A5LO-01   22  30  29   3  10   3
#> TCGA-OR-A5LP-01    5   4   6   3   4   0
#> TCGA-OR-A5LR-01    2   0   5   2   5   0
#> TCGA-OR-A5LS-01    3   3   7   2   3   1
#> TCGA-OR-A5LT-01    5   3  13   0   4   1
#> TCGA-OU-A5PI-01    6   8  11   2   8   1
#> TCGA-P6-A5OF-01    9   2  21   4   3   1
#> TCGA-P6-A5OG-01  124  25 111  24  22   7
#> TCGA-P6-A5OH-01   23  38  56  17  19   5
#> TCGA-PA-A5YG-01    2   0   7   0   2   0
#> TCGA-PK-A5H8-01    9   3   5   1   8   2
#> TCGA-PK-A5H9-01   10   0   7   1   1   2
#> TCGA-PK-A5HA-01   16  12  30   5   6   3
#> TCGA-PK-A5HB-01  128  72 761 160 294  41
#> TCGA-PK-A5HC-01   22  23  27   4   7   2
#> 
#> $all_matrices$SBS_96
#>                 A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       1       1       0       1
#> TCGA-OR-A5J2-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       2       2       0       4       1       1       0       1
#> TCGA-OR-A5J5-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5J6-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5J7-01       1       0       0       0       1       1       0       0
#> TCGA-OR-A5J8-01       4       1       1       1       0       2       2       0
#> TCGA-OR-A5J9-01       0       0       0       1       0       2       0       0
#> TCGA-OR-A5JA-01      12       8       0       6       0       0       0       1
#> TCGA-OR-A5JB-01      10       9       4       6       3       2       2       2
#> TCGA-OR-A5JC-01       0       0       1       1       0       0       0       1
#> TCGA-OR-A5JD-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JE-01       0       1       0       0       1       1       1       0
#> TCGA-OR-A5JF-01       2       2       0       2       1       1       0       0
#> TCGA-OR-A5JG-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       1       1       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5JM-01       0       0       1       0       2       0       1       0
#> TCGA-OR-A5JO-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       1       0       1       0       1       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5JS-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5JT-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       0       0       0       2       0       0
#> TCGA-OR-A5JV-01       0       0       1       0       1       3       0       1
#> TCGA-OR-A5JW-01       1       0       0       2       0       0       0       0
#> TCGA-OR-A5JX-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5JY-01       0       2       0       0       0       0       0       1
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       3       1       1       0       0       0       1       0
#> TCGA-OR-A5K1-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5K2-01       1       0       1       1       0       0       1       1
#> TCGA-OR-A5K3-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5K4-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5K5-01       5       1       2       1       0       0       0       1
#> TCGA-OR-A5K6-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K8-01       1       1       0       1       2       0       0       0
#> TCGA-OR-A5K9-01       1       4       2       1       0       1       2       1
#> TCGA-OR-A5KB-01      69      64      56      59      24      13       9      10
#> TCGA-OR-A5KO-01       0       0       0       1       2       0       0       0
#> TCGA-OR-A5KP-01       2       1       1       0       0       0       1       0
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5KT-01       0       0       1       0       0       2       0       1
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       0       0       0       0       0       0       1       2
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       1       1
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KZ-01       0       0       0       1       0       0       0       1
#> TCGA-OR-A5L1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L2-01       2       1       1       1       1       0       0       3
#> TCGA-OR-A5L3-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5L4-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       1       1       1       0       0       1       0
#> TCGA-OR-A5L8-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5L9-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       2       1       0       0       0       0       1       0
#> TCGA-OR-A5LC-01       2       1       0       1       0       0       0       1
#> TCGA-OR-A5LD-01       0       1       0       1       0       1       0       3
#> TCGA-OR-A5LE-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LG-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       1       0       0       0       0       1       1       0
#> TCGA-OR-A5LJ-01       4       0       0       1       2       0       0       2
#> TCGA-OR-A5LK-01       2       2       0       2       1       0       0       0
#> TCGA-OR-A5LL-01       1       0       0       0       1       0       0       0
#> TCGA-OR-A5LM-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5LN-01       1       1       0       0       1       0       0       0
#> TCGA-OR-A5LO-01       0       3       1       0       1       2       1       0
#> TCGA-OR-A5LP-01       0       1       0       0       0       0       0       2
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       0       1       0       0       1       0
#> TCGA-OU-A5PI-01       0       0       1       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       1       0       0       0       0       0       0
#> TCGA-P6-A5OG-01       5       9       6       4       2       0       1       0
#> TCGA-P6-A5OH-01       0       1       0       1       1       3       1       2
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       2       1       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       3       0       0       0       1       1       0       1
#> TCGA-PK-A5HB-01      10       6       1       6       1       5       1      11
#> TCGA-PK-A5HC-01       1       0       0       0       0       0       0       0
#>                 A[C>T]A A[C>T]C A[C>T]G A[C>T]T A[T>A]A A[T>A]C A[T>A]G A[T>A]T
#> TCGA-OR-A5J1-01       0       1       6       1       0       0       0       0
#> TCGA-OR-A5J2-01       1       1       5       0       1       0       0       0
#> TCGA-OR-A5J3-01       0       0       3       1       0       0       0       0
#> TCGA-OR-A5J4-01       3       2       3       2       0       0       1       0
#> TCGA-OR-A5J5-01       3       0     143       1       1       1       0       0
#> TCGA-OR-A5J6-01       0       0       0       0       0       0       2       0
#> TCGA-OR-A5J7-01       0       1       6       0       0       0       1       0
#> TCGA-OR-A5J8-01       2       0       2       1       1       0       0       0
#> TCGA-OR-A5J9-01       1       0       6       0       0       1       1       0
#> TCGA-OR-A5JA-01       0       1       1       0       0       0       1       0
#> TCGA-OR-A5JB-01       3       1       5       3       4       1       6       1
#> TCGA-OR-A5JC-01       0       0       4       0       0       0       0       1
#> TCGA-OR-A5JD-01       2       3       1       0       0       1       0       0
#> TCGA-OR-A5JE-01       2       0       5       2       0       0       1       0
#> TCGA-OR-A5JF-01       2       2       4       0       0       0       0       0
#> TCGA-OR-A5JG-01       1       1       2       0       0       0       0       1
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       1       0       0       1       1       0
#> TCGA-OR-A5JJ-01       1       1       0       1       0       0       0       0
#> TCGA-OR-A5JK-01       0       2       1       0       0       0       0       0
#> TCGA-OR-A5JL-01       1       0       1       0       0       0       1       0
#> TCGA-OR-A5JM-01       1       1       3       0       0       1       0       0
#> TCGA-OR-A5JO-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       6       0       0       0       0       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       1       5       0       0       0       0       0
#> TCGA-OR-A5JT-01       3       1       3       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       2       1       0       0       1       0
#> TCGA-OR-A5JV-01       0       1       1       2       0       0       1       0
#> TCGA-OR-A5JW-01       1       3       4       0       1       0       0       0
#> TCGA-OR-A5JX-01       1       0       1       1       0       0       1       0
#> TCGA-OR-A5JY-01       0       0       3       0       0       0       1       0
#> TCGA-OR-A5JZ-01       1       0       0       0       1       0       0       0
#> TCGA-OR-A5K0-01       3       0       0       1       0       0       1       0
#> TCGA-OR-A5K1-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5K2-01       0       1       2       0       0       0       0       0
#> TCGA-OR-A5K3-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       3      78       1       2       1       0       1
#> TCGA-OR-A5K5-01       3       2       6       1       0       1       0       1
#> TCGA-OR-A5K6-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5K8-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5K9-01       1       0       9       1       0       1       0       0
#> TCGA-OR-A5KB-01      25      20      17      15       7      10      17       3
#> TCGA-OR-A5KO-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KP-01       2       0       1       1       0       0       0       0
#> TCGA-OR-A5KQ-01       1       0       3       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5KT-01       0       1       0       0       1       1       0       0
#> TCGA-OR-A5KU-01       0       0       5       1       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5KW-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KZ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5L2-01       3       2      15       4       1       1       0       2
#> TCGA-OR-A5L3-01       0       1       1       0       1       0       0       0
#> TCGA-OR-A5L4-01       0       1       1       0       0       0       0       1
#> TCGA-OR-A5L5-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       0       3       1       0       0       0       1
#> TCGA-OR-A5L8-01       0       0       3       1       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5LB-01       2       3      41       2       0       1       1       2
#> TCGA-OR-A5LC-01       0       0       4       1       1       0       0       1
#> TCGA-OR-A5LD-01       2       0       3       1       0       0       0       0
#> TCGA-OR-A5LE-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5LF-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5LG-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LI-01       2       1       2       1       0       0       0       0
#> TCGA-OR-A5LJ-01       6       1     124       4       1       0       0       0
#> TCGA-OR-A5LK-01       0       0       9       0       0       1       0       0
#> TCGA-OR-A5LL-01       3       0       0       1       0       0       1       0
#> TCGA-OR-A5LM-01       0       1       3       0       1       0       0       0
#> TCGA-OR-A5LN-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5LO-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5LP-01       0       0       2       0       0       0       1       1
#> TCGA-OR-A5LR-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LS-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LT-01       1       1       3       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       0       2       0       0       0       0       0
#> TCGA-P6-A5OF-01       2       0       2       0       0       0       2       0
#> TCGA-P6-A5OG-01       3       5       5       3       0       1       1       0
#> TCGA-P6-A5OH-01       3       2       7       2       0       1       0       2
#> TCGA-PA-A5YG-01       0       0       1       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       0       0       9       1       0       2       1       0
#> TCGA-PK-A5HB-01      16      28      31      15      29      28       8       4
#> TCGA-PK-A5HC-01       0       0       2       1       0       0       0       0
#>                 A[T>C]A A[T>C]C A[T>C]G A[T>C]T A[T>G]A A[T>G]C A[T>G]G A[T>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J2-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       1       2       1       2       0       0       0       1
#> TCGA-OR-A5J5-01       1       1       3       0       0       0       0       0
#> TCGA-OR-A5J6-01       3       0       2       4       0       0       0       0
#> TCGA-OR-A5J7-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5J8-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5J9-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5JA-01       1       1       2       1       0       0       0       0
#> TCGA-OR-A5JB-01       2       2       6       1       1       0       0       0
#> TCGA-OR-A5JC-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JD-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5JE-01       0       2       0       0       0       0       0       1
#> TCGA-OR-A5JF-01       0       0       0       1       0       2       0       0
#> TCGA-OR-A5JG-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JK-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5JL-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JM-01       2       0       1       2       0       0       0       0
#> TCGA-OR-A5JO-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       2       0       1       2       0       1       0       0
#> TCGA-OR-A5JQ-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       1       3       1       0       0       0
#> TCGA-OR-A5JT-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JX-01       2       2       2       0       1       0       1       0
#> TCGA-OR-A5JY-01       1       0       2       0       0       0       0       0
#> TCGA-OR-A5JZ-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5K0-01       2       2       1       0       0       0       0       0
#> TCGA-OR-A5K1-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       1       0       0       1       0       0       1       0
#> TCGA-OR-A5K3-01       0       0       1       1       0       0       0       1
#> TCGA-OR-A5K4-01       1       0       3       0       0       0       0       1
#> TCGA-OR-A5K5-01       3       0       3       5       0       1       1       0
#> TCGA-OR-A5K6-01       1       0       3       1       0       0       0       0
#> TCGA-OR-A5K8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       0       0       2       2       1       0       0       1
#> TCGA-OR-A5KB-01      10       3      12       3       1       0       6       3
#> TCGA-OR-A5KO-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5KP-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KT-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       1       0       0       2       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KZ-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5L1-01       1       1       1       1       0       0       0       1
#> TCGA-OR-A5L2-01       2       3       0       2       0       0       0       1
#> TCGA-OR-A5L3-01       0       0       0       2       0       0       1       0
#> TCGA-OR-A5L4-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       2       2       0       0       0       0       1       0
#> TCGA-OR-A5L8-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LB-01       1       0       1       2       0       0       1       0
#> TCGA-OR-A5LC-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LD-01       1       0       1       1       1       0       0       0
#> TCGA-OR-A5LE-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5LF-01       0       1       1       2       0       0       0       0
#> TCGA-OR-A5LG-01       1       0       1       1       0       0       0       1
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       2       1       1       2       1       0       0       0
#> TCGA-OR-A5LJ-01       4       2       0       2       0       1       1       1
#> TCGA-OR-A5LK-01       0       0       3       0       0       2       0       0
#> TCGA-OR-A5LL-01       0       1       0       1       0       0       0       2
#> TCGA-OR-A5LM-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5LP-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5LS-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5LT-01       1       0       0       0       0       0       0       0
#> TCGA-OU-A5PI-01       1       0       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       0       1       0       0       0       0       0
#> TCGA-P6-A5OG-01       2       0       3       2       0       1       0       0
#> TCGA-P6-A5OH-01       1       2       2       2       0       2       0       0
#> TCGA-PA-A5YG-01       0       0       1       0       0       0       0       0
#> TCGA-PK-A5H8-01       2       0       0       1       0       0       1       0
#> TCGA-PK-A5H9-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       2       0       0       3       0       0       0       0
#> TCGA-PK-A5HB-01      20      13      18      12       2       2       0       4
#> TCGA-PK-A5HC-01       2       1       0       1       0       0       0       0
#>                 C[C>A]A C[C>A]C C[C>A]G C[C>A]T C[C>G]A C[C>G]C C[C>G]G C[C>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J2-01       0       2       0       1       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5J4-01       1       4       0       6       2       2       0       2
#> TCGA-OR-A5J5-01       1       6       2       4       0       0       0       0
#> TCGA-OR-A5J6-01       0       1       0       1       1       0       0       0
#> TCGA-OR-A5J7-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J8-01       4       2       3       8       1       0       0       0
#> TCGA-OR-A5J9-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5JA-01      57      16      10      29       0       0       0       3
#> TCGA-OR-A5JB-01      21      24      14      19       0       2       2       4
#> TCGA-OR-A5JC-01       1       1       1       1       0       1       0       1
#> TCGA-OR-A5JD-01       1       0       1       1       1       0       0       1
#> TCGA-OR-A5JE-01       1       1       0       0       0       0       0       1
#> TCGA-OR-A5JF-01       2       2       0       1       3       2       1       3
#> TCGA-OR-A5JG-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JJ-01       0       2       0       0       0       0       1       1
#> TCGA-OR-A5JK-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JL-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       0       0       1       0       1       1
#> TCGA-OR-A5JO-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5JP-01       3       2       0       1       0       2       0       2
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5JR-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JS-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5JT-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JV-01       1       2       0       0       1       1       0       0
#> TCGA-OR-A5JW-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       1       0       1       0       2
#> TCGA-OR-A5JY-01       1       0       1       3       0       5       0       2
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       1       1       3       1       0       0       1       2
#> TCGA-OR-A5K1-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5K2-01       3       1       0       3       2       0       2       1
#> TCGA-OR-A5K3-01       3       0       1       0       0       0       1       2
#> TCGA-OR-A5K4-01       0       1       0       3       0       0       0       1
#> TCGA-OR-A5K5-01       1       3       1       0       0       2       0       2
#> TCGA-OR-A5K6-01       2       0       0       0       0       1       0       0
#> TCGA-OR-A5K8-01       1       1       1       0       0       0       0       1
#> TCGA-OR-A5K9-01       3       2       1       1       3       4       0       1
#> TCGA-OR-A5KB-01     177     172     109     165      38      31      26      34
#> TCGA-OR-A5KO-01       2       0       1       0       0       0       1       1
#> TCGA-OR-A5KP-01       2       0       0       0       0       0       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KT-01       1       0       0       2       0       1       0       3
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KW-01       1       1       0       2       0       0       0       1
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       0       1
#> TCGA-OR-A5KY-01       1       0       0       3       1       1       0       0
#> TCGA-OR-A5KZ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5L1-01       0       0       0       1       0       1       0       0
#> TCGA-OR-A5L2-01       1       2       0       4       0       3       0       4
#> TCGA-OR-A5L3-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5L4-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5L5-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       1       1       1       1       0       0       0
#> TCGA-OR-A5L8-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       2       0       2       7       0       0       0       1
#> TCGA-OR-A5LC-01       2       4       0       4       1       0       0       0
#> TCGA-OR-A5LD-01       1       0       2       0       2       2       1       1
#> TCGA-OR-A5LE-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LF-01       1       0       0       1       0       0       0       1
#> TCGA-OR-A5LG-01       1       0       0       0       1       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       0       1       0       0       3       1       0       2
#> TCGA-OR-A5LJ-01       2       7       1       8       0       0       1       0
#> TCGA-OR-A5LK-01       2       0       1       1       1       1       0       0
#> TCGA-OR-A5LL-01       2       1       0       0       0       1       0       4
#> TCGA-OR-A5LM-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5LO-01       1       3       0       1       1       2       1       0
#> TCGA-OR-A5LP-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LR-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5LT-01       0       1       0       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       0       0       0       0       0       1       2
#> TCGA-P6-A5OF-01       1       1       1       1       0       1       1       0
#> TCGA-P6-A5OG-01      25       9      12       6       1       1       1       3
#> TCGA-P6-A5OH-01       4       2       1       1       2       2       1       2
#> TCGA-PA-A5YG-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       0       2       0       0       0       0
#> TCGA-PK-A5H9-01       0       1       1       0       0       0       0       0
#> TCGA-PK-A5HA-01       2       2       0       1       1       0       0       1
#> TCGA-PK-A5HB-01       7      16       3      19       5       4       1       3
#> TCGA-PK-A5HC-01       1       1       1       2       2       0       0       1
#>                 C[C>T]A C[C>T]C C[C>T]G C[C>T]T C[T>A]A C[T>A]C C[T>A]G C[T>A]T
#> TCGA-OR-A5J1-01       1       0       1       1       0       0       1       0
#> TCGA-OR-A5J2-01       2       0       2       0       0       1       1       0
#> TCGA-OR-A5J3-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5J4-01       0       1       1       3       1       1       0       3
#> TCGA-OR-A5J5-01       0       6      93       1       0       0       0       0
#> TCGA-OR-A5J6-01       0       2       2       0       0       0       1       0
#> TCGA-OR-A5J7-01       2       0       2       2       0       0       0       1
#> TCGA-OR-A5J8-01       2       2       3       2       0       0       0       1
#> TCGA-OR-A5J9-01       0       1       4       0       0       0       0       1
#> TCGA-OR-A5JA-01       1       0       1       2       0       2       2       0
#> TCGA-OR-A5JB-01       8       3       6       9       2       4       7       2
#> TCGA-OR-A5JC-01       1       0       2       0       0       3       1       0
#> TCGA-OR-A5JD-01       1       0       3       1       0       0       0       0
#> TCGA-OR-A5JE-01       1       3       6       2       0       0       1       0
#> TCGA-OR-A5JF-01       1       2       1       2       1       1       0       1
#> TCGA-OR-A5JG-01       0       0       4       2       0       0       1       0
#> TCGA-OR-A5JH-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5JK-01       1       1       2       2       1       0       0       0
#> TCGA-OR-A5JL-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JM-01       2       1       4       2       0       1       0       1
#> TCGA-OR-A5JO-01       2       1       1       0       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       4       2       1       2       0       0
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       1       1       2       0       1       0       0
#> TCGA-OR-A5JT-01       0       2       2       1       0       0       0       0
#> TCGA-OR-A5JU-01       0       2       4       0       0       0       0       0
#> TCGA-OR-A5JV-01       0       1       2       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       2       0       0       1       0       0
#> TCGA-OR-A5JX-01       0       1       1       0       0       0       2       0
#> TCGA-OR-A5JY-01       1       0       4       2       0       2       1       1
#> TCGA-OR-A5JZ-01       0       0       2       1       0       0       1       0
#> TCGA-OR-A5K0-01       4       2       2       4       2       0       1       0
#> TCGA-OR-A5K1-01       0       0       1       2       0       0       1       1
#> TCGA-OR-A5K2-01       0       3       7       2       0       0       2       1
#> TCGA-OR-A5K3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       2       1      71       3       0       0       0       1
#> TCGA-OR-A5K5-01       6       2       6       1       0       2       0       1
#> TCGA-OR-A5K6-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5K8-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5K9-01       4       4       2       2       0       3       0       1
#> TCGA-OR-A5KB-01      46      43      29      48      18      27      63      22
#> TCGA-OR-A5KO-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5KP-01       4       2       4       1       0       0       1       0
#> TCGA-OR-A5KQ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KS-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5KT-01       1       1       2       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       3       0       0       1       0       0
#> TCGA-OR-A5KV-01       2       1       4       1       0       0       0       0
#> TCGA-OR-A5KW-01       0       0       4       2       1       0       0       0
#> TCGA-OR-A5KX-01       3       2       6       2       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       1       1
#> TCGA-OR-A5KZ-01       2       0       1       0       0       1       0       0
#> TCGA-OR-A5L1-01       0       0       0       1       0       2       0       0
#> TCGA-OR-A5L2-01       3       0       8       3       0       1       1       0
#> TCGA-OR-A5L3-01       1       0       2       1       1       1       1       0
#> TCGA-OR-A5L4-01       1       2       0       1       0       0       1       0
#> TCGA-OR-A5L5-01       0       0       1       0       0       1       0       1
#> TCGA-OR-A5L6-01       1       1       4       3       0       0       2       0
#> TCGA-OR-A5L8-01       0       0       3       1       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LB-01       2       2      24       1       1       0       0       1
#> TCGA-OR-A5LC-01       3       0       4       0       0       0       1       0
#> TCGA-OR-A5LD-01       0       2       5       2       0       2       2       0
#> TCGA-OR-A5LE-01       2       1       1       0       0       0       1       0
#> TCGA-OR-A5LF-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LG-01       1       0       1       0       0       0       0       1
#> TCGA-OR-A5LH-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5LI-01       3       2       9       2       0       1       0       0
#> TCGA-OR-A5LJ-01       3       2      74       4       0       1       1       1
#> TCGA-OR-A5LK-01       0       2       3       0       0       0       1       0
#> TCGA-OR-A5LL-01       0       4       7       0       0       0       1       0
#> TCGA-OR-A5LM-01       1       1       1       2       0       1       0       0
#> TCGA-OR-A5LN-01       0       0       0       1       0       0       0       1
#> TCGA-OR-A5LO-01       2       1       3       2       0       0       1       0
#> TCGA-OR-A5LP-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5LS-01       0       0       1       1       0       0       0       1
#> TCGA-OR-A5LT-01       0       0       0       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       1       1       1       0       0       1       0
#> TCGA-P6-A5OF-01       2       0       1       1       0       1       0       0
#> TCGA-P6-A5OG-01       5       8      13       2       0       0       9       4
#> TCGA-P6-A5OH-01       2       2       6       1       0       1       2       2
#> TCGA-PA-A5YG-01       2       0       1       0       0       0       0       0
#> TCGA-PK-A5H8-01       1       0       0       0       0       0       0       1
#> TCGA-PK-A5H9-01       1       0       1       0       0       0       0       0
#> TCGA-PK-A5HA-01       0       1       5       0       0       0       1       0
#> TCGA-PK-A5HB-01      18      23      34      17       2       9      12       3
#> TCGA-PK-A5HC-01       0       3       1       2       0       2       1       0
#>                 C[T>C]A C[T>C]C C[T>C]G C[T>C]T C[T>G]A C[T>G]C C[T>G]G C[T>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       1       1       0
#> TCGA-OR-A5J2-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J3-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       0       2       2       1       0       0       0       0
#> TCGA-OR-A5J5-01       2       1       2       0       0       0       0       1
#> TCGA-OR-A5J6-01       1       0       2       1       0       0       0       0
#> TCGA-OR-A5J7-01       0       0       0       1       0       1       0       0
#> TCGA-OR-A5J8-01       1       0       1       1       0       0       0       1
#> TCGA-OR-A5J9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JA-01       0       1       0       1       0       0       1       0
#> TCGA-OR-A5JB-01       3       0       4       4       0       0       0       0
#> TCGA-OR-A5JC-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5JD-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JE-01       0       0       3       0       0       1       0       0
#> TCGA-OR-A5JF-01       2       1       1       1       0       0       1       0
#> TCGA-OR-A5JG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JK-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       0       0       0       1       1       1
#> TCGA-OR-A5JO-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       0       1       0       0       0       0       1       1
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5JT-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JU-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5JV-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JY-01       0       3       0       1       2       0       2       0
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       0       2       4       0       0       0       0       0
#> TCGA-OR-A5K3-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       2       0       2       1       0       0       1       1
#> TCGA-OR-A5K5-01       0       1       1       3       0       1       2       0
#> TCGA-OR-A5K6-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5K8-01       0       0       1       2       0       1       0       0
#> TCGA-OR-A5K9-01       0       1       2       0       0       0       2       1
#> TCGA-OR-A5KB-01      10       4      18       9       1       2      13       3
#> TCGA-OR-A5KO-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KP-01       2       0       1       1       0       0       0       0
#> TCGA-OR-A5KQ-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KT-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L1-01       1       0       0       1       0       0       1       0
#> TCGA-OR-A5L2-01       0       3       2       4       0       0       1       1
#> TCGA-OR-A5L3-01       0       1       3       0       0       0       0       0
#> TCGA-OR-A5L4-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5L8-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5LA-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5LB-01       2       2       2       0       0       2       1       1
#> TCGA-OR-A5LC-01       0       0       2       0       0       0       1       0
#> TCGA-OR-A5LD-01       0       1       1       0       0       0       3       1
#> TCGA-OR-A5LE-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       1       1       1       0       0       0       1
#> TCGA-OR-A5LG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       0       0       1       0       0       0       2       0
#> TCGA-OR-A5LJ-01       1       0       5       0       0       1       0       2
#> TCGA-OR-A5LK-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5LL-01       0       0       1       1       1       1       0       2
#> TCGA-OR-A5LM-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       2       1       0       0       0       1       1
#> TCGA-OR-A5LP-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       2       0       0       0       0       0
#> TCGA-OU-A5PI-01       0       4       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       1       1       0       0       0       0       0
#> TCGA-P6-A5OG-01       0       4       2       0       0       0       2       0
#> TCGA-P6-A5OH-01       0       3       1       1       0       2       0       0
#> TCGA-PA-A5YG-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       1       2       0       0       0       0
#> TCGA-PK-A5H9-01       0       1       0       0       0       0       1       0
#> TCGA-PK-A5HA-01       0       0       0       0       1       1       0       0
#> TCGA-PK-A5HB-01      16      13      17      11       5       1       6       2
#> TCGA-PK-A5HC-01       0       0       0       0       0       0       0       1
#>                 G[C>A]A G[C>A]C G[C>A]G G[C>A]T G[C>G]A G[C>G]C G[C>G]G G[C>G]T
#> TCGA-OR-A5J1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J2-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5J3-01       2       0       0       1       1       0       0       0
#> TCGA-OR-A5J4-01       2       2       0       3       0       3       0       1
#> TCGA-OR-A5J5-01       1       0       0       1       0       2       0       0
#> TCGA-OR-A5J6-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5J7-01       1       0       0       1       0       2       0       0
#> TCGA-OR-A5J8-01       7       3       2       4       1       3       0       1
#> TCGA-OR-A5J9-01       0       0       0       0       0       1       0       1
#> TCGA-OR-A5JA-01      80      19       5      56       1       2       0       0
#> TCGA-OR-A5JB-01       8       7      13       3       3       0       3       0
#> TCGA-OR-A5JC-01       1       1       0       0       1       1       0       0
#> TCGA-OR-A5JD-01       0       0       0       1       0       1       0       1
#> TCGA-OR-A5JE-01       3       0       2       0       0       0       1       2
#> TCGA-OR-A5JF-01       0       1       1       0       3       1       0       2
#> TCGA-OR-A5JG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       1       1       0       0       1
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5JM-01       1       1       2       2       0       3       0       1
#> TCGA-OR-A5JO-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JP-01       1       1       3       1       0       1       0       3
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JT-01       0       2       1       2       0       0       0       0
#> TCGA-OR-A5JU-01       0       1       1       1       0       0       0       0
#> TCGA-OR-A5JV-01       0       3       0       0       0       1       0       1
#> TCGA-OR-A5JW-01       1       1       0       2       1       1       0       0
#> TCGA-OR-A5JX-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5JY-01       2       1       0       4       2       1       0       0
#> TCGA-OR-A5JZ-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       2       1       1       0       0       0       0       1
#> TCGA-OR-A5K1-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5K3-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K5-01       1       1       0       2       0       1       2       2
#> TCGA-OR-A5K6-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5K8-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       1       3       2       0       1       3       2       2
#> TCGA-OR-A5KB-01      83     102      62      66      21      29      22      12
#> TCGA-OR-A5KO-01       1       0       0       2       1       0       0       1
#> TCGA-OR-A5KP-01       0       1       1       0       1       0       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KT-01       1       0       0       0       0       2       1       0
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5KW-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5KY-01       4       1       2       0       1       2       0       0
#> TCGA-OR-A5KZ-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5L1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L2-01       3       0       1       3       2       3       1       2
#> TCGA-OR-A5L3-01       0       2       1       0       0       1       0       0
#> TCGA-OR-A5L4-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       2       0       0       0       1
#> TCGA-OR-A5L6-01       0       2       0       0       0       0       1       0
#> TCGA-OR-A5L8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       2
#> TCGA-OR-A5LA-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LB-01       5       2       2       3       0       0       1       0
#> TCGA-OR-A5LC-01       1       2       2       1       0       0       0       0
#> TCGA-OR-A5LD-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LE-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       1       0       0       0       0       1       1       0
#> TCGA-OR-A5LG-01       1       1       1       2       0       1       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LJ-01       4       3       1       2       1       2       0       2
#> TCGA-OR-A5LK-01       0       1       0       2       0       1       0       1
#> TCGA-OR-A5LL-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5LM-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       6       0       0       2       1       0       0       0
#> TCGA-OR-A5LP-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LT-01       0       1       1       0       0       0       0       0
#> TCGA-OU-A5PI-01       1       2       1       0       1       0       1       1
#> TCGA-P6-A5OF-01       0       0       1       0       0       0       0       0
#> TCGA-P6-A5OG-01       6       8       8       7       1       2       2       1
#> TCGA-P6-A5OH-01       3       1       2       0       0       3       0       2
#> TCGA-PA-A5YG-01       0       0       0       1       0       0       0       0
#> TCGA-PK-A5H8-01       2       1       1       0       0       0       0       0
#> TCGA-PK-A5H9-01       2       1       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       1       1       0       2       0       0       0       0
#> TCGA-PK-A5HB-01       6      12       3      11       0      10       1       1
#> TCGA-PK-A5HC-01       1       1       1       2       0       1       0       2
#>                 G[C>T]A G[C>T]C G[C>T]G G[C>T]T G[T>A]A G[T>A]C G[T>A]G G[T>A]T
#> TCGA-OR-A5J1-01       3       4       1       1       0       0       0       0
#> TCGA-OR-A5J2-01       1       1       2       0       0       1       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5J4-01       3       6       5       4       0       1       0       1
#> TCGA-OR-A5J5-01      12       5     116       3       0       0       0       1
#> TCGA-OR-A5J6-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5J7-01       1       0       1       2       0       1       0       0
#> TCGA-OR-A5J8-01       3       2       7       0       0       1       0       0
#> TCGA-OR-A5J9-01       2       0       2       0       0       0       0       0
#> TCGA-OR-A5JA-01       1       1       6       1       0       0       0       0
#> TCGA-OR-A5JB-01       2       2       2       2       1       2       4       0
#> TCGA-OR-A5JC-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5JD-01       2       1       2       0       0       0       0       0
#> TCGA-OR-A5JE-01       1       0       0       1       0       0       1       0
#> TCGA-OR-A5JF-01       0       0       1       0       0       1       1       0
#> TCGA-OR-A5JG-01       2       2       3       0       0       0       0       0
#> TCGA-OR-A5JH-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       2       2       4       0       0       0       0       0
#> TCGA-OR-A5JO-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JP-01       1       0       3       1       0       2       0       0
#> TCGA-OR-A5JQ-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       1       1       4       1       0       0       0       0
#> TCGA-OR-A5JT-01       1       0       1       0       1       0       0       0
#> TCGA-OR-A5JU-01       0       0       4       0       0       0       0       0
#> TCGA-OR-A5JV-01       0       1       4       0       0       0       0       0
#> TCGA-OR-A5JW-01       1       0       1       0       1       0       0       0
#> TCGA-OR-A5JX-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5JY-01       3       2       4       0       0       1       1       0
#> TCGA-OR-A5JZ-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5K0-01       0       0       2       0       0       0       0       1
#> TCGA-OR-A5K1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       1       0       3       2       0       0       0       0
#> TCGA-OR-A5K3-01       0       0       3       0       0       0       1       0
#> TCGA-OR-A5K4-01       5       5      78       4       0       0       0       0
#> TCGA-OR-A5K5-01       1       1       3       4       0       1       1       0
#> TCGA-OR-A5K6-01       1       0       2       2       0       0       0       0
#> TCGA-OR-A5K8-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       1       3       9       1       0       0       1       0
#> TCGA-OR-A5KB-01      19      17      16      22      12       6      19       9
#> TCGA-OR-A5KO-01       1       1       2       0       0       0       0       0
#> TCGA-OR-A5KP-01       1       4       3       2       0       1       0       0
#> TCGA-OR-A5KQ-01       0       1       2       1       0       0       0       0
#> TCGA-OR-A5KS-01       2       0       1       0       0       0       0       0
#> TCGA-OR-A5KT-01       1       0       0       2       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       4       0       0       0       0       0
#> TCGA-OR-A5KV-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5KW-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5KX-01       2       2       8       0       2       0       0       0
#> TCGA-OR-A5KY-01       4       0       1       0       0       0       0       0
#> TCGA-OR-A5KZ-01       0       0       2       1       1       0       0       0
#> TCGA-OR-A5L1-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5L2-01       4       3       8       3       1       3       0       0
#> TCGA-OR-A5L3-01       1       0       1       1       0       0       0       0
#> TCGA-OR-A5L4-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       0       2       2       0       0       1       0
#> TCGA-OR-A5L8-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       2       0       0       0       1       0
#> TCGA-OR-A5LB-01      12      10      47      12       1       1       0       1
#> TCGA-OR-A5LC-01       2       3       5       0       0       0       0       0
#> TCGA-OR-A5LD-01       3       2       5       0       0       1       0       0
#> TCGA-OR-A5LE-01       0       0       2       0       0       0       0       1
#> TCGA-OR-A5LF-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LG-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5LI-01       1       2       4       2       0       0       0       1
#> TCGA-OR-A5LJ-01      16      14     114       8       0       1       1       0
#> TCGA-OR-A5LK-01       1       0       5       1       0       1       0       1
#> TCGA-OR-A5LL-01       4       2       6       2       0       1       0       0
#> TCGA-OR-A5LM-01       0       0       3       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       1       2       0       0       1       0       0
#> TCGA-OR-A5LP-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5LR-01       0       2       0       1       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5LT-01       0       0       2       1       0       0       0       0
#> TCGA-OU-A5PI-01       0       1       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       2       1       1       2       0       0       0       0
#> TCGA-P6-A5OG-01       5       3       4       3       0       3       3       0
#> TCGA-P6-A5OH-01       2       6       2       2       0       0       1       0
#> TCGA-PA-A5YG-01       0       0       2       1       0       0       0       0
#> TCGA-PK-A5H8-01       0       1       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       0       0       1       1       0       0       0       0
#> TCGA-PK-A5HA-01       1       3       2       0       0       1       0       0
#> TCGA-PK-A5HB-01      75     111     113      79      11      10       8       6
#> TCGA-PK-A5HC-01       2       1       1       0       0       0       0       0
#>                 G[T>C]A G[T>C]C G[T>C]G G[T>C]T G[T>G]A G[T>G]C G[T>G]G G[T>G]T
#> TCGA-OR-A5J1-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5J2-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       2       3       0       1       1       1       1       1
#> TCGA-OR-A5J5-01       7       0       0       2       0       0       0       0
#> TCGA-OR-A5J6-01       2       0       2       1       0       0       0       0
#> TCGA-OR-A5J7-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5J8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J9-01       1       1       0       1       0       0       0       1
#> TCGA-OR-A5JA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JB-01       3       0       0       0       1       0       1       0
#> TCGA-OR-A5JC-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JD-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JE-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5JF-01       0       1       2       0       0       0       3       0
#> TCGA-OR-A5JG-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JO-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JP-01       1       0       0       1       0       1       2       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JT-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JU-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5JV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       2       0       0       0       0
#> TCGA-OR-A5JY-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5JZ-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5K0-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5K1-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5K2-01       0       0       0       2       0       0       0       1
#> TCGA-OR-A5K3-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5K4-01       2       2       0       3       0       0       1       0
#> TCGA-OR-A5K5-01       2       2       4       2       0       1       1       1
#> TCGA-OR-A5K6-01       0       0       0       1       0       1       0       0
#> TCGA-OR-A5K8-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5K9-01       4       2       3       1       1       1       1       0
#> TCGA-OR-A5KB-01       7       5      12       5       1       0       3       3
#> TCGA-OR-A5KO-01       0       0       1       0       0       0       1       0
#> TCGA-OR-A5KP-01       0       2       1       0       0       0       1       2
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5KT-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5KU-01       3       0       0       2       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KY-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KZ-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L2-01       1       3       1       1       0       1       1       1
#> TCGA-OR-A5L3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L4-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L5-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L8-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       1       0       0       1       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       3       3       3       1       0       1       0       0
#> TCGA-OR-A5LC-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LD-01       0       3       1       0       0       0       0       0
#> TCGA-OR-A5LE-01       2       1       1       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LG-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5LI-01       0       1       2       0       0       1       0       1
#> TCGA-OR-A5LJ-01       1       2       1       1       0       0       1       0
#> TCGA-OR-A5LK-01       0       1       0       2       0       0       0       0
#> TCGA-OR-A5LL-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5LM-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LN-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5LO-01       2       1       0       0       0       0       0       0
#> TCGA-OR-A5LP-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5LT-01       0       1       0       0       0       0       0       0
#> TCGA-OU-A5PI-01       0       1       0       0       0       0       1       0
#> TCGA-P6-A5OF-01       0       0       0       0       0       0       0       0
#> TCGA-P6-A5OG-01       2       0       2       1       0       0       3       0
#> TCGA-P6-A5OH-01       4       1       0       0       0       1       0       0
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       1       1       0       0       0       0       0       1
#> TCGA-PK-A5H9-01       0       0       0       0       1       0       0       0
#> TCGA-PK-A5HA-01       1       0       0       0       0       0       0       0
#> TCGA-PK-A5HB-01      38      32      29      11       2       2       1       1
#> TCGA-PK-A5HC-01       1       0       0       1       0       0       0       0
#>                 T[C>A]A T[C>A]C T[C>A]G T[C>A]T T[C>G]A T[C>G]C T[C>G]G T[C>G]T
#> TCGA-OR-A5J1-01       1       0       0       0       0       1       0       1
#> TCGA-OR-A5J2-01       3       1       0       1       0       0       0       1
#> TCGA-OR-A5J3-01       1       0       0       1       0       1       0       0
#> TCGA-OR-A5J4-01       6       4       0       3       9       4       4      10
#> TCGA-OR-A5J5-01       2       0       0       2       0       0       0       1
#> TCGA-OR-A5J6-01       0       0       1       0       0       1       1       2
#> TCGA-OR-A5J7-01       0       2       0       3       2       6       0       4
#> TCGA-OR-A5J8-01      12       8       2       9       1       2       0       0
#> TCGA-OR-A5J9-01       0       0       1       0       1       1       0       3
#> TCGA-OR-A5JA-01     114      66      16     120       1       1       0       1
#> TCGA-OR-A5JB-01       8      17       5       7      15       5       3      19
#> TCGA-OR-A5JC-01       0       0       0       0       1       1       0       2
#> TCGA-OR-A5JD-01       0       1       0       1       0       0       0       1
#> TCGA-OR-A5JE-01       1       3       0       0       5       2       0       0
#> TCGA-OR-A5JF-01       2       0       0       2       0       3       0       5
#> TCGA-OR-A5JG-01       0       0       0       0       0       2       0       3
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5JK-01       1       0       0       1       2       0       0       2
#> TCGA-OR-A5JL-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       3       1       2       2       2       1       0       3
#> TCGA-OR-A5JO-01       1       0       0       0       0       1       0       0
#> TCGA-OR-A5JP-01       3       3       0       2       5       3       1       4
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       1       0
#> TCGA-OR-A5JR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JS-01       3       0       0       0       0       1       0       1
#> TCGA-OR-A5JT-01       0       1       0       0       0       1       0       2
#> TCGA-OR-A5JU-01       2       0       0       1       0       0       0       0
#> TCGA-OR-A5JV-01       0       0       0       3       0       0       0       0
#> TCGA-OR-A5JW-01       1       1       0       0       1       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       0       2       1       0       2
#> TCGA-OR-A5JY-01       1       2       0       1       2       1       0       4
#> TCGA-OR-A5JZ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       2       0       1       0       1       0       1       3
#> TCGA-OR-A5K1-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K2-01       0       1       0       1       1       1       1       2
#> TCGA-OR-A5K3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       1       0       1       1       1       0       1
#> TCGA-OR-A5K5-01       2       6       0       4       4       2       0       9
#> TCGA-OR-A5K6-01       2       2       0       0       2       1       2       0
#> TCGA-OR-A5K8-01       1       0       0       0       3       0       0       2
#> TCGA-OR-A5K9-01       4       3       0       4       1       4       1       9
#> TCGA-OR-A5KB-01      73     146      50      82      44      35      19      41
#> TCGA-OR-A5KO-01       0       2       1       1       0       2       0       0
#> TCGA-OR-A5KP-01       0       2       1       1       2       3       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KS-01       0       0       0       0       0       0       0       2
#> TCGA-OR-A5KT-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       1       0       1       1       0       0
#> TCGA-OR-A5KV-01       1       1       0       0       0       1       0       0
#> TCGA-OR-A5KW-01       1       0       2       0       1       0       1       0
#> TCGA-OR-A5KX-01       0       0       0       0       1       2       0       4
#> TCGA-OR-A5KY-01       1       2       0       1       2       0       0       2
#> TCGA-OR-A5KZ-01       2       0       1       2       0       3       0       1
#> TCGA-OR-A5L1-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5L2-01       1       7       1       4      11       5       0       5
#> TCGA-OR-A5L3-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5L4-01       1       2       1       1       0       1       0       1
#> TCGA-OR-A5L5-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       1       0       0       1       0       3       0       1
#> TCGA-OR-A5L8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       1       1       1       1       0       0       0       1
#> TCGA-OR-A5LC-01       0       0       0       1       1       0       0       2
#> TCGA-OR-A5LD-01       0       2       1       0       0       0       0       4
#> TCGA-OR-A5LE-01       0       0       0       0       1       0       1       2
#> TCGA-OR-A5LF-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5LG-01       0       1       0       1       1       0       0       2
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       1       1       0       1       1       2       0       2
#> TCGA-OR-A5LJ-01       1       2       1       2       1       0       1       4
#> TCGA-OR-A5LK-01       0       0       1       2       1       2       0       0
#> TCGA-OR-A5LL-01       0       0       0       1       0       1       0       2
#> TCGA-OR-A5LM-01       0       0       1       0       0       1       0       1
#> TCGA-OR-A5LN-01       0       0       0       0       0       0       1       1
#> TCGA-OR-A5LO-01       2       1       1       1       9       4       0       8
#> TCGA-OR-A5LP-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       1       0       0       1       0       0       1
#> TCGA-OR-A5LT-01       0       0       0       0       0       1       0       1
#> TCGA-OU-A5PI-01       0       0       0       1       0       1       0       1
#> TCGA-P6-A5OF-01       1       1       0       1       0       0       0       0
#> TCGA-P6-A5OG-01       6       9       1       3       3       2       4       1
#> TCGA-P6-A5OH-01       2       2       0       3       6       6       2       5
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       2       0       0       0       0       0       1       2
#> TCGA-PK-A5H9-01       1       1       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       1       1       0       2       4       0       0       3
#> TCGA-PK-A5HB-01       6      10       2      10       5      12       0      12
#> TCGA-PK-A5HC-01       4       2       0       5       7       2       1       7
#>                 T[C>T]A T[C>T]C T[C>T]G T[C>T]T T[T>A]A T[T>A]C T[T>A]G T[T>A]T
#> TCGA-OR-A5J1-01       0       1       4       0       0       0       0       0
#> TCGA-OR-A5J2-01       2       2       2       0       0       0       0       0
#> TCGA-OR-A5J3-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5J4-01       3       3       3       2       0       0       2       0
#> TCGA-OR-A5J5-01       0       1      53       0       0       1       0       0
#> TCGA-OR-A5J6-01       0       1       1       1       0       0       0       0
#> TCGA-OR-A5J7-01       1       1       4       1       0       1       0       0
#> TCGA-OR-A5J8-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J9-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JA-01       5       3       1       0       0       0       0       0
#> TCGA-OR-A5JB-01      28      11      10      16       0       1       2       1
#> TCGA-OR-A5JC-01       1       1       0       1       0       0       0       0
#> TCGA-OR-A5JD-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JE-01       2       3       0       0       0       0       0       0
#> TCGA-OR-A5JF-01       3       5       2       2       0       0       1       0
#> TCGA-OR-A5JG-01       2       0       1       0       0       0       1       0
#> TCGA-OR-A5JH-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       0       0       2       1       0       0       0       0
#> TCGA-OR-A5JK-01       1       0       2       2       0       0       2       0
#> TCGA-OR-A5JL-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JM-01       3       2       0       6       0       0       0       0
#> TCGA-OR-A5JO-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JP-01       2       1       2       3       0       0       0       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JS-01       7       0       2       2       0       0       0       0
#> TCGA-OR-A5JT-01       0       3       1       0       1       0       0       0
#> TCGA-OR-A5JU-01       0       0       0       0       0       1       0       0
#> TCGA-OR-A5JV-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5JW-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5JX-01       3       1       2       1       0       0       0       1
#> TCGA-OR-A5JY-01       6       6       4       2       0       0       0       0
#> TCGA-OR-A5JZ-01       0       1       2       1       0       0       0       0
#> TCGA-OR-A5K0-01       1       2       2       2       0       2       1       1
#> TCGA-OR-A5K1-01       1       0       1       0       0       0       0       0
#> TCGA-OR-A5K2-01       0       4       0       2       1       0       0       1
#> TCGA-OR-A5K3-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       0       2      35       4       0       0       0       0
#> TCGA-OR-A5K5-01       3       2       2       5       0       2       1       0
#> TCGA-OR-A5K6-01       3       0       1       0       0       0       0       0
#> TCGA-OR-A5K8-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5K9-01       6       6       4       6       2       0       1       1
#> TCGA-OR-A5KB-01      50      37      18      39       4       9      12       5
#> TCGA-OR-A5KO-01       2       1       0       3       0       0       0       0
#> TCGA-OR-A5KP-01       1       3       3       2       0       0       0       0
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KS-01       1       3       1       1       0       0       0       0
#> TCGA-OR-A5KT-01       4       1       0       1       0       0       0       0
#> TCGA-OR-A5KU-01       1       0       3       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       1       1       2       0       0       0       2
#> TCGA-OR-A5KW-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KX-01       2       4       0       0       1       0       0       0
#> TCGA-OR-A5KY-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5KZ-01       1       2       1       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       1       3       0       0       0       0       0
#> TCGA-OR-A5L2-01       5       5       6       2       0       2       0       3
#> TCGA-OR-A5L3-01       1       0       2       0       0       0       0       0
#> TCGA-OR-A5L4-01       4       0       1       1       0       0       0       0
#> TCGA-OR-A5L5-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       0       0       2       0       0       0       0       0
#> TCGA-OR-A5L8-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5L9-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       1       2       0       0       0       0
#> TCGA-OR-A5LB-01       1       3      14       2       0       0       1       0
#> TCGA-OR-A5LC-01       0       5       0       3       0       0       0       0
#> TCGA-OR-A5LD-01       2       1       5       1       0       2       0       0
#> TCGA-OR-A5LE-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5LF-01       0       2       0       1       0       0       0       0
#> TCGA-OR-A5LG-01       1       1       0       2       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LI-01       2       3       6       3       0       0       0       0
#> TCGA-OR-A5LJ-01       4       7      39       4       0       0       0       1
#> TCGA-OR-A5LK-01       1       2       3       1       0       0       0       0
#> TCGA-OR-A5LL-01       3       2       3       1       0       0       0       0
#> TCGA-OR-A5LM-01       1       0       4       0       0       1       0       0
#> TCGA-OR-A5LN-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5LO-01       5       3       4       3       0       0       0       1
#> TCGA-OR-A5LP-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       1       1       1       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       3       0       0       0       0       0
#> TCGA-OU-A5PI-01       2       1       1       1       0       0       1       0
#> TCGA-P6-A5OF-01       1       0       5       1       0       1       0       0
#> TCGA-P6-A5OG-01      22       7       6      17       0       0       2       1
#> TCGA-P6-A5OH-01       4       6       6       3       3       2       0       3
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       1       0       2       0       0       0       0       0
#> TCGA-PK-A5H9-01       1       1       0       1       0       0       1       0
#> TCGA-PK-A5HA-01       3       3       1       1       0       0       0       0
#> TCGA-PK-A5HB-01      52      61      35      53       9      12       3       6
#> TCGA-PK-A5HC-01       2       4       1       7       0       1       0       0
#>                 T[T>C]A T[T>C]C T[T>C]G T[T>C]T T[T>G]A T[T>G]C T[T>G]G T[T>G]T
#> TCGA-OR-A5J1-01       0       0       2       0       1       1       0       0
#> TCGA-OR-A5J2-01       0       0       0       0       1       0       0       1
#> TCGA-OR-A5J3-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5J4-01       1       0       2       0       1       1       0       1
#> TCGA-OR-A5J5-01       3       1       3       1       1       1       0       1
#> TCGA-OR-A5J6-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5J7-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5J8-01       1       0       1       0       0       0       1       1
#> TCGA-OR-A5J9-01       0       0       0       0       1       0       0       0
#> TCGA-OR-A5JA-01       0       0       1       1       0       0       0       0
#> TCGA-OR-A5JB-01       0       0       1       0       0       1       0       0
#> TCGA-OR-A5JC-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5JD-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JE-01       0       0       1       0       0       0       0       1
#> TCGA-OR-A5JF-01       0       2       0       0       1       0       1       0
#> TCGA-OR-A5JG-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5JH-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JI-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JJ-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JK-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JL-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5JM-01       1       0       2       1       0       0       1       0
#> TCGA-OR-A5JO-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JP-01       0       2       0       0       0       0       0       0
#> TCGA-OR-A5JQ-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JR-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5JS-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5JT-01       0       1       0       0       0       0       1       0
#> TCGA-OR-A5JU-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5JV-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5JW-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JX-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5JY-01       0       2       1       1       0       0       0       0
#> TCGA-OR-A5JZ-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K0-01       1       0       0       1       0       0       0       0
#> TCGA-OR-A5K1-01       0       0       0       1       0       0       0       0
#> TCGA-OR-A5K2-01       0       0       0       0       0       1       1       0
#> TCGA-OR-A5K3-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5K4-01       4       0       4       1       0       0       1       0
#> TCGA-OR-A5K5-01       0       2       2       2       0       0       0       2
#> TCGA-OR-A5K6-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5K8-01       0       1       0       0       0       1       0       0
#> TCGA-OR-A5K9-01       1       4       1       1       0       0       0       0
#> TCGA-OR-A5KB-01       5       3       5       3       1       3       5       1
#> TCGA-OR-A5KO-01       0       1       0       1       0       0       0       0
#> TCGA-OR-A5KP-01       0       1       1       2       0       1       0       1
#> TCGA-OR-A5KQ-01       0       0       0       0       0       0       0       1
#> TCGA-OR-A5KS-01       1       0       0       0       0       0       0       1
#> TCGA-OR-A5KT-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5KU-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KV-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5KW-01       1       1       0       1       0       0       0       0
#> TCGA-OR-A5KX-01       0       0       1       0       0       0       2       1
#> TCGA-OR-A5KY-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5KZ-01       1       1       0       0       0       0       0       0
#> TCGA-OR-A5L1-01       0       1       1       0       0       0       0       0
#> TCGA-OR-A5L2-01       0       0       2       0       0       1       0       0
#> TCGA-OR-A5L3-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5L4-01       0       0       1       0       0       0       0       0
#> TCGA-OR-A5L5-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5L6-01       2       1       0       0       0       0       0       0
#> TCGA-OR-A5L8-01       0       1       0       0       0       0       0       1
#> TCGA-OR-A5L9-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LA-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LB-01       1       2       0       1       1       0       0       0
#> TCGA-OR-A5LC-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LD-01       0       0       0       1       0       0       0       3
#> TCGA-OR-A5LE-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LF-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LG-01       2       0       0       0       0       0       0       0
#> TCGA-OR-A5LH-01       0       0       0       0       1       0       1       0
#> TCGA-OR-A5LI-01       1       0       0       0       0       0       0       0
#> TCGA-OR-A5LJ-01       7       2       5       4       0       0       0       1
#> TCGA-OR-A5LK-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LL-01       2       1       0       0       0       0       0       0
#> TCGA-OR-A5LM-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LN-01       0       1       0       0       0       0       0       0
#> TCGA-OR-A5LO-01       0       0       0       1       0       0       1       0
#> TCGA-OR-A5LP-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LR-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LS-01       0       0       0       0       0       0       0       0
#> TCGA-OR-A5LT-01       0       0       0       0       0       0       0       1
#> TCGA-OU-A5PI-01       1       1       0       0       0       0       0       0
#> TCGA-P6-A5OF-01       0       0       0       0       0       1       0       0
#> TCGA-P6-A5OG-01       0       1       1       2       0       0       0       1
#> TCGA-P6-A5OH-01       0       1       1       0       0       0       0       0
#> TCGA-PA-A5YG-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H8-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5H9-01       0       0       0       0       0       0       0       0
#> TCGA-PK-A5HA-01       0       0       0       0       1       0       0       0
#> TCGA-PK-A5HB-01      19      18      12      15       2       3       3       5
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#> 
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#> TCGA-OR-A5K0-01         0         0         1         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         1         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         1         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         1
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 AA[C>G]TG AA[C>G]TT AA[C>T]AA AA[C>T]AC AA[C>T]AG AA[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         1         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         1         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         1
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         1         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         1         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         1         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         1         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         2         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         1         0         1
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         2         0         0         1         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         1         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         1         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 AA[C>T]CA AA[C>T]CC AA[C>T]CG AA[C>T]CT AA[C>T]GA AA[C>T]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         1         0
#> TCGA-OR-A5J4-01         0         0         0         1         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         1        11
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         1         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         1         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         1         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         1         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         1
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         1         1         1         1         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         1
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         1         0         0         0         4         5
#> TCGA-OR-A5K5-01         0         1         0         0         1         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         2         0
#> TCGA-OR-A5KB-01         3         0         0         1         1         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         1
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         1         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         1         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         1         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         1         0
#> TCGA-OR-A5L8-01         0         0         0         0         1         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         2         4
#>                 AA[C>T]GG AA[C>T]GT AA[C>T]TA AA[C>T]TC AA[C>T]TG AA[C>T]TT
#> TCGA-OR-A5J1-01         1         0         0         0         0         0
#> TCGA-OR-A5J2-01         1         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         1
#> TCGA-OR-A5J5-01         8         6         0         1         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         1         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         1         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         1         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         1         1         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         1         0         0         1         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         1
#> TCGA-OR-A5JW-01         0         1         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         1         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         1         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         5         7         0         0         0         0
#> TCGA-OR-A5K5-01         0         2         1         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         0         0         0         2         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         1         0         0         0         1
#> TCGA-OR-A5KV-01         0         1         0         0         0         0
#> TCGA-OR-A5KW-01         1         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         1         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         1         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         1         0         0         0         0         0
#> TCGA-OR-A5LB-01         3         2         0         0         1         0
#>                 AA[T>A]AA AA[T>A]AC AA[T>A]AG AA[T>A]AT AA[T>A]CA AA[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         1         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         1         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         1         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         1         0         0         0         1
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         1
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         2         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         1         0
#>                 AA[T>A]CG AA[T>A]CT AA[T>A]GA AA[T>A]GC AA[T>A]GG AA[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
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#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         1         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         1         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 AA[T>G]CA AA[T>G]CC AA[T>G]CG AA[T>G]CT AA[T>G]GA AA[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5K4-01         0         0         0         0         0         0
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#> TCGA-OR-A5KY-01         0         0         0         0         0         0
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#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 AA[T>G]GG AA[T>G]GT AA[T>G]TA AA[T>G]TC AA[T>G]TG AA[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         1
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5JA-01         0         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
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#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         1
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         1         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 AC[C>A]AA AC[C>A]AC AC[C>A]AG AC[C>A]AT AC[C>A]CA AC[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         1         0
#> TCGA-OR-A5J5-01         0         0         0         0         2         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         1         1         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         1         0
#> TCGA-OR-A5JA-01         2         1         4         4         2         1
#> TCGA-OR-A5JB-01         1         1         1         3         2         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         1
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#> TCGA-OR-A5JG-01         0         1         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         1         0         0
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#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         1         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         1         0
#> TCGA-OR-A5K3-01         1         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         1         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01        10        11        19        11        13         8
#> TCGA-OR-A5KO-01         0         0         0         1         0         0
#> TCGA-OR-A5KP-01         0         1         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         1         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         1         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 AC[C>A]CG AC[C>A]CT AC[C>A]GA AC[C>A]GC AC[C>A]GG AC[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         1         0         0         0         1
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         1         0         2         0         1         0
#> TCGA-OR-A5JB-01         1         1         0         1         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
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#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         1
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         1         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         1         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         1         0
#> TCGA-OR-A5JV-01         0         1         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         6        12         2        13        11         5
#> TCGA-OR-A5KO-01         0         0         0         0         0         1
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         1         0
#> TCGA-OR-A5L8-01         1         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 AC[C>A]TA AC[C>A]TC AC[C>A]TG AC[C>A]TT AC[C>G]AA AC[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         1         1         0         0
#> TCGA-OR-A5J5-01         0         0         0         1         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         1         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         2         5         2         0         0
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#>                 AC[C>G]AG AC[C>G]AT AC[C>G]CA AC[C>G]CC AC[C>G]CG AC[C>G]CT
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#>                 AC[C>G]GA AC[C>G]GC AC[C>G]GG AC[C>G]GT AC[C>G]TA AC[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#>                 AC[C>G]TG AC[C>G]TT AC[C>T]AA AC[C>T]AC AC[C>T]AG AC[C>T]AT
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#>                 AC[C>T]CA AC[C>T]CC AC[C>T]CG AC[C>T]CT AC[C>T]GA AC[C>T]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#>                 AC[C>T]GG AC[C>T]GT AC[C>T]TA AC[C>T]TC AC[C>T]TG AC[C>T]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#>                 AC[T>A]AA AC[T>A]AC AC[T>A]AG AC[T>A]AT AC[T>A]CA AC[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5K3-01         0         0         0         0         0         0
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#>                 AC[T>A]CG AC[T>A]CT AC[T>A]GA AC[T>A]GC AC[T>A]GG AC[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#> TCGA-OR-A5KB-01         1         0         2         5         5         4
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#>                 AC[T>A]TA AC[T>A]TC AC[T>A]TG AC[T>A]TT AC[T>C]AA AC[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         1
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#> TCGA-OR-A5KV-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
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#>                 AC[T>C]AG AC[T>C]AT AC[T>C]CA AC[T>C]CC AC[T>C]CG AC[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#>                 AT[C>A]TA AT[C>A]TC AT[C>A]TG AT[C>A]TT AT[C>G]AA AT[C>G]AC
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#>                 AT[T>C]AG AT[T>C]AT AT[T>C]CA AT[T>C]CC AT[T>C]CG AT[T>C]CT
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#>                 CA[C>A]TA CA[C>A]TC CA[C>A]TG CA[C>A]TT CA[C>G]AA CA[C>G]AC
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#>                 CA[C>G]AG CA[C>G]AT CA[C>G]CA CA[C>G]CC CA[C>G]CG CA[C>G]CT
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#>                 CA[C>G]GA CA[C>G]GC CA[C>G]GG CA[C>G]GT CA[C>G]TA CA[C>G]TC
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#>                 CA[T>G]CA CA[T>G]CC CA[T>G]CG CA[T>G]CT CA[T>G]GA CA[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#>                 CA[T>G]GG CA[T>G]GT CA[T>G]TA CA[T>G]TC CA[T>G]TG CA[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#> TCGA-OR-A5JY-01         0         0         0         0         0         0
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#> TCGA-OR-A5K1-01         0         0         0         0         0         0
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#> TCGA-OR-A5K4-01         0         0         0         0         1         0
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5LB-01         0         1         0         0         0         0
#>                 CC[C>A]AA CC[C>A]AC CC[C>A]AG CC[C>A]AT CC[C>A]CA CC[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         1         0         0         1         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         2         1         0         0
#> TCGA-OR-A5KB-01         8        11        18        12        22         4
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5LB-01         0         1         0         0         0         0
#>                 CC[C>A]CG CC[C>A]CT CC[C>A]GA CC[C>A]GC CC[C>A]GG CC[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         1         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         1         1         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         1         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         0         0
#> TCGA-OR-A5KB-01        11        21        10         9        12         4
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
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#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
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#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
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#>                 CC[C>A]TA CC[C>A]TC CC[C>A]TG CC[C>A]TT CC[C>G]AA CC[C>G]AC
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#>                 CC[C>G]GA CC[C>G]GC CC[C>G]GG CC[C>G]GT CC[C>G]TA CC[C>G]TC
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#>                 CC[C>T]GG CC[C>T]GT CC[C>T]TA CC[C>T]TC CC[C>T]TG CC[C>T]TT
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#>                 CC[T>A]AA CC[T>A]AC CC[T>A]AG CC[T>A]AT CC[T>A]CA CC[T>A]CC
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#>                 CC[T>A]CG CC[T>A]CT CC[T>A]GA CC[T>A]GC CC[T>A]GG CC[T>A]GT
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#>                 CC[T>A]TA CC[T>A]TC CC[T>A]TG CC[T>A]TT CC[T>C]AA CC[T>C]AC
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#>                 CC[T>C]AG CC[T>C]AT CC[T>C]CA CC[T>C]CC CC[T>C]CG CC[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#> TCGA-OR-A5K9-01         1         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         3         0         0         1         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[C>A]AA CG[C>A]AC CG[C>A]AG CG[C>A]AT CG[C>A]CA CG[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         1         0         0         1         1
#> TCGA-OR-A5JB-01         0         0         0         1         2         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         3         1         0         5         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[C>A]CG CG[C>A]CT CG[C>A]GA CG[C>A]GC CG[C>A]GG CG[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         1         0         1         1         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         1         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         1
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         1         0         1
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         3         0         2         0         3         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         1         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         1         0         0         0         0
#>                 CG[C>A]TA CG[C>A]TC CG[C>A]TG CG[C>A]TT CG[C>G]AA CG[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         1         2         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         1         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         1         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         1         1         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[C>G]AG CG[C>G]AT CG[C>G]CA CG[C>G]CC CG[C>G]CG CG[C>G]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         1         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         1         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         1         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         1
#> TCGA-OR-A5KB-01         0         0         0         0         2         0
#> TCGA-OR-A5KO-01         0         1         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         1         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[C>G]GA CG[C>G]GC CG[C>G]GG CG[C>G]GT CG[C>G]TA CG[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         1         1         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[C>G]TG CG[C>G]TT CG[C>T]AA CG[C>T]AC CG[C>T]AG CG[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         1         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         1         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         1
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         1         1
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         1         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         1         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         1         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         1         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         1         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         2         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         1         0         1
#>                 CG[C>T]CA CG[C>T]CC CG[C>T]CG CG[C>T]CT CG[C>T]GA CG[C>T]GC
#> TCGA-OR-A5J1-01         1         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         1         1         0
#> TCGA-OR-A5J5-01         0         0         0         0         2         3
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         1         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         1         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         1         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         1
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         1
#> TCGA-OR-A5JV-01         0         0         0         0         0         1
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         1         0         0         1         0         9
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         0         1
#> TCGA-OR-A5KB-01         0         0         1         0         1         1
#> TCGA-OR-A5KO-01         0         0         0         1         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         1
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         1         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         1         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         1
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         2         2
#>                 CG[C>T]GG CG[C>T]GT CG[C>T]TA CG[C>T]TC CG[C>T]TG CG[C>T]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         1         0
#> TCGA-OR-A5J5-01         6         2         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         1         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         1         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         1         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         1         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         1         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         1         0         0         0         0
#> TCGA-OR-A5K0-01         1         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         2         1         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         7         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         1         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         1         2         1         0         1
#> TCGA-OR-A5KO-01         1         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         1
#> TCGA-OR-A5KQ-01         1         0         0         0         0         0
#> TCGA-OR-A5KS-01         1         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         1         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         1         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         1         0         0         0         0         0
#> TCGA-OR-A5LB-01         4         1         0         0         1         0
#>                 CG[T>A]AA CG[T>A]AC CG[T>A]AG CG[T>A]AT CG[T>A]CA CG[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         1
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         1         0         0         1         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         1         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[T>A]CG CG[T>A]CT CG[T>A]GA CG[T>A]GC CG[T>A]GG CG[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         1         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         1
#> TCGA-OR-A5KB-01         0         1         0         1         1         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         1         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[T>A]TA CG[T>A]TC CG[T>A]TG CG[T>A]TT CG[T>C]AA CG[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         1         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         1
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         2         1         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[T>C]AG CG[T>C]AT CG[T>C]CA CG[T>C]CC CG[T>C]CG CG[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         1
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         1         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         1         1         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         1         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[T>C]GA CG[T>C]GC CG[T>C]GG CG[T>C]GT CG[T>C]TA CG[T>C]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         1         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         1         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         1
#> TCGA-OR-A5K5-01         0         0         1         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         1         0         1         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         1         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         1         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[T>C]TG CG[T>C]TT CG[T>G]AA CG[T>G]AC CG[T>G]AG CG[T>G]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         1         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         1         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[T>G]CA CG[T>G]CC CG[T>G]CG CG[T>G]CT CG[T>G]GA CG[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         1
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         1         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CG[T>G]GG CG[T>G]GT CG[T>G]TA CG[T>G]TC CG[T>G]TG CG[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         1         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         1         0         1         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         1         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CT[C>A]AA CT[C>A]AC CT[C>A]AG CT[C>A]AT CT[C>A]CA CT[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         1         0         0
#> TCGA-OR-A5J5-01         1         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         1         1         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         7         1         8         6         0         0
#> TCGA-OR-A5JB-01         1         0         1         1         5         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         1
#> TCGA-OR-A5JF-01         0         0         1         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         1         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         1         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         1         1         1         0         0         1
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         1         1         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         1
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         2         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         1         1         1         1
#> TCGA-OR-A5K6-01         0         0         0         1         0         1
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         1         0         0         0         0         1
#> TCGA-OR-A5KB-01         4         3         6         4        14        11
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         1         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         1         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         1         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         1         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CT[C>A]CG CT[C>A]CT CT[C>A]GA CT[C>A]GC CT[C>A]GG CT[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         2         3         0         1         1         0
#> TCGA-OR-A5JB-01         1         2         0         0         0         2
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         1         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         0         0
#> TCGA-OR-A5KB-01         4        20         2         6         7         5
#> TCGA-OR-A5KO-01         0         0         1         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         1         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         1
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         1         0         1         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         1         0         0         0
#>                 CT[C>A]TA CT[C>A]TC CT[C>A]TG CT[C>A]TT CT[C>G]AA CT[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5J7-01         0         0         0         0         0         1
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#> TCGA-OR-A5JA-01         5         1         2         7         0         0
#> TCGA-OR-A5JB-01         0         0         1         1         3         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CT[C>G]AG CT[C>G]AT CT[C>G]CA CT[C>G]CC CT[C>G]CG CT[C>G]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5J7-01         0         0         1         1         0         1
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#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         2         1         2         0         0         0
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#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         2         0         1         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         0         0         0
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#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
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#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
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#> TCGA-OR-A5K5-01         1         0         0         1         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         1
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         1         1         0         0
#> TCGA-OR-A5KB-01         5         2         2         3         3         3
#> TCGA-OR-A5KO-01         0         0         0         1         0         1
#> TCGA-OR-A5KP-01         0         0         0         1         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         1         0         1         0         0         0
#> TCGA-OR-A5KV-01         0         0         1         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         1         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         0         0         0         1         2
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         1         1         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CT[C>G]GA CT[C>G]GC CT[C>G]GG CT[C>G]GT CT[C>G]TA CT[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         1         1         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         1         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
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#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         1         0         0         0         1
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
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#> TCGA-OR-A5JF-01         0         0         0         0         1         1
#> TCGA-OR-A5JG-01         0         0         0         0         0         1
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
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#> TCGA-OR-A5KB-01         1         4         2         4         0         4
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         1         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         1         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         1         0
#> TCGA-OR-A5L3-01         0         0         0         0         1         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CT[C>G]TG CT[C>G]TT CT[C>T]AA CT[C>T]AC CT[C>T]AG CT[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         1         0         0         1         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         1         0         0         0         1
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         1         0         0         0         1
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         1         0         0         0         0         2
#> TCGA-OR-A5JB-01         4         0         0         1         7         1
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         1         0         0         0         1
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         1         0
#> TCGA-OR-A5JY-01         1         0         0         1         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         2         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         1         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         1         1         0
#> TCGA-OR-A5K6-01         0         0         0         0         1         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         0         0
#> TCGA-OR-A5KB-01         6         3         0         1         8         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         1         0         0         1         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         1
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         1         1         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         1
#>                 CT[C>T]CA CT[C>T]CC CT[C>T]CG CT[C>T]CT CT[C>T]GA CT[C>T]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         1         0         0         0         1
#> TCGA-OR-A5J3-01         1         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         3         3
#> TCGA-OR-A5J6-01         0         0         1         0         1         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         2         0         3         0         1         2
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         1         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         1         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         1
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         1         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         1         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         1         1         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         1
#> TCGA-OR-A5K0-01         0         0         0         0         0         1
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         1         0         2         3
#> TCGA-OR-A5K5-01         1         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         1         0
#> TCGA-OR-A5K8-01         1         0         0         1         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         0         0
#> TCGA-OR-A5KB-01         3         3         1         4         0         1
#> TCGA-OR-A5KO-01         0         0         0         1         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         1
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         1         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         1         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         1         0         0         0         0         0
#> TCGA-OR-A5L1-01         1         0         0         0         0         1
#> TCGA-OR-A5L2-01         2         0         0         2         1         0
#> TCGA-OR-A5L3-01         0         0         0         0         1         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         1         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         2         1         0         0         2         0
#>                 CT[C>T]GG CT[C>T]GT CT[C>T]TA CT[C>T]TC CT[C>T]TG CT[C>T]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         5         6         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         1         0         0
#> TCGA-OR-A5J7-01         1         0         0         1         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         1         0         0         2         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         1         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         1         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         1         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         1         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         1         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         1         0         0         0         0         1
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#> TCGA-OR-A5K0-01         0         0         0         1         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         4         2         0         0         1         0
#> TCGA-OR-A5K5-01         1         0         0         0         2         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         2         0
#> TCGA-OR-A5KB-01         3         1         2         3         5         2
#> TCGA-OR-A5KO-01         0         0         0         1         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         1         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         1         0         0         0         1
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         1         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         1         0         0         1
#> TCGA-OR-A5LB-01         3         1         0         0         0         0
#>                 CT[T>A]AA CT[T>A]AC CT[T>A]AG CT[T>A]AT CT[T>A]CA CT[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         1         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         1         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         2         0         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CT[T>A]CG CT[T>A]CT CT[T>A]GA CT[T>A]GC CT[T>A]GG CT[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         1         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         1         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         1         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         1         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         1         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         1         2         1         2         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         1         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         1         0
#>                 CT[T>A]TA CT[T>A]TC CT[T>A]TG CT[T>A]TT CT[T>C]AA CT[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         2         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         1         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         1         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 CT[T>C]AG CT[T>C]AT CT[T>C]CA CT[T>C]CC CT[T>C]CG CT[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#>                 CT[T>C]GA CT[T>C]GC CT[T>C]GG CT[T>C]GT CT[T>C]TA CT[T>C]TC
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#>                 CT[T>C]TG CT[T>C]TT CT[T>G]AA CT[T>G]AC CT[T>G]AG CT[T>G]AT
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#>                 CT[T>G]CA CT[T>G]CC CT[T>G]CG CT[T>G]CT CT[T>G]GA CT[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#>                 CT[T>G]GG CT[T>G]GT CT[T>G]TA CT[T>G]TC CT[T>G]TG CT[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         1         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         1         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         1         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         1         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         1
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GA[T>G]CA GA[T>G]CC GA[T>G]CG GA[T>G]CT GA[T>G]GA GA[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         1         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         1         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         1         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         1         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GA[T>G]GG GA[T>G]GT GA[T>G]TA GA[T>G]TC GA[T>G]TG GA[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         0         0         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         1         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[C>A]AA GC[C>A]AC GC[C>A]AG GC[C>A]AT GC[C>A]CA GC[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         1         0         0
#> TCGA-OR-A5J5-01         1         0         0         0         3         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         2         2         6         1         2         2
#> TCGA-OR-A5JB-01         0         1         2         3         1         1
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         1         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         1
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         1         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         1         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         1         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         1         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         1         0
#> TCGA-OR-A5K5-01         0         0         0         0         1         1
#> TCGA-OR-A5K6-01         0         0         1         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         1
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         8         8        15         9        13        10
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         1
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[C>A]CG GC[C>A]CT GC[C>A]GA GC[C>A]GC GC[C>A]GG GC[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         1         1         0         0         0
#> TCGA-OR-A5JB-01         1         0         1         0         0         2
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         1         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         1         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         1         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         1         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         1         0
#> TCGA-OR-A5KB-01        11        10         1        10         7         7
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         1         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[C>A]TA GC[C>A]TC GC[C>A]TG GC[C>A]TT GC[C>G]AA GC[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         1         0         0
#> TCGA-OR-A5J5-01         0         1         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         1         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         1         0         1         0         0         0
#> TCGA-OR-A5JB-01         0         1         0         3         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         1         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         1         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         1         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         4        10        17         7         1         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         1         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[C>G]AG GC[C>G]AT GC[C>G]CA GC[C>G]CC GC[C>G]CG GC[C>G]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         1         0         0         1         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         1         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         1         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         1         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         1         1         1
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         2         0         0         0
#> TCGA-OR-A5KB-01         1         0         2         2         1         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         1         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         1         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[C>G]GA GC[C>G]GC GC[C>G]GG GC[C>G]GT GC[C>G]TA GC[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         1
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         1         0         1         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         1
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         1         0
#> TCGA-OR-A5K3-01         1         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         1         1         3         1         3
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[C>G]TG GC[C>G]TT GC[C>T]AA GC[C>T]AC GC[C>T]AG GC[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         1         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         1         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         1         0         0         2         1
#> TCGA-OR-A5JC-01         0         0         0         0         1         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         1
#> TCGA-OR-A5JL-01         0         0         0         1         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         1         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         1         0         0         0
#> TCGA-OR-A5K5-01         0         0         1         0         1         0
#> TCGA-OR-A5K6-01         0         0         1         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         1         0
#> TCGA-OR-A5KB-01         1         0         0         1         3         4
#> TCGA-OR-A5KO-01         0         0         0         1         0         0
#> TCGA-OR-A5KP-01         0         0         1         0         1         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         1         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         1         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         1         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[C>T]CA GC[C>T]CC GC[C>T]CG GC[C>T]CT GC[C>T]GA GC[C>T]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         1
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         1         1         1         0         4        11
#> TCGA-OR-A5J6-01         2         0         0         0         1         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         1
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         1
#> TCGA-OR-A5JC-01         0         0         0         0         0         1
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         1         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         1         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         1
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         1         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         1         0         0         0         0         0
#> TCGA-OR-A5JT-01         1         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         1         0         0         1         1
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         1         0         0         0         1         6
#> TCGA-OR-A5K5-01         0         0         0         0         0         1
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         2         0         3         2         3
#> TCGA-OR-A5KO-01         0         0         0         0         0         1
#> TCGA-OR-A5KP-01         1         1         0         0         0         3
#> TCGA-OR-A5KQ-01         0         0         0         0         0         1
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         1
#> TCGA-OR-A5KV-01         0         0         0         0         0         1
#> TCGA-OR-A5KW-01         0         0         0         0         1         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         1         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         1         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         2         1
#>                 GC[C>T]GG GC[C>T]GT GC[C>T]TA GC[C>T]TC GC[C>T]TG GC[C>T]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         1         0
#> TCGA-OR-A5J5-01         8         3         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         1         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         1         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         1         0         0         0         0
#> TCGA-OR-A5JC-01         0         1         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         2         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         1         0         1         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         1         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         1         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         1         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         1         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         1         1         0         1         0         0
#> TCGA-OR-A5JZ-01         0         1         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         6         2         0         1         0         0
#> TCGA-OR-A5K5-01         1         1         1         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         4         0         2         4         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         1         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         1         0         0         0         0
#> TCGA-OR-A5KW-01         1         0         0         0         1         0
#> TCGA-OR-A5KX-01         3         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         1         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         1
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         1         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         1         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         1         0
#> TCGA-OR-A5LB-01         1         4         0         0         1         0
#>                 GC[T>A]AA GC[T>A]AC GC[T>A]AG GC[T>A]AT GC[T>A]CA GC[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         1         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         1         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         1         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         2
#> TCGA-OR-A5KB-01         0         0         2         1         2         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         1
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[T>A]CG GC[T>A]CT GC[T>A]GA GC[T>A]GC GC[T>A]GG GC[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         1         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         1         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         1         0         1         0
#> TCGA-OR-A5JB-01         0         1         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         1
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         1         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         1         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         1         0         0         0         0
#> TCGA-OR-A5KB-01         1         2         5         6         2         6
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         1
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         1         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[T>A]TA GC[T>A]TC GC[T>A]TG GC[T>A]TT GC[T>C]AA GC[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         1         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         1         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         1         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         2         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         1
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         1         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         1         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[T>C]AG GC[T>C]AT GC[T>C]CA GC[T>C]CC GC[T>C]CG GC[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         1         1         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         1         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         1         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         1         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         1
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         1         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         0         1         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         1         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         1         0         0         0
#>                 GC[T>C]GA GC[T>C]GC GC[T>C]GG GC[T>C]GT GC[T>C]TA GC[T>C]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         2         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         1         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         1         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         1         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         1
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         2         1         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         1         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         1         0         0         1
#> TCGA-OR-A5L3-01         1         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         1         0         0         0
#>                 GC[T>C]TG GC[T>C]TT GC[T>G]AA GC[T>G]AC GC[T>G]AG GC[T>G]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         1         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         1         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         2         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         1         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         2         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[T>G]CA GC[T>G]CC GC[T>G]CG GC[T>G]CT GC[T>G]GA GC[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         1         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         1
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         1         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GC[T>G]GG GC[T>G]GT GC[T>G]TA GC[T>G]TC GC[T>G]TG GC[T>G]TT
#> TCGA-OR-A5J1-01         0         1         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         1         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
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#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         1         0         1         0         0         0
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#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
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#> TCGA-OR-A5L3-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GG[C>A]AA GG[C>A]AC GG[C>A]AG GG[C>A]AT GG[C>A]CA GG[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         1         1         0         0         0
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#> TCGA-OR-A5JA-01         8         8        12         4         3         3
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#> TCGA-OR-A5K8-01         0         0         2         0         0         0
#> TCGA-OR-A5K9-01         0         0         1         0         1         1
#> TCGA-OR-A5KB-01         2         3        10         2         9         6
#> TCGA-OR-A5KO-01         0         0         1         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5KT-01         0         0         0         0         0         0
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#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         1         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         0         1         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         1         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         1         0         1         1         0         0
#>                 GG[C>A]CG GG[C>A]CT GG[C>A]GA GG[C>A]GC GG[C>A]GG GG[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         1         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         1         1         0         1         1         1
#> TCGA-OR-A5JB-01         0         0         1         1         1         1
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#> TCGA-OR-A5JP-01         0         0         0         0         0         0
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#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         1         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         1         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         1         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         1         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         2         0         0         0
#> TCGA-OR-A5KB-01         8         7         3         3        11         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         1         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         1         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         1         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         1
#>                 GG[C>A]TA GG[C>A]TC GG[C>A]TG GG[C>A]TT GG[C>G]AA GG[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         2         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         1         0         0
#> TCGA-OR-A5J8-01         0         0         2         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         4         4         7         7         0         0
#> TCGA-OR-A5JB-01         0         0         1         1         1         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         1         0         0
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#> TCGA-OR-A5JM-01         0         0         1         1         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         1         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         1         0         0         1         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         1         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         1         0
#> TCGA-OR-A5KB-01         1         2         9         5         1         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         1         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GG[C>G]AG GG[C>G]AT GG[C>G]CA GG[C>G]CC GG[C>G]CG GG[C>G]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         1
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         1         0         0         1
#> TCGA-OR-A5J9-01         0         0         0         1         0         0
#> TCGA-OR-A5JA-01         1         0         1         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         1         0         1
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         1         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         1         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         1         3         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         1         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         1         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GG[C>G]GA GG[C>G]GC GG[C>G]GG GG[C>G]GT GG[C>G]TA GG[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#> TCGA-OR-A5LB-01         0         1         0         0         0         0
#>                 GG[C>G]TG GG[C>G]TT GG[C>T]AA GG[C>T]AC GG[C>T]AG GG[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         2
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#> TCGA-OR-A5L3-01         0         0         0         0         0         1
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         1         0
#>                 GG[C>T]CA GG[C>T]CC GG[C>T]CG GG[C>T]CT GG[C>T]GA GG[C>T]GC
#> TCGA-OR-A5J1-01         1         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5J5-01         0         0         1         0         7        11
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#> TCGA-OR-A5KB-01         7         0         0         2         0         1
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#> TCGA-OR-A5L1-01         0         0         0         0         1         1
#> TCGA-OR-A5L2-01         0         0         0         0         0         4
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         4         6
#>                 GG[C>T]GG GG[C>T]GT GG[C>T]TA GG[C>T]TC GG[C>T]TG GG[C>T]TT
#> TCGA-OR-A5J1-01         0         0         0         0         1         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5KX-01         1         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         2         3         0         0         2         1
#>                 GG[T>A]AA GG[T>A]AC GG[T>A]AG GG[T>A]AT GG[T>A]CA GG[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         3         2         1         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         1         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         1         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GG[T>A]CG GG[T>A]CT GG[T>A]GA GG[T>A]GC GG[T>A]GG GG[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         1         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5KT-01         0         0         0         0         0         0
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#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
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#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
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#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GG[T>A]TA GG[T>A]TC GG[T>A]TG GG[T>A]TT GG[T>C]AA GG[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         1         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
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#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         1         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         1         0
#> TCGA-OR-A5KB-01         0         0         2         2         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
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#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 GG[T>C]AG GG[T>C]AT GG[T>C]CA GG[T>C]CC GG[T>C]CG GG[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         1         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5JB-01         1         0         0         0         0         0
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#> TCGA-OR-A5JH-01         0         0         0         0         0         0
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#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JR-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         1         0         0         0         1
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         1         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         1         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         1         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         1         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         1         1         1         0         0
#>                 GG[T>C]GA GG[T>C]GC GG[T>C]GG GG[T>C]GT GG[T>C]TA GG[T>C]TC
#> TCGA-OR-A5J1-01         1         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
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#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         1         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         1         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         1         0         1         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         1         0         0         0
#> TCGA-OR-A5KB-01         1         1         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         1
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
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#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         1         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         1         0         1         0         0
#>                 GG[T>C]TG GG[T>C]TT GG[T>G]AA GG[T>G]AC GG[T>G]AG GG[T>G]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#>                 GT[C>T]CA GT[C>T]CC GT[C>T]CG GT[C>T]CT GT[C>T]GA GT[C>T]GC
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#>                 TA[C>A]AA TA[C>A]AC TA[C>A]AG TA[C>A]AT TA[C>A]CA TA[C>A]CC
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#>                 TA[C>A]CG TA[C>A]CT TA[C>A]GA TA[C>A]GC TA[C>A]GG TA[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TA[C>A]TA TA[C>A]TC TA[C>A]TG TA[C>A]TT TA[C>G]AA TA[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#>                 TA[C>G]AG TA[C>G]AT TA[C>G]CA TA[C>G]CC TA[C>G]CG TA[C>G]CT
#> TCGA-OR-A5J1-01         0         0         1         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TA[C>G]GA TA[C>G]GC TA[C>G]GG TA[C>G]GT TA[C>G]TA TA[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TA[C>G]TG TA[C>G]TT TA[C>T]AA TA[C>T]AC TA[C>T]AG TA[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TA[C>T]CA TA[C>T]CC TA[C>T]CG TA[C>T]CT TA[C>T]GA TA[C>T]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TA[C>T]GG TA[C>T]GT TA[C>T]TA TA[C>T]TC TA[C>T]TG TA[C>T]TT
#> TCGA-OR-A5J1-01         0         1         1         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         1         0
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#>                 TA[T>A]AA TA[T>A]AC TA[T>A]AG TA[T>A]AT TA[T>A]CA TA[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         1         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TA[T>A]CG TA[T>A]CT TA[T>A]GA TA[T>A]GC TA[T>A]GG TA[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
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#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         3         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TA[T>A]TA TA[T>A]TC TA[T>A]TG TA[T>A]TT TA[T>C]AA TA[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         1
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         0         0         1
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#> TCGA-OR-A5JP-01         0         0         0         0         1         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         1         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         1         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         1         0         0         1         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         1
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         1         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TA[T>C]AG TA[T>C]AT TA[T>C]CA TA[T>C]CC TA[T>C]CG TA[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         1         1         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         1         0         0         0         0         1
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5JK-01         1         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         1         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         1         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         1         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         0         0         1         0         0
#> TCGA-OR-A5KO-01         0         0         1         0         0         0
#> TCGA-OR-A5KP-01         0         0         1         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         1         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TA[T>C]GA TA[T>C]GC TA[T>C]GG TA[T>C]GT TA[T>C]TA TA[T>C]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         1         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         1         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         1         1         1         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         1         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         1         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         1         0         0         0
#> TCGA-OR-A5JT-01         1         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         1         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         1         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         1         0         0         0         0         0
#> TCGA-OR-A5K5-01         1         0         0         0         0         1
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         0         2         0         1         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         1
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         1         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TA[T>C]TG TA[T>C]TT TA[T>G]AA TA[T>G]AC TA[T>G]AG TA[T>G]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         1         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         2         0         0         0         0         0
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#> TCGA-OR-A5J8-01         0         0         0         0         0         0
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#> TCGA-OR-A5JC-01         0         0         0         0         0         0
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#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         1         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
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#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
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#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         1         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         1         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TA[T>G]CA TA[T>G]CC TA[T>G]CG TA[T>G]CT TA[T>G]GA TA[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5J5-01         0         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         0         0         0
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#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
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#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TA[T>G]GG TA[T>G]GT TA[T>G]TA TA[T>G]TC TA[T>G]TG TA[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5JB-01         0         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         1         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         1         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TC[C>A]AA TC[C>A]AC TC[C>A]AG TC[C>A]AT TC[C>A]CA TC[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         1
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         1         1
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         0         1         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         3         1         3         3         3         1
#> TCGA-OR-A5JB-01         1         0         3         0         1         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         1         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         1         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         0         0         0
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#> TCGA-OR-A5JP-01         1         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         1         0         0         0         0
#> TCGA-OR-A5JW-01         1         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         1         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         1         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         6         8         9        14        10         7
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         1
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         1         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         1
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         1         0         0         0         0
#>                 TC[C>A]CG TC[C>A]CT TC[C>A]GA TC[C>A]GC TC[C>A]GG TC[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         1         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         1         1         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         1         0         0         1
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         1         0         0         0
#> TCGA-OR-A5JB-01         5         2         0         1         1         0
#> TCGA-OR-A5JC-01         0         1         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         1         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         1         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         1         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         1         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         1         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         4        10         3         5         4         6
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         1         0         0         0
#>                 TC[C>A]TA TC[C>A]TC TC[C>A]TG TC[C>A]TT TC[C>G]AA TC[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5L1-01         0         0         1         0         0         0
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#> TCGA-OR-A5L3-01         0         0         0         1         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         1         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         3         1         0         0         0
#>                 TC[C>G]AG TC[C>G]AT TC[C>G]CA TC[C>G]CC TC[C>G]CG TC[C>G]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
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#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         1
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
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#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         1         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         1         0         0         0
#> TCGA-OR-A5KB-01         8         1         2         3         1         4
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
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#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
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#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TC[C>G]GA TC[C>G]GC TC[C>G]GG TC[C>G]GT TC[C>G]TA TC[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5K3-01         0         0         0         0         0         0
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#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         1         0         3         3         5
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5KU-01         0         0         0         0         0         0
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#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
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#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TC[C>G]TG TC[C>G]TT TC[C>T]AA TC[C>T]AC TC[C>T]AG TC[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         1         1         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         1         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         1         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         1         1         0
#> TCGA-OR-A5K6-01         0         0         0         0         1         0
#> TCGA-OR-A5K8-01         0         0         0         0         1         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         3         1         3         5         9         5
#> TCGA-OR-A5KO-01         0         0         0         0         0         1
#> TCGA-OR-A5KP-01         0         0         1         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         1
#> TCGA-OR-A5KT-01         0         0         0         1         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         1         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         1         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         1         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         1         0         0
#>                 TC[C>T]CA TC[C>T]CC TC[C>T]CG TC[C>T]CT TC[C>T]GA TC[C>T]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         1
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         4        12
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         1
#> TCGA-OR-A5J9-01         0         0         0         0         0         1
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         0         1         0         2
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         1         0         0         0         0         0
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#> TCGA-OR-A5JG-01         0         0         0         0         1         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         2         0         0         0         0         1
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         1         0         1         0         2
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         3         8
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         2         0         0         1         0         0
#> TCGA-OR-A5KB-01         3         4         3         3         1         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         1         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         1
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         1         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
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#> TCGA-OR-A5L9-01         0         0         0         0         0         1
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         1         0         0         0         0         1
#>                 TC[C>T]GG TC[C>T]GT TC[C>T]TA TC[C>T]TC TC[C>T]TG TC[C>T]TT
#> TCGA-OR-A5J1-01         1         0         0         0         1         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         0         0         0         1         0
#> TCGA-OR-A5J5-01        10         5         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5JB-01         0         0         0         1         1         2
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#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         1         0         0         0         0         0
#> TCGA-OR-A5JP-01         1         0         0         0         1         0
#> TCGA-OR-A5JQ-01         1         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         1         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         1         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         1         1         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         1         0
#> TCGA-OR-A5K2-01         0         2         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01        10         7         0         0         1         0
#> TCGA-OR-A5K5-01         1         1         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         1         1         0         0         0
#> TCGA-OR-A5KB-01         3         1         1         2         6         4
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         1         1         0         0         1         0
#> TCGA-OR-A5KW-01         0         1         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         1         0         0         1
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         1         0
#> TCGA-OR-A5L2-01         1         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         1         0         0         1         0         1
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         2         1         0         0         0         0
#>                 TC[T>A]AA TC[T>A]AC TC[T>A]AG TC[T>A]AT TC[T>A]CA TC[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         1
#> TCGA-OR-A5JB-01         0         0         0         0         1         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         1
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         1         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         1
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         1         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         1         2         2         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         1         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         1         0         0         0
#>                 TC[T>A]CG TC[T>A]CT TC[T>A]GA TC[T>A]GC TC[T>A]GG TC[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         1         1         0
#> TCGA-OR-A5JC-01         0         1         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         1         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         1         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         2         5         1         0         6
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         1         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TC[T>A]TA TC[T>A]TC TC[T>A]TG TC[T>A]TT TC[T>C]AA TC[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         1         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         1         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         1         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         1         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         1         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         1         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         1         1         2         0         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#>                 TC[T>C]AG TC[T>C]AT TC[T>C]CA TC[T>C]CC TC[T>C]CG TC[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TC[T>C]GA TC[T>C]GC TC[T>C]GG TC[T>C]GT TC[T>C]TA TC[T>C]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#>                 TC[T>C]TG TC[T>C]TT TC[T>G]AA TC[T>G]AC TC[T>G]AG TC[T>G]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TC[T>G]CA TC[T>G]CC TC[T>G]CG TC[T>G]CT TC[T>G]GA TC[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#>                 TC[T>G]GG TC[T>G]GT TC[T>G]TA TC[T>G]TC TC[T>G]TG TC[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         1         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         1
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         1         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         1         0         0
#>                 TG[C>A]AA TG[C>A]AC TG[C>A]AG TG[C>A]AT TG[C>A]CA TG[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         1         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         2         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         9         2         5         6         4         1
#> TCGA-OR-A5JB-01         2         2         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
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#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         1         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         1         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         1         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         3         8        10         8        10         6
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         1
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         1         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         1         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         1         0         0         0
#>                 TG[C>A]CG TG[C>A]CT TG[C>A]GA TG[C>A]GC TG[C>A]GG TG[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         1         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         1         0         0         0
#> TCGA-OR-A5JB-01         0         0         1         3         2         0
#> TCGA-OR-A5JC-01         0         1         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         1         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         1         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         1         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         6         2         3         5         3
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         1         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         1         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TG[C>A]TA TG[C>A]TC TG[C>A]TG TG[C>A]TT TG[C>G]AA TG[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         4         4         7         4         0         0
#> TCGA-OR-A5JB-01         1         0         0         0         0         1
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         1         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         1         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         1         0         1
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         1         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         4        13         5         2         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         1         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         1         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         1         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         1         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         2         0         0         0
#>                 TG[C>G]AG TG[C>G]AT TG[C>G]CA TG[C>G]CC TG[C>G]CG TG[C>G]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         1         0         0         0
#> TCGA-OR-A5J5-01         0         0         1         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         1         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         1         1         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         1         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         1         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         1         0         0
#> TCGA-OR-A5JW-01         0         0         1         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         1         3         4         2         3         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         1         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         1         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         1         0         0
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#> TCGA-OR-A5L5-01         0         0         0         0         0         0
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#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TG[C>G]GA TG[C>G]GC TG[C>G]GG TG[C>G]GT TG[C>G]TA TG[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5J5-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TG[C>G]TG TG[C>G]TT TG[C>T]AA TG[C>T]AC TG[C>T]AG TG[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         1         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
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#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         1         0         0         1
#> TCGA-OR-A5K5-01         0         1         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         2         0         0         4         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         1         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         1         4         1
#>                 TG[C>T]CA TG[C>T]CC TG[C>T]CG TG[C>T]CT TG[C>T]GA TG[C>T]GC
#> TCGA-OR-A5J1-01         0         1         0         0         0         0
#> TCGA-OR-A5J2-01         0         1         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         1         0         1
#> TCGA-OR-A5J5-01         0         1         0         1         5         9
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
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#> TCGA-OR-A5K8-01         0         0         0         0         0         0
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5KY-01         0         0         0         0         1         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
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#> TCGA-OR-A5L3-01         0         0         0         0         1         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         4         2         1         0         2         1
#>                 TG[C>T]GG TG[C>T]GT TG[C>T]TA TG[C>T]TC TG[C>T]TG TG[C>T]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         1         0         0         0         1
#> TCGA-OR-A5J5-01        12         5         0         0         2         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         1         0         1
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#> TCGA-OR-A5K3-01         1         0         0         0         0         0
#> TCGA-OR-A5K4-01        10         4         0         0         2         1
#> TCGA-OR-A5K5-01         1         0         0         0         1         1
#> TCGA-OR-A5K6-01         1         0         0         1         1         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         2         0         0         0         0         0
#> TCGA-OR-A5KB-01         2         0         0         4         3         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         1         0         0         0         1
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         1         0
#> TCGA-OR-A5KU-01         1         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         2         2         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         1         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         1         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         4         7         1         1         3         0
#>                 TG[T>A]AA TG[T>A]AC TG[T>A]AG TG[T>A]AT TG[T>A]CA TG[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5JP-01         0         0         0         0         0         1
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
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#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         1         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         1         1         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         1         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         1         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         1         0         0         1
#>                 TG[T>A]CG TG[T>A]CT TG[T>A]GA TG[T>A]GC TG[T>A]GG TG[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
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#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         1         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         2         0         1         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         1         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TG[T>A]TA TG[T>A]TC TG[T>A]TG TG[T>A]TT TG[T>C]AA TG[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         1
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#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
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#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
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#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         0         0         0
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#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         1         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         1         0         0         0         0         1
#>                 TG[T>C]AG TG[T>C]AT TG[T>C]CA TG[T>C]CC TG[T>C]CG TG[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         2         0         0
#> TCGA-OR-A5J5-01         3         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         1         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
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#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         1         0         0         0         0         0
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#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         1         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         0         0         0
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#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         1
#> TCGA-OR-A5K5-01         1         0         0         1         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         1
#> TCGA-OR-A5K9-01         1         1         1         1         0         0
#> TCGA-OR-A5KB-01         2         1         0         1         0         2
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         1         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         1
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
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#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         1         0         0         1         0         0
#>                 TG[T>C]GA TG[T>C]GC TG[T>C]GG TG[T>C]GT TG[T>C]TA TG[T>C]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
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#> TCGA-OR-A5JF-01         1         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
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#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         1
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         1
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         1         1         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         2         1         0         1
#> TCGA-OR-A5KO-01         0         0         1         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         1         0         0         0         0
#>                 TG[T>C]TG TG[T>C]TT TG[T>G]AA TG[T>G]AC TG[T>G]AG TG[T>G]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         1         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         1         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         1         0         0         0         0         0
#> TCGA-OR-A5JX-01         1         1         0         0         0         0
#> TCGA-OR-A5JY-01         0         1         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         1         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         1         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         1         1         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         2         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TG[T>G]CA TG[T>G]CC TG[T>G]CG TG[T>G]CT TG[T>G]GA TG[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         1         0
#> TCGA-OR-A5JF-01         0         0         0         0         1         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         1         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         0         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TG[T>G]GG TG[T>G]GT TG[T>G]TA TG[T>G]TC TG[T>G]TG TG[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         0         0         0         0         0
#> TCGA-OR-A5J9-01         0         0         0         1         0         0
#> TCGA-OR-A5JA-01         0         0         0         0         0         0
#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         1         0         0
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         1         0         0         0         0
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TT[C>A]AA TT[C>A]AC TT[C>A]AG TT[C>A]AT TT[C>A]CA TT[C>A]CC
#> TCGA-OR-A5J1-01         0         0         0         1         0         0
#> TCGA-OR-A5J2-01         0         0         1         1         1         0
#> TCGA-OR-A5J3-01         1         0         0         0         0         0
#> TCGA-OR-A5J4-01         1         1         0         1         0         1
#> TCGA-OR-A5J5-01         1         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         1         0         0         2         1         1
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01        14         6        12        16        13         5
#> TCGA-OR-A5JB-01         0         0         0         1         1         1
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         1         0
#> TCGA-OR-A5JF-01         0         0         1         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         1         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         1         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         1         0         0         0
#> TCGA-OR-A5JO-01         1         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         1         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         1         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         0         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         2         0
#> TCGA-OR-A5K6-01         0         0         1         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         2         0         0
#> TCGA-OR-A5KB-01         3         3         3         3        15         5
#> TCGA-OR-A5KO-01         0         0         0         0         2         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         0         0
#> TCGA-OR-A5KT-01         0         1         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         1         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         1
#> TCGA-OR-A5KZ-01         0         0         1         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         1         0         0
#> TCGA-OR-A5L2-01         1         0         0         0         0         2
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         1
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         1         1         0
#>                 TT[C>A]CG TT[C>A]CT TT[C>A]GA TT[C>A]GC TT[C>A]GG TT[C>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         2         0         0         0         0         0
#> TCGA-OR-A5J5-01         0         0         0         0         0         0
#> TCGA-OR-A5J6-01         0         0         0         0         0         0
#> TCGA-OR-A5J7-01         0         0         0         0         0         0
#> TCGA-OR-A5J8-01         0         2         0         1         1         0
#> TCGA-OR-A5J9-01         0         0         0         0         0         0
#> TCGA-OR-A5JA-01         2         8         3         0         1         1
#> TCGA-OR-A5JB-01         0         1         0         0         0         2
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         1         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         0         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         0         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         0         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         1         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
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#>                 TT[C>A]TA TT[C>A]TC TT[C>A]TG TT[C>A]TT TT[C>G]AA TT[C>G]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#> TCGA-OR-A5LB-01         0         0         1         0         0         0
#>                 TT[C>G]AG TT[C>G]AT TT[C>G]CA TT[C>G]CC TT[C>G]CG TT[C>G]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TT[C>G]GA TT[C>G]GC TT[C>G]GG TT[C>G]GT TT[C>G]TA TT[C>G]TC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#>                 TT[C>G]TG TT[C>G]TT TT[C>T]AA TT[C>T]AC TT[C>T]AG TT[C>T]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
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#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
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#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TT[C>T]CA TT[C>T]CC TT[C>T]CG TT[C>T]CT TT[C>T]GA TT[C>T]GC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         1         0         1
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5J5-01         0         0         1         0         4         1
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#> TCGA-OR-A5J7-01         0         0         0         0         1         1
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#>                 TT[C>T]GG TT[C>T]GT TT[C>T]TA TT[C>T]TC TT[C>T]TG TT[C>T]TT
#> TCGA-OR-A5J1-01         1         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5L5-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         2         1         0         1         0         0
#>                 TT[T>A]AA TT[T>A]AC TT[T>A]AG TT[T>A]AT TT[T>A]CA TT[T>A]CC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
#> TCGA-OR-A5J4-01         0         0         0         0         0         0
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#> TCGA-OR-A5J7-01         0         0         0         0         0         0
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#> TCGA-OR-A5L3-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TT[T>A]CG TT[T>A]CT TT[T>A]GA TT[T>A]GC TT[T>A]GG TT[T>A]GT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
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#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>                 TT[T>A]TA TT[T>A]TC TT[T>A]TG TT[T>A]TT TT[T>C]AA TT[T>C]AC
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         1         0
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#>                 TT[T>C]AG TT[T>C]AT TT[T>C]CA TT[T>C]CC TT[T>C]CG TT[T>C]CT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
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#>                 TT[T>C]GA TT[T>C]GC TT[T>C]GG TT[T>C]GT TT[T>C]TA TT[T>C]TC
#> TCGA-OR-A5J1-01         0         0         0         1         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#>                 TT[T>C]TG TT[T>C]TT TT[T>G]AA TT[T>G]AC TT[T>G]AG TT[T>G]AT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         0         1         0         0
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#>                 TT[T>G]CA TT[T>G]CC TT[T>G]CG TT[T>G]CT TT[T>G]GA TT[T>G]GC
#> TCGA-OR-A5J1-01         0         0         0         1         0         0
#> TCGA-OR-A5J2-01         0         0         0         0         0         0
#> TCGA-OR-A5J3-01         0         0         0         0         0         0
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#>                 TT[T>G]GG TT[T>G]GT TT[T>G]TA TT[T>G]TC TT[T>G]TG TT[T>G]TT
#> TCGA-OR-A5J1-01         0         0         0         0         0         0
#> TCGA-OR-A5J2-01         0         0         1         0         0         0
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#> TCGA-OR-A5JB-01         0         0         0         0         0         0
#> TCGA-OR-A5JC-01         0         0         0         0         0         0
#> TCGA-OR-A5JD-01         0         0         0         0         0         0
#> TCGA-OR-A5JE-01         0         0         0         0         0         0
#> TCGA-OR-A5JF-01         0         0         0         0         0         0
#> TCGA-OR-A5JG-01         0         0         0         0         0         0
#> TCGA-OR-A5JH-01         0         0         0         0         0         0
#> TCGA-OR-A5JI-01         0         0         0         0         0         0
#> TCGA-OR-A5JJ-01         0         0         0         0         0         0
#> TCGA-OR-A5JK-01         0         0         0         0         0         0
#> TCGA-OR-A5JL-01         0         0         0         0         0         0
#> TCGA-OR-A5JM-01         1         0         0         0         0         0
#> TCGA-OR-A5JO-01         0         0         0         0         0         0
#> TCGA-OR-A5JP-01         0         0         0         0         0         0
#> TCGA-OR-A5JQ-01         0         0         0         0         0         0
#> TCGA-OR-A5JR-01         0         0         0         0         0         0
#> TCGA-OR-A5JS-01         0         0         0         0         0         0
#> TCGA-OR-A5JT-01         1         0         0         0         0         0
#> TCGA-OR-A5JU-01         0         0         0         0         1         0
#> TCGA-OR-A5JV-01         0         0         0         0         0         0
#> TCGA-OR-A5JW-01         0         0         0         0         0         0
#> TCGA-OR-A5JX-01         0         0         0         0         0         0
#> TCGA-OR-A5JY-01         0         0         0         0         0         0
#> TCGA-OR-A5JZ-01         0         0         0         0         0         0
#> TCGA-OR-A5K0-01         0         0         0         0         0         0
#> TCGA-OR-A5K1-01         0         0         0         0         0         0
#> TCGA-OR-A5K2-01         0         0         0         0         0         0
#> TCGA-OR-A5K3-01         0         0         0         0         0         0
#> TCGA-OR-A5K4-01         1         0         0         0         0         0
#> TCGA-OR-A5K5-01         0         0         0         0         0         1
#> TCGA-OR-A5K6-01         0         0         0         0         0         0
#> TCGA-OR-A5K8-01         0         0         0         0         0         0
#> TCGA-OR-A5K9-01         0         0         0         0         0         0
#> TCGA-OR-A5KB-01         0         2         0         0         0         1
#> TCGA-OR-A5KO-01         0         0         0         0         0         0
#> TCGA-OR-A5KP-01         0         0         0         0         0         0
#> TCGA-OR-A5KQ-01         0         0         0         0         0         0
#> TCGA-OR-A5KS-01         0         0         0         0         1         0
#> TCGA-OR-A5KT-01         0         0         0         0         0         0
#> TCGA-OR-A5KU-01         0         0         0         0         0         0
#> TCGA-OR-A5KV-01         0         0         0         0         0         0
#> TCGA-OR-A5KW-01         0         0         0         0         0         0
#> TCGA-OR-A5KX-01         0         0         0         0         0         0
#> TCGA-OR-A5KY-01         0         0         0         0         0         0
#> TCGA-OR-A5KZ-01         0         0         0         0         0         0
#> TCGA-OR-A5L1-01         0         0         0         0         0         0
#> TCGA-OR-A5L2-01         0         0         0         0         0         0
#> TCGA-OR-A5L3-01         0         0         0         0         0         0
#> TCGA-OR-A5L4-01         0         0         0         0         0         0
#> TCGA-OR-A5L5-01         0         0         0         0         0         0
#> TCGA-OR-A5L6-01         0         0         0         0         0         0
#> TCGA-OR-A5L8-01         0         0         0         0         0         0
#> TCGA-OR-A5L9-01         0         0         0         0         0         0
#> TCGA-OR-A5LA-01         0         0         0         0         0         0
#> TCGA-OR-A5LB-01         0         0         0         0         0         0
#>  [ reached getOption("max.print") -- omitted 27 rows ]
#> 
#> 
#> $APOBEC_scores
#> Index: <APOBEC_Enriched>
#>     Tumor_Sample_Barcode   T>C   C>T   T>A   T>G   C>A   C>G   A>G   G>A   A>T
#>                   <fctr> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#>  1:      TCGA-OR-A5LG-01     2     8     1     1     3     3     3     1     0
#>  2:      TCGA-PK-A5H8-01     5     2     0     1     1     1     3     3     1
#>  3:      TCGA-OR-A5L4-01     3     7     0     0     3     2     2     5     2
#>  4:      TCGA-PK-A5H9-01     0     3     0     2     3     0     1     4     1
#>  5:      TCGA-PK-A5HC-01     6    17     1     1    12    14     1    10     3
#>  6:      TCGA-OR-A5LA-01     0     3     1     0     1     0     2     5     0
#>  7:      TCGA-OR-A5JK-01     3     9     2     1     1     3     3     5     2
#>  8:      TCGA-OR-A5LS-01     2     2     2     0     2     2     1     5     0
#>  9:      TCGA-OR-A5JI-01     0     4     1     0     0     0     4     0     1
#> 10:      TCGA-OR-A5LO-01     3     9     2     1    12    12     7    20     1
#> 11:      TCGA-OR-A5K8-01     3     3     0     0     3     6     3     5     1
#> 12:      TCGA-OR-A5KS-01     2     4     0     2     0     3     1     7     1
#> 13:      TCGA-OR-A5JX-01     4     6     2     2     4     4     4     8     2
#> 14:      TCGA-OR-A5JL-01     1     2     1     0     2     2     1     3     0
#> 15:      TCGA-OR-A5LE-01     4     8     1     1     2     2     2     2     2
#> 16:      TCGA-OR-A5K6-01     6     6     0     2     2     3     1     6     0
#> 17:      TCGA-OR-A5KY-01     0     6     2     0     9     4     1     3     0
#> 18:      TCGA-OR-A5J6-01     9     2     2     0     2     2     9     6     2
#> 19:      TCGA-OR-A5K1-01     1     4     2     0     1     2     2     2     1
#> 20:      TCGA-OR-A5JO-01     2     5     0     0     0     2     3     2     0
#> 21:      TCGA-OR-A5JS-01     4    11     0     0     6     1     4    17     1
#> 22:      TCGA-OU-A5PI-01     6     7     1     1     3     3     2     4     1
#> 23:      TCGA-OR-A5LF-01     4     8     0     0     2     2     3     2     0
#> 24:      TCGA-OR-A5KO-01     4    10     0     1     5     2     1     4     0
#> 25:      TCGA-OR-A5KQ-01     1     4     0     0     0     0     1     5     0
#> 26:      TCGA-OR-A5JB-01    17    51    18     1    90    33     9    60    20
#> 27:      TCGA-OR-A5JC-01     1     7     3     1     6     6     4     6     2
#> 28:      TCGA-OR-A5LN-01     2     3     0     0     1     1     1     3     1
#> 29:      TCGA-OR-A5JJ-01     1     7     0     0     1     3     0     4     0
#> 30:      TCGA-OR-A5JZ-01     3     5     1     0     0     0     3     6     1
#> 31:      TCGA-OR-A5KT-01     3     4     0     0     2     5     2    10     2
#> 32:      TCGA-OR-A5JM-01     5    14     0     2     9    12     6    19     3
#> 33:      TCGA-OR-A5JG-01     1     8     2     0     1     2     4    12     1
#> 34:      TCGA-OR-A5L8-01     2     8     0     1     0     0     2     5     0
#> 35:      TCGA-PK-A5HA-01     3    17     4     2     9     6     3    13     1
#> 36:      TCGA-OR-A5JW-01     1     9     1     0     7     2     2     5     2
#> 37:      TCGA-OR-A5KZ-01     2     4     0     0     3     3     2     7     2
#> 38:      TCGA-OR-A5L3-01     4    10     2     0     1     3     3     2     2
#> 39:      TCGA-OR-A5KW-01     5     8     1     0     6     4     2     5     0
#> 40:      TCGA-OR-A5J9-01     0     8     2     2     1     6     5    10     1
#> 41:      TCGA-OR-A5J2-01     1    12     1     2     7     2     1     9     3
#> 42:      TCGA-OR-A5KV-01     0     7     0     0     3     3     0     9     3
#> 43:      TCGA-OR-A5JP-01     4    11     4     3    11    11     6    16     1
#> 44:      TCGA-OR-A5JA-01     2     9     1     1   323     8     7    15     4
#> 45:      TCGA-OR-A5K0-01     3    13     7     0     7     4     5    12     2
#> 46:      TCGA-OR-A5LT-01     2     8     0     1     3     2     2     5     0
#> 47:      TCGA-OR-A5JY-01     9    14     3     2     9     8     5    23     4
#> 48:      TCGA-OR-A5KU-01     3     9     1     0     0     1     6     8     0
#> 49:      TCGA-OR-A5JT-01     5     7     1     1     3     2     1    11     1
#> 50:      TCGA-OR-A5LM-01     1     6     0     0     2     3     2    11     3
#> 51:      TCGA-OR-A5LC-01     3    15     2     1     6     3     3    15     1
#> 52:      TCGA-OR-A5K5-01    19    22     7     3    14    14    13    26     3
#> 53:      TCGA-P6-A5OF-01     2    11     1     1     2     2     1    10     3
#> 54:      TCGA-OR-A5J7-01     0    14     3     1     4     4     4    10     1
#> 55:      TCGA-OR-A5JD-01     2    11     0     0     2     3     3     5     2
#> 56:      TCGA-OR-A5J4-01    10    19     6     5    19    17    10    25     4
#> 57:      TCGA-OR-A5JE-01     4    16     1     0     3     5     3    12     2
#> 58:      TCGA-OR-A5KX-01     1    17     2     1     0     8     1    16     1
#> 59:      TCGA-OR-A5JF-01     4    18     2     5     8    11     7     9     4
#> 60:      TCGA-OR-A5K2-01     3    12     2     1     7     6     7    15     3
#> 61:      TCGA-OR-A5KP-01     5    19     1     4     9     6     8    15     1
#> 62:      TCGA-P6-A5OG-01     9    63     9     0    51    11    13    48    15
#> 63:      TCGA-OR-A5LD-01     6    14     4     3     5     5     4    20     3
#> 64:      TCGA-OR-A5L6-01     3     9     2     1     2     5     6    11     2
#> 65:      TCGA-OR-A5LK-01     5    13     2     0     8     5     4    15     2
#> 66:      TCGA-OR-A5LL-01     3    15     2     4     4     5     4    23     1
#> 67:      TCGA-OR-A5K9-01    12    27     2     3    21    19    12    32     8
#> 68:      TCGA-OR-A5J1-01     3    17     1     3     1     5     0     8     0
#> 69:      TCGA-OR-A5LI-01     3    25     1     2     3     6     8    20     1
#> 70:      TCGA-P6-A5OH-01    12    32     9     5    11    18     7    24     8
#> 71:      TCGA-OR-A5J8-01     4    15     1     2    43     6     4    11     2
#> 72:      TCGA-OR-A5L2-01    11    42     8     3    16    22    13    32     7
#> 73:      TCGA-OR-A5J3-01     1     3     1     0     1     2     2     3     1
#> 74:      TCGA-OR-A5J5-01    13   210     3     1    13     1    14   227     1
#> 75:      TCGA-OR-A5JH-01     0     0     1     1     2     0     0     3     0
#> 76:      TCGA-OR-A5JQ-01     1     1     1     0     1     1     0     1     1
#> 77:      TCGA-OR-A5JR-01     0     0     0     0     0     0     1     3     0
#> 78:      TCGA-OR-A5JU-01     2     7     1     1     4     0     3     6     1
#> 79:      TCGA-OR-A5JV-01     1     4     0     0     7     4     1    10     1
#> 80:      TCGA-OR-A5K3-01     0     1     0     1     3     2     5     3     1
#> 81:      TCGA-OR-A5K4-01    13   155     2     4     3     3    12   137     3
#> 82:      TCGA-OR-A5KB-01    54   233   136    22   813   196    60   228   107
#> 83:      TCGA-OR-A5L1-01     4     6     2     2     2     1     5     4     0
#> 84:      TCGA-OR-A5L5-01     1     1     1     0     1     1     1     2     1
#> 85:      TCGA-OR-A5L9-01     1     4     0     2     1     2     1     0     0
#> 86:      TCGA-OR-A5LB-01    11    96     5     4    20     4    13    82     5
#> 87:      TCGA-OR-A5LH-01     0     3     1     1     0     0     1     1     0
#> 88:      TCGA-OR-A5LJ-01    14   217     4     5    18     7    23   207     3
#> 89:      TCGA-OR-A5LP-01     1     3     1     0     2     2     3     3     2
#> 90:      TCGA-OR-A5LR-01     2     1     1     0     1     0     3     4     1
#> 91:      TCGA-PA-A5YG-01     1     6     0     0     1     0     1     1     0
#> 92:      TCGA-PK-A5HB-01   144   391    91    15    61    33   150   370    69
#>     Tumor_Sample_Barcode   T>C   C>T   T>A   T>G   C>A   C>G   A>G   G>A   A>T
#>       A>C   G>T   G>C   n_A   n_T   n_G   n_C n_mutations n_C>G_and_C>T
#>     <int> <int> <int> <num> <num> <num> <num>       <num>         <num>
#>  1:     0     6     2     3     4     9    14          30            14
#>  2:     1     8     2     5     6    13     4          28             8
#>  3:     0     5     1     4     3    11    12          30            15
#>  4:     0     7     0     2     2    11     6          21             7
#>  5:     1    10     9     5     8    29    43          85            50
#>  6:     1     1     0     3     1     6     4          14             8
#>  7:     0     2     4     5     6    11    13          35            21
#>  8:     1     1     1     2     4     7     6          19            10
#>  9:     0     2     1     5     1     3     4          13             5
#> 10:     2    10    18    10     6    48    33          97            59
#> 11:     2     6     2     6     3    13    12          34            16
#> 12:     0     1     0     2     4     8     7          21            14
#> 13:     0     1     4     6     8    13    14          41            22
#> 14:     0     0     0     1     2     3     6          12             7
#> 15:     0     0     2     4     6     4    12          26            14
#> 16:     1     5     4     2     8    15    11          36            19
#> 17:     1     6     6     2     2    15    19          38            19
#> 18:     0     3     4    11    11    13     6          41            14
#> 19:     0     1     0     3     3     3     7          16             8
#> 20:     0     4     0     3     2     6     7          18             9
#> 21:     1     2     2     6     4    21    18          49            31
#> 22:     0     3     5     3     8    12    13          36            19
#> 23:     1     2     2     4     4     6    12          26            14
#> 24:     0     6     6     1     5    16    17          39            22
#> 25:     1     0     1     2     1     6     4          13            10
#> 26:     3    85    32    32    36   177   174         419           176
#> 27:     0     2     3     6     5    11    19          41            22
#> 28:     0     2     3     2     2     8     5          17            10
#> 29:     1     3     1     1     1     8    11          21            15
#> 30:     0     1     0     4     4     7     5          20            11
#> 31:     0     4     5     4     3    19    11          37            24
#> 32:     2     7     4    11     7    30    35          83            49
#> 33:     0     2     4     5     3    18    11          37            26
#> 34:     1     3     0     3     3     8     8          22            13
#> 35:     1     7     6     5     9    26    32          72            42
#> 36:     0     5     1     4     2    11    18          35            17
#> 37:     0     5     3     4     2    15    10          31            17
#> 38:     1     3     1     6     6     6    14          32            16
#> 39:     0     2     2     2     6     9    18          35            19
#> 40:     0     2     4     6     4    16    15          41            28
#> 41:     0     3     0     4     4    12    21          41            23
#> 42:     0     1     0     3     0    10    13          26            19
#> 43:     3    11    12    10    11    39    33          93            50
#> 44:     0   291     2    11     4   308   340         663            34
#> 45:     0    11     6     7    10    29    24          70            35
#> 46:     0     2     1     2     3     8    13          26            16
#> 47:     2     9    10    11    14    42    31          98            55
#> 48:     0     1     1     6     4    10    10          30            19
#> 49:     0     6     1     2     7    18    12          39            21
#> 50:     0     3     1     5     1    15    11          32            21
#> 51:     0    15     2     4     6    32    24          66            35
#> 52:     7    16    11    23    29    53    50         155            73
#> 53:     0     7     0     4     4    17    15          40            23
#> 54:     1     4    12     6     4    26    22          58            40
#> 55:     0     5     2     5     2    12    16          35            21
#> 56:     3    20    23    17    21    68    55         161            84
#> 57:     4     9     9     9     5    30    24          68            42
#> 58:     2     3     3     4     4    22    25          55            44
#> 59:     3     9    14    14    11    32    37          94            52
#> 60:     3     7     7    13     6    29    25          73            40
#> 61:     1     3     4    10    10    22    34          76            44
#> 62:     7    73    14    35    18   135   125         313           136
#> 63:     5     5     9    12    13    34    24          83            48
#> 64:     0     9     2     8     6    22    16          52            27
#> 65:     2     8     3     8     7    26    26          67            36
#> 66:     3     4     4     8     9    31    24          72            47
#> 67:     5    11    16    25    17    59    67         168            94
#> 68:     1     0     0     1     7     8    23          39            30
#> 69:     3     3     8    12     6    31    34          83            59
#> 70:     0    12    20    15    26    56    61         158            94
#> 71:     1    28     7     7     7    46    64         124            39
#> 72:     4    16    18    24    22    66    80         192           114
#> 73:     0     4     1     3     2     8     6          19             9
#> 74:     3     8     2    18    17   237   224         496           440
#> 75:     0     3     0     0     2     6     2          10             3
#> 76:     0     1     1     1     2     3     3           9             4
#> 77:     0     1     2     1     0     6     0           7             5
#> 78:     1     3     2     5     4    11    11          31            15
#> 79:     0     3     5     2     1    18    15          36            23
#> 80:     0     2     2     6     1     7     6          20             8
#> 81:     1     4     2    16    19   143   161         339           297
#> 82:    24   722   212   191   212  1162  1242        2807           869
#> 83:     0     1     0     5     8     5     9          27            11
#> 84:     0     2     0     2     2     4     3          11             4
#> 85:     0     0     0     1     3     0     7          11             6
#> 86:     3    10     0    21    20    92   120         253           182
#> 87:     1     0     0     2     2     1     3           8             4
#> 88:     3    21     9    29    23   237   242         531           440
#> 89:     0     3     2     5     2     8     7          22            10
#> 90:     0     1     0     4     3     5     2          14             5
#> 91:     0     1     0     1     1     2     7          11             7
#> 92:    26    67    39   245   250   476   485        1456           833
#>       A>C   G>T   G>C   n_A   n_T   n_G   n_C n_mutations n_C>G_and_C>T
#>     tCw_to_A tCw_to_T tCw_to_G   tCw wGa_to_C wGa_to_T wGa_to_A   wGa
#>        <num>    <num>    <num> <num>    <num>    <num>    <num> <num>
#>  1:        0        3        2     5        1        1        0     2
#>  2:        0        0        1     1        1        2        1     4
#>  3:        1        2        1     4        0        1        3     4
#>  4:        0        0        0     0        0        1        2     3
#>  5:        5        6        8    19        6        4        3    13
#>  6:        0        1        0     1        0        0        1     1
#>  7:        1        2        2     5        2        1        1     4
#>  8:        0        0        2     2        0        0        1     1
#>  9:        0        1        0     1        0        0        0     0
#> 10:        1        4        6    11       11        2        4    17
#> 11:        0        0        4     4        1        1        0     2
#> 12:        0        1        2     3        0        0        1     1
#> 13:        0        1        1     2        3        0        3     6
#> 14:        0        1        0     1        0        0        0     0
#> 15:        0        0        1     1        2        0        0     2
#> 16:        1        1        1     3        1        1        2     4
#> 17:        1        1        1     3        3        1        0     4
#> 18:        0        0        1     1        1        0        1     2
#> 19:        0        1        0     1        0        0        0     0
#> 20:        0        1        0     1        0        1        0     1
#> 21:        1        4        1     6        0        2        5     7
#> 22:        1        1        1     3        0        0        2     2
#> 23:        0        1        1     2        0        0        0     0
#> 24:        0        4        0     4        0        1        1     2
#> 25:        0        0        0     0        1        0        0     1
#> 26:       10       20       19    49       15        5       24    44
#> 27:        0        2        3     5        0        0        0     0
#> 28:        0        0        1     1        0        0        0     0
#> 29:        0        1        0     1        1        0        0     1
#> 30:        0        1        0     1        0        0        0     0
#> 31:        0        1        0     1        0        1        4     5
#> 32:        3        2        3     8        2        2        7    11
#> 33:        0        1        1     2        2        0        1     3
#> 34:        0        1        0     1        0        0        0     0
#> 35:        2        2        3     7        4        1        2     7
#> 36:        1        1        0     2        1        0        0     1
#> 37:        2        0        0     2        1        2        1     4
#> 38:        0        1        0     1        1        0        0     1
#> 39:        0        0        1     1        0        1        1     2
#> 40:        0        1        2     3        2        0        0     2
#> 41:        2        0        1     3        0        2        2     4
#> 42:        1        0        0     1        0        0        2     2
#> 43:        2        2        4     8        5        3        3    11
#> 44:      127        1        1   129        1      107        4   112
#> 45:        1        2        1     4        3        1        1     5
#> 46:        0        0        1     1        0        0        0     0
#> 47:        1        4        2     7        4        1        4     9
#> 48:        0        0        1     1        0        0        1     1
#> 49:        0        0        1     1        1        0        0     1
#> 50:        0        0        1     1        0        0        1     1
#> 51:        0        1        1     2        2        1        2     5
#> 52:        2        4        8    14        5        4        4    13
#> 53:        1        1        0     2        0        1        1     2
#> 54:        1        0        1     2        5        2        2     9
#> 55:        0        0        0     0        1        1        0     2
#> 56:        4        3        7    14       12        5        2    19
#> 57:        0        2        2     4        3        1        0     4
#> 58:        0        1        3     4        2        0        1     3
#> 59:        2        5        2     9        3        2        0     5
#> 60:        1        2        2     5        1        0        0     1
#> 61:        1        2        2     5        1        0        1     2
#> 62:        3       19        1    23        3        6       20    29
#> 63:        0        2        2     4        2        0        1     3
#> 64:        0        0        1     1        0        2        0     2
#> 65:        0        1        1     2        0        2        1     3
#> 66:        1        2        1     4        1        0        2     3
#> 67:        6        6        4    16        6        2        6    14
#> 68:        1        0        1     2        0        0        0     0
#> 69:        1        3        1     5        2        1        2     5
#> 70:        3        6        2    11        9        2        1    12
#> 71:       15        0        0    15        1        6        0     7
#> 72:        2        5        9    16        7        3        2    12
#> 73:        0        0        0     0        0        2        0     2
#> 74:        2        0        0     2        1        2        0     3
#> 75:        0        0        0     0        0        0        0     0
#> 76:        0        0        0     0        0        0        0     0
#> 77:        0        0        0     0        0        0        0     0
#> 78:        1        0        0     1        0        2        0     2
#> 79:        1        0        0     1        0        2        0     2
#> 80:        0        0        0     0        0        0        0     0
#> 81:        0        4        0     4        2        1        0     3
#> 82:       73       44       36   153       49       82       45   176
#> 83:        2        0        0     2        0        0        0     0
#> 84:        0        0        0     0        0        0        0     0
#> 85:        0        0        0     0        0        0        0     0
#> 86:        2        0        1     3        0        0        3     3
#> 87:        0        0        0     0        0        0        0     0
#> 88:        2        2        1     5        4        1        6    11
#> 89:        1        0        0     1        0        0        0     0
#> 90:        0        0        0     0        0        0        0     0
#> 91:        0        0        0     0        0        0        0     0
#> 92:        6       51        6    63       11       10       54    75
#>     tCw_to_A tCw_to_T tCw_to_G   tCw wGa_to_C wGa_to_T wGa_to_A   wGa
#>     tCw_to_G+tCw_to_T n_bg_A n_bg_T n_bg_G n_bg_C n_bg_tcw n_bg_wga n_bg_bases
#>                 <num>  <int>  <int>  <int>  <int>    <num>    <num>      <int>
#>  1:                 6    133    133    151    157       19       23        574
#>  2:                 3     74     88     82     84       11       12        328
#>  3:                 6    150    126    164    175       20       26        615
#>  4:                 2     65     72     84     66        4       14        287
#>  5:                23    483    542    489    536       89       70       2050
#>  6:                 2     64     56     92    116        8        7        328
#>  7:                 7    219    177    227    238       19       25        861
#>  8:                 3    100     98    112    100       17        9        410
#>  9:                 1     39     42     59     65       11        6        205
#> 10:                25    618    566    639    596       77      111       2419
#> 11:                 5    182    123    178    173       24       33        656
#> 12:                 4    125    154    133    162       21       15        574
#> 13:                 8    230    256    208    208       44       26        902
#> 14:                 1     52     70     88     77        9        9        287
#> 15:                 3    142    114    154    164       14       28        574
#> 16:                 5    171    176    208    224       29       31        779
#> 17:                 5    190    171    217    201       28       31        779
#> 18:                 3    122    128    173    151       19       22        574
#> 19:                 1     72     70     91     95       13       11        328
#> 20:                 1    104     97     77     91        7       19        369
#> 21:                10    285    337    302    347       60       37       1271
#> 22:                 4    191    170    188    230       23       28        779
#> 23:                 2    128    125    154    167       18       23        574
#> 24:                 5    231    183    240    248       36       39        902
#> 25:                 1     97     99    109    105       15       15        410
#> 26:                78   1760   1782   1776   1898      280      285       7216
#> 27:                 5    215    236    217    234       35       34        902
#> 28:                 1     65    116    117    112       17       14        410
#> 29:                 2    140    137    173    165       18       19        615
#> 30:                 1    122    110    115    104       18       17        451
#> 31:                 5    225    249    251    259       44       32        984
#> 32:                14    447    485    541    536       64       74       2009
#> 33:                 5    258    222    302    284       33       46       1066
#> 34:                 1    104    117    136    176       19       15        533
#> 35:                11    388    395    468    471       56       62       1722
#> 36:                 2    136    165    208    188       21       30        697
#> 37:                 2    162    179    191    165       19       23        697
#> 38:                 2    162    163    150    181       31       33        656
#> 39:                 2    182    153    223    221       19       36        779
#> 40:                 5    277    281    309    281       36       45       1148
#> 41:                 3    196    225    267    255       26       32        943
#> 42:                 2    191    170    212    206       25       26        779
#> 43:                14    497    466    553    534       89       94       2050
#> 44:                 7    354    337    363    340       46       55       1394
#> 45:                 7    305    329    399    402       45       55       1435
#> 46:                 1    150    132    217    157       17       22        656
#> 47:                14    513    495    617    630       70       85       2255
#> 48:                 2    200    186    228    165       31       38        779
#> 49:                 2    177    192    249    243       30       28        861
#> 50:                 2    188    230    220    223       36       29        861
#> 51:                 6    329    330    386    390       50       53       1435
#> 52:                21    629    754    751    859      124      108       2993
#> 53:                 2    225    191    252    275       30       24        943
#> 54:                 8    366    395    451    428       68       58       1640
#> 55:                 1    220    176    246    219       23       25        861
#> 56:                24    767    833    930    914      133      120       3444
#> 57:                 7    413    368    480    461       56       65       1722
#> 58:                 7    402    421    506    475       65       57       1804
#> 59:                10    530    536    531    535       79       84       2132
#> 60:                 5    367    372    485    416       59       68       1640
#> 61:                 6    485    398    459    462       62       76       1804
#> 62:                43   1343   1308   1445   1480      221      183       5576
#> 63:                 7    443    422    553    550       70       53       1968
#> 64:                 1    251    278    323    255       33       47       1107
#> 65:                 3    325    336    386    429       54       36       1476
#> 66:                 6    449    407    521    550       64       66       1927
#> 67:                22    873    823   1067   1091      128      135       3854
#> 68:                 1    244    298    353    335       52       26       1230
#> 69:                 8    545    525    651    698       80       80       2419
#> 70:                18    859    855   1017   1123      130      139       3854
#> 71:                 1    367    318    447    467       48       44       1599
#> 72:                23   1058   1043   1265   1308      178      178       4674
#> 73:                 0     83     78     97    111        8        8        369
#> 74:                 1   3968   3799   5143   5130      566      588      18040
#> 75:                 0     26     34     28     35        7        3        123
#> 76:                 0     35     43     45     41       11        3        164
#> 77:                 0     44     34     65     62        5       12        205
#> 78:                 0    114    137    176    188       23       15        615
#> 79:                 0    227    201    243    272       27       35        943
#> 80:                 0     64     93     81     90       20       11        328
#> 81:                 6   2506   2574   3491   3606      344      339      12177
#> 82:               174   8311   8575   9200   9543     1370     1274      35629
#> 83:                 0    108    105    108    130       14       17        451
#> 84:                 0     45     30     54     35        3       13        164
#> 85:                 0     47     52     73     74        6        4        246
#> 86:                 4   1600   1475   2141   2246      207      250       7462
#> 87:                 0     42     33     51     38        2        8        164
#> 88:                13   3748   3923   5147   5222      593      526      18040
#> 89:                 0     71     91    119    129       12       12        410
#> 90:                 0     46     47     70     42        7        7        205
#> 91:                 0     57     71     80     79        9       10        287
#> 92:               122   7489   7540   9571   9553     1129     1093      34153
#>     tCw_to_G+tCw_to_T n_bg_A n_bg_T n_bg_G n_bg_C n_bg_tcw n_bg_wga n_bg_bases
#>     APOBEC_Enrichment non_APOBEC_mutations fraction_APOBEC_mutations
#>                 <num>                <num>                     <num>
#>  1:         3.1428571                   24                     0.200
#>  2:         2.7065217                   25                     0.107
#>  3:         2.9478261                   24                     0.200
#>  4:         2.3809524                   19                     0.095
#>  5:         2.9654088                   62                     0.271
#>  6:         3.4666667                   12                     0.143
#>  7:         3.5227273                   28                     0.200
#>  8:         2.4461538                   16                     0.158
#>  9:         1.4588235                   12                     0.077
#> 10:         2.7835377                   72                     0.258
#> 11:         1.9243421                   29                     0.147
#> 12:         2.3412698                   17                     0.190
#> 13:         2.1610390                   33                     0.195
#> 14:         1.3095238                   11                     0.083
#> 15:         1.6224490                   23                     0.115
#> 16:         1.8947368                   31                     0.139
#> 17:         1.8644068                   33                     0.132
#> 18:         1.6933798                   38                     0.073
#> 19:         0.9687500                   15                     0.062
#> 20:         0.7179487                   17                     0.056
#> 21:         2.1582973                   39                     0.204
#> 22:         1.7254902                   32                     0.111
#> 23:         1.1184669                   24                     0.077
#> 24:         1.4787879                   34                     0.128
#> 25:         0.7133333                   12                     0.077
#> 26:         2.8818584                  341                     0.186
#> 27:         1.4855072                   36                     0.122
#> 28:         0.7387097                   16                     0.059
#> 29:         1.2180180                   19                     0.095
#> 30:         0.5688312                   19                     0.050
#> 31:         1.3980263                   32                     0.135
#> 32:         2.2298137                   69                     0.169
#> 33:         1.4264849                   32                     0.135
#> 34:         0.7058824                   21                     0.045
#> 35:         2.0841404                   61                     0.153
#> 36:         0.9134948                   33                     0.057
#> 37:         0.9971989                   29                     0.065
#> 38:         0.6464844                   30                     0.062
#> 39:         0.8497608                   33                     0.057
#> 40:         1.3007055                   36                     0.122
#> 41:         1.1739130                   38                     0.073
#> 42:         0.8627451                   24                     0.077
#> 43:         1.6631694                   79                     0.151
#> 44:         1.4330227                  656                     0.011
#> 45:         1.6020000                   63                     0.100
#> 46:         0.5993590                   25                     0.038
#> 47:         2.0478592                   84                     0.143
#> 48:         0.5995423                   28                     0.067
#> 49:         0.8078818                   37                     0.051
#> 50:         0.6490842                   30                     0.062
#> 51:         1.2915395                   60                     0.091
#> 52:         1.9963392                  134                     0.135
#> 53:         0.8486312                   38                     0.050
#> 54:         1.3952381                   50                     0.138
#> 55:         0.4613095                   34                     0.029
#> 56:         2.0824393                  137                     0.149
#> 57:         1.2961433                   61                     0.103
#> 58:         1.2792474                   48                     0.127
#> 59:         1.2576687                   84                     0.106
#> 60:         0.8868110                   68                     0.068
#> 61:         0.9100791                   70                     0.079
#> 62:         2.2891490                  270                     0.137
#> 63:         1.3077575                   76                     0.084
#> 64:         0.2675926                   51                     0.019
#> 65:         0.7546296                   64                     0.045
#> 66:         1.0517185                   66                     0.083
#> 67:         1.9203948                  146                     0.131
#> 68:         0.2940171                   38                     0.026
#> 69:         1.1432203                   75                     0.096
#> 70:         1.5233726                  140                     0.114
#> 71:         0.2547380                  123                     0.008
#> 72:         1.4581855                  169                     0.120
#> 73:         0.0000000                   19                     0.000
#> 74:         0.0202320                  495                     0.002
#> 75:         0.0000000                   10                     0.000
#> 76:         0.0000000                    9                     0.000
#> 77:         0.0000000                    7                     0.000
#> 78:         0.0000000                   31                     0.000
#> 79:         0.0000000                   36                     0.000
#> 80:         0.0000000                   20                     0.000
#> 81:         0.2099176                  333                     0.018
#> 82:         1.4194076                 2633                     0.062
#> 83:         0.0000000                   27                     0.000
#> 84:         0.0000000                   11                     0.000
#> 85:         0.0000000                   11                     0.000
#> 86:         0.2109794                  249                     0.016
#> 87:         0.0000000                    8                     0.000
#> 88:         0.2737773                  518                     0.024
#> 89:         0.0000000                   22                     0.000
#> 90:         0.0000000                   14                     0.000
#> 91:         0.0000000                   11                     0.000
#> 92:         1.2605193                 1334                     0.084
#>     APOBEC_Enrichment non_APOBEC_mutations fraction_APOBEC_mutations
#>     fisher_pvalue          or        ci.up ci.low APOBEC_Enriched   fdr
#>             <num>       <num>        <num>  <num>          <char> <num>
#>  1:     0.8934315 0.589040068 1.993448e-01    Inf             yes     1
#>  2:     0.9226390 0.463086928 9.368122e-02    Inf             yes     1
#>  3:     0.9281081 0.530849769 1.840557e-01    Inf             yes     1
#>  4:     0.9527883 0.356817108 4.874095e-02    Inf             yes     1
#>  5:     0.9684128 0.609534004 3.615543e-01    Inf             yes     1
#>  6:     0.9763650 0.291719090 4.178781e-02    Inf             yes     1
#>  7:     0.9817466 0.426784457 1.697109e-01    Inf             yes     1
#>  8:     0.9825856 0.305742819 6.640707e-02    Inf             yes     1
#>  9:     0.9867836 0.179747836 7.218311e-03    Inf              no     1
#> 10:     0.9878915 0.567310611 3.495925e-01    Inf             yes     1
#> 11:     0.9889244 0.344794073 1.131812e-01    Inf              no     1
#> 12:     0.9905897 0.309240273 8.808370e-02    Inf             yes     1
#> 13:     0.9929701 0.372743980 1.553137e-01    Inf             yes     1
#> 14:     0.9963081 0.133206620 5.731398e-03    Inf              no     1
#> 15:     0.9970682 0.230726417 5.413504e-02    Inf              no     1
#> 16:     0.9978463 0.275998688 9.390200e-02    Inf              no     1
#> 17:     0.9980831 0.270616781 9.195820e-02    Inf              no     1
#> 18:     0.9981275 0.212728924 4.982995e-02    Inf              no     1
#> 19:     0.9986089 0.109485765 4.820747e-03    Inf              no     1
#> 20:     0.9988716 0.108139585 4.830566e-03    Inf              no     1
#> 21:     0.9989875 0.336296225 1.597789e-01    Inf             yes     1
#> 22:     0.9993605 0.218813809 6.587155e-02    Inf              no     1
#> 23:     0.9997198 0.134900189 2.129648e-02    Inf              no     1
#> 24:     0.9997317 0.220158579 7.663601e-02    Inf              no     1
#> 25:     0.9997380 0.084086974 3.806035e-03    Inf              no     1
#> 26:     0.9997472 0.591367054 4.522571e-01    Inf             yes     1
#> 27:     0.9997477 0.218221664 7.589436e-02    Inf              no     1
#> 28:     0.9997662 0.082529054 3.738940e-03    Inf              no     1
#> 29:     0.9998633 0.124214943 1.975243e-02    Inf              no     1
#> 30:     0.9999182 0.071171652 3.249253e-03    Inf              no     1
#> 31:     0.9999541 0.187271878 6.591269e-02    Inf              no     1
#> 32:     0.9999599 0.314980945 1.730261e-01    Inf             yes     1
#> 33:     0.9999634 0.188987770 6.719362e-02    Inf              no     1
#> 34:     0.9999652 0.067472102 3.146283e-03    Inf              no     1
#> 35:     0.9999672 0.279773650 1.423543e-01    Inf             yes     1
#> 36:     0.9999692 0.107037180 1.725620e-02    Inf              no     1
#> 37:     0.9999697 0.106361789 1.711625e-02    Inf              no     1
#> 38:     0.9999755 0.101605728 1.627497e-02    Inf              no     1
#> 39:     0.9999888 0.099410692 1.620821e-02    Inf              no     1
#> 40:     0.9999920 0.168447069 6.032502e-02    Inf              no     1
#> 41:     0.9999940 0.122648277 3.064410e-02    Inf              no     1
#> 42:     0.9999940 0.092591595 1.508091e-02    Inf              no     1
#> 43:     0.9999944 0.278091518 1.530629e-01    Inf              no     1
#> 44:     0.9999947 0.197881486 8.452020e-02    Inf              no     1
#> 45:     0.9999950 0.200004982 8.583462e-02    Inf              no     1
#> 46:     0.9999964 0.053975748 2.548811e-03    Inf              no     1
#> 47:     0.9999977 0.273426874 1.521705e-01    Inf             yes     1
#> 48:     0.9999982 0.080919515 1.313258e-02    Inf              no     1
#> 49:     0.9999987 0.082445427 1.355003e-02    Inf              no     1
#> 50:     0.9999994 0.076336999 1.253046e-02    Inf              no     1
#> 51:     0.9999995 0.160223297 6.427228e-02    Inf              no     1
#> 52:     0.9999996 0.302157375 1.873324e-01    Inf              no     1
#> 53:     0.9999996 0.076763450 1.270643e-02    Inf              no     1
#> 54:     0.9999997 0.181772108 8.313302e-02    Inf              no     1
#> 55:     0.9999999 0.040683051 1.953011e-03    Inf              no     1
#> 56:     0.9999999 0.298560596 1.914626e-01    Inf             yes     1
#> 57:     1.0000000 0.156963572 6.844370e-02    Inf              no     1
#> 58:     1.0000000 0.143911953 6.300038e-02    Inf              no     1
#> 59:     1.0000000 0.177073018 8.939443e-02    Inf              no     1
#> 60:     1.0000000 0.107605530 3.976487e-02    Inf              no     1
#> 61:     1.0000000 0.120764665 4.928745e-02    Inf              no     1
#> 62:     1.0000000 0.342338185 2.457853e-01    Inf             yes     1
#> 63:     1.0000000 0.132392635 5.834844e-02    Inf              no     1
#> 64:     1.0000000 0.029771290 1.442885e-03    Inf              no     1
#> 65:     1.0000000 0.070740638 1.828017e-02    Inf              no     1
#> 66:     1.0000000 0.116020729 4.761444e-02    Inf              no     1
#> 67:     1.0000000 0.241527861 1.541352e-01    Inf              no     1
#> 68:     1.0000000 0.025290608 1.231412e-03    Inf              no     1
#> 69:     1.0000000 0.124761392 5.881375e-02    Inf              no     1
#> 70:     1.0000000 0.187801486 1.152565e-01    Inf              no     1
#> 71:     1.0000000 0.021482321 1.052925e-03    Inf              no     1
#> 72:     1.0000000 0.192303513 1.251871e-01    Inf              no     1
#> 73:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 74:     1.0000000 0.001832107 9.530095e-05    Inf              no     1
#> 75:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 76:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 77:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 78:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 79:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 80:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 81:     1.0000000 0.017043915 7.358546e-03    Inf              no     1
#> 82:     1.0000000 0.187514814 1.619488e-01    Inf              no     1
#> 83:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 84:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 85:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 86:     1.0000000 0.018702858 6.310610e-03    Inf              no     1
#> 87:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 88:     1.0000000 0.024215563 1.421815e-02    Inf              no     1
#> 89:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 90:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 91:     1.0000000 0.000000000 0.000000e+00    Inf              no     1
#> 92:     1.0000000 0.135343101 1.141845e-01    Inf              no     1
#>     fisher_pvalue          or        ci.up ci.low APOBEC_Enriched   fdr
#> 
# }