Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Retrieve the annotation of a
|
object |
Object of class |
elements |
Character. The name of the element(s) in the annotation slot to be extracted.
If set to |
... |
not supported |
Value
If only a single value for elements is provided, the element is returned directly.
If multiple values are provided, a named list with the requested elements is returned.
Examples
data(SNPhood.o, package="SNPhood")
annotation(SNPhood.o)
annotation(SNPhood.o, elements = "regions")
annotation(SNPhood.o, elements = c("regions", "bins"))
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(SNPhood)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
Loading required package: checkmate
------------------------------------------------------------------------------------------------------------------
| Welcome to the SNPhood package and thank you for using our software. This is SNPhood version 1.2.2. |
| See the vignettes (type browseVignettes("SNPhood") or the help pages for how to use SNPhood for your analyses. |
| Thank you for using our software. Please do not hesitate to contact us if there are any questions. |
------------------------------------------------------------------------------------------------------------------
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPhood/annotation-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annotation,SNPhood-method
> ### Title: Retrieve the annotation of a 'SNPhood' object.
> ### Aliases: annotation annotation,SNPhood-method
>
> ### ** Examples
>
> data(SNPhood.o, package="SNPhood")
> annotation(SNPhood.o)
$regions
GRanges object with 174 ranges and 2 metadata columns:
seqnames ranges strand | annotation SNPPos
<Rle> <IRanges> <Rle> | <character> <integer>
rs75359783 chr21 [15353988, 15354987] * | rs75359783 15354488
rs8132276 chr21 [15459575, 15460574] * | rs8132276 15460075
rs113783782 chr21 [15465922, 15466921] * | rs113783782 15466422
rs7275860 chr21 [15468105, 15469104] * | rs7275860 15468605
rs2822405 chr21 [15473675, 15474674] * | rs2822405 15474175
... ... ... ... . ... ...
rs2839277 chr21 [47895101, 47896100] * | rs2839277 47895601
rs2839298 chr21 [47923469, 47924468] * | rs2839298 47923969
rs2070429 chr21 [47980070, 47981069] * | rs2070429 47980570
rs9647249 chr21 [48033417, 48034416] * | rs9647249 48033917
rs59121565 chr21 [48042523, 48043522] * | rs59121565 48043023
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
$genotype
$genotype$readsDerived
$genotype$readsDerived$paternal
$genotype$readsDerived$paternal$GM10847
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A 0 0 1 0 0 0 0 0 1 0 0 0 0 0
C 0 8 0 0 0 0 47 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 2 0 0 0 4 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 4 0 0 0 0 0 0 0 18 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 1 0 0 0 0 0 0 0 0
G 0 0 0 1 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 7
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50] [,51] [,52] [,53]
A 0 0 0 0 0 0 0 2 0 32 0 0 0
C 0 0 0 0 3 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66]
A 0 0 0 0 0 19 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 1 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
A 0 0 0 0 0 29 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 2 0 0 0 19 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
A 0 0 0 0 0 0 0 0 0 0 0 0 2
C 0 0 0 0 19 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
A 0 0 0 0 0 0 0 0 3 0 0 1
C 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 28
T 0 0 0 0 0 0 0 0 0 0 0 0
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115]
A 0 0 0 3 0 0 0 0 0 0 0
C 0 0 20 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 11 0
T 0 0 0 0 0 0 0 0 0 0 0
[,116] [,117] [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126]
A 0 0 0 0 0 0 0 0 2 0 0
C 2 0 0 0 0 2 0 2 0 0 0
G 0 2 1 0 0 0 1 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,127] [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
A 0 0 4 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 1 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
A 0 0 8 0 0 0 0 0 0 0 0
C 0 1 0 0 6 2 0 0 0 9 0
G 0 0 0 0 0 0 0 0 1 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158] [,159]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 2 2 0 0 0 0 0 0 0
T 1 0 0 0 0 0 0 0 0 0 0
[,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168] [,169] [,170]
A 0 0 0 0 0 0 0 0 0 0 1
C 0 0 0 0 0 0 0 0 0 0 0
G 0 1 0 0 0 0 0 0 0 1 0
T 2 0 0 0 0 0 0 0 0 0 0
[,171] [,172] [,173] [,174]
A 0 0 0 0
C 0 0 0 0
G 0 0 0 0
T 0 0 0 0
$genotype$readsDerived$paternal$GM12890
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A 0 0 0 0 0 0 4 0 1 0 0 0 0 0
C 0 1 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 11 0 0 0 0 0 0 0 0
T 0 0 0 2 0 0 0 0 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 4 0 0
[,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
A 0 0 0 0 0 0 0 0 0 0 105 0 0
C 0 0 0 0 0 0 0 0 3 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 4 0 0 0
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50] [,51] [,52] [,53]
A 0 0 0 0 0 0 0 0 0 61 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 3 0 0 0 0 0 0 0 0 0
T 0 0 0 0 2 0 21 0 0 0 0 0 0
[,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 13 0 0 0 0 3 0
G 0 0 0 0 0 4 0 0 0 0 0 0 0
T 8 32 0 0 0 0 0 0 0 0 0 0 0
[,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 2 0 0 0 0 0 0
G 0 0 0 0 2 139 0 0 0 0 0 0 3
T 0 0 0 2 0 0 0 0 0 0 0 0 0
[,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
A 0 0 0 0 0 0 0 91 0 0 0 0 0
C 0 6 0 0 0 0 0 0 0 0 0 5 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 5 0 0 0 0 0 0 0 0
[,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
A 0 0 0 0 43 1 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 56
T 0 0 0 0 0 0 0 0 0 0 0 0
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115]
A 0 0 0 0 0 5 0 0 0 0 0
C 0 0 0 0 0 0 0 0 3 0 0
G 0 0 0 0 0 0 0 0 0 0 0
T 1 0 0 0 0 0 1 0 0 0 1
[,116] [,117] [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126]
A 0 0 0 7 0 0 0 0 0 0 0
C 1 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,127] [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
A 0 0 0 0 0 0 1 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 1 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 33 0
G 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158] [,159]
A 1 0 0 0 0 1 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 1
G 0 0 0 2 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 1 0
[,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168] [,169] [,170]
A 0 0 0 0 0 0 0 3 0 0 0
C 1 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 1 0 0 0 0
T 0 2 0 0 0 0 0 0 0 0 0
[,171] [,172] [,173] [,174]
A 0 0 0 0
C 0 0 0 0
G 0 0 0 0
T 0 0 0 0
$genotype$readsDerived$maternal
$genotype$readsDerived$maternal$GM10847
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A 0 0 1 0 0 0 16 0 0 0 0 0 0 0
C 0 0 0 0 2 0 0 0 2 0 0 0 0 0
G 0 0 0 5 0 0 0 1 0 0 0 0 0 0
T 0 11 0 0 0 0 0 0 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 3 0 13 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 2 0 0 0 0 0 0 0 0 0 0
[,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 7
G 0 0 0 0 0 1 0 0 0 0 0 0 0
T 0 0 0 4 2 0 0 0 0 0 0 0 0
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50] [,51] [,52] [,53]
A 0 0 0 0 0 0 0 1 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 21 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 2 0 0 0 0
G 0 0 0 0 0 24 0 0 0 1 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 3 47 0 0 19 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 4
T 0 0 0 0 12 0 0 0 0 0 0 0 0
[,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
A 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 3 0 0 33
T 0 0 0 0 0 0 0 0 0 0 0 0
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115]
A 0 0 6 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 2 0 0 0 0 0 13 0
T 1 0 0 0 0 0 0 0 0 0 0
[,116] [,117] [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126]
A 0 0 2 0 0 0 0 0 0 0 0
C 0 0 0 0 0 2 0 0 0 0 0
G 0 0 0 1 0 0 3 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,127] [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
A 0 0 2 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
A 0 0 0 0 0 0 0 0 2 0 0
C 0 0 0 0 0 2 0 0 0 0 0
G 0 0 3 0 0 0 0 0 0 0 0
T 0 0 0 0 12 1 0 0 0 8 0
[,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158] [,159]
A 1 0 0 3 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 1
G 0 0 5 0 0 1 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 1 0
[,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168] [,169] [,170]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 1 0 0 0 0 0 2 0 0
G 0 0 0 0 0 0 0 0 0 1 2
T 0 1 0 0 0 0 0 0 0 0 0
[,171] [,172] [,173] [,174]
A 0 0 0 0
C 0 0 0 0
G 0 0 0 0
T 0 0 0 0
$genotype$readsDerived$maternal$GM12890
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A 0 0 7 0 0 0 0 0 0 0 1 0 0 0
C 0 0 0 0 0 0 5 0 4 0 0 0 0 0
G 0 0 0 22 0 12 0 0 0 0 0 2 0 0
T 0 24 0 0 0 0 0 0 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 5 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 3 0
[,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 7 0 0 0
G 0 0 0 0 0 0 0 2 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 119 0 0
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50] [,51] [,52] [,53]
A 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 16 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 55 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66]
A 0 0 0 0 0 10 0 0 0 0 0 0 0
C 0 28 0 0 0 0 13 0 0 0 0 1 0
G 0 0 0 0 0 0 0 0 0 0 0 0 0
T 8 0 0 0 0 0 0 0 0 0 0 0 0
[,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
A 0 0 0 0 0 137 0 0 0 0 0 0 2
C 0 0 0 1 0 0 0 0 0 0 0 0 0
G 0 0 0 0 4 0 6 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
A 0 0 0 0 0 0 0 77 0 0 0 0 0
C 0 0 0 0 18 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 16 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0
[,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
A 0 0 0 0 0 3 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 41 0 0 0 0 0 0 69
T 0 0 2 0 0 0 0 0 0 0 0 0
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 26 0 0 5 0 0
T 1 0 0 0 0 0 0 0 0 0 0
[,116] [,117] [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 1 0 0 0 0 0 0 0
T 1 0 0 0 0 0 0 0 0 0 0
[,127] [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 2 0 0 0 0 0 0 16 0 0
G 0 0 0 0 0 1 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0
[,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 36 0
[,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158] [,159]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 1 0 0 0 0 0
T 1 0 0 0 0 0 0 0 0 0 0
[,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168] [,169] [,170]
A 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0
G 0 11 0 0 0 0 0 0 0 0 0
T 3 0 0 0 0 0 0 0 0 0 0
[,171] [,172] [,173] [,174]
A 0 0 0 1
C 0 0 0 0
G 0 0 0 0
T 0 0 0 0
$genotype$readsDerived$ambiguous
$genotype$readsDerived$ambiguous$GM10847
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A 0 0 1 0 0 0 0 0 0 0 1 0 0 0
C 0 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 160 0 0 0 0 0 7 9 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0 3
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
A 0 0 0 0 2 1 0 0 0 0 0 0 1
C 0 0 0 0 0 0 0 0 0 0 11 0 0
G 20 0 0 0 0 0 0 1 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 7 0
[,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
A 0 0 0 0 0 0 0 0 0 0 145 0 0
C 0 1 20 0 0 0 0 0 19 0 0 0 0
G 1 0 0 0 0 1 0 0 0 0 0 3 0
T 0 6 0 0 0 0 0 0 0 7 1 0 0
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50] [,51] [,52] [,53]
A 0 0 0 2 0 0 0 21 25 0 4 0 0
C 0 0 0 0 10 0 29 0 0 0 0 0 0
G 2 3 0 4 0 1 0 0 0 0 0 4 0
T 0 0 0 0 0 0 0 0 1 0 0 0 3
[,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66]
A 0 0 0 33 4 0 0 0 0 0 1 0 0
C 0 105 0 0 0 0 48 0 1 0 0 9 0
G 0 0 0 0 0 0 0 21 0 7 0 0 134
T 100 0 2 0 0 0 0 0 0 0 0 0 0
[,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
A 0 0 0 0 0 0 0 3 0 9 0 0 0
C 0 4 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0 2 0 29 4 2
T 34 0 2 2 0 0 0 0 0 0 0 0 0
[,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
A 0 0 0 15 0 0 0 3 18 0 0 0 0
C 0 7 0 1 0 0 0 0 0 9 0 0 0
G 29 0 36
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and