| Back to Build/check report for BioC 3.10 experimental data |
This page was generated on 2020-04-14 17:46:30 -0400 (Tue, 14 Apr 2020).
| Package 242/384 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| MTseekerData 1.4.0 Tim Triche, Jr.
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ ERROR ] |
| Package: MTseekerData |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MTseekerData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MTseekerData_1.4.0.tar.gz |
| StartedAt: 2020-04-14 13:56:13 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 14:02:17 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 364.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MTseekerData.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MTseekerData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MTseekerData_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/MTseekerData.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MTseekerData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MTseekerData’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MTseekerData’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 20.6Mb
sub-directories of 1Mb or more:
data 8.6Mb
extdata 11.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
Error loading dataset 'RONKSreads':
Error in .requirePackage(package) :
unable to find required package 'MTseeker'
Error loading dataset 'RONKSvariants':
Error in .requirePackage(package) :
unable to find required package 'MTseeker'
The dataset(s) may use package(s) not declared in the DESCRIPTION file.
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘MTseekerData-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RONKSvariants
> ### Title: RONKSvariants: mitochondrial variant calls from RONKSreads
> ### Aliases: RONKSvariants
> ### Keywords: datasets
>
> ### ** Examples
>
> library(MTseeker)
Loading required package: viridis
Loading required package: viridisLite
Loading required package: S4Vectors
Loading required package: stats4
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, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: GenomeInfoDb
Loading required package: IRanges
Loading required package: GenomicAlignments
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: Rsamtools
Loading required package: VariantAnnotation
Attaching package: ‘VariantAnnotation’
The following object is masked from ‘package:base’:
tabulate
> data(RONKSvariants)
> show(RONKSvariants)
An object of class "MVRangesList"
Slot "elementMetadata":
DataFrame with 22 rows and 0 columns
Slot "elementType":
[1] "MVRanges"
Slot "metadata":
$seqinfo
Seqinfo object with 1 sequence (1 circular) from rCRS genome:
seqnames seqlengths isCircular genome
chrM 16569 TRUE rCRS
Slot "listData":
$NKS_1
MVRanges object with 204 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.55-56 chrM 55-56 * TA T
m.56-57 chrM 56-57 * AT A
m.56-59 chrM 56-59 * ATTT A
m.60 chrM 60 * T C
m.65 chrM 65 * T TG
... ... ... ... ... ...
m.16311 chrM 16311 * T C
m.16373-16374 chrM 16373-16374 * GA G
m.16391 chrM 16391 * G A
m.16502-16503 chrM 16502-16503 * TG T
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.55-56 4 0 4
m.56-57 17 0 17
m.56-59 2 0 2
m.60 1913 1820 87
m.65 2 0 2
... ... ... ...
m.16311 3798 2360 1436
m.16373-16374 2 0 2
m.16391 2944 1947 997
m.16502-16503 2 0 2
m.16519 2227 5 2222
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.55-56 NKS_1.merged.hg19chrm TRUE:TRUE | 2
m.56-57 NKS_1.merged.hg19chrm TRUE:TRUE | 12
m.56-59 NKS_1.merged.hg19chrm TRUE:TRUE | 2
m.60 NKS_1.merged.hg19chrm TRUE:FALSE | 55
m.65 NKS_1.merged.hg19chrm TRUE:TRUE | 2
... ... ... . ...
m.16311 NKS_1.merged.hg19chrm FALSE:FALSE | 167
m.16373-16374 NKS_1.merged.hg19chrm TRUE:TRUE | 2
m.16391 NKS_1.merged.hg19chrm FALSE:FALSE | 152
m.16502-16503 NKS_1.merged.hg19chrm TRUE:TRUE | 1
m.16519 NKS_1.merged.hg19chrm TRUE:FALSE | 163
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.55-56 <NA> 4 0 0
m.56-57 <NA> 17 8 0
m.56-59 <NA> 2 1 0
m.60 171 2048 33 1528
m.65 <NA> 2 1 0
... ... ... ... ...
m.16311 192 4033 1315 2109
m.16373-16374 <NA> 2 0 0
m.16391 177 3117 907 1772
m.16502-16503 <NA> 2 2 0
m.16519 4 2314 2042 3
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.55-56 4 0 <NA> <NA>
m.56-57 9 0 <NA> <NA>
m.56-59 1 0 <NA> <NA>
m.60 54 292 1 0
m.65 1 0 <NA> <NA>
... ... ... ... ...
m.16311 121 251 0 0
m.16373-16374 2 0 <NA> <NA>
m.16391 90 175 0 0
m.16502-16503 0 0 <NA> <NA>
m.16519 180 2 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.55-56 37.5 <NA> 471.75
m.56-57 60.3529411764706 <NA> 1088.27249134948
m.56-59 70.5 <NA> 480.5
m.60 47.8620689655172 46.7049450549451 672.803749688909
m.65 73.5 <NA> 1104.5
... ... ... ...
m.16311 52.8426183844011 52.0953389830508 854.592873918185
m.16373-16374 86 <NA> 72
m.16391 55.8224674022066 52.4232152028762 798.881249595443
m.16502-16503 47 <NA> 0
m.16519 56.0454545454545 55 733.692706918557
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.55-56 <NA> 12.5 <NA> 4
m.56-57 <NA> 25 <NA> 17
m.56-59 <NA> 19 <NA> 2
m.60 730.614572505272 31 <NA> 87
m.65 <NA> 13.5 <NA> 2
... ... ... ... ...
m.16311 823.661497699268 <NA> <NA> 1436
m.16373-16374 <NA> 13 <NA> 2
m.16391 820.996641400327 <NA> <NA> 997
m.16502-16503 <NA> 12.5 <NA> 2
m.16519 2536.25 48.5 3 2222
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.55-56 <NA> TRUE 1
m.56-57 <NA> TRUE 1
m.56-59 <NA> TRUE 1
m.60 1820 FALSE 0.0454783063251438
m.65 <NA> TRUE 1
... ... ... ...
m.16311 2360 FALSE 0.378093733543971
m.16373-16374 <NA> TRUE 1
m.16391 1947 FALSE 0.338654891304348
m.16502-16503 <NA> TRUE 1
m.16519 5 FALSE 0.997754827121688
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~2097x read coverage
$RO_1
MVRanges object with 311 ranges and 19 metadata columns:
seqnames ranges strand ref alt totalDepth
<Rle> <IRanges> <Rle> <character> <characterOrRle> <integerOrRle>
m.55-56 chrM 55-56 * TA T 2
m.56-57 chrM 56-57 * AT A 9
m.65 chrM 65 * T TG 2
m.65-66 chrM 65-66 * TG T 7
m.71-73 chrM 71-73 * GTA G 4
... ... ... ... ... ... ...
m.16291 chrM 16291 * C T 8618
m.16292 chrM 16292 * C T 8520
m.16311 chrM 16311 * T C 8553
m.16391 chrM 16391 * G A 6696
m.16519 chrM 16519 * T C 5097
refDepth altDepth sampleNames softFilterMatrix |
<integerOrRle> <integerOrRle> <factorOrRle> <matrix> |
m.55-56 0 2 RO_1.merged.hg19chrm TRUE:TRUE |
m.56-57 0 9 RO_1.merged.hg19chrm TRUE:TRUE |
m.65 0 2 RO_1.merged.hg19chrm TRUE:TRUE |
m.65-66 0 7 RO_1.merged.hg19chrm TRUE:TRUE |
m.71-73 0 4 RO_1.merged.hg19chrm FALSE:TRUE |
... ... ... ... ... .
m.16291 7362 1256 RO_1.merged.hg19chrm FALSE:FALSE |
m.16292 7289 1230 RO_1.merged.hg19chrm FALSE:FALSE |
m.16311 4107 4445 RO_1.merged.hg19chrm FALSE:FALSE |
m.16391 3340 3356 RO_1.merged.hg19chrm FALSE:FALSE |
m.16519 8 5088 RO_1.merged.hg19chrm FALSE:FALSE |
n.read.pos n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer> <integer>
m.55-56 1 <NA> 2 0 0
m.56-57 7 <NA> 9 6 0
m.65 2 <NA> 2 1 0
m.65-66 7 <NA> 7 3 0
m.71-73 2 <NA> 4 0 0
... ... ... ... ... ...
m.16291 164 201 8971 1129 6835
m.16292 164 201 8949 1112 6798
m.16311 199 199 9036 4189 3686
m.16391 193 201 7145 3158 2986
m.16519 189 8 5325 4672 5
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.55-56 2 0 <NA> <NA>
m.56-57 3 0 <NA> <NA>
m.65 1 0 <NA> <NA>
m.65-66 4 0 <NA> <NA>
m.71-73 4 0 <NA> <NA>
... ... ... ... ...
m.16291 127 527 0 0
m.16292 118 491 0 0
m.16311 256 421 0 0
m.16391 198 354 0 0
m.16519 416 3 0 0
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
<numeric> <numeric> <numeric> <numeric>
m.55-56 36 <NA> 0 <NA>
m.56-57 76.1111111111111 <NA> 1077.4737654321 <NA>
m.65 73.5 <NA> 1104.5 <NA>
m.65-66 58.5714285714286 <NA> 1418.05442176871 <NA>
m.71-73 95.5 <NA> 3040.41666666667 <NA>
... ... ... ... ...
m.16291 50.8447452229299 50.3401249660418 687.717859310961 816.32719131458
m.16292 50.8666666666667 50.5336808890108 668.321847934183 808.349840044723
m.16311 51.1721034870641 51.5473581689798 820.161549281657 825.579315384884
m.16391 54.184147794994 52.7682634730539 796.97648838598 815.600217298025
m.16519 55.470322327044 57.5 744.179767118233 850.892857142857
mdfne mdfne.ref count.high.nm count.high.nm.ref PASS
<numeric> <numeric> <integer> <integer> <logical>
m.55-56 12.5 <NA> 2 <NA> TRUE
m.56-57 22 <NA> 9 <NA> TRUE
m.65 13.5 <NA> 2 <NA> TRUE
m.65-66 25 <NA> 7 <NA> TRUE
m.71-73 3.5 <NA> 4 <NA> FALSE
... ... ... ... ... ...
m.16291 <NA> <NA> 1256 7362 FALSE
m.16292 <NA> <NA> 1230 7289 FALSE
m.16311 <NA> <NA> 4445 4107 FALSE
m.16391 <NA> <NA> 3356 3340 FALSE
m.16519 <NA> 24.5 5088 8 FALSE
VAF
<numeric>
m.55-56 1
m.56-57 1
m.65 1
m.65-66 1
m.71-73 1
... ...
m.16291 0.145741471339058
m.16292 0.144366197183099
m.16311 0.519700689816439
m.16391 0.501194743130227
m.16519 0.998234255444379
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~4578x read coverage
$NKS_2
MVRanges object with 63 ranges and 19 metadata columns:
seqnames ranges strand ref alt totalDepth
<Rle> <IRanges> <Rle> <character> <characterOrRle> <integerOrRle>
m.56-57 chrM 56-57 * AT A 2
m.72 chrM 72 * T C 237
m.73 chrM 73 * A G 281
m.94 chrM 94 * G A 310
m.152 chrM 152 * T C 241
... ... ... ... ... ... ...
m.16145 chrM 16145 * G A 382
m.16176 chrM 16176 * C G 454
m.16223 chrM 16223 * C T 487
m.16390 chrM 16390 * G A 412
m.16519 chrM 16519 * T C 341
refDepth altDepth sampleNames softFilterMatrix
<integerOrRle> <integerOrRle> <factorOrRle> <matrix>
m.56-57 0 2 NKS_2.merged.hg19chrm TRUE:TRUE
m.72 224 13 NKS_2.merged.hg19chrm TRUE:FALSE
m.73 3 278 NKS_2.merged.hg19chrm FALSE:FALSE
m.94 292 18 NKS_2.merged.hg19chrm TRUE:FALSE
m.152 1 240 NKS_2.merged.hg19chrm FALSE:FALSE
... ... ... ... ...
m.16145 2 380 NKS_2.merged.hg19chrm TRUE:FALSE
m.16176 3 451 NKS_2.merged.hg19chrm FALSE:FALSE
m.16223 6 481 NKS_2.merged.hg19chrm FALSE:FALSE
m.16390 7 405 NKS_2.merged.hg19chrm FALSE:FALSE
m.16519 2 339 NKS_2.merged.hg19chrm TRUE:FALSE
| n.read.pos n.read.pos.ref raw.count.total count.plus count.plus.ref
| <integer> <integer> <integer> <integer> <integer>
m.56-57 | 2 <NA> 2 1 0
m.72 | 12 97 308 7 141
m.73 | 116 3 314 183 0
m.94 | 18 110 338 12 181
m.152 | 111 1 253 158 0
... . ... ... ... ... ...
m.16145 | 117 2 392 346 2
m.16176 | 125 3 470 400 2
m.16223 | 137 7 516 420 5
m.16390 | 127 8 442 276 3
m.16519 | 105 3 360 269 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.56-57 1 0 <NA> <NA>
m.72 6 83 0 0
m.73 95 3 0 0
m.94 6 111 0 0
m.152 82 1 0 0
... ... ... ... ...
m.16145 34 0 0 0
m.16176 51 1 0 0
m.16223 61 1 0 0
m.16390 129 4 0 0
m.16519 70 2 0 0
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
<numeric> <numeric> <numeric> <numeric>
m.56-57 39.5 <NA> 1012.5 <NA>
m.72 57.5384615384615 45.3883928571429 1113.82544378698 770.92069967526
m.73 45.6510791366906 68.6666666666667 794.791248023839 2917.88888888889
m.94 62.3888888888889 48.6849315068493 1064.50889615105 834.739643486106
m.152 58.0291666666667 66 897.33129714377 <NA>
... ... ... ... ...
m.16145 46.8842105263158 55 763.401146332015 200
m.16176 49.8159645232816 89.3333333333333 842.531900837372 4123.55555555556
m.16223 49.0665280665281 32.3333333333333 808.69874016328 347.355555555555
m.16390 54.9234567901235 41.8571428571429 703.02775560958 1269.81292517007
m.16519 56.5486725663717 37.5 755.15295642507 180.5
mdfne mdfne.ref count.high.nm count.high.nm.ref PASS
<numeric> <numeric> <integer> <integer> <logical>
m.56-57 20.5 <NA> 2 <NA> TRUE
m.72 25 47.5 13 224 FALSE
m.73 <NA> 25 278 3 FALSE
m.94 24.5 <NA> 18 292 FALSE
m.152 <NA> 25 240 1 FALSE
... ... ... ... ... ...
m.16145 40.5 12.5 380 2 FALSE
m.16176 <NA> 23 451 3 FALSE
m.16223 <NA> 25.5 481 6 FALSE
m.16390 <NA> 25 405 7 FALSE
m.16519 44 12.5 339 2 FALSE
VAF
<numeric>
m.56-57 1
m.72 0.0548523206751055
m.73 0.98932384341637
m.94 0.0580645161290323
m.152 0.995850622406639
... ...
m.16145 0.994764397905759
m.16176 0.993392070484581
m.16223 0.987679671457906
m.16390 0.983009708737864
m.16519 0.994134897360704
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~333x read coverage
$RO_2
MVRanges object with 77 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.73 chrM 73 * A G
m.152 chrM 152 * T C
m.263 chrM 263 * A G
m.297 chrM 297 * A AC
m.302 chrM 302 * A AC
... ... ... ... ... ...
m.16176 chrM 16176 * C G
m.16223 chrM 16223 * C T
m.16390 chrM 16390 * G A
m.16519 chrM 16519 * T C
m.16529-16530 chrM 16529-16530 * TA T
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.73 692 2 690
m.152 624 2 622
m.263 543 1 542
m.297 2 0 2
m.302 32 0 32
... ... ... ...
m.16176 1057 3 1053
m.16223 1209 1 1207
m.16390 1034 1 1031
m.16519 859 2 857
m.16529-16530 2 0 2
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.73 RO_2.merged.hg19chrm FALSE:FALSE | 137
m.152 RO_2.merged.hg19chrm FALSE:FALSE | 134
m.263 RO_2.merged.hg19chrm FALSE:FALSE | 153
m.297 RO_2.merged.hg19chrm TRUE:TRUE | 2
m.302 RO_2.merged.hg19chrm FALSE:TRUE | 11
... ... ... . ...
m.16176 RO_2.merged.hg19chrm TRUE:FALSE | 158
m.16223 RO_2.merged.hg19chrm FALSE:FALSE | 166
m.16390 RO_2.merged.hg19chrm FALSE:FALSE | 169
m.16519 RO_2.merged.hg19chrm TRUE:FALSE | 137
m.16529-16530 RO_2.merged.hg19chrm TRUE:TRUE | 1
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.73 3 758 593 1
m.152 2 646 528 0
m.263 1 596 467 1
m.297 <NA> 2 1 0
m.302 <NA> 32 26 0
... ... ... ... ...
m.16176 2 1092 979 3
m.16223 3 1277 1109 1
m.16390 1 1107 886 1
m.16519 2 891 751 1
m.16529-16530 <NA> 2 2 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.73 97 1 0 0
m.152 94 2 0 0
m.263 75 0 0 0
m.297 1 0 <NA> <NA>
m.302 6 0 <NA> <NA>
... ... ... ... ...
m.16176 74 0 0 0
m.16223 98 0 0 0
m.16390 145 0 0 0
m.16519 106 1 0 0
m.16529-16530 0 0 <NA> <NA>
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.73 47.6391304347826 73 733.292641838669
m.152 57.8167202572347 35 826.96276851953
m.263 51.1291512915129 54 832.830220926774
m.297 79.5 <NA> 312.5
m.302 70.1875 <NA> 1238.48903729839
... ... ... ...
m.16176 47.6210826210826 76.3333333333333 815.431159197543
m.16223 49.0886495443248 52 842.080605317448
m.16390 52.7041707080504 88 807.872331724251
m.16519 55.3827304550758 96 728.861812200228
m.16529-16530 76 <NA> 0
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.73 1568 <NA> 12.5 690
m.152 0 <NA> 12.5 622
m.263 <NA> <NA> 25 542
m.297 <NA> 16 <NA> 2
m.302 <NA> 9.5 <NA> 32
... ... ... ... ...
m.16176 2998.72222222222 48 25 1053
m.16223 <NA> <NA> 25 1207
m.16390 <NA> <NA> 11 1031
m.16519 32 49 16 857
m.16529-16530 <NA> 11.5 <NA> 2
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.73 2 FALSE 0.997109826589595
m.152 2 FALSE 0.996794871794872
m.263 1 FALSE 0.998158379373849
m.297 <NA> TRUE 1
m.302 <NA> FALSE 1
... ... ... ...
m.16176 3 FALSE 0.996215704824976
m.16223 1 FALSE 0.998345740281224
m.16390 1 FALSE 0.997098646034816
m.16519 2 FALSE 0.9976717112922
m.16529-16530 <NA> TRUE 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~734x read coverage
$NKS_3
MVRanges object with 40 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.56-57 chrM 56-57 * AT A
m.60 chrM 60 * T C
m.72 chrM 72 * T C
m.152 chrM 152 * T C
m.263 chrM 263 * A G
... ... ... ... ... ...
m.15326 chrM 15326 * A G
m.15961 chrM 15961 * G GA
m.16161-16162 chrM 16161-16162 * TA T
m.16262-16263 chrM 16262-16263 * CT C
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.56-57 4 0 4
m.60 433 390 43
m.72 427 344 83
m.152 422 8 414
m.263 363 0 362
... ... ... ...
m.15326 456 1 455
m.15961 2 0 2
m.16161-16162 3 0 3
m.16262-16263 8 0 8
m.16519 489 7 482
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.56-57 NKS_3.merged.hg19chrm TRUE:TRUE | 4
m.60 NKS_3.merged.hg19chrm TRUE:FALSE | 29
m.72 NKS_3.merged.hg19chrm TRUE:FALSE | 55
m.152 NKS_3.merged.hg19chrm FALSE:FALSE | 130
m.263 NKS_3.merged.hg19chrm FALSE:TRUE | 125
... ... ... . ...
m.15326 NKS_3.merged.hg19chrm TRUE:FALSE | 134
m.15961 NKS_3.merged.hg19chrm TRUE:TRUE | 2
m.16161-16162 NKS_3.merged.hg19chrm TRUE:TRUE | 3
m.16262-16263 NKS_3.merged.hg19chrm TRUE:TRUE | 8
m.16519 NKS_3.merged.hg19chrm TRUE:FALSE | 116
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.56-57 <NA> 4 3 0
m.60 129 456 21 279
m.72 128 505 41 236
m.152 6 433 315 3
m.263 0 387 307 0
... ... ... ... ...
m.15326 1 474 396 0
m.15961 <NA> 2 1 0
m.16161-16162 <NA> 3 2 0
m.16262-16263 <NA> 8 5 0
m.16519 6 513 384 4
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.56-57 1 0 <NA> <NA>
m.60 22 111 0 0
m.72 42 108 0 0
m.152 99 5 0 0
m.263 55 0 0 0
... ... ... ... ...
m.15326 59 1 0 0
m.15961 1 0 <NA> <NA>
m.16161-16162 1 0 <NA> <NA>
m.16262-16263 3 0 <NA> <NA>
m.16519 98 3 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.56-57 21.25 <NA> 517.4375
m.60 57.6046511627907 49.7153846153846 732.204164413196
m.72 45.1927710843374 47.7267441860465 839.235392938194
m.152 52.3937198067633 41.375 889.32185362394
m.263 50.5580110497238 NaN 810.884748612908
... ... ... ...
m.15326 50.2879120879121 62 865.273474930936
m.15961 67.5 <NA> 1740.5
m.16161-16162 73 <NA> 3415.5
m.16262-16263 44.25 <NA> 792.508928571428
m.16519 53.5954356846473 38.5714285714286 697.951311194872
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.56-57 <NA> 13 <NA> 4
m.60 822.532203495536 28 <NA> 43
m.72 883.994624093553 33 <NA> 83
m.152 1002.82366071429 <NA> 20 414
m.263 <NA> <NA> <NA> 362
... ... ... ... ...
m.15326 <NA> 49 25 455
m.15961 <NA> 13.5 <NA> 2
m.16161-16162 <NA> 16 <NA> 3
m.16262-16263 <NA> 22 <NA> 8
m.16519 774.91156462585 47.5 25 482
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.56-57 <NA> TRUE 1
m.60 390 FALSE 0.0993071593533487
m.72 344 FALSE 0.194379391100703
m.152 8 FALSE 0.981042654028436
m.263 0 FALSE 0.997245179063361
... ... ... ...
m.15326 1 FALSE 0.99780701754386
m.15961 <NA> TRUE 1
m.16161-16162 <NA> TRUE 1
m.16262-16263 <NA> TRUE 1
m.16519 7 FALSE 0.985685071574642
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~508x read coverage
$RO_3
MVRanges object with 125 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.152 chrM 152 * T C
m.209-210 chrM 209-210 * TA T
m.263 chrM 263 * A G
m.290 chrM 290 * A AAT
m.300 chrM 300 * A AC
... ... ... ... ... ...
m.16245-16246 chrM 16245-16246 * CA C
m.16462-16463 chrM 16462-16463 * TA T
m.16479-16480 chrM 16479-16480 * TA T
m.16502-16503 chrM 16502-16503 * TG T
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.152 1690 1 1687
m.209-210 2 0 2
m.263 1612 0 1611
m.290 12 0 12
m.300 2 0 2
... ... ... ...
m.16245-16246 2 0 2
m.16462-16463 2 0 2
m.16479-16480 2 0 2
m.16502-16503 3 0 3
m.16519 2236 0 2236
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.152 RO_3.merged.hg19chrm FALSE:FALSE | 169
m.209-210 RO_3.merged.hg19chrm TRUE:TRUE | 2
m.263 RO_3.merged.hg19chrm FALSE:TRUE | 179
m.290 RO_3.merged.hg19chrm TRUE:TRUE | 12
m.300 RO_3.merged.hg19chrm TRUE:TRUE | 2
... ... ... . ...
m.16245-16246 RO_3.merged.hg19chrm TRUE:TRUE | 2
m.16462-16463 RO_3.merged.hg19chrm TRUE:TRUE | 2
m.16479-16480 RO_3.merged.hg19chrm TRUE:TRUE | 2
m.16502-16503 RO_3.merged.hg19chrm TRUE:TRUE | 2
m.16519 RO_3.merged.hg19chrm TRUE:TRUE | 172
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.152 1 1730 1529 0
m.209-210 <NA> 2 1 0
m.263 0 1743 1494 0
m.290 <NA> 12 6 0
m.300 <NA> 2 2 0
... ... ... ... ...
m.16245-16246 <NA> 2 1 0
m.16462-16463 <NA> 2 1 0
m.16479-16480 <NA> 2 1 0
m.16502-16503 <NA> 3 2 0
m.16519 0 2345 2006 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.152 158 1 1 0
m.209-210 1 0 <NA> <NA>
m.263 117 0 0 0
m.290 6 0 <NA> <NA>
m.300 0 0 <NA> <NA>
... ... ... ... ...
m.16245-16246 1 0 <NA> <NA>
m.16462-16463 1 0 <NA> <NA>
m.16479-16480 1 0 <NA> <NA>
m.16502-16503 1 0 <NA> <NA>
m.16519 230 0 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.152 52.6544161232958 69 814.266911113385
m.209-210 85.5 <NA> 24.5
m.263 52.5226567349472 NaN 822.391647515324
m.290 56.5833333333333 <NA> 1175.32638888889
m.300 43 <NA> 50
... ... ... ...
m.16245-16246 72.5 <NA> 220.5
m.16462-16463 78 <NA> 338
m.16479-16480 65 <NA> 1800
m.16502-16503 68 <NA> 2675
m.16519 55.8483899821109 NaN 733.083063475405
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.152 <NA> <NA> 25 1687
m.209-210 <NA> 13.5 <NA> 2
m.263 <NA> <NA> <NA> 1611
m.290 <NA> 19.5 <NA> 12
m.300 <NA> 12.5 <NA> 2
... ... ... ... ...
m.16245-16246 <NA> 20.5 <NA> 2
m.16462-16463 <NA> 16.5 <NA> 2
m.16479-16480 <NA> 14.5 <NA> 2
m.16502-16503 <NA> 25 <NA> 3
m.16519 <NA> 48.5 <NA> 2236
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.152 1 FALSE 0.998224852071006
m.209-210 <NA> TRUE 1
m.263 0 FALSE 0.999379652605459
m.290 <NA> TRUE 1
m.300 <NA> TRUE 1
... ... ... ...
m.16245-16246 <NA> TRUE 1
m.16462-16463 <NA> TRUE 1
m.16479-16480 <NA> TRUE 1
m.16502-16503 <NA> TRUE 1
m.16519 0 TRUE 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~1967x read coverage
$NKS_4
MVRanges object with 73 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.56-57 chrM 56-57 * AT A
m.65-66 chrM 65-66 * TG T
m.72 chrM 72 * T C
m.73 chrM 73 * A G
m.94 chrM 94 * G A
... ... ... ... ... ...
m.16192 chrM 16192 * C T
m.16192 chrM 16192 * C CT
m.16262-16263 chrM 16262-16263 * CT C
m.16270 chrM 16270 * C T
m.16390 chrM 16390 * G A
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.56-57 6 0 6
m.65-66 7 0 7
m.72 528 464 64
m.73 585 2 583
m.94 646 589 57
... ... ... ...
m.16192 873 5 868
m.16192 2 0 2
m.16262-16263 2 0 2
m.16270 985 4 981
m.16390 826 3 823
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.56-57 NKS_4.merged.hg19chrm TRUE:TRUE | 6
m.65-66 NKS_4.merged.hg19chrm TRUE:TRUE | 5
m.72 NKS_4.merged.hg19chrm TRUE:FALSE | 39
m.73 NKS_4.merged.hg19chrm FALSE:FALSE | 146
m.94 NKS_4.merged.hg19chrm TRUE:FALSE | 45
... ... ... . ...
m.16192 NKS_4.merged.hg19chrm FALSE:FALSE | 143
m.16192 NKS_4.merged.hg19chrm FALSE:TRUE | 1
m.16262-16263 NKS_4.merged.hg19chrm TRUE:TRUE | 2
m.16270 NKS_4.merged.hg19chrm FALSE:FALSE | 165
m.16390 NKS_4.merged.hg19chrm FALSE:FALSE | 158
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.56-57 <NA> 6 4 0
m.65-66 <NA> 7 4 0
m.72 132 634 29 335
m.73 1 637 415 0
m.94 143 693 22 440
... ... ... ... ...
m.16192 5 913 808 2
m.16192 <NA> 2 0 0
m.16262-16263 <NA> 2 1 0
m.16270 7 1031 860 3
m.16390 3 892 710 1
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.56-57 2 0 <NA> <NA>
m.65-66 3 0 <NA> <NA>
m.72 35 129 0 0
m.73 168 2 0 0
m.94 35 149 0 0
... ... ... ... ...
m.16192 60 3 0 0
m.16192 2 0 <NA> <NA>
m.16262-16263 1 0 <NA> <NA>
m.16270 121 1 0 0
m.16390 113 2 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.56-57 82.1666666666667 <NA> 1414.83888888889
m.65-66 49.2857142857143 <NA> 718.418367346939
m.72 38.15625 48.0387931034483 779.338681175595
m.73 46.4888507718696 52 731.211152536265
m.94 53.0350877192982 47.9439728353141 901.654470606341
... ... ... ...
m.16192 51.4896313364055 64.8 765.287299673802
m.16192 98 <NA> 0
m.16262-16263 35.5 <NA> 420.5
m.16270 49.6167176350663 40.75 812.530310713942
m.16390 55.1142162818955 67.6666666666667 829.726083340474
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.56-57 <NA> 18.5 <NA> 6
m.65-66 <NA> 26 <NA> 7
m.72 694.010858244004 26.5 <NA> 64
m.73 0 <NA> 12.5 583
m.94 866.071046997957 29 <NA> 57
... ... ... ... ...
m.16192 2722.46 <NA> 1 868
m.16192 <NA> 0.5 <NA> 2
m.16262-16263 <NA> 22.5 <NA> 2
m.16270 1498.4375 <NA> 21 981
m.16390 3223.72222222222 <NA> 25 823
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.56-57 <NA> TRUE 1
m.65-66 <NA> TRUE 1
m.72 464 FALSE 0.121212121212121
m.73 2 FALSE 0.996581196581197
m.94 589 FALSE 0.0882352941176471
... ... ... ...
m.16192 5 FALSE 0.994272623138603
m.16192 <NA> FALSE 1
m.16262-16263 <NA> TRUE 1
m.16270 4 FALSE 0.995939086294416
m.16390 3 FALSE 0.99636803874092
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~649x read coverage
$RO_4
MVRanges object with 73 ranges and 19 metadata columns:
seqnames ranges strand ref alt totalDepth
<Rle> <IRanges> <Rle> <character> <characterOrRle> <integerOrRle>
m.73 chrM 73 * A G 868
m.150 chrM 150 * C T 838
m.263 chrM 263 * A G 751
m.301 chrM 301 * A AC 2
m.302 chrM 302 * A AC 4
... ... ... ... ... ... ...
m.15115 chrM 15115 * T C 1022
m.15326 chrM 15326 * A G 983
m.16192 chrM 16192 * C T 1390
m.16270 chrM 16270 * C T 1608
m.16390 chrM 16390 * G A 1369
refDepth altDepth sampleNames softFilterMatrix |
<integerOrRle> <integerOrRle> <factorOrRle> <matrix> |
m.73 2 866 RO_4.merged.hg19chrm FALSE:FALSE |
m.150 3 835 RO_4.merged.hg19chrm FALSE:FALSE |
m.263 1 749 RO_4.merged.hg19chrm FALSE:FALSE |
m.301 0 2 RO_4.merged.hg19chrm TRUE:TRUE |
m.302 0 4 RO_4.merged.hg19chrm TRUE:TRUE |
... ... ... ... ... .
m.15115 6 1016 RO_4.merged.hg19chrm TRUE:FALSE |
m.15326 0 983 RO_4.merged.hg19chrm FALSE:TRUE |
m.16192 12 1378 RO_4.merged.hg19chrm FALSE:FALSE |
m.16270 14 1594 RO_4.merged.hg19chrm TRUE:FALSE |
m.16390 8 1360 RO_4.merged.hg19chrm FALSE:FALSE |
n.read.pos n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer> <integer>
m.73 149 1 948 746 0
m.150 151 2 868 739 1
m.263 157 3 801 657 0
m.301 2 <NA> 2 0 0
m.302 4 <NA> 4 2 0
... ... ... ... ... ...
m.15115 154 6 1040 940 5
m.15326 165 0 1031 894 0
m.16192 175 15 1461 1293 4
m.16270 180 16 1668 1466 8
m.16390 180 11 1448 1229 2
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.73 120 2 0 0
m.150 96 2 0 0
m.263 92 1 0 0
m.301 2 0 <NA> <NA>
m.302 2 0 <NA> <NA>
... ... ... ... ...
m.15115 76 1 0 0
m.15326 89 0 0 0
m.16192 85 8 0 0
m.16270 128 6 0 0
m.16390 131 6 0 0
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
<numeric> <numeric> <numeric> <numeric>
m.73 48.8406466512702 35 749.139211564381 0
m.150 53.4826347305389 34 807.634161176634 605
m.263 53.3738317757009 61 865.141835589872 <NA>
m.301 80 <NA> 338 <NA>
m.302 39.5 <NA> 1263.08333333333 <NA>
... ... ... ... ...
m.15115 49.8513779527559 47.1666666666667 807.148490595719 1713.10555555556
m.15326 47.4089521871821 NaN 812.453370639755 <NA>
m.16192 52.910740203193 63.5833333333333 854.4005573521 1436.52335858586
m.16270 48 49.2857142857143 857.903327055869 872.764521193093
m.16390 54.0558823529412 40.375 812.999110638802 1086.57366071429
mdfne mdfne.ref count.high.nm count.high.nm.ref PASS
<numeric> <numeric> <integer> <integer> <logical>
m.73 <NA> 12.5 866 2 FALSE
m.150 <NA> 25 835 3 FALSE
m.263 <NA> 25 749 1 FALSE
m.301 15.5 <NA> 2 <NA> TRUE
m.302 24.5 <NA> 4 <NA> TRUE
... ... ... ... ... ...
m.15115 48.5 24.5 1016 6 FALSE
m.15326 <NA> <NA> 983 0 FALSE
m.16192 <NA> 20 1378 12 FALSE
m.16270 48.5 26.5 1594 14 FALSE
m.16390 <NA> 25.5 1360 8 FALSE
VAF
<numeric>
m.73 0.997695852534562
m.150 0.996420047732697
m.263 0.997336884154461
m.301 1
m.302 1
... ...
m.15115 0.99412915851272
m.15326 1
m.16192 0.99136690647482
m.16270 0.991293532338308
m.16390 0.993425858290723
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~1000x read coverage
$NKS_5
MVRanges object with 69 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.189 chrM 189 * A G
m.202-203 chrM 202-203 * AG A
m.239 chrM 239 * T C
m.263 chrM 263 * A G
m.301 chrM 301 * A ACC
... ... ... ... ... ...
m.15326 chrM 15326 * A G
m.15728-15729 chrM 15728-15729 * CT C
m.15961 chrM 15961 * G A
m.16362 chrM 16362 * T C
m.16362 chrM 16362 * T A
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.189 633 597 36
m.202-203 2 0 2
m.239 633 2 631
m.263 626 0 626
m.301 3 0 3
... ... ... ...
m.15326 840 0 840
m.15728-15729 2 0 2
m.15961 455 311 144
m.16362 1521 10 1430
m.16362 1521 10 81
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.189 NKS_5.merged.hg19chrm TRUE:FALSE | 29
m.202-203 NKS_5.merged.hg19chrm TRUE:TRUE | 2
m.239 NKS_5.merged.hg19chrm FALSE:FALSE | 153
m.263 NKS_5.merged.hg19chrm FALSE:TRUE | 160
m.301 NKS_5.merged.hg19chrm TRUE:TRUE | 3
... ... ... . ...
m.15326 NKS_5.merged.hg19chrm FALSE:TRUE | 164
m.15728-15729 NKS_5.merged.hg19chrm FALSE:TRUE | 2
m.15961 NKS_5.merged.hg19chrm TRUE:FALSE | 83
m.16362 NKS_5.merged.hg19chrm FALSE:FALSE | 175
m.16362 NKS_5.merged.hg19chrm TRUE:FALSE | 61
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.189 130 655 20 534
m.202-203 <NA> 2 1 0
m.239 3 666 546 1
m.263 0 681 530 0
m.301 <NA> 3 0 0
... ... ... ... ...
m.15326 0 882 750 0
m.15728-15729 <NA> 2 1 0
m.15961 112 463 112 275
m.16362 13 1631 1307 5
m.16362 13 1631 43 5
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.189 16 63 0 0
m.202-203 1 0 <NA> <NA>
m.239 85 1 0 0
m.263 96 0 0 0
m.301 3 0 <NA> <NA>
... ... ... ... ...
m.15326 90 0 0 0
m.15728-15729 1 0 <NA> <NA>
m.15961 32 36 0 0
m.16362 123 5 0 0
m.16362 38 5 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.189 49.25 50.5159128978224 972.008928571428
m.202-203 62.5 <NA> 24.5
m.239 52.6687797147385 46 800.126627487333
m.263 55.5527156549521 NaN 870.689383360043
m.301 50.3333333333333 <NA> 2184.05555555556
... ... ... ...
m.15326 47.8095238095238 NaN 845.081375895611
m.15728-15729 90 <NA> 72
m.15961 48.0625 50.1543408360129 947.233855987762
m.16362 51.2524475524475 52.5 894.074653473536
m.16362 56.7901234567901 52.5 911.056877762536
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.189 946.696235374784 23 <NA> 36
m.202-203 <NA> 12.5 <NA> 2
m.239 288 <NA> 12.5 631
m.263 <NA> <NA> <NA> 626
m.301 <NA> 26 <NA> 3
... ... ... ... ...
m.15326 <NA> <NA> <NA> 840
m.15728-15729 <NA> 9 <NA> 2
m.15961 787.47757917602 32.5 45 144
m.16362 1236.75 <NA> 22.5 1430
m.16362 1236.75 30 22.5 81
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.189 597 FALSE 0.0568720379146919
m.202-203 <NA> TRUE 1
m.239 2 FALSE 0.996840442338073
m.263 0 FALSE 1
m.301 <NA> TRUE 1
... ... ... ...
m.15326 0 FALSE 1
m.15728-15729 <NA> FALSE 1
m.15961 311 FALSE 0.316483516483516
m.16362 10 FALSE 0.94017094017094
m.16362 10 FALSE 0.0532544378698225
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~964x read coverage
$RO_5
MVRanges object with 74 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.65 chrM 65 * T TG
m.239 chrM 239 * T C
m.263 chrM 263 * A G
m.302 chrM 302 * A AC
m.302 chrM 302 * A ACC
... ... ... ... ... ...
m.16073-16074 chrM 16073-16074 * CA C
m.16256-16258 chrM 16256-16258 * CCA C
m.16362 chrM 16362 * T C
m.16506-16507 chrM 16506-16507 * TC T
m.16535-16536 chrM 16535-16536 * GC G
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.65 2 0 2
m.239 597 3 594
m.263 582 0 582
m.302 23 0 23
m.302 11 0 11
... ... ... ...
m.16073-16074 2 0 2
m.16256-16258 2 0 2
m.16362 1429 12 1417
m.16506-16507 2 0 2
m.16535-16536 3 0 3
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.65 RO_5.merged.hg19chrm FALSE:TRUE | 1
m.239 RO_5.merged.hg19chrm FALSE:FALSE | 153
m.263 RO_5.merged.hg19chrm FALSE:TRUE | 162
m.302 RO_5.merged.hg19chrm TRUE:TRUE | 11
m.302 RO_5.merged.hg19chrm TRUE:TRUE | 11
... ... ... . ...
m.16073-16074 RO_5.merged.hg19chrm FALSE:TRUE | 1
m.16256-16258 RO_5.merged.hg19chrm FALSE:TRUE | 1
m.16362 RO_5.merged.hg19chrm FALSE:FALSE | 180
m.16506-16507 RO_5.merged.hg19chrm TRUE:TRUE | 2
m.16535-16536 RO_5.merged.hg19chrm TRUE:TRUE | 1
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.65 <NA> 2 0 0
m.239 2 622 493 0
m.263 0 624 469 0
m.302 <NA> 23 17 0
m.302 <NA> 11 9 0
... ... ... ... ...
m.16073-16074 <NA> 2 2 0
m.16256-16258 <NA> 2 0 0
m.16362 17 1535 1286 5
m.16506-16507 <NA> 2 1 0
m.16535-16536 <NA> 3 3 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.65 2 0 <NA> <NA>
m.239 101 3 0 0
m.263 113 0 0 0
m.302 6 0 <NA> <NA>
m.302 2 0 <NA> <NA>
... ... ... ... ...
m.16073-16074 0 0 <NA> <NA>
m.16256-16258 2 0 <NA> <NA>
m.16362 131 7 0 0
m.16506-16507 1 0 <NA> <NA>
m.16535-16536 0 0 <NA> <NA>
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.65 97 <NA> 0
m.239 55.0218855218855 7.66666666666667 768.111506533894
m.263 54.4896907216495 NaN 810.238493182911
m.302 67.1304347826087 <NA> 1304.77745317065
m.302 39 <NA> 675.1
... ... ... ...
m.16073-16074 81 <NA> 0
m.16256-16258 96 <NA> 0
m.16362 52.42413549753 48.1666666666667 906.620328071078
m.16506-16507 76 <NA> 288
m.16535-16536 38 <NA> 722
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.65 <NA> 1 <NA> 2
m.239 37.7222222222222 <NA> 5 594
m.263 <NA> <NA> <NA> 582
m.302 <NA> 11 <NA> 23
m.302 <NA> 25 <NA> 11
... ... ... ... ...
m.16073-16074 <NA> 9 <NA> 2
m.16256-16258 <NA> 1.5 <NA> 2
m.16362 1070.33585858586 <NA> 26.5 1417
m.16506-16507 <NA> 18 <NA> 2
m.16535-16536 <NA> 25 <NA> 3
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.65 <NA> FALSE 1
m.239 3 FALSE 0.994974874371859
m.263 0 FALSE 1
m.302 <NA> TRUE 1
m.302 <NA> TRUE 1
... ... ... ...
m.16073-16074 <NA> FALSE 1
m.16256-16258 <NA> FALSE 1
m.16362 12 FALSE 0.991602519244227
m.16506-16507 <NA> TRUE 1
m.16535-16536 <NA> TRUE 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~906x read coverage
$NKS_6
MVRanges object with 90 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.16 chrM 16 * A T
m.56-57 chrM 56-57 * AT A
m.56-58 chrM 56-58 * ATT A
m.65-66 chrM 65-66 * TG T
m.72 chrM 72 * T C
... ... ... ... ... ...
m.16161-16162 chrM 16161-16162 * TA T
m.16179-16180 chrM 16179-16180 * CA C
m.16224 chrM 16224 * T C
m.16311 chrM 16311 * T C
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.16 323 5 318
m.56-57 5 0 5
m.56-58 2 0 2
m.65-66 4 0 4
m.72 530 486 44
... ... ... ...
m.16161-16162 2 0 2
m.16179-16180 2 0 2
m.16224 1520 13 1507
m.16311 1713 16 1697
m.16519 579 3 575
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.16 NKS_6.merged.hg19chrm TRUE:FALSE | 95
m.56-57 NKS_6.merged.hg19chrm TRUE:TRUE | 5
m.56-58 NKS_6.merged.hg19chrm TRUE:TRUE | 2
m.65-66 NKS_6.merged.hg19chrm TRUE:TRUE | 4
m.72 NKS_6.merged.hg19chrm TRUE:FALSE | 42
... ... ... . ...
m.16161-16162 NKS_6.merged.hg19chrm TRUE:TRUE | 2
m.16179-16180 NKS_6.merged.hg19chrm TRUE:TRUE | 2
m.16224 NKS_6.merged.hg19chrm FALSE:FALSE | 175
m.16311 NKS_6.merged.hg19chrm FALSE:FALSE | 182
m.16519 NKS_6.merged.hg19chrm FALSE:FALSE | 123
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.16 6 344 265 4
m.56-57 <NA> 5 2 0
m.56-58 <NA> 2 1 0
m.65-66 <NA> 4 3 0
m.72 153 654 23 382
... ... ... ... ...
m.16161-16162 <NA> 2 1 0
m.16179-16180 <NA> 2 1 0
m.16224 13 1566 1389 9
m.16311 16 1785 1547 5
m.16519 4 604 498 2
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.16 53 1 0 0
m.56-57 3 0 <NA> <NA>
m.56-58 1 0 <NA> <NA>
m.65-66 1 0 <NA> <NA>
m.72 21 104 0 0
... ... ... ... ...
m.16161-16162 1 0 <NA> <NA>
m.16179-16180 1 0 <NA> <NA>
m.16224 118 4 0 0
m.16311 150 11 0 0
m.16519 77 1 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.16 46.3427672955975 51 801.62552190976
m.56-57 62 <NA> 1851
m.56-58 57 <NA> 512
m.65-66 31.5 <NA> 560.416666666667
m.72 52.1363636363636 47.5102880658436 863.985633288488
... ... ... ...
m.16161-16162 53 <NA> 2888
m.16179-16180 77.5 <NA> 24.5
m.16224 49.0152621101526 45.3076923076923 860.777652650195
m.16311 52.8933411903359 60.75 832.912382251019
m.16519 56.1965217391304 54.3333333333333 760.963139545392
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.16 1198.75 41.5 25 318
m.56-57 <NA> 18 <NA> 5
m.56-58 <NA> 12.5 <NA> 2
m.65-66 <NA> 18.5 <NA> 4
m.72 774.735414498495 27.5 <NA> 44
... ... ... ... ...
m.16161-16162 <NA> 11 <NA> 2
m.16179-16180 <NA> 21.5 <NA> 2
m.16224 1510.96301775148 <NA> 16 1507
m.16311 1098.77083333333 <NA> 23 1697
m.16519 2920.38888888889 <NA> 17 575
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.16 5 FALSE 0.984520123839009
m.56-57 <NA> TRUE 1
m.56-58 <NA> TRUE 1
m.65-66 <NA> TRUE 1
m.72 486 FALSE 0.0830188679245283
... ... ... ...
m.16161-16162 <NA> TRUE 1
m.16179-16180 <NA> TRUE 1
m.16224 13 FALSE 0.991447368421053
m.16311 16 FALSE 0.990659661412726
m.16519 3 FALSE 0.993091537132988
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~820x read coverage
$RO_6
MVRanges object with 85 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.16 chrM 16 * A T
m.73 chrM 73 * A G
m.150 chrM 150 * C T
m.152 chrM 152 * T C
m.151-152 chrM 151-152 * CT C
... ... ... ... ... ...
m.16224 chrM 16224 * T C
m.16258-16260 chrM 16258-16260 * ACC A
m.16262 chrM 16262 * C CG
m.16311 chrM 16311 * T C
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.16 295 2 293
m.73 462 0 462
m.150 467 7 460
m.152 475 7 466
m.151-152 2 0 2
... ... ... ...
m.16224 1143 2 1140
m.16258-16260 2 0 2
m.16262 2 0 2
m.16311 1316 3 1313
m.16519 637 9 628
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.16 RO_6.merged.hg19chrm TRUE:FALSE | 85
m.73 RO_6.merged.hg19chrm FALSE:TRUE | 129
m.150 RO_6.merged.hg19chrm FALSE:FALSE | 122
m.152 RO_6.merged.hg19chrm FALSE:FALSE | 125
m.151-152 RO_6.merged.hg19chrm FALSE:TRUE | 1
... ... ... . ...
m.16224 RO_6.merged.hg19chrm FALSE:FALSE | 163
m.16258-16260 RO_6.merged.hg19chrm TRUE:TRUE | 1
m.16262 RO_6.merged.hg19chrm TRUE:TRUE | 1
m.16311 RO_6.merged.hg19chrm FALSE:FALSE | 175
m.16519 RO_6.merged.hg19chrm FALSE:FALSE | 133
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.16 2 323 244 2
m.73 0 534 363 0
m.150 5 487 371 5
m.152 7 495 371 4
m.151-152 <NA> 2 2 0
... ... ... ... ...
m.16224 2 1181 1039 1
m.16258-16260 <NA> 2 2 0
m.16262 <NA> 2 0 0
m.16311 3 1386 1155 3
m.16519 5 664 533 5
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.16 49 0 0 0
m.73 99 0 0 0
m.150 89 2 0 0
m.152 95 3 2 0
m.151-152 0 0 <NA> <NA>
... ... ... ... ...
m.16224 101 1 0 0
m.16258-16260 0 0 <NA> <NA>
m.16262 2 0 <NA> <NA>
m.16311 158 0 0 0
m.16519 95 4 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.16 38.9897610921502 82 704.969762853765
m.73 49.9632034632035 NaN 755.099123989544
m.150 51.8782608695652 26.4285714285714 684.388968539317
m.152 51.6394849785408 30.7142857142857 733.135634161815
m.151-152 4 <NA> 0
... ... ... ...
m.16224 48.6035087719298 50 852.176546997239
m.16258-16260 44 <NA> 0
m.16262 55 <NA> 0
m.16311 50.4028941355674 39.3333333333333 843.463659100249
m.16519 55.6353503184713 30.7777777777778 744.26600865708
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.16 0 32 8.5 293
m.73 <NA> <NA> <NA> 462
m.150 488.697278911565 <NA> 25 460
m.152 593.465986394558 <NA> 25 466
m.151-152 <NA> 1.5 <NA> 2
... ... ... ... ...
m.16224 72 <NA> 12.5 1140
m.16258-16260 <NA> 12.5 <NA> 2
m.16262 <NA> 12.5 <NA> 2
m.16311 1673.88888888889 <NA> 25 1313
m.16519 452.603395061728 <NA> 25 628
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.16 2 FALSE 0.993220338983051
m.73 0 FALSE 1
m.150 7 FALSE 0.985010706638116
m.152 7 FALSE 0.981052631578947
m.151-152 <NA> FALSE 1
... ... ... ...
m.16224 2 FALSE 0.99737532808399
m.16258-16260 <NA> TRUE 1
m.16262 <NA> TRUE 1
m.16311 3 FALSE 0.997720364741641
m.16519 9 FALSE 0.985871271585557
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~652x read coverage
$NKS_7
MVRanges object with 84 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.56-57 chrM 56-57 * AT A
m.65-66 chrM 65-66 * TG T
m.72 chrM 72 * T C
m.73 chrM 73 * A G
m.94 chrM 94 * G A
... ... ... ... ... ...
m.16256 chrM 16256 * C T
m.16270 chrM 16270 * C T
m.16304 chrM 16304 * T C
m.16526 chrM 16526 * G A
m.16525-16526 chrM 16525-16526 * AG A
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.56-57 3 0 3
m.65-66 2 0 2
m.72 737 667 68
m.73 821 4 817
m.94 940 877 63
... ... ... ...
m.16256 1319 7 1312
m.16270 1389 6 1382
m.16304 1459 6 1451
m.16526 953 7 944
m.16525-16526 2 0 2
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.56-57 NKS_7.merged.hg19chrm TRUE:TRUE | 2
m.65-66 NKS_7.merged.hg19chrm TRUE:TRUE | 1
m.72 NKS_7.merged.hg19chrm TRUE:FALSE | 53
m.73 NKS_7.merged.hg19chrm FALSE:FALSE | 165
m.94 NKS_7.merged.hg19chrm TRUE:FALSE | 44
... ... ... . ...
m.16256 NKS_7.merged.hg19chrm FALSE:FALSE | 165
m.16270 NKS_7.merged.hg19chrm FALSE:FALSE | 164
m.16304 NKS_7.merged.hg19chrm FALSE:FALSE | 165
m.16526 NKS_7.merged.hg19chrm TRUE:FALSE | 114
m.16525-16526 NKS_7.merged.hg19chrm TRUE:TRUE | 1
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.56-57 <NA> 3 1 0
m.65-66 <NA> 2 0 0
m.72 140 900 26 527
m.73 2 900 631 0
m.94 164 995 33 706
... ... ... ... ...
m.16256 11 1400 1228 4
m.16270 7 1439 1296 3
m.16304 8 1508 1344 3
m.16526 6 1004 878 6
m.16525-16526 <NA> 2 2 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.56-57 2 0 <NA> <NA>
m.65-66 2 0 <NA> <NA>
m.72 42 140 0 0
m.73 186 4 0 0
m.94 30 171 0 0
... ... ... ... ...
m.16256 84 3 0 0
m.16270 86 3 0 0
m.16304 107 3 0 0
m.16526 66 1 2 0
m.16525-16526 0 0 <NA> <NA>
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.56-57 38.3333333333333 <NA> 756.055555555555
m.65-66 69 <NA> 0
m.72 48.2941176470588 47.5577211394303 618.693126065175
m.73 47.5764993880049 74.5 725.427686375327
m.94 47.3650793650794 47.6442417331813 1047.74280512683
... ... ... ...
m.16256 50.4314024390244 37.2857142857143 826.952824234538
m.16270 49.8842257597684 28.8333333333333 855.982557640271
m.16304 49.6946933149552 39.6666666666667 824.914008056685
m.16526 58.4353813559322 54.1428571428571 633.8120382364
m.16525-16526 48 <NA> 0
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.56-57 <NA> 25 <NA> 3
m.65-66 <NA> 12.5 <NA> 2
m.72 745.543940804966 27.5 <NA> 68
m.73 1906.41666666667 <NA> 21.5 817
m.94 874.439471679317 29 <NA> 63
... ... ... ... ...
m.16256 1054.60884353742 <NA> 25 1312
m.16270 604.038888888889 <NA> 15 1382
m.16304 974.955555555556 <NA> 22.5 1451
m.16526 1471.05102040816 41.5 25 944
m.16525-16526 <NA> 12.5 <NA> 2
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.56-57 <NA> TRUE 1
m.65-66 <NA> TRUE 1
m.72 667 FALSE 0.0922659430122117
m.73 4 FALSE 0.995127892813642
m.94 877 FALSE 0.0670212765957447
... ... ... ...
m.16256 7 FALSE 0.994692949203942
m.16270 6 FALSE 0.994960403167747
m.16304 6 FALSE 0.994516792323509
m.16526 7 FALSE 0.990556138509968
m.16525-16526 <NA> TRUE 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~938x read coverage
$RO_7
MVRanges object with 79 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.31-32 chrM 31-32 * CA C
m.65 chrM 65 * T TG
m.73 chrM 73 * A G
m.263 chrM 263 * A G
m.296-297 chrM 296-297 * CA C
... ... ... ... ... ...
m.16192 chrM 16192 * C CT
m.16256 chrM 16256 * C T
m.16270 chrM 16270 * C T
m.16304 chrM 16304 * T C
m.16526 chrM 16526 * G A
totalDepth refDepth altDepth sampleNames
<integerOrRle> <integerOrRle> <integerOrRle> <factorOrRle>
m.31-32 2 0 2 RO_7.merged.hg19chrm
m.65 2 0 2 RO_7.merged.hg19chrm
m.73 729 2 727 RO_7.merged.hg19chrm
m.263 560 0 558 RO_7.merged.hg19chrm
m.296-297 2 0 2 RO_7.merged.hg19chrm
... ... ... ... ...
m.16192 2 0 2 RO_7.merged.hg19chrm
m.16256 1212 18 1192 RO_7.merged.hg19chrm
m.16270 1296 18 1275 RO_7.merged.hg19chrm
m.16304 1324 15 1309 RO_7.merged.hg19chrm
m.16526 866 4 860 RO_7.merged.hg19chrm
softFilterMatrix | n.read.pos n.read.pos.ref raw.count.total
<matrix> | <integer> <integer> <integer>
m.31-32 TRUE:TRUE | 1 <NA> 2
m.65 TRUE:TRUE | 1 <NA> 2
m.73 FALSE:FALSE | 150 1 815
m.263 FALSE:TRUE | 156 0 606
m.296-297 FALSE:TRUE | 1 <NA> 2
... ... . ... ... ...
m.16192 FALSE:TRUE | 1 <NA> 2
m.16256 FALSE:FALSE | 173 22 1300
m.16270 FALSE:FALSE | 181 18 1350
m.16304 FALSE:FALSE | 183 15 1388
m.16526 TRUE:FALSE | 126 4 915
count.plus count.plus.ref count.minus count.minus.ref
<integer> <integer> <integer> <integer>
m.31-32 0 0 2 0
m.65 0 0 2 0
m.73 622 0 105 2
m.263 463 0 95 0
m.296-297 0 0 2 0
... ... ... ... ...
m.16192 0 0 2 0
m.16256 1083 13 109 5
m.16270 1151 12 124 6
m.16304 1175 6 134 9
m.16526 782 4 78 0
count.del.plus count.del.minus read.pos.mean read.pos.mean.ref
<integer> <integer> <numeric> <numeric>
m.31-32 <NA> <NA> 78 <NA>
m.65 <NA> <NA> 62 <NA>
m.73 0 0 50.5804676753783 54
m.263 0 0 50.0501792114695 NaN
m.296-297 <NA> <NA> 81 <NA>
... ... ... ... ...
m.16192 <NA> <NA> 98 <NA>
m.16256 0 0 51.1552013422819 57.6666666666667
m.16270 0 0 50.9890196078431 65
m.16304 0 0 49.4140565317036 67.1333333333333
m.16526 0 0 57.0686046511628 38.5
read.pos.var read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <numeric> <integer>
m.31-32 0 <NA> 10.5 <NA> 2
m.65 0 <NA> 12.5 <NA> 2
m.73 756.754030786847 0 <NA> 12.5 727
m.263 780.552271851309 <NA> <NA> <NA> 558
m.296-297 0 <NA> 9 <NA> 2
... ... ... ... ... ...
m.16192 0 <NA> 0.5 <NA> 2
m.16256 814.610530962256 866.790849673203 <NA> 24.5 1192
m.16270 861.156771110736 938.529411764706 <NA> 26.5 1275
m.16304 822.496429925638 819.615555555554 <NA> 27 1309
m.16526 604.868193204205 614.416666666667 42.5 12.5 860
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.31-32 <NA> TRUE 1
m.65 <NA> TRUE 1
m.73 2 FALSE 0.997256515775034
m.263 0 FALSE 0.996428571428571
m.296-297 <NA> FALSE 1
... ... ... ...
m.16192 <NA> FALSE 1
m.16256 18 FALSE 0.983498349834984
m.16270 18 FALSE 0.983796296296296
m.16304 15 FALSE 0.988670694864048
m.16526 4 FALSE 0.993071593533487
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~870x read coverage
$NKS_8
MVRanges object with 81 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.56-57 chrM 56-57 * AT A
m.60 chrM 60 * T C
m.64-65 chrM 64-65 * CT C
m.65-66 chrM 65-66 * TG T
m.70 chrM 70 * G GC
... ... ... ... ... ...
m.16223 chrM 16223 * C T
m.16257 chrM 16257 * C A
m.16261 chrM 16261 * C T
m.16502-16503 chrM 16502-16503 * TG T
m.16549-16550 chrM 16549-16550 * CT C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.56-57 7 0 7
m.60 655 592 60
m.64-65 2 0 2
m.65-66 11 0 11
m.70 2 0 2
... ... ... ...
m.16223 1154 3 1150
m.16257 1213 7 1206
m.16261 1205 13 1192
m.16502-16503 2 0 2
m.16549-16550 2 0 2
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.56-57 NKS_8.merged.hg19chrm TRUE:TRUE | 7
m.60 NKS_8.merged.hg19chrm TRUE:FALSE | 40
m.64-65 NKS_8.merged.hg19chrm TRUE:TRUE | 2
m.65-66 NKS_8.merged.hg19chrm TRUE:TRUE | 10
m.70 NKS_8.merged.hg19chrm TRUE:TRUE | 1
... ... ... . ...
m.16223 NKS_8.merged.hg19chrm FALSE:FALSE | 160
m.16257 NKS_8.merged.hg19chrm FALSE:FALSE | 162
m.16261 NKS_8.merged.hg19chrm FALSE:FALSE | 155
m.16502-16503 NKS_8.merged.hg19chrm TRUE:TRUE | 1
m.16549-16550 NKS_8.merged.hg19chrm TRUE:TRUE | 2
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.56-57 <NA> 7 5 0
m.60 137 687 31 465
m.64-65 <NA> 2 1 0
m.65-66 <NA> 11 5 0
m.70 <NA> 2 0 0
... ... ... ... ...
m.16223 4 1195 1066 2
m.16257 7 1236 1117 5
m.16261 13 1241 1114 6
m.16502-16503 <NA> 2 2 0
m.16549-16550 <NA> 2 1 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.56-57 2 0 <NA> <NA>
m.60 29 127 0 0
m.64-65 1 0 <NA> <NA>
m.65-66 6 0 <NA> <NA>
m.70 2 0 <NA> <NA>
... ... ... ... ...
m.16223 84 1 0 0
m.16257 89 2 0 0
m.16261 78 7 0 0
m.16502-16503 0 0 <NA> <NA>
m.16549-16550 1 0 <NA> <NA>
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.56-57 65 <NA> 1031.83333333333
m.60 54.2666666666667 49.9459459459459 763.739058380414
m.64-65 56.5 <NA> 24.5
m.65-66 53.2727272727273 <NA> 1085.01652892562
m.70 76 <NA> 0
... ... ... ...
m.16223 48.4017391304348 68 848.340404588851
m.16257 50.5082918739635 41.7142857142857 758.785481020154
m.16261 51.3447986577181 57.3076923076923 765.401827120806
m.16502-16503 54 <NA> 0
m.16549-16550 61 <NA> 32
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.56-57 <NA> 25 <NA> 7
m.60 667.832263598487 29.5 <NA> 60
m.64-65 <NA> 12.5 <NA> 2
m.65-66 <NA> 25 <NA> 11
m.70 <NA> 11.5 <NA> 2
... ... ... ... ...
m.16223 2751 <NA> 25 1150
m.16257 1194.91836734694 <NA> 20 1206
m.16261 1241.74506903353 <NA> 25 1192
m.16502-16503 <NA> 12.5 <NA> 2
m.16549-16550 <NA> 12.5 <NA> 2
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.56-57 <NA> TRUE 1
m.60 592 FALSE 0.0916030534351145
m.64-65 <NA> TRUE 1
m.65-66 <NA> TRUE 1
m.70 <NA> TRUE 1
... ... ... ...
m.16223 3 FALSE 0.996533795493934
m.16257 7 FALSE 0.994229183841715
m.16261 13 FALSE 0.989211618257261
m.16502-16503 <NA> TRUE 1
m.16549-16550 <NA> TRUE 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~784x read coverage
$RO_8
MVRanges object with 98 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.73 chrM 73 * A G
m.146 chrM 146 * T C
m.150 chrM 150 * C T
m.186-187 chrM 186-187 * CG C
m.263 chrM 263 * A G
... ... ... ... ... ...
m.16129 chrM 16129 * G A
m.16223 chrM 16223 * C T
m.16257 chrM 16257 * C A
m.16261 chrM 16261 * C T
m.16502-16503 chrM 16502-16503 * TG T
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.73 1501 10 1490
m.146 1502 8 1493
m.150 1486 5 1481
m.186-187 2 0 2
m.263 1479 1 1477
... ... ... ...
m.16129 2271 12 2259
m.16223 2801 21 2777
m.16257 2872 23 2849
m.16261 2837 16 2819
m.16502-16503 2 0 2
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.73 RO_8.merged.hg19chrm FALSE:FALSE | 182
m.146 RO_8.merged.hg19chrm FALSE:FALSE | 175
m.150 RO_8.merged.hg19chrm FALSE:FALSE | 173
m.186-187 RO_8.merged.hg19chrm TRUE:TRUE | 2
m.263 RO_8.merged.hg19chrm FALSE:FALSE | 186
... ... ... . ...
m.16129 RO_8.merged.hg19chrm TRUE:FALSE | 188
m.16223 RO_8.merged.hg19chrm FALSE:FALSE | 194
m.16257 RO_8.merged.hg19chrm FALSE:FALSE | 191
m.16261 RO_8.merged.hg19chrm FALSE:FALSE | 191
m.16502-16503 RO_8.merged.hg19chrm TRUE:TRUE | 2
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.73 8 1683 1312 3
m.146 8 1561 1341 6
m.150 6 1541 1340 4
m.186-187 <NA> 2 1 0
m.263 2 1594 1327 1
... ... ... ... ...
m.16129 13 2346 2100 9
m.16223 21 2930 2564 8
m.16257 22 2968 2629 12
m.16261 21 2994 2611 10
m.16502-16503 <NA> 2 1 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.73 178 7 0 0
m.146 152 2 0 0
m.150 141 1 0 0
m.186-187 1 0 <NA> <NA>
m.263 150 0 0 0
... ... ... ... ...
m.16129 159 3 0 0
m.16223 213 13 0 0
m.16257 220 11 0 0
m.16261 208 6 0 0
m.16502-16503 1 0 <NA> <NA>
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.73 48.0751677852349 28.6 761.037476807006
m.146 52.914266577361 36.875 761.032805448607
m.150 52.696151249156 23 759.062265147699
m.186-187 64.5 <NA> 2112.5
m.263 51.1123899796886 97 814.659769426021
... ... ... ...
m.16129 47.427180168216 55.5833333333333 882.862758439495
m.16223 49.0234065538351 51.7142857142857 861.165264036075
m.16257 50.2295542295542 41.5652173913044 765.186404372181
m.16261 49.9169918410784 39.9375 771.437999348926
m.16502-16503 83 <NA> 200
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.73 925.817777777778 <NA> 15.5 1490
m.146 562.948660714286 <NA> 23.5 1493
m.150 506.25 <NA> 25 1481
m.186-187 <NA> 13.5 <NA> 2
m.263 <NA> <NA> 2 1477
... ... ... ... ...
m.16129 1302.03851010101 46 19 2259
m.16223 988.332653061224 <NA> 26 2777
m.16257 692.150885031792 <NA> 28 2849
m.16261 929.729427083333 <NA> 24.5 2819
m.16502-16503 <NA> 15.5 <NA> 2
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.73 10 FALSE 0.992671552298468
m.146 8 FALSE 0.994007989347537
m.150 5 FALSE 0.996635262449529
m.186-187 <NA> TRUE 1
m.263 1 FALSE 0.998647734956051
... ... ... ...
m.16129 12 FALSE 0.994715984147952
m.16223 21 FALSE 0.991431631560157
m.16257 23 FALSE 0.991991643454039
m.16261 16 FALSE 0.99365526965104
m.16502-16503 <NA> TRUE 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~1749x read coverage
$NKS_9
MVRanges object with 50 ranges and 19 metadata columns:
seqnames ranges strand ref alt totalDepth
<Rle> <IRanges> <Rle> <character> <characterOrRle> <integerOrRle>
m.56-57 chrM 56-57 * AT A 3
m.60 chrM 60 * T C 418
m.62-63 chrM 62-63 * GT G 3
m.72 chrM 72 * T C 423
m.152 chrM 152 * T C 427
... ... ... ... ... ... ...
m.15326 chrM 15326 * A G 491
m.16261 chrM 16261 * C T 970
m.16261 chrM 16261 * C CT 3
m.16311 chrM 16311 * T C 973
m.16519 chrM 16519 * T C 571
refDepth altDepth sampleNames softFilterMatrix
<integerOrRle> <integerOrRle> <factorOrRle> <matrix>
m.56-57 0 3 NKS_9.merged.hg19chrm TRUE:TRUE
m.60 393 19 NKS_9.merged.hg19chrm TRUE:FALSE
m.62-63 0 3 NKS_9.merged.hg19chrm TRUE:TRUE
m.72 330 91 NKS_9.merged.hg19chrm TRUE:FALSE
m.152 0 427 NKS_9.merged.hg19chrm FALSE:TRUE
... ... ... ... ...
m.15326 0 490 NKS_9.merged.hg19chrm TRUE:TRUE
m.16261 6 963 NKS_9.merged.hg19chrm FALSE:FALSE
m.16261 0 3 NKS_9.merged.hg19chrm FALSE:TRUE
m.16311 1 972 NKS_9.merged.hg19chrm FALSE:FALSE
m.16519 0 571 NKS_9.merged.hg19chrm TRUE:TRUE
| n.read.pos n.read.pos.ref raw.count.total count.plus count.plus.ref
| <integer> <integer> <integer> <integer> <integer>
m.56-57 | 3 <NA> 3 2 0
m.60 | 16 133 449 13 277
m.62-63 | 2 <NA> 3 0 0
m.72 | 59 128 509 45 223
m.152 | 127 0 437 328 0
... . ... ... ... ... ...
m.15326 | 123 0 506 434 0
m.16261 | 156 5 1007 901 2
m.16261 | 1 <NA> 3 0 0
m.16311 | 158 2 1004 875 0
m.16519 | 116 0 585 506 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.56-57 1 0 <NA> <NA>
m.60 6 116 2 0
m.62-63 3 0 <NA> <NA>
m.72 46 107 0 0
m.152 99 0 0 0
... ... ... ... ...
m.15326 56 0 0 0
m.16261 62 4 0 0
m.16261 3 0 <NA> <NA>
m.16311 97 1 0 0
m.16519 65 0 0 0
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
<numeric> <numeric> <numeric> <numeric>
m.56-57 58.6666666666667 <NA> 2946.22222222222 <NA>
m.60 44.2105263157895 48.9363867684478 671.873807325331 743.480050048883
m.62-63 48.3333333333333 <NA> 1784.38888888889 <NA>
m.72 53.3516483516484 44.5909090909091 891.52384038428 807.289124318621
m.152 52.6791569086651 NaN 836.995629270175 <NA>
... ... ... ... ...
m.15326 45.6938775510204 NaN 834.33949300266 <NA>
m.16261 49.8193146417445 64.1666666666667 756.580587171556 2307.23888888889
m.16261 98 <NA> 4802 <NA>
m.16311 54.179012345679 95 838.504858115968 <NA>
m.16519 55.5113835376532 NaN 697.926648612754 <NA>
mdfne mdfne.ref count.high.nm count.high.nm.ref PASS
<numeric> <numeric> <integer> <integer> <logical>
m.56-57 23 <NA> 3 <NA> TRUE
m.60 26 <NA> 19 393 FALSE
m.62-63 25 <NA> 3 <NA> TRUE
m.72 38 <NA> 91 330 FALSE
m.152 <NA> <NA> 427 0 FALSE
... ... ... ... ... ...
m.15326 46.5 <NA> 490 0 TRUE
m.16261 <NA> 9.5 963 6 FALSE
m.16261 1 <NA> 3 <NA> FALSE
m.16311 <NA> 4 972 1 FALSE
m.16519 44 <NA> 571 0 TRUE
VAF
<numeric>
m.56-57 1
m.60 0.0454545454545455
m.62-63 1
m.72 0.215130023640662
m.152 1
... ...
m.15326 0.9979633401222
m.16261 0.992783505154639
m.16261 1
m.16311 0.998972250770812
m.16519 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~537x read coverage
$RO_9
MVRanges object with 47 ranges and 19 metadata columns:
seqnames ranges strand ref alt totalDepth
<Rle> <IRanges> <Rle> <character> <characterOrRle> <integerOrRle>
m.152 chrM 152 * T C 350
m.195 chrM 195 * T C 299
m.263 chrM 263 * A G 322
m.302 chrM 302 * A AC 5
m.310 chrM 310 * T C 234
... ... ... ... ... ... ...
m.15326 chrM 15326 * A G 434
m.16261 chrM 16261 * C T 866
m.16293 chrM 16293 * A G 833
m.16311 chrM 16311 * T C 913
m.16519 chrM 16519 * T C 446
refDepth altDepth sampleNames softFilterMatrix |
<integerOrRle> <integerOrRle> <factorOrRle> <matrix> |
m.152 0 350 RO_9.merged.hg19chrm FALSE:TRUE |
m.195 1 298 RO_9.merged.hg19chrm FALSE:FALSE |
m.263 0 321 RO_9.merged.hg19chrm FALSE:TRUE |
m.302 0 5 RO_9.merged.hg19chrm TRUE:TRUE |
m.310 221 13 RO_9.merged.hg19chrm TRUE:FALSE |
... ... ... ... ... .
m.15326 0 434 RO_9.merged.hg19chrm FALSE:TRUE |
m.16261 1 865 RO_9.merged.hg19chrm FALSE:FALSE |
m.16293 754 79 RO_9.merged.hg19chrm TRUE:FALSE |
m.16311 2 911 RO_9.merged.hg19chrm FALSE:FALSE |
m.16519 0 446 RO_9.merged.hg19chrm TRUE:TRUE |
n.read.pos n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer> <integer>
m.152 128 0 368 247 0
m.195 120 1 314 213 1
m.263 133 0 355 252 0
m.302 5 <NA> 5 0 0
m.310 19 129 356 5 180
... ... ... ... ... ...
m.15326 134 0 457 383 0
m.16261 169 3 911 782 0
m.16293 62 160 970 52 695
m.16311 175 2 957 779 1
m.16519 118 0 458 364 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.152 103 0 0 0
m.195 85 0 0 0
m.263 69 0 0 0
m.302 5 0 <NA> <NA>
m.310 8 41 0 0
... ... ... ... ...
m.15326 51 0 0 0
m.16261 83 1 0 0
m.16293 27 59 0 0
m.16311 132 1 0 0
m.16519 82 0 0 0
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
<numeric> <numeric> <numeric> <numeric>
m.152 52.8971428571429 NaN 912.58568729314 <NA>
m.195 47.1610738255034 43 808.149613941921 <NA>
m.263 48.3551401869159 NaN 847.842917503712 <NA>
m.302 43.4 <NA> 757.19 <NA>
m.310 31.5384615384615 45.6923076923077 934.992110453649 863.340290478752
... ... ... ... ...
m.15326 46.6958525345622 NaN 820.730612421459 <NA>
m.16261 49.9248554913295 99 819.257646762461 <NA>
m.16293 47.3924050632911 52.1538461538462 958.80609616309 794.539412370243
m.16311 53.7167947310648 43.5 835.385084699773 480.5
m.16519 49.567264573991 NaN 733.987406247479 <NA>
mdfne mdfne.ref count.high.nm count.high.nm.ref PASS
<numeric> <numeric> <integer> <integer> <logical>
m.152 <NA> <NA> 350 0 FALSE
m.195 <NA> 25 298 1 FALSE
m.263 <NA> <NA> 321 0 FALSE
m.302 26 <NA> 5 <NA> TRUE
m.310 28 <NA> 13 221 FALSE
... ... ... ... ... ...
m.15326 <NA> <NA> 434 0 FALSE
m.16261 <NA> 25 865 1 FALSE
m.16293 30 <NA> 79 754 FALSE
m.16311 <NA> 12.5 911 2 FALSE
m.16519 40.5 <NA> 446 0 TRUE
VAF
<numeric>
m.152 1
m.195 0.996655518394649
m.263 0.996894409937888
m.302 1
m.310 0.0555555555555556
... ...
m.15326 1
m.16261 0.998845265588915
m.16293 0.0948379351740696
m.16311 0.997809419496167
m.16519 1
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~471x read coverage
$NKS_10
MVRanges object with 58 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.55-56 chrM 55-56 * TA T
m.56-57 chrM 56-57 * AT A
m.56-59 chrM 56-59 * ATTT A
m.60 chrM 60 * T C
m.62 chrM 62 * G C
... ... ... ... ... ...
m.15657-15658 chrM 15657-15658 * TC T
m.16262-16263 chrM 16262-16263 * CT C
m.16373-16374 chrM 16373-16374 * GA G
m.16502-16503 chrM 16502-16503 * TG T
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.55-56 2 0 2
m.56-57 8 0 8
m.56-59 2 0 2
m.60 530 460 69
m.62 541 518 23
... ... ... ...
m.15657-15658 2 0 2
m.16262-16263 3 0 3
m.16373-16374 2 0 2
m.16502-16503 2 0 2
m.16519 642 1 641
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.55-56 NKS_10.merged.hg19chrm TRUE:TRUE | 1
m.56-57 NKS_10.merged.hg19chrm TRUE:TRUE | 5
m.56-59 NKS_10.merged.hg19chrm TRUE:TRUE | 2
m.60 NKS_10.merged.hg19chrm TRUE:FALSE | 45
m.62 NKS_10.merged.hg19chrm TRUE:FALSE | 16
... ... ... . ...
m.15657-15658 NKS_10.merged.hg19chrm TRUE:TRUE | 2
m.16262-16263 NKS_10.merged.hg19chrm TRUE:TRUE | 3
m.16373-16374 NKS_10.merged.hg19chrm TRUE:TRUE | 2
m.16502-16503 NKS_10.merged.hg19chrm TRUE:TRUE | 1
m.16519 NKS_10.merged.hg19chrm TRUE:FALSE | 121
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.55-56 <NA> 2 0 0
m.56-57 <NA> 8 2 0
m.56-59 <NA> 2 1 0
m.60 128 560 25 326
m.62 145 572 7 352
... ... ... ... ...
m.15657-15658 <NA> 2 1 0
m.16262-16263 <NA> 3 1 0
m.16373-16374 <NA> 2 0 0
m.16502-16503 <NA> 2 2 0
m.16519 1 657 565 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.55-56 2 0 <NA> <NA>
m.56-57 6 0 <NA> <NA>
m.56-59 1 0 <NA> <NA>
m.60 44 134 1 0
m.62 16 166 0 0
... ... ... ... ...
m.15657-15658 1 0 <NA> <NA>
m.16262-16263 2 0 <NA> <NA>
m.16373-16374 2 0 <NA> <NA>
m.16502-16503 0 0 <NA> <NA>
m.16519 76 1 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.55-56 39 <NA> 0
m.56-57 42.625 <NA> 1144.39508928571
m.56-59 70.5 <NA> 480.5
m.60 50.7101449275362 48.3804347826087 699.437083781212
m.62 66.4347826086957 46.7258687258687 677.692387008076
... ... ... ...
m.15657-15658 62 <NA> 288
m.16262-16263 37 <NA> 1285.5
m.16373-16374 86 <NA> 72
m.16502-16503 47 <NA> 0
m.16519 58.1341653666147 1 745.8063171271
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.55-56 <NA> 12.5 <NA> 2
m.56-57 <NA> 24 <NA> 8
m.56-59 <NA> 19 <NA> 2
m.60 737.139630463612 34 <NA> 69
m.62 742.201895874778 25 <NA> 23
... ... ... ... ...
m.15657-15658 <NA> 25.5 <NA> 2
m.16262-16263 <NA> 25 <NA> 3
m.16373-16374 <NA> 13 <NA> 2
m.16502-16503 <NA> 12.5 <NA> 2
m.16519 <NA> 47 0 641
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.55-56 <NA> TRUE 1
m.56-57 <NA> TRUE 1
m.56-59 <NA> TRUE 1
m.60 460 FALSE 0.130188679245283
m.62 518 FALSE 0.0425138632162662
... ... ... ...
m.15657-15658 <NA> TRUE 1
m.16262-16263 <NA> TRUE 1
m.16373-16374 <NA> TRUE 1
m.16502-16503 <NA> TRUE 1
m.16519 1 FALSE 0.998442367601246
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~600x read coverage
$RO_10
MVRanges object with 78 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.147-149 chrM 147-149 * CAT C
m.152 chrM 152 * T C
m.152 chrM 152 * T TCC
m.217-218 chrM 217-218 * TA T
m.263 chrM 263 * A G
... ... ... ... ... ...
m.15326 chrM 15326 * A G
m.15982-15983 chrM 15982-15983 * AT A
m.16016-16018 chrM 16016-16018 * ATT A
m.16032-16033 chrM 16032-16033 * TG T
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.147-149 2 0 2
m.152 1287 1 1286
m.152 2 0 2
m.217-218 2 0 2
m.263 1248 0 1247
... ... ... ...
m.15326 1425 0 1422
m.15982-15983 2 0 2
m.16016-16018 2 0 2
m.16032-16033 2 0 2
m.16519 1687 6 1681
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.147-149 RO_10.merged.hg19chrm TRUE:TRUE | 1
m.152 RO_10.merged.hg19chrm FALSE:FALSE | 153
m.152 RO_10.merged.hg19chrm TRUE:TRUE | 1
m.217-218 RO_10.merged.hg19chrm TRUE:TRUE | 2
m.263 RO_10.merged.hg19chrm FALSE:TRUE | 164
... ... ... . ...
m.15326 RO_10.merged.hg19chrm FALSE:TRUE | 174
m.15982-15983 RO_10.merged.hg19chrm TRUE:TRUE | 2
m.16016-16018 RO_10.merged.hg19chrm TRUE:TRUE | 2
m.16032-16033 RO_10.merged.hg19chrm TRUE:TRUE | 2
m.16519 RO_10.merged.hg19chrm TRUE:FALSE | 162
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.147-149 <NA> 2 0 0
m.152 3 1335 1182 0
m.152 <NA> 2 0 0
m.217-218 <NA> 2 1 0
m.263 0 1341 1161 0
... ... ... ... ...
m.15326 0 1487 1300 0
m.15982-15983 <NA> 2 1 0
m.16016-16018 <NA> 2 0 0
m.16032-16033 <NA> 2 1 0
m.16519 4 1760 1532 4
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.147-149 2 0 <NA> <NA>
m.152 104 1 0 0
m.152 2 0 <NA> <NA>
m.217-218 1 0 <NA> <NA>
m.263 86 0 0 0
... ... ... ... ...
m.15326 122 0 0 0
m.15982-15983 1 0 <NA> <NA>
m.16016-16018 2 0 <NA> <NA>
m.16032-16033 1 0 <NA> <NA>
m.16519 149 2 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.147-149 42 <NA> 0
m.152 52.4261275272162 10 807.728389854152
m.152 39 <NA> 0
m.217-218 75.5 <NA> 144.5
m.263 51.5445068163593 NaN 824.666224762949
... ... ... ...
m.15326 49.4247538677918 NaN 888.14796267329
m.15982-15983 16 <NA> 50
m.16016-16018 47 <NA> 1250
m.16032-16033 82 <NA> 338
m.16519 55.2938726948245 58.6666666666667 724.795380503779
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.147-149 <NA> 12.5 <NA> 2
m.152 <NA> <NA> 9 1286
m.152 <NA> 12.5 <NA> 2
m.217-218 <NA> 20 <NA> 2
m.263 <NA> <NA> <NA> 1247
... ... ... ... ...
m.15326 <NA> <NA> <NA> 1422
m.15982-15983 <NA> 15 <NA> 2
m.16016-16018 <NA> 23 <NA> 2
m.16032-16033 <NA> 14.5 <NA> 2
m.16519 1210.22222222222 47 24.5 1681
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.147-149 <NA> TRUE 1
m.152 1 FALSE 0.999222999222999
m.152 <NA> TRUE 1
m.217-218 <NA> TRUE 1
m.263 0 FALSE 0.999198717948718
... ... ... ...
m.15326 0 FALSE 0.997894736842105
m.15982-15983 <NA> TRUE 1
m.16016-16018 <NA> TRUE 1
m.16032-16033 <NA> TRUE 1
m.16519 6 FALSE 0.996443390634262
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~1552x read coverage
$NKS_11
MVRanges object with 103 ranges and 19 metadata columns:
seqnames ranges strand ref alt
<Rle> <IRanges> <Rle> <character> <characterOrRle>
m.65-66 chrM 65-66 * TG T
m.73 chrM 73 * A G
m.199 chrM 199 * T C
m.203 chrM 203 * G A
m.204 chrM 204 * T C
... ... ... ... ... ...
m.16223 chrM 16223 * C T
m.16264-16265 chrM 16264-16265 * CA C
m.16311 chrM 16311 * T C
m.16391 chrM 16391 * G A
m.16519 chrM 16519 * T C
totalDepth refDepth altDepth
<integerOrRle> <integerOrRle> <integerOrRle>
m.65-66 11 0 11
m.73 702 0 702
m.199 392 2 390
m.203 363 3 360
m.204 376 8 368
... ... ... ...
m.16223 1319 2 1317
m.16264-16265 2 0 2
m.16311 1436 7 1428
m.16391 1012 15 997
m.16519 687 3 684
sampleNames softFilterMatrix | n.read.pos
<factorOrRle> <matrix> | <integer>
m.65-66 NKS_11.merged.hg19chrm TRUE:TRUE | 9
m.73 NKS_11.merged.hg19chrm TRUE:TRUE | 123
m.199 NKS_11.merged.hg19chrm TRUE:FALSE | 109
m.203 NKS_11.merged.hg19chrm TRUE:FALSE | 102
m.204 NKS_11.merged.hg19chrm TRUE:FALSE | 101
... ... ... . ...
m.16223 NKS_11.merged.hg19chrm FALSE:FALSE | 167
m.16264-16265 NKS_11.merged.hg19chrm FALSE:TRUE | 1
m.16311 NKS_11.merged.hg19chrm FALSE:FALSE | 165
m.16391 NKS_11.merged.hg19chrm FALSE:FALSE | 152
m.16519 NKS_11.merged.hg19chrm TRUE:FALSE | 112
n.read.pos.ref raw.count.total count.plus count.plus.ref
<integer> <integer> <integer> <integer>
m.65-66 <NA> 11 5 0
m.73 0 765 609 0
m.199 1 396 331 2
m.203 2 376 312 2
m.204 6 384 323 2
... ... ... ... ...
m.16223 3 1377 1203 1
m.16264-16265 <NA> 2 0 0
m.16311 8 1490 1309 4
m.16391 14 1063 907 6
m.16519 2 709 583 2
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.65-66 6 0 <NA> <NA>
m.73 93 0 0 0
m.199 59 0 0 0
m.203 48 1 0 0
m.204 45 6 0 0
... ... ... ... ...
m.16223 114 1 0 0
m.16264-16265 2 0 <NA> <NA>
m.16311 119 3 0 0
m.16391 90 9 0 0
m.16519 101 1 0 0
read.pos.mean read.pos.mean.ref read.pos.var
<numeric> <numeric> <numeric>
m.65-66 49 <NA> 579.3
m.73 45.4487179487179 NaN 723.97323795911
m.199 43.8025641025641 54 685.569311202716
m.203 45.5611111111111 42.6666666666667 600.591839557756
m.204 45.7228260869565 30.75 634.932711406669
... ... ... ...
m.16223 48.5596051632498 2.5 873.117481951592
m.16264-16265 82 <NA> 0
m.16311 52.8025210084034 60.8571428571429 855.09769947387
m.16391 55.8224674022066 57 798.881249595443
m.16519 53.1827485380117 72.6666666666667 753.04913788405
read.pos.var.ref mdfne mdfne.ref count.high.nm
<numeric> <numeric> <numeric> <integer>
m.65-66 <NA> 26 <NA> 11
m.73 <NA> 43.5 <NA> 702
m.199 0 44.5 12.5 390
m.203 1615.55555555556 43.5 25 360
m.204 338.151785714286 41.5 25.5 368
... ... ... ... ...
m.16223 0.5 <NA> 1.5 1317
m.16264-16265 <NA> 8.5 <NA> 2
m.16311 960.408163265306 <NA> 25 1428
m.16391 1102.21428571429 <NA> 24 997
m.16519 4273.55555555555 41.5 3 684
count.high.nm.ref PASS VAF
<integer> <logical> <numeric>
m.65-66 <NA> TRUE 1
m.73 0 TRUE 1
m.199 2 FALSE 0.994897959183674
m.203 3 FALSE 0.991735537190083
m.204 8 FALSE 0.978723404255319
... ... ... ...
m.16223 2 FALSE 0.998483699772555
m.16264-16265 <NA> FALSE 1
m.16311 7 FALSE 0.994428969359331
m.16391 15 FALSE 0.985177865612648
m.16519 3 FALSE 0.995633187772926
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~683x read coverage
$RO_11
MVRanges object with 167 ranges and 19 metadata columns:
seqnames ranges strand ref alt totalDepth
<Rle> <IRanges> <Rle> <character> <characterOrRle> <integerOrRle>
m.71-73 chrM 71-73 * GTA G 4
m.73 chrM 73 * A G 2067
m.199 chrM 199 * T C 1436
m.203 chrM 203 * G A 1351
m.204 chrM 204 * T C 1379
... ... ... ... ... ... ...
m.16191 chrM 16191 * C CT 2
m.16223 chrM 16223 * C T 4162
m.16311 chrM 16311 * T C 4438
m.16391 chrM 16391 * G A 3356
m.16519 chrM 16519 * T C 2512
refDepth altDepth sampleNames softFilterMatrix
<integerOrRle> <integerOrRle> <factorOrRle> <matrix>
m.71-73 0 4 RO_11.merged.hg19chrm FALSE:TRUE
m.73 3 2060 RO_11.merged.hg19chrm FALSE:FALSE
m.199 0 1436 RO_11.merged.hg19chrm TRUE:TRUE
m.203 1 1350 RO_11.merged.hg19chrm TRUE:FALSE
m.204 0 1379 RO_11.merged.hg19chrm TRUE:TRUE
... ... ... ... ...
m.16191 0 2 RO_11.merged.hg19chrm TRUE:TRUE
m.16223 2 4159 RO_11.merged.hg19chrm FALSE:FALSE
m.16311 2 4436 RO_11.merged.hg19chrm FALSE:FALSE
m.16391 1 3355 RO_11.merged.hg19chrm FALSE:FALSE
m.16519 1 2510 RO_11.merged.hg19chrm TRUE:FALSE
| n.read.pos n.read.pos.ref raw.count.total count.plus count.plus.ref
| <integer> <integer> <integer> <integer> <integer>
m.71-73 | 2 <NA> 4 0 0
m.73 | 159 2 2215 1957 1
m.199 | 131 0 1457 1363 0
m.203 | 122 3 1386 1286 0
m.204 | 128 0 1411 1312 0
... . ... ... ... ... ...
m.16191 | 1 <NA> 2 0 0
m.16223 | 194 3 4347 3964 1
m.16311 | 198 3 4604 4184 2
m.16391 | 193 2 3554 3157 1
m.16519 | 169 3 2617 2317 0
count.minus count.minus.ref count.del.plus count.del.minus
<integer> <integer> <integer> <integer>
m.71-73 4 0 <NA> <NA>
m.73 103 2 0 4
m.199 73 0 0 0
m.203 64 1 0 0
m.204 67 0 0 0
... ... ... ... ...
m.16191 2 0 <NA> <NA>
m.16223 195 1 0 0
m.16311 252 0 0 0
m.16391 198 0 0 0
m.16519 193 1 0 0
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
<numeric> <numeric> <numeric> <numeric>
m.71-73 95.5 <NA> 3040.41666666667 <NA>
m.73 48.0533980582524 32.3333333333333 786.176423156162 803.055555555555
m.199 50.2771587743733 NaN 709.528559931862 <NA>
m.203 51.522962962963 85 623.135214129452 <NA>
m.204 51.9448875997099 NaN 653.561743690366 <NA>
... ... ... ... ...
m.16191 75 <NA> 0 <NA>
m.16223 51.1372926184179 14 839.319295000294 98
m.16311 51.1916140667268 25 820.76115206179 8
m.16391 54.1770491803279 26 797.044718379479 <NA>
m.16519 55.3115537848606 52 770.593755648599 <NA>
mdfne mdfne.ref count.high.nm count.high.nm.ref PASS
<numeric> <numeric> <integer> <integer> <logical>
m.71-73 3.5 <NA> 4 <NA> FALSE
m.73 <NA> 25 2060 3 FALSE
m.199 48.5 <NA> 1436 0 TRUE
m.203 46.5 14 1350 1 FALSE
m.204 46 <NA> 1379 0 TRUE
... ... ... ... ... ...
m.16191 12 <NA> 2 <NA> TRUE
m.16223 <NA> 13 4159 2 FALSE
m.16311 <NA> 23.5 4436 2 FALSE
m.16391 <NA> 25 3355 1 FALSE
m.16519 47.5 25 2510 1 FALSE
VAF
<numeric>
m.71-73 1
m.73 0.996613449443638
m.199 1
m.203 0.999259807549963
m.204 1
... ...
m.16191 1
m.16223 0.999279192695819
m.16311 0.999549346552501
m.16391 0.999702026221692
m.16519 0.999203821656051
-------
seqinfo: 1 sequence (1 circular) from rCRS genome
hardFilters(4): nonRef nonNRef readCount likelihoodRatio
genome: rCRS, ~2212x read coverage
Error: C stack usage 7971556 is too close to the limit
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.10-data-experiment/meat/MTseekerData.Rcheck/00check.log’
for details.
MTseekerData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MTseekerData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘MTseekerData’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MTseekerData)
MTseekerData.Rcheck/MTseekerData-Ex.timings
| name | user | system | elapsed | |
| RONKSreads | 5.272 | 0.308 | 5.602 | |