BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR975192.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 39,605,836
number of mapped reads = 39,541,394 (99.84%)
number of supplementary alignments = 101,391 (0.26%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 19,771,455
number of mapped paired reads (second in pair) = 19,769,939
number of mapped paired reads (both in pair) = 39,496,998
number of mapped paired reads (singletons) = 44,396
number of mapped bases = 3,704,316,363 bp
number of sequenced bases = 3,702,947,098 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 22,763,147
duplication rate = 43.26%
>>>>>>> Insert size
mean insert size = 172,613.4497
std insert size = 4,116,996.3647
median insert size = 232
>>>>>>> Mapping quality
mean mapping quality = 55.6955
>>>>>>> ACTG content
number of A's = 997,821,292 bp (26.95%)
number of C's = 804,012,298 bp (21.71%)
number of T's = 1,045,453,435 bp (28.23%)
number of G's = 855,406,057 bp (23.1%)
number of N's = 254,016 bp (0.01%)
GC percentage = 44.81%
>>>>>>> Mismatches and indels
general error rate = 0.0061
number of mismatches = 21,940,241
number of insertions = 363,671
mapped reads with insertion percentage = 0.91%
number of deletions = 943,595
mapped reads with deletion percentage = 2.35%
homopolymer indels = 48.6%
>>>>>>> Coverage
mean coverageData = 1.1966X
std coverageData = 17.8921X
There is a 8.28% of reference with a coverageData >= 1X
There is a 3.95% of reference with a coverageData >= 2X
There is a 2.57% of reference with a coverageData >= 3X
There is a 2.09% of reference with a coverageData >= 4X
There is a 1.85% of reference with a coverageData >= 5X
There is a 1.7% of reference with a coverageData >= 6X
There is a 1.59% of reference with a coverageData >= 7X
There is a 1.5% of reference with a coverageData >= 8X
There is a 1.43% of reference with a coverageData >= 9X
There is a 1.37% of reference with a coverageData >= 10X
There is a 1.31% of reference with a coverageData >= 11X
There is a 1.26% of reference with a coverageData >= 12X
There is a 1.22% of reference with a coverageData >= 13X
There is a 1.18% of reference with a coverageData >= 14X
There is a 1.14% of reference with a coverageData >= 15X
There is a 1.1% of reference with a coverageData >= 16X
There is a 1.07% of reference with a coverageData >= 17X
There is a 1.04% of reference with a coverageData >= 18X
There is a 1.01% of reference with a coverageData >= 19X
There is a 0.98% of reference with a coverageData >= 20X
There is a 0.96% of reference with a coverageData >= 21X
There is a 0.93% of reference with a coverageData >= 22X
There is a 0.91% of reference with a coverageData >= 23X
There is a 0.89% of reference with a coverageData >= 24X
There is a 0.87% of reference with a coverageData >= 25X
There is a 0.85% of reference with a coverageData >= 26X
There is a 0.83% of reference with a coverageData >= 27X
There is a 0.81% of reference with a coverageData >= 28X
There is a 0.79% of reference with a coverageData >= 29X
There is a 0.78% of reference with a coverageData >= 30X
There is a 0.76% of reference with a coverageData >= 31X
There is a 0.74% of reference with a coverageData >= 32X
There is a 0.73% of reference with a coverageData >= 33X
There is a 0.72% of reference with a coverageData >= 34X
There is a 0.7% of reference with a coverageData >= 35X
There is a 0.69% of reference with a coverageData >= 36X
There is a 0.68% of reference with a coverageData >= 37X
There is a 0.66% of reference with a coverageData >= 38X
There is a 0.65% of reference with a coverageData >= 39X
There is a 0.64% of reference with a coverageData >= 40X
There is a 0.63% of reference with a coverageData >= 41X
There is a 0.62% of reference with a coverageData >= 42X
There is a 0.61% of reference with a coverageData >= 43X
There is a 0.6% of reference with a coverageData >= 44X
There is a 0.59% of reference with a coverageData >= 45X
There is a 0.58% of reference with a coverageData >= 46X
There is a 0.57% of reference with a coverageData >= 47X
There is a 0.56% of reference with a coverageData >= 48X
There is a 0.55% of reference with a coverageData >= 49X
There is a 0.54% of reference with a coverageData >= 50X
There is a 0.53% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 533145437 2.138993414985313 26.738807418719794
chr2 243199373 232660615 0.9566661793984148 13.446735449436476
chr3 198022430 269303279 1.3599635101942744 18.07176993400335
chr4 191154276 146785317 0.7678892676196267 12.281447738267326
chr5 180915260 258720459 1.4300643240376738 19.781977328723457
chr6 171115067 205553093 1.201256538093165 18.20629486816015
chr7 159138663 155872102 0.9794734922461928 15.823701671526585
chr8 146364022 164311284 1.122620721641552 17.496145436417986
chr9 141213431 125676013 0.8899720947931645 13.123302343733796
chr10 135534747 141472491 1.0438097545568887 15.420046030901682
chr11 135006516 179409067 1.3288919106689636 17.448827281683727
chr12 133851895 173084552 1.2931049799481733 17.288963685515313
chr13 115169878 50133060 0.4352966319891387 9.390334766245822
chr14 107349540 121785624 1.1344773717707592 16.448234723982278
chr15 102531392 109699862 1.0699148803129483 14.488704781563309
chr16 90354753 87566400 0.969139941094189 13.657570091325024
chr17 81195210 106127461 1.3070655399499551 16.47310291986713
chr18 78077248 56306220 0.7211604077028945 12.090329103474842
chr19 59128983 133582851 2.2591772126369905 33.63247277451068
chr20 63025520 68447621 1.0860302461606028 15.396891295951415
chr21 48129895 29269339 0.6081322014103708 9.252323826223948
chr22 51304566 47574004 0.9272859651517177 13.404628822306547
chrMT 16571 60401 3.6449821978154606 9.289301536425237
chrX 155270560 306282219 1.97257109783078 27.626703053478632
chrY 59373566 1487592 0.02505478616527766 1.552985095824612