BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084813.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,525,174 number of mapped reads = 2,276,514 (90.15%) number of supplementary alignments = 29,831 (1.18%) number of secondary alignments = 0 number of mapped bases = 152,193,611 bp number of sequenced bases = 152,135,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,816 duplication rate = 4.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2933 >>>>>>> ACTG content number of A's = 41,384,962 bp (27.2%) number of C's = 28,721,429 bp (18.88%) number of T's = 47,559,093 bp (31.26%) number of G's = 34,448,617 bp (22.64%) number of N's = 21,791 bp (0.01%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,200,880 number of insertions = 12,124 mapped reads with insertion percentage = 0.53% number of deletions = 34,860 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.358X There is a 3.99% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11514264 0.04619552783381029 0.5365717169172606 chr2 243199373 12900884 0.053046534786913284 0.5893557666749898 chr3 198022430 11265333 0.05688917664529215 0.28474916677675344 chr4 191154276 8622829 0.045109265565160574 0.2558443645330421 chr5 180915260 7663755 0.0423610202920417 0.25055141990589413 chr6 171115067 8661983 0.050620808277508374 0.29146544267113195 chr7 159138663 8407439 0.052830901312775264 0.32935636214150366 chr8 146364022 8423961 0.0575548613989304 0.3790120250199014 chr9 141213431 10931555 0.07741158133888837 0.4200849345764023 chr10 135534747 5270177 0.03888432388485589 0.26485960215352505 chr11 135006516 6752610 0.05001691918336742 0.31022668567218215 chr12 133851895 6764812 0.05053953102419656 0.27010494870849056 chr13 115169878 3632347 0.03153903662205842 0.21130197995098843 chr14 107349540 3337481 0.031089849104150795 0.21563115209361608 chr15 102531392 3502948 0.03416463906000613 0.23105265374529046 chr16 90354753 3227096 0.03571584109139228 0.23896393027966792 chr17 81195210 5010863 0.06171377597274519 0.301135707422465 chr18 78077248 6536290 0.08371568116745098 0.5783606028974221 chr19 59128983 3504432 0.059267584561703016 0.41563124435058496 chr20 63025520 3294554 0.0522733330879301 0.2764064080276187 chr21 48129895 1246759 0.02590404570797422 0.19850229616624043 chr22 51304566 1392058 0.027133218513143646 0.19285843566251845 chrMT 16571 35996 2.1722285921187616 1.848796684461185 chrX 155270560 9951751 0.0640929677847494 0.3197465394258791 chrY 59373566 341434 0.005750606254642007 0.12908587697457397