BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472816.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,955,275 number of mapped reads = 2,205,283 (74.62%) number of supplementary alignments = 22,755 (0.77%) number of secondary alignments = 0 number of mapped bases = 138,555,734 bp number of sequenced bases = 138,493,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,389 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4566 >>>>>>> ACTG content number of A's = 36,852,369 bp (26.61%) number of C's = 28,223,701 bp (20.38%) number of T's = 40,417,933 bp (29.18%) number of G's = 32,996,774 bp (23.83%) number of N's = 3,027 bp (0%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,245,555 number of insertions = 10,871 mapped reads with insertion percentage = 0.49% number of deletions = 34,135 mapped reads with deletion percentage = 1.53% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.0448X std coverageData = 0.3469X There is a 3.59% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 11673695 0.04683516916894662 0.4105522877303346 chr2 243199373 12726308 0.05232870398888734 0.4720769586657775 chr3 198022430 8644728 0.04365529702872548 0.26353145556576807 chr4 191154276 6744506 0.03528305063916017 0.2636203783884154 chr5 180915260 7888898 0.04360548690033113 0.2625627536478042 chr6 171115067 9509990 0.055576578770822095 0.31628254623298213 chr7 159138663 7935749 0.049866882443268985 0.47113469302898686 chr8 146364022 7860954 0.05370823985692331 0.3479765365813256 chr9 141213431 6011991 0.04257379030752394 0.3688226079679886 chr10 135534747 6380393 0.047075699340774955 0.3372993217257715 chr11 135006516 5512117 0.04082852563945877 0.3612573129482895 chr12 133851895 5540661 0.041393967563925785 0.26772977860898123 chr13 115169878 5751163 0.04993634707158412 0.2867638050990416 chr14 107349540 3726036 0.03470938021718584 0.2728599290117665 chr15 102531392 3492737 0.0340650500482818 0.2615349405889889 chr16 90354753 4344802 0.048086037045555315 0.2965117154649534 chr17 81195210 3800066 0.046801603198021166 0.2947821207697861 chr18 78077248 2789675 0.035729678894420046 0.5886993054332691 chr19 59128983 3082789 0.052136682276439625 0.3626237452830599 chr20 63025520 4550480 0.0722005942989443 0.34654051242990613 chr21 48129895 2157049 0.044817238849160175 0.2956581514196706 chr22 51304566 1631763 0.0318054147461261 0.23488604367073032 chrMT 16571 127819 7.713415002112123 6.07080431493101 chrX 155270560 6031586 0.03884565110089124 0.28408530429735096 chrY 59373566 639779 0.01077548550814684 0.16059656903860503