BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174008.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,381,396 number of mapped reads = 4,264,784 (97.34%) number of supplementary alignments = 440,333 (10.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,133,870 number of mapped paired reads (second in pair) = 2,130,914 number of mapped paired reads (both in pair) = 4,185,216 number of mapped paired reads (singletons) = 79,568 number of mapped bases = 504,618,884 bp number of sequenced bases = 504,328,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,393,862 duplication rate = 65.28% >>>>>>> Insert size mean insert size = 1,068,356.8364 std insert size = 9,892,493.7277 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.5951 >>>>>>> ACTG content number of A's = 151,887,357 bp (30.12%) number of C's = 98,633,099 bp (19.56%) number of T's = 151,673,250 bp (30.07%) number of G's = 102,129,300 bp (20.25%) number of N's = 5,875 bp (0%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 5,226,273 number of insertions = 50,508 mapped reads with insertion percentage = 1.15% number of deletions = 119,780 mapped reads with deletion percentage = 2.74% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.163X std coverageData = 2.5567X There is a 3.2% of reference with a coverageData >= 1X There is a 2.55% of reference with a coverageData >= 2X There is a 2.01% of reference with a coverageData >= 3X There is a 1.68% of reference with a coverageData >= 4X There is a 1.31% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.82% of reference with a coverageData >= 7X There is a 0.67% of reference with a coverageData >= 8X There is a 0.5% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 46075716 0.18485697574249976 1.95075280807523 chr2 243199373 57314071 0.23566701794087275 7.326170521111435 chr3 198022430 35810291 0.18083956953765287 1.279208654142322 chr4 191154276 30413821 0.15910615046874493 1.3329977096246772 chr5 180915260 31367946 0.17338474377451632 1.2495633895587421 chr6 171115067 28615816 0.16723142211667427 1.263750168257635 chr7 159138663 32700571 0.20548476645175787 2.2893054962923594 chr8 146364022 21248623 0.14517654482055706 1.3637466385779933 chr9 141213431 12554452 0.08890409298248692 1.1262228930082894 chr10 135534747 21177105 0.1562485301278498 3.014883826577253 chr11 135006516 23781568 0.17615126072877846 1.2671810377352364 chr12 133851895 19747312 0.14753106035592548 1.1502788843233869 chr13 115169878 16558865 0.14377774195436763 1.1486547360771815 chr14 107349540 12694137 0.11825050205152253 1.027170198023554 chr15 102531392 16209887 0.15809681975253004 1.1756880454819623 chr16 90354753 20969946 0.2320845921630708 2.161810425826211 chr17 81195210 11432598 0.14080384791171793 1.1971490365588022 chr18 78077248 7906994 0.10127142288621648 1.787392380894604 chr19 59128983 11606794 0.19629618862208403 2.232365416125071 chr20 63025520 15304234 0.2428259854103544 1.4560466481802863 chr21 48129895 7443299 0.15465022310977408 1.2009920252213901 chr22 51304566 4454577 0.08682613161565386 0.8346752135428884 chrMT 16571 1457206 87.93711906342405 68.6750035221026 chrX 155270560 17125322 0.1102934258754525 0.9923818118239995 chrY 59373566 647733 0.010909450848884502 0.3986519333028858