BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716339.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,685,295 number of mapped reads = 1,946,424 (72.48%) number of supplementary alignments = 12,883 (0.48%) number of secondary alignments = 0 number of mapped bases = 113,839,488 bp number of sequenced bases = 113,807,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,916 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8804 >>>>>>> ACTG content number of A's = 28,410,414 bp (24.96%) number of C's = 21,180,513 bp (18.61%) number of T's = 36,490,136 bp (32.06%) number of G's = 27,724,767 bp (24.36%) number of N's = 1,407 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 565,630 number of insertions = 7,540 mapped reads with insertion percentage = 0.39% number of deletions = 20,296 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.02% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3069X There is a 3.17% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9230498 0.03703299900705162 0.4941969843615913 chr2 243199373 9611616 0.03952154925991524 0.41862236715351275 chr3 198022430 7483139 0.037789350428635786 0.22017225894399495 chr4 191154276 7202784 0.03768047542917638 0.25421890702199357 chr5 180915260 6778164 0.037465960582871785 0.21970227252686444 chr6 171115067 6501099 0.037992557370766185 0.24063022415307014 chr7 159138663 6217304 0.039068469489403714 0.4005215074028275 chr8 146364022 5756396 0.039329310040414164 0.32348367829607616 chr9 141213431 4761058 0.03371533406053989 0.25233505122418315 chr10 135534747 5442446 0.040155355880805974 0.3155339200991071 chr11 135006516 5100352 0.037778561739938536 0.2797834359632152 chr12 133851895 5152883 0.03849689987579182 0.22600018563415253 chr13 115169878 3466183 0.03009626353863117 0.19867843598027113 chr14 107349540 3532778 0.03290911167388328 0.21365229811115466 chr15 102531392 3350352 0.03267635340403844 0.20982813651491883 chr16 90354753 3376374 0.037367973326206755 0.23285458099758002 chr17 81195210 3220432 0.03966283232717792 0.24774694193166902 chr18 78077248 2974025 0.03809080207335177 0.43267634391793436 chr19 59128983 2437172 0.04121789140192044 0.38631258975464694 chr20 63025520 2453042 0.038921408343794706 0.22809403825498634 chr21 48129895 1513599 0.03144820906008625 0.22802069374749773 chr22 51304566 1463101 0.028517949065196262 0.19197884931167145 chrMT 16571 54412 3.2835676784744434 2.97189427097869 chrX 155270560 6414450 0.041311437274393806 0.2504585981832005 chrY 59373566 345829 0.00582462909504206 0.16788378052234637