BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525142.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 = 794,769 number of mapped reads = 706,870 (88.94%) number of supplementary alignments = 23,748 (2.99%) number of secondary alignments = 0 number of mapped bases = 53,853,335 bp number of sequenced bases = 53,832,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,267 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3367 >>>>>>> ACTG content number of A's = 13,984,415 bp (25.98%) number of C's = 10,558,513 bp (19.61%) number of T's = 16,444,153 bp (30.55%) number of G's = 12,842,948 bp (23.86%) number of N's = 2,210 bp (0%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 416,143 number of insertions = 5,086 mapped reads with insertion percentage = 0.71% number of deletions = 11,705 mapped reads with deletion percentage = 1.63% homopolymer indels = 41.55% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.2237X There is a 1.61% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5138308 0.020615025869885395 0.41468421592448657 chr2 243199373 4379874 0.01800939675942339 0.283354025871063 chr3 198022430 3389905 0.017118793057937932 0.13820652046733087 chr4 191154276 3341719 0.01748179046750699 0.15387986294530084 chr5 180915260 3122636 0.01726021342809888 0.13878788984576096 chr6 171115067 2923997 0.01708789910358975 0.15043031694979442 chr7 159138663 2932261 0.018425824024925985 0.26773432952289555 chr8 146364022 2686190 0.01835280257603197 0.26855064848267635 chr9 141213431 2143463 0.015178889039244433 0.19341097794896017 chr10 135534747 2478251 0.01828498635851661 0.23863588861398488 chr11 135006516 3070430 0.022742828205417877 0.2501658121751 chr12 133851895 2356310 0.017603859848230017 0.138586932323405 chr13 115169878 1819856 0.015801492817418803 0.1310970406095096 chr14 107349540 1590123 0.014812573952342973 0.14055550072173942 chr15 102531392 1489523 0.01452748247092949 0.1250289179001403 chr16 90354753 1252449 0.013861462274153967 0.135852538585683 chr17 81195210 1750454 0.021558587015169984 0.1756778631546304 chr18 78077248 1417357 0.018153265340499707 0.3273667873298006 chr19 59128983 1106422 0.018712007950483438 0.2851649573376088 chr20 63025520 1081937 0.017166649319196415 0.14087000166502014 chr21 48129895 697093 0.014483576164045235 0.1346796355235335 chr22 51304566 573763 0.011183468543521058 0.10965917610699578 chrMT 16571 12609 0.7609076096795607 0.950855704208375 chrX 155270560 2943204 0.018955325465432726 0.17299536116388806 chrY 59373566 155201 0.002613974710563957 0.08045788432361009