BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716318.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 = 1,456,164 number of mapped reads = 1,318,762 (90.56%) number of supplementary alignments = 5,732 (0.39%) number of secondary alignments = 0 number of mapped bases = 75,225,999 bp number of sequenced bases = 75,205,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,008 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.922 >>>>>>> ACTG content number of A's = 18,914,608 bp (25.15%) number of C's = 13,977,945 bp (18.59%) number of T's = 23,058,659 bp (30.66%) number of G's = 19,253,076 bp (25.6%) number of N's = 1,692 bp (0%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 363,671 number of insertions = 4,853 mapped reads with insertion percentage = 0.37% number of deletions = 11,757 mapped reads with deletion percentage = 0.88% homopolymer indels = 40.36% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2015X There is a 2.22% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 8420625 0.033783767383271636 0.28396531925136004 chr2 243199373 6301728 0.02591177733011672 0.2278839379347262 chr3 198022430 4978823 0.02514272246835876 0.16991577130301647 chr4 191154276 4754547 0.02487282575881274 0.18093432994578504 chr5 180915260 3714873 0.02053377365734654 0.15539415311094348 chr6 171115067 3980649 0.023262995303622212 0.1720371023870962 chr7 159138663 3228440 0.02028696194337136 0.1759554970666949 chr8 146364022 4744754 0.032417488500008564 0.2140264971869444 chr9 141213431 2731716 0.01934459052977758 0.2057522227038017 chr10 135534747 3554347 0.026224618252321672 0.22756754168214002 chr11 135006516 2366666 0.01753001314395818 0.18713350164869824 chr12 133851895 3362606 0.02512184082264954 0.17167533517128633 chr13 115169878 2339585 0.02031420924141293 0.1519107153368986 chr14 107349540 2651247 0.024697329862801463 0.17788073538136465 chr15 102531392 2171517 0.021179045340572376 0.15685403749302695 chr16 90354753 2226409 0.02464075132826715 0.18204239471978978 chr17 81195210 1694191 0.02086565205016404 0.15941556347535457 chr18 78077248 1842080 0.02359304467288601 0.3500554464970731 chr19 59128983 1475920 0.024961024612921212 0.23655070361479627 chr20 63025520 2352755 0.037330195768317344 0.21299847117327866 chr21 48129895 973364 0.02022368841652366 0.16831561554763746 chr22 51304566 908507 0.01770811198363904 0.14232624571336983 chrMT 16571 3614 0.21809184720294492 0.4667326448719688 chrX 155270560 4224405 0.027206735133820603 0.1956562554865319 chrY 59373566 222631 0.0037496652971795563 0.09122806495606238