BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063553.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,310,744 number of mapped reads = 2,995,607 (90.48%) number of supplementary alignments = 25,291 (0.76%) number of secondary alignments = 0 number of mapped bases = 197,464,501 bp number of sequenced bases = 197,380,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 176,356 duplication rate = 4.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9226 >>>>>>> ACTG content number of A's = 55,046,821 bp (27.89%) number of C's = 36,041,231 bp (18.26%) number of T's = 62,633,322 bp (31.73%) number of G's = 43,654,572 bp (22.12%) number of N's = 4,844 bp (0%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,589,033 number of insertions = 14,999 mapped reads with insertion percentage = 0.5% number of deletions = 51,308 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0638X std coverageData = 0.5575X There is a 4.93% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20583429 0.08258125463205968 1.0675343482702062 chr2 243199373 19600207 0.08059316419372513 0.7266296371593023 chr3 198022430 12239416 0.06180823051206876 0.30650558090555496 chr4 191154276 10945202 0.05725847325539294 0.31077141607381564 chr5 180915260 7938812 0.04388138402476386 0.26167047935592863 chr6 171115067 15279131 0.08929155841080903 0.44274030460739267 chr7 159138663 13008696 0.08174440927658165 0.6912336050974085 chr8 146364022 8706576 0.05948576624930408 0.9074436502716475 chr9 141213431 7359256 0.052114419626274784 0.4853783594079896 chr10 135534747 10655805 0.07862046623365151 0.4536811038661958 chr11 135006516 9610504 0.07118548263255679 0.46828103061772386 chr12 133851895 8026320 0.05996418653617119 0.3197736553814609 chr13 115169878 3646920 0.03166557144394996 0.2239485109161767 chr14 107349540 4640305 0.04322612840259958 0.30940905523882534 chr15 102531392 3194924 0.03116044693902137 0.23986946818298707 chr16 90354753 4127457 0.04568057421395419 0.2868560531060631 chr17 81195210 5445629 0.0670683529237747 0.34836588475483804 chr18 78077248 4937756 0.06324193188776325 0.7710160713630673 chr19 59128983 4527259 0.07656581883033571 0.7473890024152635 chr20 63025520 2569612 0.04077097658218449 0.265616925881302 chr21 48129895 2802947 0.05823713099727311 0.32111567221552184 chr22 51304566 1720086 0.03352695742519292 0.2196744972033128 chrMT 16571 44736 2.6996560255868687 2.5193258353948407 chrX 155270560 15358125 0.09891202169941295 0.4565003962498678 chrY 59373566 495391 0.008343628880232662 0.1490529349089412