BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536744.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 22,131,201 number of mapped reads = 17,959,377 (81.15%) number of supplementary alignments = 382 (0%) number of secondary alignments = 0 number of mapped bases = 895,280,328 bp number of sequenced bases = 895,202,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,449 duplication rate = 0.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5296 >>>>>>> ACTG content number of A's = 281,752,125 bp (31.47%) number of C's = 165,405,782 bp (18.48%) number of T's = 280,308,551 bp (31.31%) number of G's = 167,716,939 bp (18.74%) number of N's = 19,159 bp (0%) GC percentage = 37.21% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,060,302 number of insertions = 62,332 mapped reads with insertion percentage = 0.35% number of deletions = 46,500 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.24% >>>>>>> Coverage mean coverageData = 0.2892X std coverageData = 2.2944X There is a 22.44% of reference with a coverageData >= 1X There is a 5.07% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.01% 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 67084944 0.2691465470812207 0.6685467541797596 chr2 243199373 83982788 0.345324854106429 0.6801244307775021 chr3 198022430 73519977 0.3712709565275004 0.686335893853764 chr4 191154276 79406732 0.4154065169852648 0.9665134467491063 chr5 180915260 66926008 0.3699301429851744 0.6743893911236821 chr6 171115067 62064855 0.3627082996729914 9.334647120165544 chr7 159138663 51697462 0.32485796364897196 0.6458881125053757 chr8 146364022 51544739 0.3521680963372269 0.6584104922197767 chr9 141213431 37143012 0.26302747364023754 1.1793075059333018 chr10 135534747 36761393 0.27123223980342104 0.6712332354458326 chr11 135006516 40495767 0.29995416665666713 0.6164111926987691 chr12 133851895 40661087 0.30377670035975207 0.6184457246904213 chr13 115169878 41182226 0.3575780986761139 0.6784263184630347 chr14 107349540 27904451 0.259940107801114 0.5804473137148827 chr15 102531392 21741923 0.21205137837200141 0.5191079317754852 chr16 90354753 13923049 0.154093155453593 0.4368682119848823 chr17 81195210 10898081 0.13422073789820851 0.41065816266052924 chr18 78077248 29043903 0.3719893278000782 0.9636705157071108 chr19 59128983 3881802 0.06564973390460647 0.27455847814082474 chr20 63025520 13603823 0.21584626354530673 0.5258581291000636 chr21 48129895 12015320 0.24964359469306965 0.5853793347462154 chr22 51304566 3328399 0.06487529784386052 0.27584700025805337 chrMT 16571 3382 0.20409148512461528 0.4816193415029581 chrX 155270560 23143367 0.14905186791365987 0.4065647449562706 chrY 59373566 3321838 0.05594809649802742 0.2589215906848476