BamQC report ----------------------------------- >>>>>>> Input bam file = SRR052047.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 6,888,013 number of mapped reads = 5,527,951 (80.25%) number of supplementary alignments = 144 (0%) number of secondary alignments = 0 number of mapped bases = 259,137,297 bp number of sequenced bases = 259,086,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,547,375 duplication rate = 20.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5963 >>>>>>> ACTG content number of A's = 82,239,279 bp (31.74%) number of C's = 51,470,843 bp (19.87%) number of T's = 70,369,454 bp (27.16%) number of G's = 54,967,760 bp (21.22%) number of N's = 38,861 bp (0.01%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,615,602 number of insertions = 11,232 mapped reads with insertion percentage = 0.2% number of deletions = 34,228 mapped reads with deletion percentage = 0.62% homopolymer indels = 44.25% >>>>>>> Coverage mean coverageData = 0.0837X std coverageData = 0.7844X There is a 3.34% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 20493853 0.08222187338100954 0.8150746710276188 chr2 243199373 21766833 0.08950201117500414 0.8414203668490056 chr3 198022430 17196038 0.08683883941834265 0.7628402186691792 chr4 191154276 16667394 0.08719341439162993 0.7966033027778394 chr5 180915260 16134195 0.08918095134705607 0.7800600279933873 chr6 171115067 15283531 0.08931727210205283 0.8389642290702554 chr7 159138663 14073053 0.088432645685857 0.8117388630286994 chr8 146364022 13339545 0.0911395083144135 0.8373241766323826 chr9 141213431 10911592 0.07727021376599794 0.7618758482847109 chr10 135534747 11791274 0.08699816291389838 0.7889572980458442 chr11 135006516 11612139 0.08601169294673155 0.8302296040723449 chr12 133851895 12200152 0.09114665130441374 0.8112321418659955 chr13 115169878 8519486 0.07397321372520686 0.7172260876734528 chr14 107349540 8111669 0.07556314633486087 0.7583344902803214 chr15 102531392 7526411 0.0734059184527603 0.6888777841151721 chr16 90354753 7520294 0.08323075156876363 0.7982776570857253 chr17 81195210 7092458 0.08735069470231065 0.7450034596655613 chr18 78077248 6723663 0.0861155224118555 0.7866379385191153 chr19 59128983 4828230 0.08165589453821656 0.768652943800191 chr20 63025520 5550132 0.08806166137145716 0.7746848613528514 chr21 48129895 3297982 0.06852252638406961 0.7414729379566075 chr22 51304566 2926167 0.057035215929903786 0.5723400695941206 chrMT 16571 51811 3.126606722587653 6.951579756904435 chrX 155270560 14907865 0.09601218028710658 0.8172582342869976 chrY 59373566 611530 0.010299701385630097 0.2251593548523308