BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818959.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,929,154 number of mapped reads = 2,888,976 (98.63%) number of supplementary alignments = 37,927 (1.29%) number of secondary alignments = 0 number of mapped bases = 267,722,030 bp number of sequenced bases = 267,568,125 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,468,353 duplication rate = 39.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3248 >>>>>>> ACTG content number of A's = 74,840,570 bp (27.97%) number of C's = 55,188,821 bp (20.63%) number of T's = 77,820,034 bp (29.08%) number of G's = 59,707,960 bp (22.32%) number of N's = 10,740 bp (0%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,691,434 number of insertions = 36,953 mapped reads with insertion percentage = 1.24% number of deletions = 83,308 mapped reads with deletion percentage = 2.82% homopolymer indels = 41.14% >>>>>>> Coverage mean coverageData = 0.0865X std coverageData = 0.9926X There is a 3.45% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 31259259 0.1254129633642919 1.6242090379339293 chr2 243199373 23744221 0.09763273937387988 1.5866896931827312 chr3 198022430 17898410 0.0903857709452409 0.6399435144915564 chr4 191154276 16947387 0.08865816321053681 0.6972889157496247 chr5 180915260 14414379 0.07967475491011648 0.629620650872852 chr6 171115067 14215275 0.08307436188538558 0.6790710821261917 chr7 159138663 13438699 0.08444647420470033 0.7517868639278569 chr8 146364022 17151903 0.11718660614560045 0.8425860920204415 chr9 141213431 9951267 0.07046969207907709 1.057078712902305 chr10 135534747 13084096 0.09653683863076086 1.214104042903494 chr11 135006516 12026620 0.08908177439376333 0.7584253508488444 chr12 133851895 11991112 0.08958492518914282 0.6586249151979197 chr13 115169878 4214287 0.036591920328334464 0.4009958709452036 chr14 107349540 5723621 0.053317610862608264 0.5626706586098847 chr15 102531392 7713161 0.07522731184611246 0.5975949803681034 chr16 90354753 8212334 0.09088989485699772 1.2017203471763662 chr17 81195210 6026556 0.07422304837933173 0.6588990026282471 chr18 78077248 6632159 0.08494355487529479 1.333269231894767 chr19 59128983 4351649 0.07359587091156294 1.4709771691618252 chr20 63025520 5856374 0.09292067721138993 0.7102278476310677 chr21 48129895 3521638 0.07316945112803591 0.6542193644335002 chr22 51304566 3314814 0.06461050659701517 0.6045715239302484 chrMT 16571 14475 0.8735139701888842 2.0082184860558003 chrX 155270560 15161572 0.09764614747315911 0.7778334940707836 chrY 59373566 856762 0.014430024297344714 1.160909325480857