BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153314.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 147,553,632 number of mapped reads = 143,160,278 (97.02%) number of supplementary alignments = 932,835 (0.63%) number of secondary alignments = 0 number of mapped bases = 14,092,340,744 bp number of sequenced bases = 14,090,665,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,900,735 duplication rate = 53.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.457 >>>>>>> ACTG content number of A's = 3,189,277,977 bp (22.63%) number of C's = 3,859,002,037 bp (27.39%) number of T's = 3,196,991,389 bp (22.69%) number of G's = 3,830,039,595 bp (27.18%) number of N's = 15,354,020 bp (0.11%) GC percentage = 54.57% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 88,238,613 number of insertions = 584,962 mapped reads with insertion percentage = 0.4% number of deletions = 654,276 mapped reads with deletion percentage = 0.45% homopolymer indels = 40.67% >>>>>>> Coverage mean coverageData = 4.5522X std coverageData = 55.9808X There is a 12.02% of reference with a coverageData >= 1X There is a 7.91% of reference with a coverageData >= 2X There is a 5.96% of reference with a coverageData >= 3X There is a 5.3% of reference with a coverageData >= 4X There is a 4.81% of reference with a coverageData >= 5X There is a 4.52% of reference with a coverageData >= 6X There is a 4.28% of reference with a coverageData >= 7X There is a 4.1% of reference with a coverageData >= 8X There is a 3.94% of reference with a coverageData >= 9X There is a 3.81% of reference with a coverageData >= 10X There is a 3.69% of reference with a coverageData >= 11X There is a 3.58% of reference with a coverageData >= 12X There is a 3.48% of reference with a coverageData >= 13X There is a 3.39% of reference with a coverageData >= 14X There is a 3.3% of reference with a coverageData >= 15X There is a 3.22% of reference with a coverageData >= 16X There is a 3.15% of reference with a coverageData >= 17X There is a 3.08% of reference with a coverageData >= 18X There is a 3.01% of reference with a coverageData >= 19X There is a 2.95% of reference with a coverageData >= 20X There is a 2.89% of reference with a coverageData >= 21X There is a 2.84% of reference with a coverageData >= 22X There is a 2.78% of reference with a coverageData >= 23X There is a 2.73% of reference with a coverageData >= 24X There is a 2.68% of reference with a coverageData >= 25X There is a 2.63% of reference with a coverageData >= 26X There is a 2.59% of reference with a coverageData >= 27X There is a 2.54% of reference with a coverageData >= 28X There is a 2.5% of reference with a coverageData >= 29X There is a 2.46% of reference with a coverageData >= 30X There is a 2.42% of reference with a coverageData >= 31X There is a 2.38% of reference with a coverageData >= 32X There is a 2.34% of reference with a coverageData >= 33X There is a 2.31% of reference with a coverageData >= 34X There is a 2.27% of reference with a coverageData >= 35X There is a 2.24% of reference with a coverageData >= 36X There is a 2.2% of reference with a coverageData >= 37X There is a 2.17% of reference with a coverageData >= 38X There is a 2.14% of reference with a coverageData >= 39X There is a 2.11% of reference with a coverageData >= 40X There is a 2.08% of reference with a coverageData >= 41X There is a 2.05% of reference with a coverageData >= 42X There is a 2.02% of reference with a coverageData >= 43X There is a 2% of reference with a coverageData >= 44X There is a 1.97% of reference with a coverageData >= 45X There is a 1.94% of reference with a coverageData >= 46X There is a 1.92% of reference with a coverageData >= 47X There is a 1.89% of reference with a coverageData >= 48X There is a 1.87% of reference with a coverageData >= 49X There is a 1.85% of reference with a coverageData >= 50X There is a 1.82% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1401548591 5.62304954497987 56.32321931501751 chr2 243199373 661456712 2.7198125712273113 27.859012055292204 chr3 198022430 633544874 3.1993591534049957 34.49689525368221 chr4 191154276 353447701 1.8490180203973046 32.95364975122595 chr5 180915260 781255765 4.318351945546219 91.53756400377236 chr6 171115067 331039619 1.9346023982797493 22.460562999687077 chr7 159138663 790854489 4.969593649281822 68.86024330214941 chr8 146364022 743118901 5.077196505299643 82.14726566643901 chr9 141213431 347081483 2.457850365522243 24.3410192791068 chr10 135534747 586130170 4.324574937229934 42.344557876519005 chr11 135006516 733478781 5.432913926910016 46.244849382246976 chr12 133851895 580421798 4.336298697900392 36.689938933631254 chr13 115169878 102376247 0.8889151293535277 12.572171685663319 chr14 107349540 309946523 2.8872645658286005 29.41950540002801 chr15 102531392 815222494 7.950955098707721 68.97577219319737 chr16 90354753 891613297 9.867918038578447 84.93317823761149 chr17 81195210 919041729 11.318915598592577 77.89923247590423 chr18 78077248 94043713 1.2044957450344562 15.644568333188355 chr19 59128983 1262886069 21.358156439118865 109.36495273673464 chr20 63025520 418890491 6.646363108150476 54.80430022119953 chr21 48129895 225730521 4.690027289691781 141.29563120622714 chr22 51304566 445903428 8.691301043263868 66.58028258161453 chrMT 16571 2902 0.17512521875565748 0.5074894167634566 chrX 155270560 650436461 4.189052071429381 40.057621202271484 chrY 59373566 12867985 0.2167291922469336 11.683449077909746