BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153381.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 = 81,611,374 number of mapped reads = 81,064,562 (99.33%) number of supplementary alignments = 424,748 (0.52%) number of secondary alignments = 0 number of mapped bases = 7,891,598,481 bp number of sequenced bases = 7,890,770,837 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,604,964 duplication rate = 45.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6456 >>>>>>> ACTG content number of A's = 1,951,037,107 bp (24.73%) number of C's = 1,992,757,243 bp (25.25%) number of T's = 1,948,057,829 bp (24.69%) number of G's = 1,997,858,961 bp (25.32%) number of N's = 1,059,697 bp (0.01%) GC percentage = 50.57% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 22,442,946 number of insertions = 560,909 mapped reads with insertion percentage = 0.68% number of deletions = 359,862 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 2.5492X std coverageData = 41.3595X There is a 8.95% of reference with a coverageData >= 1X There is a 5.92% of reference with a coverageData >= 2X There is a 4.22% of reference with a coverageData >= 3X There is a 3.71% of reference with a coverageData >= 4X There is a 3.3% of reference with a coverageData >= 5X There is a 3.07% of reference with a coverageData >= 6X There is a 2.87% of reference with a coverageData >= 7X There is a 2.72% of reference with a coverageData >= 8X There is a 2.59% of reference with a coverageData >= 9X There is a 2.48% of reference with a coverageData >= 10X There is a 2.38% of reference with a coverageData >= 11X There is a 2.3% of reference with a coverageData >= 12X There is a 2.22% of reference with a coverageData >= 13X There is a 2.14% of reference with a coverageData >= 14X There is a 2.08% of reference with a coverageData >= 15X There is a 2.02% of reference with a coverageData >= 16X There is a 1.96% of reference with a coverageData >= 17X There is a 1.91% of reference with a coverageData >= 18X There is a 1.85% of reference with a coverageData >= 19X There is a 1.81% of reference with a coverageData >= 20X There is a 1.76% of reference with a coverageData >= 21X There is a 1.72% of reference with a coverageData >= 22X There is a 1.68% of reference with a coverageData >= 23X There is a 1.64% of reference with a coverageData >= 24X There is a 1.61% of reference with a coverageData >= 25X There is a 1.57% of reference with a coverageData >= 26X There is a 1.54% of reference with a coverageData >= 27X There is a 1.51% of reference with a coverageData >= 28X There is a 1.48% of reference with a coverageData >= 29X There is a 1.45% of reference with a coverageData >= 30X There is a 1.42% of reference with a coverageData >= 31X There is a 1.39% of reference with a coverageData >= 32X There is a 1.37% of reference with a coverageData >= 33X There is a 1.34% of reference with a coverageData >= 34X There is a 1.32% of reference with a coverageData >= 35X There is a 1.3% of reference with a coverageData >= 36X There is a 1.27% of reference with a coverageData >= 37X There is a 1.25% of reference with a coverageData >= 38X There is a 1.23% of reference with a coverageData >= 39X There is a 1.21% of reference with a coverageData >= 40X There is a 1.19% of reference with a coverageData >= 41X There is a 1.17% of reference with a coverageData >= 42X There is a 1.15% of reference with a coverageData >= 43X There is a 1.14% of reference with a coverageData >= 44X There is a 1.12% of reference with a coverageData >= 45X There is a 1.1% of reference with a coverageData >= 46X There is a 1.08% of reference with a coverageData >= 47X There is a 1.07% of reference with a coverageData >= 48X There is a 1.05% of reference with a coverageData >= 49X There is a 1.04% of reference with a coverageData >= 50X There is a 1.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1269880140 5.094792281380113 55.783584734948356 chr2 243199373 259164839 1.065647644576781 17.742430212198347 chr3 198022430 170406368 0.8605407377335992 14.46163049304896 chr4 191154276 412660222 2.1587810151837776 41.033547969938404 chr5 180915260 393507119 2.1750908077074316 31.479403714063597 chr6 171115067 206579138 1.2072527663504933 19.12394723102972 chr7 159138663 403575225 2.535997333344443 40.748824003549544 chr8 146364022 751213555 5.132501449024132 111.33144898639425 chr9 141213431 312135004 2.2103775950320195 27.86539600100883 chr10 135534747 444231577 3.277621324662966 34.734872155123476 chr11 135006516 101590341 0.7524847245150745 13.051206467996876 chr12 133851895 213131839 1.5922960149350145 25.74053931625451 chr13 115169878 79013128 0.6860572345140454 13.127650636713168 chr14 107349540 270269503 2.5176586970004715 27.08880449261707 chr15 102531392 466582230 4.55062806520758 39.205764396143216 chr16 90354753 453633579 5.0205834661514706 47.483715332668005 chr17 81195210 216255368 2.66340056266866 37.881191875325044 chr18 78077248 117800882 1.5087734905820451 21.324064254620808 chr19 59128983 405079315 6.8507742641201865 57.191776895242256 chr20 63025520 152727256 2.423260545886809 24.87760974725491 chr21 48129895 142880877 2.9686513340617093 65.11496300722285 chr22 51304566 80856259 1.5760051259375238 18.80135617416796 chrMT 16571 977 0.05895842133848289 0.391000507106292 chrX 155270560 560643516 3.6107521992578633 43.7649883619296 chrY 59373566 7780224 0.13103851636602054 7.324128933218223