BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153393.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 = 87,261,464 number of mapped reads = 86,611,710 (99.26%) number of supplementary alignments = 464,297 (0.53%) number of secondary alignments = 0 number of mapped bases = 8,371,049,189 bp number of sequenced bases = 8,370,162,729 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,139,901 duplication rate = 46.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0088 >>>>>>> ACTG content number of A's = 2,064,079,003 bp (24.66%) number of C's = 2,119,641,367 bp (25.32%) number of T's = 2,057,080,418 bp (24.58%) number of G's = 2,128,250,778 bp (25.43%) number of N's = 1,111,163 bp (0.01%) GC percentage = 50.75% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 23,686,655 number of insertions = 604,731 mapped reads with insertion percentage = 0.69% number of deletions = 393,280 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 2.7041X std coverageData = 39.9519X There is a 9.49% of reference with a coverageData >= 1X There is a 6.42% of reference with a coverageData >= 2X There is a 4.64% of reference with a coverageData >= 3X There is a 4.11% of reference with a coverageData >= 4X There is a 3.67% of reference with a coverageData >= 5X There is a 3.42% of reference with a coverageData >= 6X There is a 3.21% of reference with a coverageData >= 7X There is a 3.05% of reference with a coverageData >= 8X There is a 2.91% of reference with a coverageData >= 9X There is a 2.79% of reference with a coverageData >= 10X There is a 2.68% of reference with a coverageData >= 11X There is a 2.58% of reference with a coverageData >= 12X There is a 2.49% of reference with a coverageData >= 13X There is a 2.41% of reference with a coverageData >= 14X There is a 2.34% of reference with a coverageData >= 15X There is a 2.27% of reference with a coverageData >= 16X There is a 2.2% of reference with a coverageData >= 17X There is a 2.14% of reference with a coverageData >= 18X There is a 2.09% of reference with a coverageData >= 19X There is a 2.03% of reference with a coverageData >= 20X There is a 1.98% of reference with a coverageData >= 21X There is a 1.93% of reference with a coverageData >= 22X There is a 1.89% of reference with a coverageData >= 23X There is a 1.85% of reference with a coverageData >= 24X There is a 1.8% of reference with a coverageData >= 25X There is a 1.76% of reference with a coverageData >= 26X There is a 1.73% of reference with a coverageData >= 27X There is a 1.69% of reference with a coverageData >= 28X There is a 1.66% of reference with a coverageData >= 29X There is a 1.62% of reference with a coverageData >= 30X There is a 1.59% of reference with a coverageData >= 31X There is a 1.56% of reference with a coverageData >= 32X There is a 1.53% of reference with a coverageData >= 33X There is a 1.5% of reference with a coverageData >= 34X There is a 1.47% of reference with a coverageData >= 35X There is a 1.45% of reference with a coverageData >= 36X There is a 1.42% of reference with a coverageData >= 37X There is a 1.4% of reference with a coverageData >= 38X There is a 1.37% of reference with a coverageData >= 39X There is a 1.35% of reference with a coverageData >= 40X There is a 1.33% of reference with a coverageData >= 41X There is a 1.3% of reference with a coverageData >= 42X There is a 1.28% of reference with a coverageData >= 43X There is a 1.26% of reference with a coverageData >= 44X There is a 1.24% of reference with a coverageData >= 45X There is a 1.22% of reference with a coverageData >= 46X There is a 1.2% of reference with a coverageData >= 47X There is a 1.19% of reference with a coverageData >= 48X There is a 1.17% of reference with a coverageData >= 49X There is a 1.15% of reference with a coverageData >= 50X There is a 1.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 900626153 3.613335643404475 38.14426695302006 chr2 243199373 551786689 2.2688655903730477 26.506703155577277 chr3 198022430 415508530 2.098290229041225 28.917988154969414 chr4 191154276 296900727 1.5531995057228016 24.099839710684964 chr5 180915260 444818051 2.4587094035074766 59.17961587789379 chr6 171115067 408659504 2.38821461584093 29.983619488187443 chr7 159138663 406594067 2.5549672174888136 33.531083830706216 chr8 146364022 519639656 3.5503236990850113 97.7740864799936 chr9 141213431 376729664 2.6678033479690755 31.0696216421267 chr10 135534747 307746294 2.27060809727265 24.374970784061816 chr11 135006516 434246081 3.2164823881537687 33.231144014575875 chr12 133851895 411757654 3.076218338186396 33.84442811430907 chr13 115169878 138601173 1.2034498551782784 16.801047047105328 chr14 107349540 193629579 1.8037299368027102 22.584284021004624 chr15 102531392 348375367 3.3977434637774158 34.799847041458065 chr16 90354753 306273394 3.38967662276715 33.46708264054593 chr17 81195210 394970313 4.864453371079402 43.22178341250281 chr18 78077248 121904686 1.561334308299391 21.78503090470975 chr19 59128983 487343821 8.242046392037556 65.35049074626852 chr20 63025520 173553288 2.753698628745943 28.123045312183457 chr21 48129895 97560414 2.0270232046007997 31.30275730860826 chr22 51304566 177484594 3.4594307648952727 34.569648498812825 chrMT 16571 6173 0.37251825478245126 0.7726014297405207 chrX 155270560 449498644 2.894937997261039 45.89167488082493 chrY 59373566 6834673 0.11511306226747438 7.160676882001971