BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163091.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 = 83,375,384 number of mapped reads = 82,241,733 (98.64%) number of supplementary alignments = 349,099 (0.42%) number of secondary alignments = 0 number of mapped bases = 7,720,111,191 bp number of sequenced bases = 7,719,236,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,657,643 duplication rate = 48.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8396 >>>>>>> ACTG content number of A's = 1,858,753,045 bp (24.08%) number of C's = 2,001,058,071 bp (25.92%) number of T's = 1,839,027,384 bp (23.82%) number of G's = 2,020,096,832 bp (26.17%) number of N's = 300,737 bp (0%) GC percentage = 52.09% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 27,958,069 number of insertions = 473,455 mapped reads with insertion percentage = 0.57% number of deletions = 395,220 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 2.4938X std coverageData = 33.855X There is a 7.85% of reference with a coverageData >= 1X There is a 5.53% of reference with a coverageData >= 2X There is a 4.16% of reference with a coverageData >= 3X There is a 3.73% of reference with a coverageData >= 4X There is a 3.37% of reference with a coverageData >= 5X There is a 3.15% of reference with a coverageData >= 6X There is a 2.97% of reference with a coverageData >= 7X There is a 2.82% of reference with a coverageData >= 8X There is a 2.69% of reference with a coverageData >= 9X There is a 2.58% of reference with a coverageData >= 10X There is a 2.48% of reference with a coverageData >= 11X There is a 2.4% of reference with a coverageData >= 12X There is a 2.32% of reference with a coverageData >= 13X There is a 2.24% of reference with a coverageData >= 14X There is a 2.17% of reference with a coverageData >= 15X There is a 2.11% of reference with a coverageData >= 16X There is a 2.05% of reference with a coverageData >= 17X There is a 2% of reference with a coverageData >= 18X There is a 1.94% of reference with a coverageData >= 19X There is a 1.9% of reference with a coverageData >= 20X There is a 1.85% of reference with a coverageData >= 21X There is a 1.81% of reference with a coverageData >= 22X There is a 1.76% of reference with a coverageData >= 23X There is a 1.72% of reference with a coverageData >= 24X There is a 1.69% of reference with a coverageData >= 25X There is a 1.65% of reference with a coverageData >= 26X There is a 1.61% of reference with a coverageData >= 27X There is a 1.58% of reference with a coverageData >= 28X There is a 1.55% of reference with a coverageData >= 29X There is a 1.52% of reference with a coverageData >= 30X There is a 1.49% of reference with a coverageData >= 31X There is a 1.46% of reference with a coverageData >= 32X There is a 1.43% of reference with a coverageData >= 33X There is a 1.41% of reference with a coverageData >= 34X There is a 1.38% of reference with a coverageData >= 35X There is a 1.36% of reference with a coverageData >= 36X There is a 1.33% of reference with a coverageData >= 37X There is a 1.31% of reference with a coverageData >= 38X There is a 1.29% of reference with a coverageData >= 39X There is a 1.27% of reference with a coverageData >= 40X There is a 1.24% of reference with a coverageData >= 41X There is a 1.22% of reference with a coverageData >= 42X There is a 1.2% of reference with a coverageData >= 43X There is a 1.19% of reference with a coverageData >= 44X There is a 1.17% of reference with a coverageData >= 45X There is a 1.15% of reference with a coverageData >= 46X There is a 1.13% of reference with a coverageData >= 47X There is a 1.11% of reference with a coverageData >= 48X There is a 1.1% of reference with a coverageData >= 49X There is a 1.08% of reference with a coverageData >= 50X There is a 1.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1164335560 4.6713446703910115 49.30991087124213 chr2 243199373 326170720 1.3411659576934847 17.62932373439567 chr3 198022430 327533152 1.6540204662673819 21.673095514706926 chr4 191154276 171608997 0.8977512854590812 15.770562346858128 chr5 180915260 414088391 2.2888527534935417 34.299675948078836 chr6 171115067 457436609 2.6732690289628325 34.040575440527824 chr7 159138663 449895479 2.8270658463430727 35.05028628084396 chr8 146364022 416120827 2.843054060102284 61.486877299885904 chr9 141213431 352870479 2.4988450213351165 28.17817125013787 chr10 135534747 162800644 1.2011727442852718 14.831417121776065 chr11 135006516 436786317 3.2352980429477936 34.92895233441669 chr12 133851895 203711158 1.5219146355753872 19.063967215827454 chr13 115169878 116986030 1.0157693316302723 17.7098097084057 chr14 107349540 225991938 2.1051970786274445 24.548613449826348 chr15 102531392 344115463 3.356196149175464 31.122811103919386 chr16 90354753 339203565 3.754130842458282 35.06368762098142 chr17 81195210 229201380 2.8228436135579917 32.28160376505724 chr18 78077248 131533607 1.68465987684402 20.46475157023937 chr19 59128983 618972007 10.468165958477588 77.19654775130878 chr20 63025520 197459891 3.1330148644549065 36.12149655985354 chr21 48129895 112081590 2.328731238661543 54.566358845515595 chr22 51304566 93541422 1.8232572516060266 19.858293656969746 chrMT 16571 896 0.05407036388872126 0.3036153877199783 chrX 155270560 421330386 2.713523967453972 33.5253064918082 chrY 59373566 6334683 0.10669197467438624 6.1008058838935755