BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163156.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 = 75,722,878 number of mapped reads = 73,619,340 (97.22%) number of supplementary alignments = 345,928 (0.46%) number of secondary alignments = 0 number of mapped bases = 7,194,422,933 bp number of sequenced bases = 7,193,578,202 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,214,578 duplication rate = 41.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1162 >>>>>>> ACTG content number of A's = 1,790,159,614 bp (24.89%) number of C's = 1,800,992,691 bp (25.04%) number of T's = 1,787,996,596 bp (24.86%) number of G's = 1,802,064,039 bp (25.05%) number of N's = 12,365,262 bp (0.17%) GC percentage = 50.09% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 46,164,768 number of insertions = 499,283 mapped reads with insertion percentage = 0.67% number of deletions = 361,331 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.86% >>>>>>> Coverage mean coverageData = 2.324X std coverageData = 27.5567X There is a 9.56% of reference with a coverageData >= 1X There is a 6.21% of reference with a coverageData >= 2X There is a 4.76% of reference with a coverageData >= 3X There is a 4.23% of reference with a coverageData >= 4X There is a 3.84% of reference with a coverageData >= 5X There is a 3.58% of reference with a coverageData >= 6X There is a 3.37% of reference with a coverageData >= 7X There is a 3.19% of reference with a coverageData >= 8X There is a 3.04% of reference with a coverageData >= 9X There is a 2.9% of reference with a coverageData >= 10X There is a 2.78% of reference with a coverageData >= 11X There is a 2.68% of reference with a coverageData >= 12X There is a 2.58% of reference with a coverageData >= 13X There is a 2.49% of reference with a coverageData >= 14X There is a 2.4% of reference with a coverageData >= 15X There is a 2.33% of reference with a coverageData >= 16X There is a 2.25% of reference with a coverageData >= 17X There is a 2.19% of reference with a coverageData >= 18X There is a 2.12% of reference with a coverageData >= 19X There is a 2.06% of reference with a coverageData >= 20X There is a 2.01% of reference with a coverageData >= 21X There is a 1.95% of reference with a coverageData >= 22X There is a 1.9% of reference with a coverageData >= 23X There is a 1.85% of reference with a coverageData >= 24X There is a 1.81% of reference with a coverageData >= 25X There is a 1.76% of reference with a coverageData >= 26X There is a 1.72% of reference with a coverageData >= 27X There is a 1.68% of reference with a coverageData >= 28X There is a 1.64% of reference with a coverageData >= 29X There is a 1.61% of reference with a coverageData >= 30X There is a 1.57% of reference with a coverageData >= 31X There is a 1.54% of reference with a coverageData >= 32X There is a 1.5% of reference with a coverageData >= 33X There is a 1.47% of reference with a coverageData >= 34X There is a 1.44% of reference with a coverageData >= 35X There is a 1.41% of reference with a coverageData >= 36X There is a 1.38% of reference with a coverageData >= 37X There is a 1.36% of reference with a coverageData >= 38X There is a 1.33% of reference with a coverageData >= 39X There is a 1.3% of reference with a coverageData >= 40X There is a 1.28% of reference with a coverageData >= 41X There is a 1.25% of reference with a coverageData >= 42X There is a 1.23% of reference with a coverageData >= 43X There is a 1.21% of reference with a coverageData >= 44X There is a 1.19% of reference with a coverageData >= 45X There is a 1.17% of reference with a coverageData >= 46X There is a 1.15% of reference with a coverageData >= 47X There is a 1.13% of reference with a coverageData >= 48X There is a 1.11% of reference with a coverageData >= 49X There is a 1.09% of reference with a coverageData >= 50X There is a 1.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 822497472 3.2998813351000638 38.92454156221638 chr2 243199373 495156034 2.0360086783611897 22.616343958888603 chr3 198022430 358031888 1.8080370390364364 20.188155554221535 chr4 191154276 256334846 1.340984106471152 22.573043467631027 chr5 180915260 329305259 1.8202182557734488 26.112241787099283 chr6 171115067 371174592 2.169152012779798 24.262964804047495 chr7 159138663 398957262 2.5069788477486457 32.410055783225964 chr8 146364022 320097857 2.1869982296605652 34.453531683975406 chr9 141213431 334493862 2.368711386950155 28.48258295123925 chr10 135534747 272852711 2.0131568991677096 21.22257076754542 chr11 135006516 366690132 2.7160921032878145 26.409508566590546 chr12 133851895 330538195 2.469432315470767 26.439543926712403 chr13 115169878 132232338 1.1481503696652349 15.608929126054385 chr14 107349540 190480210 1.7743924193806513 18.72071185805551 chr15 102531392 344824154 3.3631080908371946 35.33587359381765 chr16 90354753 249226638 2.7583124265748364 24.540012868555575 chr17 81195210 342295694 4.215712897349486 33.33985155524108 chr18 78077248 114265620 1.4634944612801926 17.14128856781482 chr19 59128983 407897915 6.898442934491196 47.78505282327637 chr20 63025520 157775343 2.5033564657618057 24.468278703872283 chr21 48129895 99885566 2.075333137543724 36.385846524449825 chr22 51304566 138539199 2.7003288362287288 25.01053528204042 chrMT 16571 981 0.059199806891557544 0.3383379552004722 chrX 155270560 352155825 2.268014136098949 26.16990799314166 chrY 59373566 8713340 0.14675453382739384 7.458390027727728