BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617502.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,208,719 (94.4%) number of supplementary alignments = 175,153 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,264,099 number of mapped paired reads (second in pair) = 14,944,620 number of mapped paired reads (both in pair) = 29,559,310 number of mapped paired reads (singletons) = 649,409 number of mapped bases = 2,933,358,127 bp number of sequenced bases = 2,931,617,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,206,990 duplication rate = 9.94% >>>>>>> Insert size mean insert size = 48,683.6587 std insert size = 2,082,880.0401 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.6227 >>>>>>> ACTG content number of A's = 865,396,087 bp (29.52%) number of C's = 591,540,326 bp (20.18%) number of T's = 865,028,626 bp (29.51%) number of G's = 606,639,546 bp (20.69%) number of N's = 3,012,732 bp (0.1%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 36,025,261 number of insertions = 439,623 mapped reads with insertion percentage = 1.43% number of deletions = 1,020,321 mapped reads with deletion percentage = 3.31% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.9476X std coverageData = 9.5099X There is a 37.99% of reference with a coverageData >= 1X There is a 20.39% of reference with a coverageData >= 2X There is a 11.46% of reference with a coverageData >= 3X There is a 6.78% of reference with a coverageData >= 4X There is a 4.17% of reference with a coverageData >= 5X There is a 2.67% of reference with a coverageData >= 6X There is a 1.76% of reference with a coverageData >= 7X There is a 1.2% of reference with a coverageData >= 8X There is a 0.84% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188972724 0.7581635032315527 9.257336663449538 chr2 243199373 302944774 1.245664288780876 11.240271229425002 chr3 198022430 241951046 1.2218365666960052 2.2375144345287006 chr4 191154276 151662467 0.7934034758395884 5.990121620505781 chr5 180915260 187815525 1.038140867718953 2.068286203830316 chr6 171115067 138226023 0.8077957448364264 5.225207190595936 chr7 159138663 226072922 1.4206033765660078 12.998952876885868 chr8 146364022 130393753 0.8908866483595265 3.831010059462733 chr9 141213431 121400867 0.8596977365417883 17.902345596666457 chr10 135534747 124544183 0.918909621014012 18.41406047010209 chr11 135006516 165286057 1.2242820709483386 12.365514811235649 chr12 133851895 128418695 0.9594088675397535 2.0859773039246208 chr13 115169878 124712669 1.082858392886376 2.162556950431974 chr14 107349540 85404861 0.7955773354967334 2.205545838179253 chr15 102531392 66501624 0.6485976899640649 1.6456409148805633 chr16 90354753 79144638 0.8759322046954188 14.59831925378695 chr17 81195210 81832604 1.0078501428840445 13.185809862750924 chr18 78077248 52585399 0.6735047705574868 16.618129101443067 chr19 59128983 35075908 0.5932100675568867 5.550884169077978 chr20 63025520 86582268 1.3737652303384407 2.7673513087950665 chr21 48129895 42105618 0.874832949458959 3.7183574691880827 chr22 51304566 21998899 0.42879027570372585 1.251864349769667 chrMT 16571 2071193 124.98901695733511 91.381960044992 chrX 155270560 137498483 0.8855412320275009 4.041481210166045 chrY 59373566 10154927 0.1710344802264361 13.400351900006514