BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472767.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,422,146 number of mapped reads = 15,216,361 (98.67%) number of supplementary alignments = 51,608 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,658,776 number of mapped paired reads (second in pair) = 7,557,585 number of mapped paired reads (both in pair) = 15,080,736 number of mapped paired reads (singletons) = 135,625 number of mapped bases = 1,499,640,807 bp number of sequenced bases = 1,499,416,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,300,452 duplication rate = 47.24% >>>>>>> Insert size mean insert size = 24,854.3867 std insert size = 1,573,265.931 median insert size = 252 >>>>>>> Mapping quality mean mapping quality = 55.2428 >>>>>>> ACTG content number of A's = 419,458,580 bp (27.97%) number of C's = 332,092,394 bp (22.15%) number of T's = 417,305,594 bp (27.83%) number of G's = 330,268,391 bp (22.03%) number of N's = 291,263 bp (0.02%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 9,662,687 number of insertions = 92,599 mapped reads with insertion percentage = 0.6% number of deletions = 90,925 mapped reads with deletion percentage = 0.59% homopolymer indels = 44.97% >>>>>>> Coverage mean coverageData = 0.4844X std coverageData = 15.6527X There is a 4.29% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 169497115 0.6800268513674034 20.80526867527451 chr2 243199373 116849702 0.4804687633795832 19.857662258637507 chr3 198022430 186801550 0.9433353080254595 20.730372289638588 chr4 191154276 65905931 0.3447787430086053 15.752093444351349 chr5 180915260 81900820 0.4527026631142116 13.687735355634146 chr6 171115067 108512437 0.6341489320750463 16.592825511987847 chr7 159138663 66928185 0.42056520859421825 11.859399010144008 chr8 146364022 59202247 0.4044863361297901 11.36560110500524 chr9 141213431 72431751 0.512923951263531 13.185223423986258 chr10 135534747 34585034 0.2551746674968892 7.697418459724418 chr11 135006516 58956714 0.43669532217244983 16.360692354119106 chr12 133851895 87949155 0.6570632040734276 20.157584545480766 chr13 115169878 36141800 0.31381295723869745 12.571587904060014 chr14 107349540 36707829 0.34194677499316717 16.55385802478074 chr15 102531392 40455219 0.3945642228284582 12.719108163987631 chr16 90354753 48821813 0.5403347513992983 15.30803584289127 chr17 81195210 62543783 0.770289072471147 20.625728269203044 chr18 78077248 23046891 0.2951806267556971 10.222362639935469 chr19 59128983 24913103 0.42133488073014885 9.378846224965924 chr20 63025520 29219403 0.4636122478640398 12.242245590808272 chr21 48129895 6399861 0.13297059966575867 4.765621175848422 chr22 51304566 16066017 0.3131498471305653 10.159423318874934 chrMT 16571 4733 0.28561945567557784 0.9349846105475029 chrX 155270560 59583327 0.38373872677473436 12.704355613506635 chrY 59373566 6216387 0.10469957287052625 6.444409405938086