BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080793.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,411,839 number of mapped reads = 2,175,645 (90.21%) number of supplementary alignments = 22,181 (0.92%) number of secondary alignments = 0 number of mapped bases = 142,750,930 bp number of sequenced bases = 142,700,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,113 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2356 >>>>>>> ACTG content number of A's = 41,470,749 bp (29.06%) number of C's = 27,542,652 bp (19.3%) number of T's = 43,455,109 bp (30.45%) number of G's = 30,228,812 bp (21.18%) number of N's = 2,768 bp (0%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,094,234 number of insertions = 11,002 mapped reads with insertion percentage = 0.5% number of deletions = 32,312 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.3749X There is a 3.78% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 18848524 0.0756207704694144 0.7628179286019535 chr2 243199373 10494577 0.04315215483717551 0.38528314738031794 chr3 198022430 7798172 0.039380245965065674 0.2361749408409118 chr4 191154276 6679607 0.03494353953138877 0.2256571515425755 chr5 180915260 11017462 0.060898467050264304 0.29171256713189275 chr6 171115067 9795161 0.05724312400847788 0.3368303333055924 chr7 159138663 9502057 0.05970929264373674 0.43393311362528053 chr8 146364022 5548229 0.03790705478153641 0.45156173586959797 chr9 141213431 4490729 0.03180100482085164 0.2549719641400496 chr10 135534747 6789169 0.05009172297344533 0.3799605416507822 chr11 135006516 6850954 0.0507453580981232 0.33911271415830907 chr12 133851895 6091440 0.0455088065805867 0.2521610730667686 chr13 115169878 6432680 0.05585384053285183 0.28048562228182616 chr14 107349540 3576104 0.03331270911826916 0.22406123148971177 chr15 102531392 3747486 0.03654964520524602 0.22863547263292358 chr16 90354753 3257621 0.036053676113751314 0.23644317204493298 chr17 81195210 3996256 0.04921787873939854 0.29283342473571383 chr18 78077248 1935813 0.024793560859112246 0.4241900324807422 chr19 59128983 1974164 0.033387416793554524 0.5461709631641165 chr20 63025520 2755085 0.04371380037800561 0.25306364182771435 chr21 48129895 2487670 0.05168658689157747 0.27259201878398426 chr22 51304566 875606 0.017066824032777123 0.14919554996000836 chrMT 16571 23763 1.434011224428218 1.540483394637348 chrX 155270560 7495479 0.04827366501415336 0.2799979985109246 chrY 59373566 287122 0.004835855740920126 0.09556476081967556