BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080820.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 = 3,024,619 number of mapped reads = 2,773,771 (91.71%) number of supplementary alignments = 18,754 (0.62%) number of secondary alignments = 0 number of mapped bases = 190,408,225 bp number of sequenced bases = 190,329,174 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,912 duplication rate = 4.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.871 >>>>>>> ACTG content number of A's = 54,375,416 bp (28.57%) number of C's = 35,525,654 bp (18.67%) number of T's = 60,101,775 bp (31.58%) number of G's = 40,299,363 bp (21.17%) number of N's = 26,966 bp (0.01%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,598,170 number of insertions = 14,362 mapped reads with insertion percentage = 0.51% number of deletions = 44,937 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.37% >>>>>>> Coverage mean coverageData = 0.0615X std coverageData = 0.5504X There is a 4.8% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 24065560 0.0965516551310819 1.2533269644627192 chr2 243199373 13983214 0.05749691632634267 0.43987978188647864 chr3 198022430 11720025 0.059185340771749945 0.30777845639652734 chr4 191154276 11401034 0.05964310209832816 0.3153588752810675 chr5 180915260 15478754 0.0855580341868342 0.3543025701979049 chr6 171115067 13805496 0.08067960491170541 0.49531484679357535 chr7 159138663 13522812 0.08497502583643046 0.7271775715113264 chr8 146364022 8341014 0.05698814425856649 0.6865637668965056 chr9 141213431 5137242 0.03637927330014381 0.32698777061930934 chr10 135534747 8083681 0.05964286781750513 0.5911407908227645 chr11 135006516 7461404 0.055266991705792926 0.3412824637231048 chr12 133851895 7195935 0.05376042677617676 0.28494508552352754 chr13 115169878 8130989 0.07059996191017932 0.32339044072965223 chr14 107349540 4929299 0.04591821259783693 0.27521433866360684 chr15 102531392 4627063 0.0451282569147213 0.25627510951722376 chr16 90354753 4312274 0.047726033847937145 0.3126641584245821 chr17 81195210 4828811 0.05947162400343567 0.3162158835246602 chr18 78077248 2501956 0.03204462329409971 0.6528963926380802 chr19 59128983 3032460 0.05128550917237998 0.8662575237011254 chr20 63025520 3337788 0.05295930918142365 0.287528647472809 chr21 48129895 3071935 0.06382592357618898 0.3287908953823362 chr22 51304566 965724 0.018823353851195233 0.16134289425536266 chrMT 16571 106482 6.42580411562368 4.57035402536634 chrX 155270560 9901922 0.06377205054197009 0.33288054678126305 chrY 59373566 465351 0.007837679818658695 0.19011166696218745