BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081957.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 = 2,704,699 number of mapped reads = 2,463,977 (91.1%) number of supplementary alignments = 15,209 (0.56%) number of secondary alignments = 0 number of mapped bases = 171,045,489 bp number of sequenced bases = 170,974,664 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,361 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.842 >>>>>>> ACTG content number of A's = 49,315,080 bp (28.84%) number of C's = 31,999,846 bp (18.72%) number of T's = 53,565,751 bp (31.33%) number of G's = 36,071,860 bp (21.1%) number of N's = 22,127 bp (0.01%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,365,052 number of insertions = 13,100 mapped reads with insertion percentage = 0.53% number of deletions = 39,726 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0553X std coverageData = 0.5488X There is a 4.69% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 15610288 0.0626288830790917 0.9631160274822516 chr2 243199373 15476798 0.06363831373858024 0.8475052970098836 chr3 198022430 10813931 0.054609626798337946 0.2648084959179564 chr4 191154276 7123897 0.03726778782599663 0.25201594832965624 chr5 180915260 8728218 0.04824478598433322 0.25539096958441687 chr6 171115067 15310676 0.08947590804496486 0.42577602339618825 chr7 159138663 11162410 0.07014266545647678 0.5779017635668814 chr8 146364022 10285337 0.0702723036676322 0.80403356276108 chr9 141213431 8669449 0.061392524341399225 0.6681952891671494 chr10 135534747 6702851 0.04945485307911483 0.4740332181506443 chr11 135006516 7710630 0.057113021122624924 0.4341169585885614 chr12 133851895 7353121 0.05493475456585803 0.2837942782876152 chr13 115169878 4418924 0.03836874777274662 0.21904124716150383 chr14 107349540 4680891 0.043604201750654915 0.284047767477766 chr15 102531392 3763370 0.036704563613063984 0.21589775999728206 chr16 90354753 3392653 0.03754814093731184 0.29668992998280436 chr17 81195210 4783311 0.05891124611907525 0.3080799846349332 chr18 78077248 5161456 0.06610704311709348 1.0439773409200934 chr19 59128983 3511040 0.05937934024672807 0.6509871779864139 chr20 63025520 4692129 0.0744480807139711 0.3184148939574531 chr21 48129895 1978833 0.0411144258677481 0.2788137185235206 chr22 51304566 1414192 0.027564642102225364 0.1842059776511307 chrMT 16571 214925 12.969947498642206 7.825249720028765 chrX 155270560 7696420 0.049567799588022356 0.32877407395404934 chrY 59373566 389739 0.006564183798561131 0.18553596982691592