BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081949.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 = 3,157,668 number of mapped reads = 2,908,153 (92.1%) number of supplementary alignments = 18,653 (0.59%) number of secondary alignments = 0 number of mapped bases = 199,709,669 bp number of sequenced bases = 199,633,860 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,037 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5986 >>>>>>> ACTG content number of A's = 57,191,789 bp (28.65%) number of C's = 36,722,051 bp (18.39%) number of T's = 63,409,229 bp (31.76%) number of G's = 42,285,101 bp (21.18%) number of N's = 25,690 bp (0.01%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,527,452 number of insertions = 14,312 mapped reads with insertion percentage = 0.49% number of deletions = 42,766 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.31% >>>>>>> Coverage mean coverageData = 0.0645X std coverageData = 0.54X There is a 5.34% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.14% 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 0.01% 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 16915109 0.06786385900318379 0.9008158330728608 chr2 243199373 16267662 0.06689023001716374 0.7859996853416888 chr3 198022430 13235874 0.06684027662926871 0.305110017537799 chr4 191154276 10358899 0.05419130148048584 0.2919721936196291 chr5 180915260 11843359 0.06546357117691454 0.29817775258184986 chr6 171115067 18025926 0.10534388535172066 0.48146502308068717 chr7 159138663 13217103 0.08305400303633316 0.567361064904629 chr8 146364022 11221475 0.07666826072871925 0.8267341047261128 chr9 141213431 11427915 0.08092654444462864 0.6166202015103467 chr10 135534747 7762669 0.057274382930009825 0.5477683542618291 chr11 135006516 8696484 0.06441529088862644 0.4060583016969514 chr12 133851895 8152650 0.060907990880517605 0.30135712603557446 chr13 115169878 6077593 0.05277068193125984 0.2624788049754703 chr14 107349540 4639727 0.04322074412242474 0.27858324934507234 chr15 102531392 4381002 0.04272839678212893 0.23737433201939653 chr16 90354753 4241406 0.04694170322174419 0.310934011598373 chr17 81195210 5837421 0.07189366220002387 0.3418456853424205 chr18 78077248 6672994 0.08546656255097516 0.9365906037441276 chr19 59128983 2500348 0.04228633528163338 0.7537965626705041 chr20 63025520 4888603 0.07756545285147985 0.3334722849702851 chr21 48129895 2294887 0.04768111378593284 0.28114098957704015 chr22 51304566 1704226 0.033217823146579194 0.20576742403688866 chrMT 16571 230376 13.902359543781305 7.508352958477888 chrX 155270560 8697148 0.05601285910220199 0.33741715708464226 chrY 59373566 418813 0.007053862993507919 0.1649530881050847