BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081027.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 = 2,595,399 number of mapped reads = 1,987,020 (76.56%) number of supplementary alignments = 8,669 (0.33%) number of secondary alignments = 0 number of mapped bases = 123,395,073 bp number of sequenced bases = 123,353,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,255 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3248 >>>>>>> ACTG content number of A's = 35,627,010 bp (28.88%) number of C's = 24,706,186 bp (20.03%) number of T's = 35,631,712 bp (28.89%) number of G's = 27,386,611 bp (22.2%) number of N's = 1,663 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 986,979 number of insertions = 8,592 mapped reads with insertion percentage = 0.43% number of deletions = 24,743 mapped reads with deletion percentage = 1.23% homopolymer indels = 45.05% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.3402X There is a 3.52% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9764277 0.039174534293336824 0.5099527250259508 chr2 243199373 9519234 0.03914168808321722 0.3651761804208582 chr3 198022430 8576691 0.043311714738577846 0.22791089200194842 chr4 191154276 8156965 0.04267215555251299 0.23987802258103244 chr5 180915260 7494668 0.04142640040425556 0.2251172435216781 chr6 171115067 7309720 0.04271815526332348 0.31117373249571567 chr7 159138663 7442888 0.04676982864937102 0.6727606631557076 chr8 146364022 5278125 0.036061628587932625 0.3147527471405024 chr9 141213431 5254573 0.03721015035744015 0.3121812831263594 chr10 135534747 5492761 0.040526589096742845 0.28931005657095027 chr11 135006516 5612136 0.04156937136278667 0.3136959489250439 chr12 133851895 5646533 0.04218493133772966 0.2286053090061895 chr13 115169878 4195906 0.03643232130540244 0.20960094426233594 chr14 107349540 3680411 0.03428436675182772 0.220783359099666 chr15 102531392 3778035 0.03684759297913365 0.2244175749777146 chr16 90354753 3829891 0.042387266555861204 0.24707527558788442 chr17 81195210 3063063 0.037724676123135834 0.24325871472864577 chr18 78077248 3607854 0.046208775186338535 0.5785961629309365 chr19 59128983 2310932 0.039082897806647546 0.40137019766742393 chr20 63025520 2604999 0.04133244755457789 0.2312418675146101 chr21 48129895 1507529 0.03132209201786125 0.2091350783018715 chr22 51304566 1301576 0.025369593809642595 0.17421769917372484 chrMT 16571 11360 0.6855349707320016 0.9776657703941617 chrX 155270560 7621685 0.049086478467006235 0.28529515333358835 chrY 59373566 333261 0.00561295240376837 0.1251306146211655