BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083670.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 = 3,500,742 number of mapped reads = 2,632,012 (75.18%) number of supplementary alignments = 20,662 (0.59%) number of secondary alignments = 0 number of mapped bases = 153,948,754 bp number of sequenced bases = 153,904,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,953 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0001 >>>>>>> ACTG content number of A's = 44,979,720 bp (29.23%) number of C's = 31,573,946 bp (20.52%) number of T's = 43,927,651 bp (28.54%) number of G's = 33,404,118 bp (21.7%) number of N's = 19,366 bp (0.01%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,252,880 number of insertions = 9,847 mapped reads with insertion percentage = 0.37% number of deletions = 28,225 mapped reads with deletion percentage = 1.06% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.3984X There is a 4.16% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.11% 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% 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 14753334 0.059190761253910776 0.9164222860947357 chr2 243199373 15587495 0.06409348349759109 0.37146962075826273 chr3 198022430 13146166 0.06638725724151552 0.3029306569196395 chr4 191154276 6572103 0.034381145625013376 0.22540672014084398 chr5 180915260 7833291 0.0432981220047441 0.24151893035229027 chr6 171115067 10030059 0.05861587279161104 0.3379605995330508 chr7 159138663 9675513 0.06079926032808256 0.46264895615723356 chr8 146364022 12106200 0.08271294977122179 0.4665430395434355 chr9 141213431 6842391 0.04845425078581937 0.29272541481318937 chr10 135534747 6744926 0.04976529007723754 0.3397129978005821 chr11 135006516 5764033 0.042694480020505084 0.26019445728653834 chr12 133851895 6315119 0.04717989984377883 0.25158024703517756 chr13 115169878 5866329 0.050936313399585265 0.2598789131448974 chr14 107349540 2641178 0.02460353346646851 0.18398948868404558 chr15 102531392 3805014 0.037110722148393345 0.22520348886338268 chr16 90354753 4154175 0.045976275315588545 0.2571562478579846 chr17 81195210 2907094 0.03580376231553561 0.22723173481142558 chr18 78077248 4711282 0.06034129174224993 0.42226636673969503 chr19 59128983 3840443 0.06495026305458357 0.6088370052004791 chr20 63025520 2560237 0.04062222731363422 0.23887344562642224 chr21 48129895 1914814 0.0397842962258696 0.23550561327077532 chr22 51304566 942132 0.01836351173889669 0.15355757523586594 chrMT 16571 23664 1.4280369319896205 1.409565463933766 chrX 155270560 4904970 0.03158982617181261 0.22339178447358404 chrY 59373566 306792 0.0051671479526764486 0.10385592463256982