BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013260.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,757,067 number of mapped reads = 1,474,727 (83.93%) number of supplementary alignments = 9,200 (0.52%) number of secondary alignments = 0 number of mapped bases = 95,922,208 bp number of sequenced bases = 95,871,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,517 duplication rate = 6.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.122 >>>>>>> ACTG content number of A's = 26,256,452 bp (27.39%) number of C's = 16,801,654 bp (17.53%) number of T's = 31,562,893 bp (32.92%) number of G's = 21,249,317 bp (22.16%) number of N's = 1,336 bp (0%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 789,458 number of insertions = 7,103 mapped reads with insertion percentage = 0.48% number of deletions = 28,835 mapped reads with deletion percentage = 1.93% homopolymer indels = 49.86% >>>>>>> Coverage mean coverageData = 0.031X std coverageData = 0.3532X There is a 2.25% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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% 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 6519688 0.026157158501121647 0.4712605085657599 chr2 243199373 11027754 0.045344500127473604 0.41621117101693594 chr3 198022430 6907452 0.034882169661285344 0.2433288742058443 chr4 191154276 8236161 0.0430864596510517 0.28041879039046236 chr5 180915260 3876885 0.02142928683849002 0.18957729487168573 chr6 171115067 4863063 0.0284198410184417 0.26855312429401085 chr7 159138663 6553768 0.04118275142226123 0.7383136857429267 chr8 146364022 6938269 0.0474041974604934 0.5393458926851389 chr9 141213431 3117794 0.02207859392638084 0.2793556809463221 chr10 135534747 3335332 0.024608685771184566 0.3280284008427383 chr11 135006516 3980501 0.02948376950931761 0.27191927129781573 chr12 133851895 4308064 0.03218530451137804 0.23705560192855024 chr13 115169878 2563557 0.022258919124669038 0.19579089029283492 chr14 107349540 4142919 0.038592796950969704 0.26427118401633487 chr15 102531392 1748294 0.017051304638485743 0.17278343275890104 chr16 90354753 2489582 0.02755341492660602 0.22774228650511968 chr17 81195210 2823499 0.034774206507994745 0.2567839449857843 chr18 78077248 2411909 0.030891316763623635 0.5171099934233836 chr19 59128983 1056635 0.017870001247949758 0.34803887691038954 chr20 63025520 1832969 0.029082965122699502 0.22432647114679546 chr21 48129895 1856849 0.03857995119249689 0.26022705846594335 chr22 51304566 913499 0.01780541326477647 0.16910343710596648 chrMT 16571 104141 6.2845332206867415 5.078380508836653 chrX 155270560 4142901 0.026681819142018937 0.22840735275881144 chrY 59373566 170723 0.002875404182393222 0.07550174832559209