BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068155.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 = 4,906,856 number of mapped reads = 4,668,226 (95.14%) number of supplementary alignments = 44,868 (0.91%) number of secondary alignments = 0 number of mapped bases = 297,696,219 bp number of sequenced bases = 297,573,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 655,694 duplication rate = 11.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5959 >>>>>>> ACTG content number of A's = 77,316,544 bp (25.98%) number of C's = 54,798,787 bp (18.42%) number of T's = 95,063,057 bp (31.95%) number of G's = 70,360,809 bp (23.64%) number of N's = 34,480 bp (0.01%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,606,853 number of insertions = 18,774 mapped reads with insertion percentage = 0.4% number of deletions = 70,205 mapped reads with deletion percentage = 1.49% homopolymer indels = 44.55% >>>>>>> Coverage mean coverageData = 0.0962X std coverageData = 0.7309X There is a 6.44% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 42908872 0.17215151492039812 1.1420326575108881 chr2 243199373 22802462 0.09376036508120439 1.471819781664761 chr3 198022430 17705190 0.08941002289488115 0.41895976812321106 chr4 191154276 7925550 0.04146153654444016 0.33693939453847216 chr5 180915260 15706837 0.08681875149724794 0.41600830202103356 chr6 171115067 18513561 0.10819363440391838 0.6552127318030091 chr7 159138663 23760052 0.14930408206332613 0.5809406534753365 chr8 146364022 4427222 0.030248020924158535 0.5503569634169746 chr9 141213431 20702278 0.14660275480453414 0.7758882003748883 chr10 135534747 4693343 0.03462833777968391 0.47115575158685724 chr11 135006516 13604951 0.10077255085969332 0.5526878051147248 chr12 133851895 18241074 0.13627804074047664 0.5392265943350943 chr13 115169878 7203582 0.06254744838750285 0.3901191650533311 chr14 107349540 5016688 0.0467322729095998 0.35988018398601546 chr15 102531392 5324145 0.05192697471619229 0.37431181762205995 chr16 90354753 5352296 0.05923646318860503 0.39736224744989185 chr17 81195210 9716439 0.11966763802938622 0.5227566080145029 chr18 78077248 6452058 0.08263685215954333 1.1877072687217045 chr19 59128983 7269783 0.12294787820044191 0.8949033717923414 chr20 63025520 3132062 0.049695139365768026 0.32147535820743034 chr21 48129895 3699283 0.07686040038109371 0.41641238325578067 chr22 51304566 4866309 0.09485138223369827 0.4268345133865589 chrMT 16571 14171 0.8551686681552109 1.2820400014899689 chrX 155270560 27771458 0.17885849062436562 0.660845459215621 chrY 59373566 886553 0.014931779573421613 0.386460192312179