BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238632.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 = 1,756,079 number of mapped reads = 1,511,140 (86.05%) number of supplementary alignments = 13,857 (0.79%) number of secondary alignments = 0 number of mapped bases = 93,261,497 bp number of sequenced bases = 93,210,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 417,286 duplication rate = 19.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4188 >>>>>>> ACTG content number of A's = 23,498,822 bp (25.21%) number of C's = 16,261,849 bp (17.45%) number of T's = 31,325,045 bp (33.61%) number of G's = 22,120,699 bp (23.73%) number of N's = 4,506 bp (0%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 545,696 number of insertions = 6,016 mapped reads with insertion percentage = 0.39% number of deletions = 29,462 mapped reads with deletion percentage = 1.93% homopolymer indels = 41.02% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.4931X There is a 1.38% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 12098713 0.048540352483214075 0.5733181002887724 chr2 243199373 3645472 0.014989643908333596 0.9982759556169268 chr3 198022430 3373817 0.017037549736158678 0.24558038771340177 chr4 191154276 2844010 0.014878087268107987 0.22790441570591435 chr5 180915260 8859210 0.04896883767571624 0.42303138381378386 chr6 171115067 7920287 0.04628632147279 0.535038102359133 chr7 159138663 2227259 0.013995712657206377 0.30457316452702826 chr8 146364022 7268218 0.049658501458780625 0.5845557482676121 chr9 141213431 8023596 0.056818929638498765 0.47519128831848434 chr10 135534747 3240553 0.023909389080867947 0.30358382996927574 chr11 135006516 1516866 0.011235502144207618 0.19741366738841448 chr12 133851895 1315424 0.009827458923909894 0.1887722573139259 chr13 115169878 1214563 0.010545839077818595 0.29312312471937246 chr14 107349540 5073571 0.04726215873864015 0.42487315170756124 chr15 102531392 1575050 0.015361636756087345 0.30972669154838905 chr16 90354753 1502069 0.01662412822931407 0.25567569600420864 chr17 81195210 1839780 0.02265872580414534 0.2843176859821414 chr18 78077248 2926173 0.03747792186527886 1.044713802964635 chr19 59128983 2211299 0.03739788658296389 0.4298404619634036 chr20 63025520 5445494 0.08640141326878382 0.587430577384079 chr21 48129895 2463182 0.051177797084327736 0.4348023016044214 chr22 51304566 847879 0.016526384805594107 0.232984103676959 chrMT 16571 58250 3.5151771166495687 4.117618481245369 chrX 155270560 5594640 0.03603155678706897 0.3721389106477139 chrY 59373566 176122 0.0029663369048778376 0.16822644843764764