BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068953.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 = 2,367,309 number of mapped reads = 1,942,363 (82.05%) number of supplementary alignments = 8,168 (0.35%) number of secondary alignments = 0 number of mapped bases = 124,270,923 bp number of sequenced bases = 124,214,071 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,603 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0027 >>>>>>> ACTG content number of A's = 32,458,850 bp (26.13%) number of C's = 21,041,393 bp (16.94%) number of T's = 41,443,420 bp (33.36%) number of G's = 28,977,646 bp (23.33%) number of N's = 292,762 bp (0.24%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,152,403 number of insertions = 11,001 mapped reads with insertion percentage = 0.56% number of deletions = 35,239 mapped reads with deletion percentage = 1.8% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.3644X There is a 3.48% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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 11740797 0.04710438414514522 0.6192942140463517 chr2 243199373 6805638 0.02798378102726441 0.3730386312989897 chr3 198022430 7908680 0.039938303958799014 0.22496845283596156 chr4 191154276 10747609 0.05622478986554295 0.2707731472416959 chr5 180915260 4039773 0.02232964206557258 0.17061240336695993 chr6 171115067 5925051 0.03462612091312801 0.2703272095659317 chr7 159138663 5504359 0.03458844567520339 0.32836278280724973 chr8 146364022 8017147 0.05477539418806078 0.5031947364791967 chr9 141213431 5915500 0.04189049128053549 0.4668269433664054 chr10 135534747 9407636 0.06941124846752397 0.4049848574716766 chr11 135006516 6552714 0.04853627953779653 0.41116898035877975 chr12 133851895 8002319 0.059784876411350024 0.2851602671851705 chr13 115169878 1530129 0.013285843716878819 0.12865547451860906 chr14 107349540 6531201 0.06084051221831039 0.30495568814453883 chr15 102531392 2357713 0.022995035510685352 0.1686161933130804 chr16 90354753 2187432 0.02420937391085558 0.22722825257847767 chr17 81195210 2723215 0.033539109018869466 0.23765702622382495 chr18 78077248 2458331 0.03148588177698066 0.7530274277947886 chr19 59128983 2757109 0.04662872351449035 0.3663646751334954 chr20 63025520 1765364 0.028010304397329842 0.20671143559807395 chr21 48129895 2470330 0.05132631184838446 0.2680868091476488 chr22 51304566 1698199 0.033100348222417475 0.20366123000169217 chrMT 16571 82120 4.955645404622533 3.9098573892266746 chrX 155270560 6891685 0.04438500769237903 0.2834232004996956 chrY 59373566 250872 0.004225314679600009 0.10319415006442079