BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238068.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 = 1,883,985 number of mapped reads = 1,650,883 (87.63%) number of supplementary alignments = 17,872 (0.95%) number of secondary alignments = 0 number of mapped bases = 110,542,286 bp number of sequenced bases = 110,489,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,036 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7725 >>>>>>> ACTG content number of A's = 30,269,574 bp (27.4%) number of C's = 21,101,660 bp (19.1%) number of T's = 34,367,424 bp (31.1%) number of G's = 24,737,031 bp (22.39%) number of N's = 14,164 bp (0.01%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 833,523 number of insertions = 7,823 mapped reads with insertion percentage = 0.47% number of deletions = 29,487 mapped reads with deletion percentage = 1.76% homopolymer indels = 46.01% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3405X There is a 2.94% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 8107411 0.032527144636482166 0.6445130096927401 chr2 243199373 7730422 0.031786356620253295 0.34017696369057165 chr3 198022430 9605447 0.04850686359115985 0.25822666398769656 chr4 191154276 3830725 0.02003996499665014 0.18432127758419792 chr5 180915260 7625082 0.04214725722971075 0.24266068279883177 chr6 171115067 6588355 0.038502483244213674 0.2655327436320026 chr7 159138663 4650159 0.029220799724828654 0.3961517581759229 chr8 146364022 4631064 0.0316407265714521 0.3666928507161719 chr9 141213431 5160757 0.03654579428779689 0.32004039708269233 chr10 135534747 6968067 0.05141166493637237 0.3794793938503143 chr11 135006516 6432380 0.0476449595958761 0.3216947211771696 chr12 133851895 4402693 0.03289227246278433 0.2193255142610791 chr13 115169878 3693516 0.0320701563997489 0.20809748027101682 chr14 107349540 4586777 0.04272749561851872 0.2647117987284717 chr15 102531392 3938608 0.03841367919787922 0.22868930908826557 chr16 90354753 2344041 0.025942641888468225 0.21716359076821348 chr17 81195210 2034567 0.025057722001088488 0.19602942691066821 chr18 78077248 3464473 0.044372375932102526 0.5991883201993163 chr19 59128983 2403000 0.04063996838910624 0.42421488618616876 chr20 63025520 1787069 0.028354688703877414 0.2074232781708549 chr21 48129895 1823931 0.037896010369438786 0.25161438978450934 chr22 51304566 1682258 0.03278963513695837 0.2119770918299226 chrMT 16571 80943 4.884617705630318 3.7301365223645804 chrX 155270560 6672683 0.04297455357924902 0.2746924670342746 chrY 59373566 297858 0.005016676950143099 0.13595128688834685