BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082934.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,027,615 number of mapped reads = 1,790,399 (88.3%) number of supplementary alignments = 25,020 (1.23%) number of secondary alignments = 0 number of mapped bases = 118,700,133 bp number of sequenced bases = 118,656,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,651 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1945 >>>>>>> ACTG content number of A's = 32,233,994 bp (27.17%) number of C's = 22,197,470 bp (18.71%) number of T's = 37,369,546 bp (31.49%) number of G's = 26,849,541 bp (22.63%) number of N's = 5,775 bp (0%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 858,946 number of insertions = 8,962 mapped reads with insertion percentage = 0.5% number of deletions = 26,862 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.78% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.2893X There is a 2.93% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 10885030 0.043671024594959786 0.38973413064858886 chr2 243199373 12662389 0.052065878475764 0.4527005575713986 chr3 198022430 8494454 0.042896423400116845 0.26054481299335464 chr4 191154276 6216917 0.032523033907962386 0.23434519347456223 chr5 180915260 7046746 0.03895053407877257 0.24946147654912176 chr6 171115067 7399341 0.043241902245814506 0.29556509068239073 chr7 159138663 5892719 0.037028833150370255 0.255214194073929 chr8 146364022 9586924 0.06550055040165541 0.36895109092138495 chr9 141213431 3125762 0.02213501915409165 0.2034834249052134 chr10 135534747 4988256 0.03680425950107097 0.24988810680672266 chr11 135006516 5966951 0.04419750377085503 0.2771629288713688 chr12 133851895 3557667 0.026579130612980863 0.2046748130055054 chr13 115169878 2887576 0.02507231969109145 0.2018041976879002 chr14 107349540 1948586 0.018151787143195958 0.17419750373207007 chr15 102531392 2876322 0.02805308641474408 0.22337310888980913 chr16 90354753 5832925 0.06455581810953542 0.32707501769123687 chr17 81195210 2906276 0.035793687829614576 0.24595882565899976 chr18 78077248 2999027 0.038411023400824786 0.33334815909513016 chr19 59128983 1490004 0.025199215755156823 0.27380001370903784 chr20 63025520 2285454 0.036262358485895874 0.24451314390858417 chr21 48129895 2658769 0.055241529199263784 0.29993678906606785 chr22 51304566 1467589 0.028605426659295784 0.21202093616698608 chrMT 16571 10060 0.6070846659827409 0.8772798094750486 chrX 155270560 5320032 0.034262979408330854 0.23818679056200354 chrY 59373566 194357 0.003273460111861902 0.0688838687568394