BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008790.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 = 1,734,122 number of mapped reads = 1,364,919 (78.71%) number of supplementary alignments = 10,154 (0.59%) number of secondary alignments = 0 number of mapped bases = 86,606,878 bp number of sequenced bases = 86,558,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,414 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3031 >>>>>>> ACTG content number of A's = 23,249,905 bp (26.86%) number of C's = 15,700,202 bp (18.14%) number of T's = 27,678,947 bp (31.98%) number of G's = 19,894,904 bp (22.98%) number of N's = 34,829 bp (0.04%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 755,400 number of insertions = 5,882 mapped reads with insertion percentage = 0.43% number of deletions = 27,768 mapped reads with deletion percentage = 2.01% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.305X There is a 2.31% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% 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 9577473 0.038425071767424004 0.6124851600351835 chr2 243199373 7359033 0.03025925975557511 0.3275038974146047 chr3 198022430 8040144 0.04060218834805734 0.24578375110804743 chr4 191154276 4857231 0.02541000443013893 0.1962410032467163 chr5 180915260 4204842 0.02324205266045551 0.17851501292794555 chr6 171115067 4890767 0.02858174376894584 0.22152025746144832 chr7 159138663 4510576 0.028343684149212692 0.3037441008126478 chr8 146364022 7031506 0.04804121876344721 0.35469984280954975 chr9 141213431 2729096 0.019326037053798373 0.23277274161385583 chr10 135534747 4789606 0.035338583691752495 0.45673001400305224 chr11 135006516 2409432 0.017846783039716395 0.20817808439510027 chr12 133851895 1926622 0.014393684900762892 0.14169966844490922 chr13 115169878 1841773 0.01599179431274556 0.1459426316425397 chr14 107349540 2714391 0.025285539183493473 0.19100473911686175 chr15 102531392 2808328 0.027389933416684716 0.1936469225783022 chr16 90354753 2045240 0.02263566588467128 0.207379099184508 chr17 81195210 2155212 0.026543585514465694 0.23680509886612527 chr18 78077248 2272712 0.029108505463717165 0.43083303606641626 chr19 59128983 1476722 0.024974588181230852 0.38968921495240144 chr20 63025520 1894353 0.030056919800106368 0.20585320696175638 chr21 48129895 1015102 0.02109088332729585 0.17947168710999611 chr22 51304566 1118454 0.021800281869648795 0.17055617784646865 chrMT 16571 13269 0.8007362259368777 1.2640863621915108 chrX 155270560 4642064 0.029896614013628857 0.21653568672492782 chrY 59373566 282930 0.004765251930463466 0.18093722256463293