BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068187.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 = 1,624,252 number of mapped reads = 1,479,852 (91.11%) number of supplementary alignments = 7,794 (0.48%) number of secondary alignments = 0 number of mapped bases = 101,472,853 bp number of sequenced bases = 101,429,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,765 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7635 >>>>>>> ACTG content number of A's = 29,750,714 bp (29.33%) number of C's = 18,819,280 bp (18.55%) number of T's = 31,659,065 bp (31.21%) number of G's = 21,084,010 bp (20.79%) number of N's = 116,097 bp (0.11%) GC percentage = 39.34% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 862,009 number of insertions = 6,964 mapped reads with insertion percentage = 0.47% number of deletions = 25,054 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0328X std coverageData = 0.3802X There is a 2.74% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.07% 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 11314556 0.04539429412294223 0.6178288385427082 chr2 243199373 11658166 0.04793666141565258 0.34484130410104236 chr3 198022430 9035824 0.045630305617398996 0.2531667299360452 chr4 191154276 13883407 0.07262933003915643 0.3191592201541965 chr5 180915260 4904876 0.027111455385245002 0.18847909426675202 chr6 171115067 7105327 0.04152367833277943 0.25934805125618104 chr7 159138663 6349861 0.03990143488889309 0.9228854045068774 chr8 146364022 5535807 0.03782218419769853 0.5077205346018546 chr9 141213431 1855399 0.013138969762727456 0.25910447614051785 chr10 135534747 3582121 0.026429539872900636 0.40862319348514176 chr11 135006516 2189030 0.016214254429023262 0.2261385632206773 chr12 133851895 3449618 0.025771902594281536 0.20152585859572603 chr13 115169878 2612306 0.022682198204638196 0.17174422920594204 chr14 107349540 3507495 0.032673591335370414 0.23057842768871978 chr15 102531392 2276400 0.022201980833343217 0.16880300481834046 chr16 90354753 1245318 0.013782540028635793 0.16723616143857192 chr17 81195210 3171900 0.03906511233852342 0.2661610179191791 chr18 78077248 1906380 0.02441658804367695 0.43064201573461386 chr19 59128983 343047 0.0058016725909187375 0.413380091141686 chr20 63025520 1975293 0.03134116148506193 0.22296156934905928 chr21 48129895 319819 0.006644913727736161 0.11577380401521448 chr22 51304566 546726 0.010656478411687568 0.11502757439583251 chrMT 16571 16495 0.9954136744915817 1.2244518016122328 chrX 155270560 2427905 0.015636608768590774 0.16398867183758076 chrY 59373566 259777 0.004375297249284303 0.1406570846540062