BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695978.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 13,602,712 number of mapped reads = 12,299,403 (90.42%) number of supplementary alignments = 19,761 (0.15%) number of secondary alignments = 0 number of mapped bases = 1,667,564,712 bp number of sequenced bases = 1,655,121,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,751,025 duplication rate = 18.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.9429 >>>>>>> ACTG content number of A's = 456,246,707 bp (27.57%) number of C's = 365,782,416 bp (22.1%) number of T's = 454,203,605 bp (27.44%) number of G's = 378,888,621 bp (22.89%) number of N's = 0 bp (0%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.021 number of mismatches = 24,262,084 number of insertions = 9,788,723 mapped reads with insertion percentage = 47.67% number of deletions = 11,191,450 mapped reads with deletion percentage = 53.24% homopolymer indels = 36.6% >>>>>>> Coverage mean coverageData = 0.5387X std coverageData = 1.8232X There is a 18.52% of reference with a coverageData >= 1X There is a 10.67% of reference with a coverageData >= 2X There is a 6.71% of reference with a coverageData >= 3X There is a 4.47% of reference with a coverageData >= 4X There is a 3.11% of reference with a coverageData >= 5X There is a 2.23% of reference with a coverageData >= 6X There is a 1.64% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.94% of reference with a coverageData >= 9X There is a 0.72% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.45% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 190604000 0.7647082251401893 2.4580864377235314 chr2 243199373 130557337 0.5368325394490223 1.8376630276998727 chr3 198022430 112669008 0.568970939302179 1.7293753305743773 chr4 191154276 56802567 0.297155617905194 1.2220265399651156 chr5 180915260 133563771 0.7382670262309547 2.228482495642658 chr6 171115067 77885340 0.45516354208598125 1.5044215291934258 chr7 159138663 100132792 0.6292172506187261 1.8926273612660862 chr8 146364022 74274734 0.5074657896460375 1.6632633530109766 chr9 141213431 70690260 0.5005916186541775 1.7511090788828392 chr10 135534747 75169589 0.5546148914860924 1.7262943837713074 chr11 135006516 94403194 0.6992491680920053 2.037562174703505 chr12 133851895 80876320 0.6042224504927629 1.8325895544913704 chr13 115169878 30716748 0.2667081752053258 1.0514573170595372 chr14 107349540 36329055 0.3384183574517413 1.2227393646319362 chr15 102531392 64195139 0.6261022868001246 1.9838609438041641 chr16 90354753 69818806 0.7727186858670291 2.3582788257829232 chr17 81195210 49068444 0.604326831595115 1.8325941293311103 chr18 78077248 30648817 0.3925447910254214 1.5689277175137646 chr19 59128983 24450505 0.4135113401155572 1.6135154832528165 chr20 63025520 60307260 0.9568704867488598 2.624635402174124 chr21 48129895 15118254 0.3141135878231191 1.9981669903986083 chr22 51304566 20223439 0.39418399913956975 1.3991530252970803 chrMT 16571 258556 15.602920765192204 16.60668968656966 chrX 155270560 66819602 0.4303430218838652 1.4211293561650689 chrY 59373566 1981175 0.033367963783748476 0.6652503961874519