BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236073.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 = 2,395,244 number of mapped reads = 2,055,636 (85.82%) number of supplementary alignments = 13,568 (0.57%) number of secondary alignments = 0 number of mapped bases = 141,273,626 bp number of sequenced bases = 141,195,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,033 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5705 >>>>>>> ACTG content number of A's = 40,133,778 bp (28.42%) number of C's = 26,287,046 bp (18.62%) number of T's = 44,240,811 bp (31.33%) number of G's = 30,455,817 bp (21.57%) number of N's = 77,650 bp (0.05%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,126,232 number of insertions = 9,859 mapped reads with insertion percentage = 0.48% number of deletions = 44,821 mapped reads with deletion percentage = 2.15% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.4357X There is a 3.21% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16675200 0.06690133783056854 0.5427077295422083 chr2 243199373 12671738 0.05210432018671364 0.3620117140538881 chr3 198022430 14796928 0.07472349470714 0.36206135422153124 chr4 191154276 8655163 0.045278416895052874 0.2865409013964284 chr5 180915260 5548253 0.030667689392260222 0.23176491364722437 chr6 171115067 11379579 0.06650249565691371 0.5920766571193107 chr7 159138663 10613930 0.06669611142830828 0.9527658860607643 chr8 146364022 8576394 0.058596326356759994 0.8230806621000248 chr9 141213431 7729048 0.054733094049672935 0.35732121560692537 chr10 135534747 4847004 0.03576207656919152 0.35343957895973765 chr11 135006516 2206276 0.016341996411491724 0.19949562467353532 chr12 133851895 3869020 0.028905231412674433 0.2385724604911638 chr13 115169878 4504127 0.03910855058820154 0.26299242340207024 chr14 107349540 3368937 0.03138287318231638 0.24202595147396044 chr15 102531392 4768121 0.046504011181278025 0.2873557167232505 chr16 90354753 1593781 0.017639149542027967 0.1957916423176726 chr17 81195210 3948459 0.04862921100887602 0.3213619326819691 chr18 78077248 2412278 0.030896042852330042 0.4364331587249629 chr19 59128983 1989216 0.03364197892596935 0.353876564360447 chr20 63025520 1230489 0.019523662795642147 0.1886685147539784 chr21 48129895 1896391 0.03940151957530761 0.26897496914433383 chr22 51304566 872235 0.017001118379989806 0.16890899193482806 chrMT 16571 71213 4.297447347776235 3.3489146439086297 chrX 155270560 6775133 0.043634369580427865 0.29007209722676097 chrY 59373566 274713 0.004626857009060227 0.11307881220611417