BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004146.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 = 3,394,357 number of mapped reads = 2,862,155 (84.32%) number of supplementary alignments = 20,821 (0.61%) number of secondary alignments = 0 number of mapped bases = 193,246,537 bp number of sequenced bases = 193,162,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,429 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0589 >>>>>>> ACTG content number of A's = 54,418,684 bp (28.17%) number of C's = 34,910,015 bp (18.07%) number of T's = 62,719,413 bp (32.47%) number of G's = 41,091,988 bp (21.27%) number of N's = 21,921 bp (0.01%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,799,691 number of insertions = 16,942 mapped reads with insertion percentage = 0.59% number of deletions = 50,651 mapped reads with deletion percentage = 1.75% homopolymer indels = 47.6% >>>>>>> Coverage mean coverageData = 0.0624X std coverageData = 0.6071X There is a 5.01% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17335180 0.06954919482427288 1.1147878966617455 chr2 243199373 14535408 0.0597674567195533 0.6662749667000359 chr3 198022430 13156090 0.0664373727764072 0.30660029442651904 chr4 191154276 12663098 0.06624543413300364 0.3193066332759332 chr5 180915260 12875791 0.07117028712779674 0.31989404749347156 chr6 171115067 10042622 0.05868929122413282 0.35442140117240184 chr7 159138663 13936638 0.08757543727761494 0.9874314708088677 chr8 146364022 15402351 0.10523317677072307 1.0353605129344474 chr9 141213431 5632877 0.039889102333332586 0.5486033450874586 chr10 135534747 8376080 0.06180024078991345 0.44924906128681785 chr11 135006516 7500436 0.0555561036772477 0.4144452885016855 chr12 133851895 4047690 0.0302400649613515 0.22798252784557058 chr13 115169878 6034796 0.052399083031068244 0.27271631607049146 chr14 107349540 5786964 0.0539076739406615 0.3193464363582044 chr15 102531392 6229261 0.0607546711157496 0.2916293305259261 chr16 90354753 3870214 0.04283354080996713 0.3167530932292135 chr17 81195210 5056498 0.062275816516762506 0.324131888660231 chr18 78077248 6547742 0.0838623564191197 1.1817683041082794 chr19 59128983 2779849 0.04701330648626242 0.7800860974401129 chr20 63025520 4925313 0.07814791532065106 0.3515036614194569 chr21 48129895 2702724 0.056154786957253906 0.3059255313594896 chr22 51304566 2300354 0.04483721780240769 0.246395261368703 chrMT 16571 221287 13.353871220807434 7.648016300015551 chrX 155270560 10811770 0.06963180914656326 0.36297225650890724 chrY 59373566 475504 0.008008681843364436 0.1539889432914464