BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068063.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 = 1,736,501 number of mapped reads = 1,463,714 (84.29%) number of supplementary alignments = 15,838 (0.91%) number of secondary alignments = 0 number of mapped bases = 93,071,976 bp number of sequenced bases = 93,034,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,357 duplication rate = 7.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1569 >>>>>>> ACTG content number of A's = 24,900,075 bp (26.76%) number of C's = 16,946,387 bp (18.22%) number of T's = 29,729,894 bp (31.96%) number of G's = 21,456,637 bp (23.06%) number of N's = 1,733 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 719,405 number of insertions = 6,795 mapped reads with insertion percentage = 0.46% number of deletions = 23,322 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.3682X There is a 2.13% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.06% 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% 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 8723654 0.034999527644105646 0.2978518361351248 chr2 243199373 4750126 0.0195318184475747 0.44610986092189553 chr3 198022430 4858794 0.02453658406272461 0.20958843275664268 chr4 191154276 2422491 0.012672962649289623 0.16188068508314002 chr5 180915260 5350863 0.02957662609555435 0.23182734297228105 chr6 171115067 6865053 0.04011951209416293 0.29258702196567415 chr7 159138663 9360596 0.058820376038976774 1.110866838926294 chr8 146364022 7249409 0.049529993101720036 0.36415396493803964 chr9 141213431 1868556 0.013232140786948232 0.19220984998160473 chr10 135534747 10082741 0.07439229587376586 0.42841002484955004 chr11 135006516 1705204 0.01263053110710597 0.1584086886901546 chr12 133851895 5964044 0.04455703821003057 0.284832250600004 chr13 115169878 4091394 0.03552486180457706 0.25597684859913034 chr14 107349540 1164978 0.010852193684295247 0.14568710466432558 chr15 102531392 3694149 0.036029443548371995 0.2653816574758102 chr16 90354753 2194875 0.024291749212130544 0.21227396616948876 chr17 81195210 1917531 0.023616306922538903 0.2030469062395873 chr18 78077248 2166865 0.027752835243373332 0.2579821648695322 chr19 59128983 1174305 0.019860057461160797 0.22787894331668213 chr20 63025520 2843194 0.045111789636959755 0.29012836468204595 chr21 48129895 951512 0.019769667064513646 0.1943957264867843 chr22 51304566 597886 0.011653660611805975 0.14261513942602702 chrMT 16571 70485 4.2535151771166495 3.4612533890422537 chrX 155270560 2742151 0.017660469570020227 0.18722864523306382 chrY 59373566 261120 0.004397916742949211 0.2367052342831