BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716763.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,150,474 number of mapped reads = 982,661 (85.41%) number of supplementary alignments = 2,660 (0.23%) number of secondary alignments = 0 number of mapped bases = 55,114,485 bp number of sequenced bases = 55,100,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,481 duplication rate = 1.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0895 >>>>>>> ACTG content number of A's = 13,288,938 bp (24.12%) number of C's = 12,030,764 bp (21.83%) number of T's = 16,023,760 bp (29.08%) number of G's = 13,755,056 bp (24.96%) number of N's = 1,648 bp (0%) GC percentage = 46.8% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 286,098 number of insertions = 4,011 mapped reads with insertion percentage = 0.41% number of deletions = 8,859 mapped reads with deletion percentage = 0.89% homopolymer indels = 36.56% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.1627X There is a 1.63% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5389384 0.02162234933809854 0.19160297405019855 chr2 243199373 4755681 0.01955465978935727 0.19811819550709303 chr3 198022430 3730340 0.018837966991921067 0.15206423777627837 chr4 191154276 3515981 0.018393420610690395 0.15857987083341626 chr5 180915260 3406038 0.018826703728585418 0.14796679641890234 chr6 171115067 2383718 0.013930497423701444 0.13025899074466665 chr7 159138663 3129870 0.019667565009013555 0.18653601678232723 chr8 146364022 3417077 0.02334642730711513 0.17354300468119105 chr9 141213431 2397368 0.016976912061572952 0.15112959713022467 chr10 135534747 2846717 0.021003595483894622 0.2207046399298161 chr11 135006516 2288927 0.016954196492264123 0.1628134523030204 chr12 133851895 2690284 0.020098960870146815 0.15344212019414327 chr13 115169878 972395 0.008443136494422613 0.09989991670729548 chr14 107349540 1768416 0.01647343807900807 0.1435407709517761 chr15 102531392 1107309 0.010799707078979285 0.1128290056968156 chr16 90354753 1501476 0.016617565209878886 0.1482954465491188 chr17 81195210 2182744 0.026882669556492312 0.18359253277508672 chr18 78077248 1491984 0.019109075155927628 0.18212443646164378 chr19 59128983 1455687 0.02461884047625172 0.1926063655982025 chr20 63025520 1393800 0.022114851253904767 0.16607419576732144 chr21 48129895 741972 0.015416031969319692 0.14496649369567777 chr22 51304566 608970 0.011869703760869939 0.11898498055976928 chrMT 16571 25405 1.5330999939653611 1.7894894836205428 chrX 155270560 1757818 0.01132099993714198 0.12090499455275894 chrY 59373566 155124 0.002612677837137153 0.08202887990021589