BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716936.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 = 1,023,554 number of mapped reads = 802,863 (78.44%) number of supplementary alignments = 911 (0.09%) number of secondary alignments = 0 number of mapped bases = 43,173,263 bp number of sequenced bases = 43,161,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,420 duplication rate = 5.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2967 >>>>>>> ACTG content number of A's = 9,260,242 bp (21.45%) number of C's = 7,439,041 bp (17.24%) number of T's = 13,754,487 bp (31.87%) number of G's = 12,707,528 bp (29.44%) number of N's = 699 bp (0%) GC percentage = 46.68% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 283,805 number of insertions = 2,462 mapped reads with insertion percentage = 0.3% number of deletions = 6,591 mapped reads with deletion percentage = 0.82% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0139X std coverageData = 0.149X There is a 1.22% of reference with a coverageData >= 1X There is a 0.13% 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 4290992 0.0172155719523764 0.18188732147694264 chr2 243199373 3761546 0.015466923099345326 0.20410193214752956 chr3 198022430 2859725 0.014441419590699903 0.13588925010539246 chr4 191154276 2816318 0.0147332199882361 0.14478401756076598 chr5 180915260 2649978 0.014647620106783695 0.1355347012405011 chr6 171115067 1858676 0.010862141087786267 0.12833486640006925 chr7 159138663 2497489 0.01569379152066899 0.16009407023124517 chr8 146364022 2683448 0.0183340684639016 0.1566574669099105 chr9 141213431 1888786 0.01337539911483349 0.1381576223052982 chr10 135534747 2184611 0.016118457062527295 0.16775004504959398 chr11 135006516 1847620 0.013685413524781278 0.14334758178000537 chr12 133851895 2083941 0.015569006325984402 0.1411365647772799 chr13 115169878 758435 0.006585359064112233 0.09081135497454547 chr14 107349540 1368698 0.012749919561835105 0.12876113902444053 chr15 102531392 846526 0.008256261653016473 0.10233535364770822 chr16 90354753 1145707 0.012680096640848544 0.1334385519808748 chr17 81195210 1678302 0.0206699631665464 0.16842090890123507 chr18 78077248 1181871 0.015137201044790922 0.1584658969044188 chr19 59128983 1111228 0.01879328788726165 0.17898829003348382 chr20 63025520 1096102 0.01739139954735796 0.15514531631341935 chr21 48129895 600763 0.012482117403331132 0.13239838684015848 chr22 51304566 466223 0.009087358813248708 0.11324231895857383 chrMT 16571 32465 1.9591454951421157 1.9563254974421198 chrX 155270560 1337087 0.008611336237854749 0.10786081077821269 chrY 59373566 126726 0.0021343841803269825 0.07457024286214652