BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524823.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 = 1,526,159 number of mapped reads = 1,378,494 (90.32%) number of supplementary alignments = 4,452 (0.29%) number of secondary alignments = 0 number of mapped bases = 77,594,248 bp number of sequenced bases = 77,570,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,023 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3729 >>>>>>> ACTG content number of A's = 17,609,791 bp (22.7%) number of C's = 14,830,991 bp (19.12%) number of T's = 25,966,716 bp (33.48%) number of G's = 19,154,176 bp (24.69%) number of N's = 8,745 bp (0.01%) GC percentage = 43.81% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 394,686 number of insertions = 5,978 mapped reads with insertion percentage = 0.43% number of deletions = 14,801 mapped reads with deletion percentage = 1.07% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2239X There is a 2.25% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 6190849 0.024837847846324923 0.2643480298587869 chr2 243199373 6518188 0.02680182896688636 0.36635573507703734 chr3 198022430 5053117 0.025517902189161095 0.17868339746240997 chr4 191154276 4895859 0.025612082044139048 0.20442762412759055 chr5 180915260 4520884 0.02498895891921997 0.17261884939159447 chr6 171115067 4411046 0.025778244296862533 0.1885582845242112 chr7 159138663 4236750 0.02662300863995571 0.26035299945785406 chr8 146364022 3863222 0.026394614927977313 0.19914567709693928 chr9 141213431 3294144 0.02332741281528667 0.20442691963857187 chr10 135534747 3832375 0.028275959374462107 0.27076228650786593 chr11 135006516 3504668 0.025959250737201456 0.2051474565127573 chr12 133851895 3527903 0.026356765438397416 0.17947563655413026 chr13 115169878 2396154 0.020805388019947368 0.15834237287940478 chr14 107349540 2342230 0.021818724141715 0.16377879033612974 chr15 102531392 2258948 0.02203176954819847 0.16418912403419644 chr16 90354753 2396001 0.026517708481810582 0.1960784440333615 chr17 81195210 2257583 0.027804386490286805 0.19165171767645636 chr18 78077248 2033474 0.026044386195579024 0.28619861284292 chr19 59128983 1763869 0.02983086991365977 0.2380344473750833 chr20 63025520 1719660 0.027285137829882244 0.19004396350491204 chr21 48129895 1028373 0.021366616320272463 0.17777896203427815 chr22 51304566 989340 0.01928366375811463 0.15309745603672215 chrMT 16571 11616 0.7009836461287792 0.986486995815188 chrX 155270560 4281269 0.02757296038605129 0.19742502398235742 chrY 59373566 266726 0.004492335865425364 0.1337228279229843