BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716624.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 = 546,411 number of mapped reads = 506,412 (92.68%) number of supplementary alignments = 2,093 (0.38%) number of secondary alignments = 0 number of mapped bases = 29,479,761 bp number of sequenced bases = 29,470,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,277 duplication rate = 1.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2328 >>>>>>> ACTG content number of A's = 7,281,911 bp (24.71%) number of C's = 5,822,511 bp (19.76%) number of T's = 9,135,995 bp (31%) number of G's = 7,229,577 bp (24.53%) number of N's = 821 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 144,450 number of insertions = 1,773 mapped reads with insertion percentage = 0.35% number of deletions = 5,521 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.57% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.1191X There is a 0.9% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2410118 0.009669456350120788 0.1758305822962299 chr2 243199373 2546919 0.010472555782452613 0.1444442741042954 chr3 198022430 1979673 0.009997215971948229 0.10398243047256844 chr4 191154276 1851797 0.00968744743120473 0.10583705048428664 chr5 180915260 1782048 0.009850180686803314 0.10351978318171584 chr6 171115067 1702942 0.009952028362294946 0.11073081726604404 chr7 159138663 1627642 0.010227822512245187 0.13299667057167758 chr8 146364022 1468286 0.01003174127040592 0.11609582968799836 chr9 141213431 1217637 0.008622671309501714 0.10767504110650462 chr10 135534747 1419314 0.01047195668576413 0.11864612789278274 chr11 135006516 1299118 0.00962263184393263 0.11481391121814574 chr12 133851895 1309586 0.00978384355335425 0.10418429907255737 chr13 115169878 880683 0.0076468171651618835 0.09101362268440638 chr14 107349540 880360 0.008200873520277777 0.09569803258491712 chr15 102531392 834836 0.008142247790803425 0.09480888401791826 chr16 90354753 881374 0.00975459475828571 0.10528451892101327 chr17 81195210 821685 0.01011987037166355 0.10605224747742634 chr18 78077248 784979 0.010053876386626743 0.1467414347331343 chr19 59128983 640898 0.01083898229739551 0.1401798086258602 chr20 63025520 649376 0.010303381868170227 0.10640751605153406 chr21 48129895 388692 0.008075895449179766 0.0970761994206447 chr22 51304566 360407 0.007024852329907634 0.08706425037158572 chrMT 16571 3637 0.21947981413312415 0.4866668295466422 chrX 155270560 1642444 0.01057794858213946 0.10956279206735281 chrY 59373566 95310 0.0016052598221909056 0.054473088131478324