BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524282.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 = 2,390,179 number of mapped reads = 2,220,018 (92.88%) number of supplementary alignments = 8,001 (0.33%) number of secondary alignments = 0 number of mapped bases = 130,329,526 bp number of sequenced bases = 130,291,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,441 duplication rate = 4.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4485 >>>>>>> ACTG content number of A's = 32,817,423 bp (25.19%) number of C's = 24,066,547 bp (18.47%) number of T's = 42,062,016 bp (32.28%) number of G's = 31,327,748 bp (24.04%) number of N's = 17,336 bp (0.01%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 628,467 number of insertions = 9,825 mapped reads with insertion percentage = 0.44% number of deletions = 24,547 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.84% >>>>>>> Coverage mean coverageData = 0.0421X std coverageData = 0.4107X There is a 3.64% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10166019 0.04078633368781055 0.8314682243620759 chr2 243199373 11788994 0.048474606881490606 0.4239823102235993 chr3 198022430 8834859 0.04461544583611059 0.23643403961950624 chr4 191154276 8246815 0.04314219473698825 0.268897506471981 chr5 180915260 7942663 0.04390267023356681 0.2370771563023493 chr6 171115067 7400221 0.04324704498406327 0.2638115026996883 chr7 159138663 7171362 0.04506360594470999 0.6044617418369456 chr8 146364022 6696835 0.04575465273836216 0.4028373037312141 chr9 141213431 5469892 0.03873492741635886 0.3449313879626606 chr10 135534747 6186110 0.04564224405126163 0.3612713745643478 chr11 135006516 6062835 0.044907721342872076 0.3562800650949219 chr12 133851895 5751646 0.04297022466510467 0.24097015059168847 chr13 115169878 4035633 0.03504069874937264 0.2139784247160759 chr14 107349540 3897623 0.03630777551538646 0.2325843135096065 chr15 102531392 3729466 0.03637389415331453 0.21439620886447058 chr16 90354753 3717666 0.04114521789462476 0.2575376600675709 chr17 81195210 3361715 0.041402873396103046 0.25537223571702566 chr18 78077248 3508284 0.04493349970531748 0.7336316252851549 chr19 59128983 2505160 0.04236771669149121 0.5650473806706585 chr20 63025520 2738576 0.04345185886605934 0.23895789829435599 chr21 48129895 1690654 0.0351268998197482 0.24042592239816166 chr22 51304566 1501365 0.029263769622376302 0.19073255557494578 chrMT 16571 284218 17.15152978094261 10.091094700368663 chrX 155270560 7231430 0.046573091512003305 0.2893256315729758 chrY 59373566 409485 0.006896756041232221 0.18658707324717086