BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525191.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 = 2,974,421 number of mapped reads = 2,703,677 (90.9%) number of supplementary alignments = 9,374 (0.32%) number of secondary alignments = 0 number of mapped bases = 157,173,890 bp number of sequenced bases = 157,120,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,533 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9549 >>>>>>> ACTG content number of A's = 38,796,660 bp (24.69%) number of C's = 28,940,675 bp (18.42%) number of T's = 51,025,707 bp (32.48%) number of G's = 38,353,465 bp (24.41%) number of N's = 3,713 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 807,467 number of insertions = 10,675 mapped reads with insertion percentage = 0.39% number of deletions = 33,396 mapped reads with deletion percentage = 1.23% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.4696X There is a 4.33% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 16019431 0.06427037547882378 0.8658403632141171 chr2 243199373 12084831 0.04969104505051499 0.6222355786937145 chr3 198022430 9079433 0.04585052814471573 0.251759000494016 chr4 191154276 9230666 0.04828908980304474 0.27849217341234084 chr5 180915260 7411563 0.04096704169675902 0.23271102218735984 chr6 171115067 10377968 0.060649060202278976 0.33369551181697127 chr7 159138663 12070428 0.07584849446674062 0.861020567615966 chr8 146364022 8486308 0.0579808335685118 0.44419749030672 chr9 141213431 5477402 0.038788109326513 0.3071545431893789 chr10 135534747 7657895 0.05650134131286643 0.4730062437254536 chr11 135006516 7514111 0.055657395084545404 0.37165950204552467 chr12 133851895 7381894 0.05514971603502513 0.27396470029314585 chr13 115169878 3815684 0.03313091987472627 0.21552793508437287 chr14 107349540 8749515 0.08150491376115818 0.3352055514830569 chr15 102531392 3171180 0.030928869082358697 0.2081660158492697 chr16 90354753 3568236 0.039491403401877484 0.2635388068153908 chr17 81195210 2928444 0.03606670886127396 0.23227324223146825 chr18 78077248 3456904 0.04427543347839309 0.6107657292724794 chr19 59128983 2732301 0.04620916615460814 0.599353199867822 chr20 63025520 2942919 0.04669408518961843 0.2542346118833643 chr21 48129895 2076107 0.04313549821789555 0.26674202021853016 chr22 51304566 1328201 0.02588855346715144 0.18429504401368624 chrMT 16571 447991 27.03463882686621 14.901515116762678 chrX 155270560 8698576 0.05602205595188167 0.30798415308588006 chrY 59373566 465902 0.00784696004279076 0.22705771014175904