BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438254.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 787,637,176 number of mapped reads = 783,615,491 (99.49%) number of supplementary alignments = 20,435,650 (2.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 391,967,796 number of mapped paired reads (second in pair) = 391,647,695 number of mapped paired reads (both in pair) = 781,220,936 number of mapped paired reads (singletons) = 2,394,555 number of mapped bases = 111,322,242,168 bp number of sequenced bases = 111,286,469,487 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 356,378,508 duplication rate = 40.48% >>>>>>> Insert size mean insert size = 93,799.6771 std insert size = 2,955,157.7569 median insert size = 440 >>>>>>> Mapping quality mean mapping quality = 54.3291 >>>>>>> ACTG content number of A's = 34,227,725,155 bp (30.76%) number of C's = 21,093,965,141 bp (18.95%) number of T's = 32,256,701,107 bp (28.99%) number of G's = 23,707,871,934 bp (21.3%) number of N's = 206,150 bp (0%) GC percentage = 40.26% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 600,869,034 number of insertions = 14,791,961 mapped reads with insertion percentage = 1.84% number of deletions = 13,093,453 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 35.9604X std coverageData = 109.3692X There is a 90.81% of reference with a coverageData >= 1X There is a 90.05% of reference with a coverageData >= 2X There is a 89.24% of reference with a coverageData >= 3X There is a 88.38% of reference with a coverageData >= 4X There is a 87.45% of reference with a coverageData >= 5X There is a 86.45% of reference with a coverageData >= 6X There is a 85.36% of reference with a coverageData >= 7X There is a 84.2% of reference with a coverageData >= 8X There is a 82.97% of reference with a coverageData >= 9X There is a 81.67% of reference with a coverageData >= 10X There is a 80.3% of reference with a coverageData >= 11X There is a 78.87% of reference with a coverageData >= 12X There is a 77.39% of reference with a coverageData >= 13X There is a 75.86% of reference with a coverageData >= 14X There is a 74.29% of reference with a coverageData >= 15X There is a 72.68% of reference with a coverageData >= 16X There is a 71.05% of reference with a coverageData >= 17X There is a 69.38% of reference with a coverageData >= 18X There is a 67.7% of reference with a coverageData >= 19X There is a 66.01% of reference with a coverageData >= 20X There is a 64.31% of reference with a coverageData >= 21X There is a 62.61% of reference with a coverageData >= 22X There is a 60.91% of reference with a coverageData >= 23X There is a 59.22% of reference with a coverageData >= 24X There is a 57.54% of reference with a coverageData >= 25X There is a 55.87% of reference with a coverageData >= 26X There is a 54.22% of reference with a coverageData >= 27X There is a 52.59% of reference with a coverageData >= 28X There is a 50.99% of reference with a coverageData >= 29X There is a 49.41% of reference with a coverageData >= 30X There is a 47.86% of reference with a coverageData >= 31X There is a 46.34% of reference with a coverageData >= 32X There is a 44.85% of reference with a coverageData >= 33X There is a 43.4% of reference with a coverageData >= 34X There is a 41.97% of reference with a coverageData >= 35X There is a 40.58% of reference with a coverageData >= 36X There is a 39.23% of reference with a coverageData >= 37X There is a 37.91% of reference with a coverageData >= 38X There is a 36.62% of reference with a coverageData >= 39X There is a 35.37% of reference with a coverageData >= 40X There is a 34.16% of reference with a coverageData >= 41X There is a 32.98% of reference with a coverageData >= 42X There is a 31.83% of reference with a coverageData >= 43X There is a 30.72% of reference with a coverageData >= 44X There is a 29.65% of reference with a coverageData >= 45X There is a 28.6% of reference with a coverageData >= 46X There is a 27.59% of reference with a coverageData >= 47X There is a 26.62% of reference with a coverageData >= 48X There is a 25.67% of reference with a coverageData >= 49X There is a 24.76% of reference with a coverageData >= 50X There is a 23.87% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8524968513 34.202396282093915 44.16538937502659 chr2 243199373 9535775252 39.20970327501625 170.80998606960438 chr3 198022430 7779442234 39.285661902038065 30.16144509474136 chr4 191154276 7630076882 39.91580539898569 38.3138234803238 chr5 180915260 7382014805 40.80371553510743 31.477667207853585 chr6 171115067 6703232779 39.17383136693626 37.80988445433704 chr7 159138663 6069765979 38.14136592940962 33.11062894742262 chr8 146364022 5793609902 39.583565843797324 33.700653249901016 chr9 141213431 4788512354 33.90975150231992 55.38830489973107 chr10 135534747 4917642238 36.283258329319786 82.05410505755152 chr11 135006516 5143335242 38.09694075802978 33.66919023953428 chr12 133851895 5034513610 37.61256880225715 31.9647868547566 chr13 115169878 3901776621 33.878447114444285 31.571965912076077 chr14 107349540 3351646709 31.221807834481638 31.56707435569712 chr15 102531392 2989343264 29.155395295910935 29.659233951383758 chr16 90354753 2923210457 32.352591977092786 85.27526657946564 chr17 81195210 2479444628 30.53683373686699 46.650356733791575 chr18 78077248 3062268729 39.22101261817015 59.82742539751187 chr19 59128983 1452837963 24.570657049859964 31.58583328046814 chr20 63025520 2133073800 33.844604534797966 33.784838323613464 chr21 48129895 1484396374 30.84146296184523 47.47620011331844 chr22 51304566 975522883 19.014348216102245 27.204992001962395 chrMT 16571 597450261 36053.96542151952 13479.918868042247 chrX 155270560 6536485109 42.097388642122496 33.41870874202318 chrY 59373566 131895580 2.2214528937002034 36.426151442029116