BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251071.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 4,435,807 number of mapped reads = 4,172,178 (94.06%) number of supplementary alignments = 32,557 (0.73%) number of secondary alignments = 0 number of mapped bases = 324,256,664 bp number of sequenced bases = 324,050,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 969,646 duplication rate = 20.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2703 >>>>>>> ACTG content number of A's = 94,387,823 bp (29.13%) number of C's = 64,750,925 bp (19.98%) number of T's = 95,815,956 bp (29.57%) number of G's = 69,093,491 bp (21.32%) number of N's = 2,687 bp (0%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,836,147 number of insertions = 39,340 mapped reads with insertion percentage = 0.92% number of deletions = 115,818 mapped reads with deletion percentage = 2.73% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.1047X std coverageData = 0.9913X There is a 6.68% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 27755446 0.11135557411509919 1.9408120520433905 chr2 243199373 28832052 0.11855315103957936 1.3407672271690385 chr3 198022430 22237233 0.11229653630651841 0.48723385241313943 chr4 191154276 20939829 0.10954413073134707 0.5487651825435765 chr5 180915260 19264064 0.10648114481885054 0.4874485063640306 chr6 171115067 18827330 0.11002730694661739 0.604197057864081 chr7 159138663 17782232 0.11174048885907757 1.4482658259799006 chr8 146364022 15480287 0.10576565735533013 0.6534335762986819 chr9 141213431 13720401 0.09716073678572401 1.0227033807412573 chr10 135534747 18912120 0.13953705908345407 1.0052937351719733 chr11 135006516 14531685 0.10763691583597343 0.6732109565897205 chr12 133851895 14416232 0.10770286068792675 0.49054591861509467 chr13 115169878 9509924 0.08257301444740611 0.4094682997454559 chr14 107349540 9431644 0.08785919343482981 0.6627234681872317 chr15 102531392 9570585 0.09334297343783259 0.4393948900194632 chr16 90354753 8689594 0.09617196341624662 0.8116698316154431 chr17 81195210 9091599 0.11197211017743534 0.5926603664544665 chr18 78077248 7892848 0.10109024334464248 1.1780859836202378 chr19 59128983 6780163 0.11466733665958706 1.983404935992614 chr20 63025520 6705642 0.10639566321705875 0.5216609994841573 chr21 48129895 3868536 0.08037698814842625 0.4412749786127964 chr22 51304566 4022908 0.07841228010777831 0.435336531128689 chrMT 16571 651903 39.33999155150564 21.20923679922952 chrX 155270560 14536737 0.09362197830676981 0.5159201031614936 chrY 59373566 805670 0.013569506672380096 0.9603919059670197