BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238324.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,469,056 number of mapped reads = 2,253,316 (91.26%) number of supplementary alignments = 27,843 (1.13%) number of secondary alignments = 0 number of mapped bases = 149,367,386 bp number of sequenced bases = 149,288,285 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,298 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5028 >>>>>>> ACTG content number of A's = 42,985,089 bp (28.79%) number of C's = 27,720,186 bp (18.57%) number of T's = 47,032,392 bp (31.5%) number of G's = 31,504,986 bp (21.1%) number of N's = 45,632 bp (0.03%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,309,775 number of insertions = 11,602 mapped reads with insertion percentage = 0.51% number of deletions = 45,415 mapped reads with deletion percentage = 1.99% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.4584X There is a 3.99% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.1% 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 14104026 0.056585720602878656 0.8504969167026849 chr2 243199373 10866401 0.04468104035778086 0.46687673182209527 chr3 198022430 9723012 0.04910055896193174 0.25707966724162207 chr4 191154276 9606175 0.05025351878605112 0.29226046716547727 chr5 180915260 10990242 0.06074800986937199 0.2879798880631765 chr6 171115067 10217234 0.05970972737310152 0.37116185861724305 chr7 159138663 7519184 0.047249259596959164 0.5406441614653712 chr8 146364022 7382766 0.05044112548369298 0.8469725174569174 chr9 141213431 6078962 0.04304804406317413 0.4074354947949916 chr10 135534747 6226369 0.04593928227128354 0.4368910782478803 chr11 135006516 5618035 0.04161306555011019 0.32103312466307404 chr12 133851895 7835339 0.058537378196999 0.2885939528890362 chr13 115169878 3180609 0.027616674214068368 0.19141984690118108 chr14 107349540 4080930 0.03801534687526374 0.25797148437403444 chr15 102531392 3603000 0.03514045727575804 0.2212197843828401 chr16 90354753 3948158 0.04369618496992626 0.28043093565445115 chr17 81195210 3155619 0.038864595583902053 0.2591378583886372 chr18 78077248 4070118 0.05212937320741633 0.7274845469795793 chr19 59128983 2346150 0.03967851095967607 0.5909406265877195 chr20 63025520 3695296 0.05863174155484953 0.2882020543159914 chr21 48129895 1799286 0.03738395855631931 0.2607802442915703 chr22 51304566 1731671 0.03375276578696719 0.21026369399825015 chrMT 16571 17923 1.0815883169392313 1.4090661840514596 chrX 155270560 11116436 0.07159397119453939 0.3492217557377008 chrY 59373566 454445 0.00765399538238953 0.1981184344508886