BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013360.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 = 2,022,918 number of mapped reads = 1,834,210 (90.67%) number of supplementary alignments = 11,309 (0.56%) number of secondary alignments = 0 number of mapped bases = 124,410,861 bp number of sequenced bases = 124,361,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,903 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4247 >>>>>>> ACTG content number of A's = 35,476,115 bp (28.53%) number of C's = 22,699,438 bp (18.25%) number of T's = 39,707,226 bp (31.93%) number of G's = 26,452,068 bp (21.27%) number of N's = 27,129 bp (0.02%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 971,432 number of insertions = 9,493 mapped reads with insertion percentage = 0.51% number of deletions = 27,931 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.439X There is a 3.44% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9257215 0.037140188308698335 0.7040232097865589 chr2 243199373 13076163 0.053767256217391646 0.49297212315397465 chr3 198022430 9986018 0.050428721635220816 0.25092119443441663 chr4 191154276 10940648 0.05723464956651035 0.28913274677025 chr5 180915260 5905845 0.032644261186148694 0.20487821371318957 chr6 171115067 8268616 0.04832196337216757 0.3169668395241398 chr7 159138663 6018289 0.03781789344302836 0.6605101745224065 chr8 146364022 8334209 0.056941650592247324 0.6998544020179411 chr9 141213431 5016741 0.0355259479532085 0.4037968933256608 chr10 135534747 4373861 0.03227114151030215 0.37075814633538934 chr11 135006516 4787417 0.03546063658142248 0.2958375533907191 chr12 133851895 5698986 0.04257680475872232 0.24068873551983125 chr13 115169878 2702447 0.023464876814404543 0.17395216442911487 chr14 107349540 4743775 0.04418998907680462 0.25928324866896585 chr15 102531392 2239702 0.02184406118274489 0.1694422069404544 chr16 90354753 2727059 0.030181688394411304 0.22521231800825975 chr17 81195210 3442259 0.042394853095398116 0.24790223461370325 chr18 78077248 3327885 0.04262298025668118 0.8112487313677299 chr19 59128983 1658742 0.028052943173401106 0.47595326352887135 chr20 63025520 2059607 0.03267893704010693 0.2155409737555497 chr21 48129895 1899757 0.03947145531898626 0.23836888100305534 chr22 51304566 1232582 0.024024801223345306 0.1711939045999892 chrMT 16571 819811 49.47263291292016 27.20994225253637 chrX 155270560 5653731 0.03641212474534773 0.24241779250618387 chrY 59373566 239496 0.004033714262673729 0.12163756441436022