BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238274.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 = 1,577,600 number of mapped reads = 1,437,876 (91.14%) number of supplementary alignments = 11,935 (0.76%) number of secondary alignments = 0 number of mapped bases = 96,167,754 bp number of sequenced bases = 96,115,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,927 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3976 >>>>>>> ACTG content number of A's = 26,979,083 bp (28.07%) number of C's = 18,341,530 bp (19.08%) number of T's = 29,402,017 bp (30.59%) number of G's = 21,373,319 bp (22.24%) number of N's = 19,995 bp (0.02%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 860,054 number of insertions = 8,521 mapped reads with insertion percentage = 0.59% number of deletions = 30,790 mapped reads with deletion percentage = 2.11% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.3445X There is a 2.77% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 9558288 0.03834810104645637 0.653580677038053 chr2 243199373 7448273 0.030626201491070457 0.3778233960259267 chr3 198022430 5875178 0.02966925514448035 0.1896206092465021 chr4 191154276 3956411 0.020697475791752625 0.18107522108588342 chr5 180915260 6211016 0.03433107853920117 0.20446974776218688 chr6 171115067 4640619 0.02711987366956996 0.2037658028800185 chr7 159138663 5959564 0.037448875638725204 0.48241285225534974 chr8 146364022 4329857 0.029582795968807144 0.4143941285580545 chr9 141213431 4422367 0.03131690072738194 0.3524605786471021 chr10 135534747 3788091 0.027949223972801602 0.32836617607137236 chr11 135006516 4643320 0.0343933029128757 0.30335060340700987 chr12 133851895 5075255 0.03791694544182583 0.21802313968904774 chr13 115169878 2420250 0.021014609392917827 0.1552310229644603 chr14 107349540 3229486 0.03008383640954586 0.22735477718409688 chr15 102531392 2406690 0.02347271360560481 0.16834866640316237 chr16 90354753 3330114 0.03685599140534422 0.24779396324365935 chr17 81195210 2679203 0.03299705733872725 0.23531249575322677 chr18 78077248 2921955 0.03742389844478125 0.6799635865931734 chr19 59128983 2252425 0.038093416895061426 0.4236139819813948 chr20 63025520 2256019 0.03579532544911966 0.20809732205136205 chr21 48129895 1059689 0.02201727221719474 0.20106226430180563 chr22 51304566 1251597 0.024395431003158666 0.169711968956032 chrMT 16571 3199 0.19304809607145013 0.5140849489935421 chrX 155270560 6163674 0.03969634681551996 0.24662674354485514 chrY 59373566 285214 0.004803720227954642 0.14392845109764843