BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505922.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,895,980 number of mapped reads = 4,366,786 (74.06%) number of supplementary alignments = 246 (0%) number of secondary alignments = 0 number of mapped bases = 202,102,108 bp number of sequenced bases = 202,061,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,936 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0022 >>>>>>> ACTG content number of A's = 59,791,614 bp (29.59%) number of C's = 41,433,327 bp (20.51%) number of T's = 59,046,647 bp (29.22%) number of G's = 41,788,879 bp (20.68%) number of N's = 648 bp (0%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 997,177 number of insertions = 9,106 mapped reads with insertion percentage = 0.21% number of deletions = 29,566 mapped reads with deletion percentage = 0.68% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.0653X std coverageData = 0.5389X There is a 5.36% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 21471456 0.08614404214463321 1.1243837848403588 chr2 243199373 13739914 0.05649650256294041 0.3968831958988829 chr3 198022430 13694973 0.06915869581036856 0.3127061462985555 chr4 191154276 8579134 0.044880680566099396 0.2517259388440512 chr5 180915260 11459848 0.06334373341419623 0.29684146951852514 chr6 171115067 14450103 0.08444670158706714 0.45185033500460436 chr7 159138663 13857955 0.08708100683238743 0.8850427309173772 chr8 146364022 12589950 0.08601806528656339 0.6809244632689432 chr9 141213431 5521616 0.039101209855881204 0.32133084871172884 chr10 135534747 6675567 0.04925354676760491 0.6457396888578627 chr11 135006516 11552601 0.08557069201015453 0.48391220071042235 chr12 133851895 5941769 0.04439062293440074 0.2592625405007631 chr13 115169878 5620731 0.04880382872334032 0.25395758041391503 chr14 107349540 7834896 0.07298490519847593 0.39670134276118146 chr15 102531392 3983535 0.03885185719511152 0.22615865137821495 chr16 90354753 6780550 0.07504364490930543 0.3908421438846212 chr17 81195210 3606618 0.04441909812167491 0.28085582102309936 chr18 78077248 5241789 0.06713593440178629 0.5757133553131382 chr19 59128983 5230209 0.08845423571719473 0.8549149170695806 chr20 63025520 5257719 0.08342206458590108 0.3414317332752577 chr21 48129895 3065236 0.06368673773337756 0.3148876107752407 chr22 51304566 1661626 0.032387487694565044 0.21157033115330354 chrMT 16571 9803 0.5915756441976948 0.9616314349016636 chrX 155270560 13694534 0.08819787859334055 0.38562735536021786 chrY 59373566 579976 0.009768252760832994 0.15573122217641833