BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238035.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 = 2,222,807 number of mapped reads = 1,987,446 (89.41%) number of supplementary alignments = 19,378 (0.87%) number of secondary alignments = 0 number of mapped bases = 133,297,280 bp number of sequenced bases = 133,240,913 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,840 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0031 >>>>>>> ACTG content number of A's = 36,097,109 bp (27.09%) number of C's = 25,711,314 bp (19.3%) number of T's = 41,167,136 bp (30.9%) number of G's = 30,246,477 bp (22.7%) number of N's = 18,877 bp (0.01%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 984,307 number of insertions = 9,134 mapped reads with insertion percentage = 0.46% number of deletions = 31,332 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.3959X There is a 3.39% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.14% 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 5967517 0.023941834030575995 0.6412703927886898 chr2 243199373 15403915 0.06333862957779912 0.45705135632912636 chr3 198022430 1456251 0.007353969951787785 0.10376359793099763 chr4 191154276 12380905 0.06476917628565107 0.33141139815054876 chr5 180915260 12295535 0.06796295127343044 0.32085486475032265 chr6 171115067 3093233 0.018076917797075112 0.18373487958764928 chr7 159138663 11332581 0.07121199076556274 0.7206694120567702 chr8 146364022 2684057 0.018338229322503858 0.32487045571479145 chr9 141213431 8952433 0.0633964697026588 0.4157770066992767 chr10 135534747 3937518 0.02905172354067994 0.34618352986245826 chr11 135006516 7114675 0.052698752703165826 0.36370311523138027 chr12 133851895 5902081 0.044094116112439054 0.2628850512653423 chr13 115169878 3640700 0.031611564266830254 0.2136568882257133 chr14 107349540 5312276 0.049485782612575704 0.32316110722723074 chr15 102531392 4584052 0.04470876587728371 0.2574501656105962 chr16 90354753 7020081 0.07769465099417626 0.3761443314206181 chr17 81195210 5018440 0.06180709428548802 0.3757683428171449 chr18 78077248 687786 0.008809045113885161 0.6335915961615101 chr19 59128983 2951228 0.049911698971720854 0.4712160655919794 chr20 63025520 3022725 0.04796033416305014 0.2752005913396123 chr21 48129895 1077501 0.022387354055104423 0.21957467225716584 chr22 51304566 3079733 0.06002843879431706 0.3027095673874182 chrMT 16571 54412 3.2835676784744434 2.937998354784207 chrX 155270560 6020639 0.038775148360384606 0.275481782542022 chrY 59373566 307006 0.0051707522502522415 0.13649470747035827