BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080979.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,118,703 number of mapped reads = 3,453,350 (83.85%) number of supplementary alignments = 24,105 (0.59%) number of secondary alignments = 0 number of mapped bases = 233,143,679 bp number of sequenced bases = 233,061,085 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 239,556 duplication rate = 5.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3107 >>>>>>> ACTG content number of A's = 65,782,361 bp (28.23%) number of C's = 41,046,431 bp (17.61%) number of T's = 76,188,261 bp (32.69%) number of G's = 49,579,939 bp (21.27%) number of N's = 464,093 bp (0.2%) GC percentage = 38.89% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 2,264,848 number of insertions = 17,474 mapped reads with insertion percentage = 0.5% number of deletions = 46,762 mapped reads with deletion percentage = 1.34% homopolymer indels = 49.27% >>>>>>> Coverage mean coverageData = 0.0753X std coverageData = 0.5847X There is a 5.41% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 19152962 0.07684218367504088 0.8903432460658971 chr2 243199373 15724274 0.06465589859888331 0.4880291822289821 chr3 198022430 21155376 0.10683323096277528 0.431490569232629 chr4 191154276 15689718 0.08207882307586988 0.3920817857381488 chr5 180915260 14094719 0.07790785033832967 0.3698902904498723 chr6 171115067 20034601 0.11708262370607025 0.6213335767326685 chr7 159138663 11478063 0.07212617464305328 0.5424375932045667 chr8 146364022 18482023 0.12627435859886388 1.2517276889328417 chr9 141213431 11947119 0.0846032768653571 0.7101208355866434 chr10 135534747 9954358 0.0734450627631304 0.4766399401612484 chr11 135006516 10204966 0.07558869232652445 0.4398579459648992 chr12 133851895 9426401 0.07042411315880137 0.3716899119272752 chr13 115169878 6246740 0.054239355884357195 0.3029581075278268 chr14 107349540 6658723 0.06202842601840679 0.40188243706571253 chr15 102531392 5835488 0.056914159519067094 0.3096310239392896 chr16 90354753 5250460 0.05810939464357785 0.3768040445990594 chr17 81195210 4906505 0.0604285031099741 0.32700203695678287 chr18 78077248 5869223 0.0751720014516905 1.1227579239821077 chr19 59128983 3981835 0.06734151000026502 0.6633481272360792 chr20 63025520 3515154 0.05577350254309683 0.33241696075303356 chr21 48129895 4152988 0.08628707791695785 0.4466058837156778 chr22 51304566 1833426 0.035736117522171415 0.24064221350894882 chrMT 16571 116221 7.013517590972181 4.782501271105667 chrX 155270560 6933611 0.04465502668374481 0.31452406442669095 chrY 59373566 498725 0.008399781815362075 0.1703622999766701