BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082445.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 = 2,291,331 number of mapped reads = 2,080,781 (90.81%) number of supplementary alignments = 17,691 (0.77%) number of secondary alignments = 0 number of mapped bases = 144,417,336 bp number of sequenced bases = 144,360,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,538 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6757 >>>>>>> ACTG content number of A's = 42,612,585 bp (29.52%) number of C's = 27,047,969 bp (18.74%) number of T's = 44,050,596 bp (30.51%) number of G's = 30,646,876 bp (21.23%) number of N's = 2,962 bp (0%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,242,579 number of insertions = 12,338 mapped reads with insertion percentage = 0.59% number of deletions = 33,967 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.21% >>>>>>> Coverage mean coverageData = 0.0467X std coverageData = 0.4503X There is a 4.11% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.05% 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 11345498 0.045518434234914106 0.8264972290403901 chr2 243199373 12399096 0.05098325644120801 0.46754360526463595 chr3 198022430 9930987 0.05015081877340865 0.2481762433590917 chr4 191154276 9891737 0.051747401141055305 0.26288580824629126 chr5 180915260 9162063 0.05064284240035915 0.24766080492195836 chr6 171115067 8654294 0.05057587360205983 0.29710739545577086 chr7 159138663 7990009 0.05020784295517174 0.59469823065329 chr8 146364022 7558031 0.051638585061566565 0.8621946642367327 chr9 141213431 6094812 0.04316028551136896 0.4000416259375251 chr10 135534747 6710719 0.04951290461330923 0.41100936004299515 chr11 135006516 6513520 0.048245967624258965 0.3565424472607045 chr12 133851895 6481114 0.048420039178376964 0.24418334761601931 chr13 115169878 4825816 0.04190172017026882 0.22255132936903005 chr14 107349540 4333330 0.040366544654033915 0.24545457985348207 chr15 102531392 3947229 0.03849776076384489 0.21542391824038898 chr16 90354753 3815470 0.04222766233448726 0.2712235808573383 chr17 81195210 3386802 0.0417118448243437 0.2558494076467081 chr18 78077248 3991727 0.05112535472561738 0.7330109548876519 chr19 59128983 2449773 0.04143100178130918 0.6363778752038521 chr20 63025520 2746002 0.04356968415333979 0.23620920927641958 chr21 48129895 1886757 0.03920135292212875 0.2383656700068834 chr22 51304566 1367902 0.026662383227255056 0.17625254035654137 chrMT 16571 4849 0.2926196367147426 0.5226213031116588 chrX 155270560 8568782 0.05518613444815295 0.28944811994461483 chrY 59373566 361017 0.0060804331678511615 0.14424501925840905