BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013361.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 = 2,231,860 number of mapped reads = 1,898,417 (85.06%) number of supplementary alignments = 10,709 (0.48%) number of secondary alignments = 0 number of mapped bases = 124,193,715 bp number of sequenced bases = 124,127,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,412 duplication rate = 5.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9149 >>>>>>> ACTG content number of A's = 34,236,558 bp (27.58%) number of C's = 22,291,441 bp (17.96%) number of T's = 39,984,415 bp (32.21%) number of G's = 27,613,494 bp (22.25%) number of N's = 1,771 bp (0%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 987,087 number of insertions = 9,258 mapped reads with insertion percentage = 0.48% number of deletions = 37,714 mapped reads with deletion percentage = 1.96% homopolymer indels = 48.84% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.4043X There is a 3.05% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 9042946 0.036280535485606676 0.6274717586011715 chr2 243199373 13080015 0.05378309507401567 0.4992843660511329 chr3 198022430 9552639 0.04824018673036181 0.2766202379784198 chr4 191154276 8832751 0.04620744659669554 0.2859504604554802 chr5 180915260 6565882 0.03629258250520161 0.24004115923995972 chr6 171115067 7507288 0.04387274675233596 0.3120496349583855 chr7 159138663 7266498 0.045661424213423236 0.7075942422517342 chr8 146364022 7428528 0.0507537842872342 0.5908972516608407 chr9 141213431 5169924 0.03661071020928597 0.35966942201133256 chr10 135534747 4949143 0.03651567667736156 0.3550506166341659 chr11 135006516 5131821 0.0380116541930465 0.33526028160795845 chr12 133851895 5776674 0.043157207449323 0.2659450451502408 chr13 115169878 3176432 0.0275804060502695 0.2082844586354167 chr14 107349540 4590570 0.04276282879274564 0.274731243012734 chr15 102531392 2770054 0.02701664286387529 0.21084692131793112 chr16 90354753 2922935 0.032349543360491506 0.2407871492252752 chr17 81195210 3434877 0.04230393640215968 0.2789792191309337 chr18 78077248 3206817 0.041072362079155246 0.6788953367586146 chr19 59128983 1948921 0.03296050263539963 0.44257772385241245 chr20 63025520 2139013 0.033938839378080496 0.24182268713513347 chr21 48129895 1787422 0.03713745895352566 0.25494769678803847 chr22 51304566 1255599 0.02447343575618591 0.1914593485281346 chrMT 16571 50506 3.047854685897049 2.8449430778820948 chrX 155270560 6339597 0.04082935618960864 0.2770535676680327 chrY 59373566 266863 0.004494643289574354 0.11207918668103084