BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524886.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,118,238 number of mapped reads = 2,858,273 (91.66%) number of supplementary alignments = 11,034 (0.35%) number of secondary alignments = 0 number of mapped bases = 166,573,090 bp number of sequenced bases = 166,523,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,911 duplication rate = 4.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0989 >>>>>>> ACTG content number of A's = 41,378,391 bp (24.85%) number of C's = 33,488,284 bp (20.11%) number of T's = 53,824,828 bp (32.32%) number of G's = 37,809,412 bp (22.71%) number of N's = 22,232 bp (0.01%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 824,698 number of insertions = 13,967 mapped reads with insertion percentage = 0.49% number of deletions = 31,609 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.0538X std coverageData = 0.4956X There is a 4.58% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 13444252 0.053938690086553484 1.0324829061110725 chr2 243199373 14252887 0.05860577198116378 0.547728323322358 chr3 198022430 11009315 0.05559630290366602 0.269190516802348 chr4 191154276 10731894 0.056142578782804736 0.31651550450152593 chr5 180915260 9764832 0.05397461772986977 0.2681750131095123 chr6 171115067 9564150 0.05589309093395031 0.3169397772319876 chr7 159138663 9075318 0.05702773813048813 0.7127830658801886 chr8 146364022 8628732 0.058953914234469454 0.44956504893986265 chr9 141213431 6899988 0.048862122753748544 0.42056795849980655 chr10 135534747 7892272 0.05823061742240903 0.4420569843632217 chr11 135006516 7697591 0.05701644059905968 0.43565474089537765 chr12 133851895 7468600 0.05579749169782019 0.28129387535143985 chr13 115169878 5234098 0.04544676169579688 0.24505009379913895 chr14 107349540 5092895 0.04744216882531588 0.2742547749129844 chr15 102531392 4848359 0.047286581264789615 0.25542827746540314 chr16 90354753 4824567 0.05339582965823613 0.3056702679186588 chr17 81195210 4462250 0.05495705965906117 0.3034670035044588 chr18 78077248 4565333 0.058472001984496175 0.9156632631070659 chr19 59128983 3349094 0.056640480354617294 0.6367443129925683 chr20 63025520 3570605 0.05665332075007076 0.279763674384897 chr21 48129895 2219150 0.04610751799894847 0.2836257863346984 chr22 51304566 1994401 0.03887375248433054 0.2265521955571015 chrMT 16571 18081 1.0911230462856798 1.301692332740847 chrX 155270560 9451209 0.06086929164163509 0.345867927660324 chrY 59373566 513217 0.008643863499793831 0.21464796226232924