BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716590.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 = 413,875 number of mapped reads = 360,440 (87.09%) number of supplementary alignments = 940 (0.23%) number of secondary alignments = 0 number of mapped bases = 21,013,391 bp number of sequenced bases = 21,006,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,497 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3323 >>>>>>> ACTG content number of A's = 5,500,788 bp (26.19%) number of C's = 3,968,890 bp (18.89%) number of T's = 6,380,614 bp (30.37%) number of G's = 5,156,121 bp (24.55%) number of N's = 196 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 101,684 number of insertions = 1,742 mapped reads with insertion percentage = 0.48% number of deletions = 4,231 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 0.0068X std coverageData = 0.0914X There is a 0.65% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1674166 0.006716797708600293 0.09877564902743174 chr2 243199373 1766413 0.0072632300741992456 0.10638783164509133 chr3 198022430 1405476 0.007097559604737706 0.08684521531685692 chr4 191154276 1329458 0.006954895426979619 0.0881101969533406 chr5 180915260 1241852 0.006864274467504842 0.08518508947553861 chr6 171115067 1185410 0.006927560622116345 0.08949483408243192 chr7 159138663 1165093 0.007321244115265691 0.10918081199525158 chr8 146364022 1060861 0.007248099536373768 0.0918707566251813 chr9 141213431 865714 0.006130535841169385 0.08457640452591424 chr10 135534747 1019394 0.0075212742308804394 0.10017757353342518 chr11 135006516 948266 0.007023853574593392 0.09100767897552557 chr12 133851895 962879 0.007193615002611655 0.08704040684291478 chr13 115169878 661427 0.005743055488866629 0.07782554434680758 chr14 107349540 636055 0.00592508361004621 0.08013893364166678 chr15 102531392 611229 0.005961384002277078 0.0793185725214183 chr16 90354753 651194 0.007207080738740993 0.08946836294840482 chr17 81195210 592439 0.007296477218298961 0.08918376242725706 chr18 78077248 561329 0.00718940554872016 0.10782917380148119 chr19 59128983 454252 0.007682391560835741 0.1015502675699146 chr20 63025520 457338 0.007256393917892308 0.08801331107253517 chr21 48129895 270255 0.005615117174055751 0.0787633198302422 chr22 51304566 254770 0.004965834814780423 0.07279221058798938 chrMT 16571 1857 0.11206324301490556 0.3281652185530924 chrX 155270560 1176500 0.007577096392258777 0.09127233278180205 chrY 59373566 59764 0.0010065758893444264 0.040992797123171526