BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525063.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 = 601,718 number of mapped reads = 489,754 (81.39%) number of supplementary alignments = 1,415 (0.24%) number of secondary alignments = 0 number of mapped bases = 28,580,620 bp number of sequenced bases = 28,571,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,883 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2561 >>>>>>> ACTG content number of A's = 7,655,940 bp (26.8%) number of C's = 5,253,208 bp (18.39%) number of T's = 8,822,358 bp (30.88%) number of G's = 6,837,254 bp (23.93%) number of N's = 2,560 bp (0.01%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 138,091 number of insertions = 2,444 mapped reads with insertion percentage = 0.5% number of deletions = 5,764 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.02% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.1206X There is a 0.86% of reference with a coverageData >= 1X There is a 0.04% 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 2303936 0.00924345139344708 0.19553309666814292 chr2 243199373 2399566 0.009866661950645736 0.13370924934398254 chr3 198022430 1925555 0.009723923698946629 0.10312951963204024 chr4 191154276 1905733 0.009969606957680613 0.10950332859861789 chr5 180915260 1749474 0.009670129540205729 0.10292202243959277 chr6 171115067 1656818 0.009682478749811084 0.10633933027104847 chr7 159138663 1590068 0.009991713955772018 0.13204064541122928 chr8 146364022 1429292 0.00976532333881888 0.12149643495219145 chr9 141213431 1208115 0.008555241462832243 0.10777506055107032 chr10 135534747 1387188 0.010234925218106617 0.13010277613271798 chr11 135006516 1309111 0.009696650493521364 0.10971824547710414 chr12 133851895 1267610 0.009470243211722927 0.1033345345888094 chr13 115169878 899431 0.007809602785200484 0.09268554204945494 chr14 107349540 867903 0.008084832035610027 0.09428759131220621 chr15 102531392 804478 0.007846162861028943 0.09215893626121481 chr16 90354753 818051 0.009053768316980513 0.10302716684776933 chr17 81195210 741456 0.0091317702115679 0.10295437811757008 chr18 78077248 772814 0.009898069153257041 0.1429642229737538 chr19 59128983 557302 0.00942519170336483 0.1406131011151347 chr20 63025520 598431 0.009495058509632288 0.10317612134197006 chr21 48129895 390595 0.008115434284658215 0.09795382439388839 chr22 51304566 325579 0.0063460043692797246 0.08352940231004526 chrMT 16571 1259 0.07597610283024561 0.2870430369461055 chrX 155270560 1579263 0.010171039506780938 0.10871467322112174 chrY 59373566 91592 0.0015426393624395072 0.06147621877664484