BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714152.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 720,660 number of mapped reads = 695,953 (96.57%) number of supplementary alignments = 12,963 (1.8%) number of secondary alignments = 0 number of mapped bases = 91,967,046 bp number of sequenced bases = 89,999,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 673,009 duplication rate = 35.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.179 >>>>>>> ACTG content number of A's = 26,303,335 bp (29.23%) number of C's = 18,127,358 bp (20.14%) number of T's = 25,955,822 bp (28.84%) number of G's = 19,612,357 bp (21.79%) number of N's = 690 bp (0%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0388 number of mismatches = 3,377,398 number of insertions = 53,298 mapped reads with insertion percentage = 7.46% number of deletions = 373,458 mapped reads with deletion percentage = 51.07% homopolymer indels = 32.26% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 34.2643X There is a 0.03% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% 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 2378699 0.009543402501693266 6.353824688287075 chr2 243199373 1505338 0.006189728128945464 3.014455841436152 chr3 198022430 23505851 0.11870297218350466 68.59539537637274 chr4 191154276 1480518 0.007745147171073484 3.1178646346145933 chr5 180915260 1574480 0.008702859007029037 5.578507974533385 chr6 171115067 973138 0.00568703865218368 1.9376122073834983 chr7 159138663 232790 0.0014628123399528623 0.3680051224684231 chr8 146364022 8145376 0.055651490637501064 37.020338365051 chr9 141213431 3564839 0.02524433387642851 14.561715086976761 chr10 135534747 491727 0.0036280511889692757 2.2558995612368298 chr11 135006516 1775495 0.01315118005119101 3.963545514939864 chr12 133851895 10360692 0.07740414881686956 44.66561074407059 chr13 115169878 3453073 0.029982431691036437 12.686392367825757 chr14 107349540 6446710 0.06005344783033071 43.941318428127516 chr15 102531392 857360 0.008361926852607249 1.9283633482923368 chr16 90354753 17457763 0.19321355457637077 145.86233142876392 chr17 81195210 57098 7.032188228837638E-4 0.11677780564818173 chr18 78077248 827024 0.010592381534759013 6.4028365872336535 chr19 59128983 201065 0.003400447459074343 1.246585238094287 chr20 63025520 667751 0.010594930434528744 2.1187342281448833 chr21 48129895 1674920 0.034799992811120825 13.88413887507317 chr22 51304566 61634 0.0012013355692356894 0.4422142207749969 chrMT 16571 49126 2.9645766700862954 24.383013471475046 chrX 155270560 4179987 0.02692066673811185 11.477123812965665 chrY 59373566 44592 7.510412967279075E-4 0.34646037633979826