BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716694.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 = 2,523,799 number of mapped reads = 2,375,652 (94.13%) number of supplementary alignments = 39,796 (1.58%) number of secondary alignments = 0 number of mapped bases = 189,225,440 bp number of sequenced bases = 189,141,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,101 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4728 >>>>>>> ACTG content number of A's = 45,807,612 bp (24.22%) number of C's = 37,895,175 bp (20.04%) number of T's = 57,613,046 bp (30.46%) number of G's = 47,814,883 bp (25.28%) number of N's = 11,075 bp (0.01%) GC percentage = 45.32% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,537,039 number of insertions = 16,109 mapped reads with insertion percentage = 0.67% number of deletions = 47,591 mapped reads with deletion percentage = 1.97% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.0611X std coverageData = 0.8066X There is a 5.02% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 15062636 0.060431688954548285 1.2955108881981174 chr2 243199373 15514179 0.06379201890458822 1.4182450516642944 chr3 198022430 14262103 0.07202266430121072 0.3345934661972492 chr4 191154276 7545744 0.03947462833632871 0.26488344411833853 chr5 180915260 11752984 0.06496402791008343 0.3157801259704889 chr6 171115067 13633235 0.07967290805548993 0.4549260112811239 chr7 159138663 10588404 0.06653571043260556 1.1240300943354549 chr8 146364022 13717312 0.09372051828419965 1.0839493227062453 chr9 141213431 8303183 0.05879881921429981 0.7606516440155632 chr10 135534747 9240031 0.0681746283113658 0.6811283353493717 chr11 135006516 7650364 0.05666662785372523 0.5438848808867169 chr12 133851895 7095349 0.05300895441188935 0.2882275741074437 chr13 115169878 6516563 0.056582182018114144 0.27473035219095626 chr14 107349540 4487280 0.04180064488399298 0.34987227107446867 chr15 102531392 3165483 0.0308733056116121 0.2160326036538395 chr16 90354753 4947047 0.054751375392504256 0.36764124862063935 chr17 81195210 6895503 0.08492499742287753 0.42160876431346705 chr18 78077248 5838120 0.0747736395627059 1.8905396474377985 chr19 59128983 4327812 0.07319273527839977 0.9919008461589052 chr20 63025520 3512537 0.055731979680611915 0.3973436930308022 chr21 48129895 3748173 0.07787619316435243 0.3546068473488411 chr22 51304566 2821997 0.05500479236097621 0.2791198243959138 chrMT 16571 160978 9.714440890712691 6.585615415886535 chrX 155270560 7982132 0.0514078908455022 0.4568968299711947 chrY 59373566 456291 0.0076850866596087555 0.21813096111728467