BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716652.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 = 2,093,831 number of mapped reads = 1,918,904 (91.65%) number of supplementary alignments = 45,820 (2.19%) number of secondary alignments = 0 number of mapped bases = 138,741,698 bp number of sequenced bases = 138,695,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,954 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9208 >>>>>>> ACTG content number of A's = 36,254,323 bp (26.14%) number of C's = 28,978,589 bp (20.89%) number of T's = 40,629,134 bp (29.29%) number of G's = 32,818,597 bp (23.66%) number of N's = 15,328 bp (0.01%) GC percentage = 44.56% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,005,602 number of insertions = 9,939 mapped reads with insertion percentage = 0.51% number of deletions = 26,759 mapped reads with deletion percentage = 1.38% homopolymer indels = 39.49% >>>>>>> Coverage mean coverageData = 0.0448X std coverageData = 0.3637X There is a 3.88% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% 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% 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 11517419 0.046208185776195114 0.5177485922320635 chr2 243199373 13351300 0.054898579035399075 0.54951049438909 chr3 198022430 10068063 0.05084304338654969 0.2604161625845161 chr4 191154276 5759447 0.030129836070211687 0.20697076740088388 chr5 180915260 8803371 0.04866019041179832 0.2518416871907169 chr6 171115067 9761077 0.05704393640567023 0.3038332982531211 chr7 159138663 6883800 0.043256615772874756 0.4887689159186156 chr8 146364022 10565189 0.07218433092799267 0.4765062969187948 chr9 141213431 5898317 0.04176881022032529 0.3224060631986696 chr10 135534747 6636862 0.04896797424205912 0.3369853594023469 chr11 135006516 5302908 0.039278904138226926 0.30410874624443296 chr12 133851895 5131541 0.03833745499083147 0.22039118741413638 chr13 115169878 4942857 0.04291796679683901 0.23269930483059462 chr14 107349540 3259302 0.03036158329136762 0.21196869689870154 chr15 102531392 2673882 0.026078666717018726 0.18266279823240059 chr16 90354753 3376295 0.03736709899478116 0.24004815014069156 chr17 81195210 4205491 0.05179481646762167 0.2844812516024185 chr18 78077248 4160209 0.0532832432823452 0.6862934481930862 chr19 59128983 2364678 0.039991859829552626 0.4611837976261769 chr20 63025520 2454340 0.03894200317585638 0.24763238403330923 chr21 48129895 3048427 0.06333749533424081 0.2965167456045862 chr22 51304566 1737499 0.033866361914064336 0.20782819761254323 chrMT 16571 34393 2.0754933317240964 1.8751986314488525 chrX 155270560 6505635 0.04189870249711214 0.283080589969661 chrY 59373566 299396 0.0050425807336551085 0.13222860280952134