BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008683.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,920,779 number of mapped reads = 1,620,186 (84.35%) number of supplementary alignments = 7,077 (0.37%) number of secondary alignments = 0 number of mapped bases = 100,776,865 bp number of sequenced bases = 100,715,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,040 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1964 >>>>>>> ACTG content number of A's = 25,962,785 bp (25.78%) number of C's = 18,426,737 bp (18.3%) number of T's = 31,460,481 bp (31.24%) number of G's = 24,824,121 bp (24.65%) number of N's = 41,862 bp (0.04%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 858,293 number of insertions = 7,307 mapped reads with insertion percentage = 0.45% number of deletions = 34,600 mapped reads with deletion percentage = 2.11% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.3847X There is a 2.88% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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% 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 8402886 0.03371259805206263 0.7156653897535487 chr2 243199373 8035610 0.03304124472393274 0.5033170934804507 chr3 198022430 7164089 0.036178169311425985 0.24188171761632352 chr4 191154276 5087932 0.026616888235343476 0.2014667278486737 chr5 180915260 4813974 0.026608999152420862 0.1795024292096151 chr6 171115067 5876049 0.034339752208962404 0.25071483515303256 chr7 159138663 4535685 0.028501464788603884 0.30313040197680663 chr8 146364022 8690269 0.059374352257141445 0.3713263091299546 chr9 141213431 2497246 0.017684196059226123 0.3181125623194585 chr10 135534747 6859345 0.05060949425758695 0.7785361086690168 chr11 135006516 4277641 0.0316847003147611 0.3058999485179214 chr12 133851895 3902335 0.0291541259090878 0.19095353622758535 chr13 115169878 3157985 0.027420233960827847 0.17801767155869744 chr14 107349540 2988029 0.027834576654916267 0.1914327572114033 chr15 102531392 2831675 0.027617639288462992 0.18281542510098858 chr16 90354753 3096897 0.0342748654296028 0.2881698079157976 chr17 81195210 3383774 0.04167455198403945 0.3125759123381393 chr18 78077248 2229175 0.02855089103550371 0.551875498924018 chr19 59128983 2346350 0.03968189339566351 0.4974598119349347 chr20 63025520 2810049 0.04458589155630925 0.23826756082451078 chr21 48129895 1219969 0.025347426999373257 0.19488321094899583 chr22 51304566 1403098 0.027348404038736045 0.17882716840340163 chrMT 16571 33067 1.9954740208798503 1.8019354244572103 chrX 155270560 4769197 0.030715397690328418 0.24061823307294825 chrY 59373566 364539 0.006139752495243422 0.22522682638174293