BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237290.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 = 3,074,468 number of mapped reads = 2,665,274 (86.69%) number of supplementary alignments = 21,534 (0.7%) number of secondary alignments = 0 number of mapped bases = 180,188,519 bp number of sequenced bases = 180,111,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,416 duplication rate = 6.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1445 >>>>>>> ACTG content number of A's = 50,602,145 bp (28.09%) number of C's = 33,465,833 bp (18.58%) number of T's = 56,707,199 bp (31.48%) number of G's = 39,333,289 bp (21.84%) number of N's = 2,939 bp (0%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,453,009 number of insertions = 14,503 mapped reads with insertion percentage = 0.54% number of deletions = 44,059 mapped reads with deletion percentage = 1.63% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.723X There is a 3.4% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 7934463 0.031833272744383655 1.2332791163658714 chr2 243199373 9652535 0.03968980216079751 0.9269490763431886 chr3 198022430 5470172 0.027624001988057617 0.24788653057046117 chr4 191154276 12138422 0.06350065640174327 0.4211101005934283 chr5 180915260 8256799 0.04563904117319899 0.33065366042440775 chr6 171115067 6102047 0.03566048920753425 0.31095498829760293 chr7 159138663 6025680 0.037864337216406044 0.5039585429900062 chr8 146364022 11866048 0.08107216403222371 1.5345726394358579 chr9 141213431 9589859 0.0679103887788124 0.7321208396804105 chr10 135534747 5712557 0.0421482839378451 0.5661929983829371 chr11 135006516 19172394 0.1420108789415764 0.9422272924255434 chr12 133851895 14364575 0.10731693413828769 0.5169053603004756 chr13 115169878 6010131 0.052184921130158705 0.35190825357851396 chr14 107349540 5681185 0.052922304091848 0.37479668027722457 chr15 102531392 3038336 0.029633226865777847 0.27118331301869114 chr16 90354753 4692752 0.051936968938424304 0.39294272234510075 chr17 81195210 5235764 0.06448365611715272 0.5161094717850525 chr18 78077248 7920029 0.10143837293035739 1.1070121824632644 chr19 59128983 4415721 0.07467946810449962 0.7772540394578166 chr20 63025520 4451913 0.07063667225593696 0.43625180821137877 chr21 48129895 6575277 0.13661523674630913 0.6094018426366475 chr22 51304566 2708097 0.05278471705617781 0.34349601516916495 chrMT 16571 153012 9.23372156176453 6.4060540507806705 chrX 155270560 12481835 0.08038764721399859 0.5096092517897134 chrY 59373566 538916 0.009076699216617712 0.21788304739839912