BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708631.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,040,064 number of mapped reads = 2,200,783 (72.39%) number of supplementary alignments = 664 (0.02%) number of secondary alignments = 0 number of mapped bases = 107,204,920 bp number of sequenced bases = 107,184,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,398 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.485 >>>>>>> ACTG content number of A's = 31,829,714 bp (29.7%) number of C's = 20,070,432 bp (18.73%) number of T's = 33,878,858 bp (31.61%) number of G's = 21,396,480 bp (19.96%) number of N's = 9,102 bp (0.01%) GC percentage = 38.69% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 699,449 number of insertions = 5,002 mapped reads with insertion percentage = 0.23% number of deletions = 13,333 mapped reads with deletion percentage = 0.6% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.3553X There is a 2.95% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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% 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 8202028 0.03290675051116523 0.615614299305689 chr2 243199373 8618522 0.03543809300857038 0.35489001375258084 chr3 198022430 7949696 0.04014543200989908 0.23015170146239805 chr4 191154276 6696622 0.035032551403663084 0.2191882614576097 chr5 180915260 6983583 0.038601403773236155 0.228120947711686 chr6 171115067 5720329 0.033429721299761406 0.24742644439825223 chr7 159138663 6564296 0.04124890756434217 0.49691926069178777 chr8 146364022 5475653 0.03741119521845335 0.6110621238370254 chr9 141213431 4725936 0.03346661834170717 0.3094466529480124 chr10 135534747 5226879 0.03856486337042412 0.28145919317995216 chr11 135006516 4931203 0.0365256666574523 0.32979700259523015 chr12 133851895 5112460 0.03819490191005514 0.23054011766996474 chr13 115169878 3268545 0.028380207192717527 0.19437794100277486 chr14 107349540 3094754 0.028828758837718356 0.21498405041162005 chr15 102531392 3010130 0.02935813062988553 0.19602939957353913 chr16 90354753 2843846 0.03147422692860441 0.2184585788091233 chr17 81195210 2768351 0.034095003880154996 0.25080172334324535 chr18 78077248 2932157 0.03755456391085915 0.6481449359463599 chr19 59128983 1821914 0.030812537398114896 0.4576105579190108 chr20 63025520 2226558 0.035327879881038665 0.2232273152238421 chr21 48129895 1329655 0.027626384807197275 0.21279232989247893 chr22 51304566 1131300 0.022050668940460386 0.16619062096092418 chrMT 16571 3621 0.21851427192082554 0.5598434127100669 chrX 155270560 6302543 0.040590714685385304 0.264388765097527 chrY 59373566 264339 0.004452132789194437 0.09615514331273599