BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549020.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,613,260 number of mapped reads = 7,452,419 (86.52%) number of secondary alignments = 0 number of mapped bases = 295,264,149 bp number of sequenced bases = 295,231,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 374,417 duplication rate = 3.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2907 >>>>>>> ACTG content number of A's = 86,213,425 bp (29.2%) number of C's = 61,219,053 bp (20.74%) number of T's = 86,524,393 bp (29.31%) number of G's = 61,272,001 bp (20.75%) number of N's = 3,103 bp (0%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 762,761 number of insertions = 8,731 mapped reads with insertion percentage = 0.12% number of deletions = 24,336 mapped reads with deletion percentage = 0.33% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.0954X std coverageData = 1.2774X There is a 6.75% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% 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 23434247 0.09401881088994359 0.9866970946958404 chr2 243199373 24885442 0.10232527203102616 0.5569730110782689 chr3 198022430 19721427 0.09959188461630332 0.4222825932383596 chr4 191154276 19495000 0.10198568615854557 0.4404587791670989 chr5 180915260 18322247 0.10127529872272797 0.42813917421951997 chr6 171115067 17274177 0.10095064860653095 0.4576854072925262 chr7 159138663 16220555 0.10192717906647236 0.7575505534436474 chr8 146364022 15449934 0.10555827715639025 5.282971719885246 chr9 141213431 12381278 0.08767776487209633 0.51808078021636 chr10 135534747 13678364 0.10092145595697316 0.5210101245349458 chr11 135006516 13500697 0.10000033628006517 0.6668991724586741 chr12 133851895 13270380 0.09914226466498663 0.4297736590288784 chr13 115169878 9707197 0.08428590156186498 0.3847629340662225 chr14 107349540 9083679 0.0846177729313046 0.4375251049453509 chr15 102531392 8634741 0.08421558345760097 0.3819458940983376 chr16 90354753 8107314 0.08972758743527305 0.41586776887130616 chr17 81195210 7687804 0.09468297452522138 0.4486842684719034 chr18 78077248 7805259 0.09996841845655216 0.8707186855902599 chr19 59128983 5556473 0.09397207119222734 0.8090929577555828 chr20 63025520 6029880 0.09567362554089201 0.4279452123371726 chr21 48129895 3848005 0.07995041335535845 0.4098098833372459 chr22 51304566 3283999 0.06400987779528239 0.38146548316775203 chrMT 16571 49225 2.970550962524893 3.901227769630634 chrX 155270560 16979268 0.10935278394049716 0.5226292453973407 chrY 59373566 857557 0.014443414094413666 0.22510858650470303