BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080804.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,493,755 number of mapped reads = 2,266,086 (90.87%) number of supplementary alignments = 20,314 (0.81%) number of secondary alignments = 0 number of mapped bases = 154,424,400 bp number of sequenced bases = 154,367,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,140 duplication rate = 5.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8136 >>>>>>> ACTG content number of A's = 43,990,094 bp (28.5%) number of C's = 28,735,749 bp (18.62%) number of T's = 48,846,744 bp (31.64%) number of G's = 32,773,169 bp (21.23%) number of N's = 21,896 bp (0.01%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,249,403 number of insertions = 11,589 mapped reads with insertion percentage = 0.51% number of deletions = 31,907 mapped reads with deletion percentage = 1.39% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.3595X There is a 3.77% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 11850833 0.04754585145045637 0.43338402259672115 chr2 243199373 13048290 0.05365264654691359 0.41315043316091826 chr3 198022430 10357883 0.05230661496275952 0.287737639317814 chr4 191154276 10469743 0.05477116818459243 0.3090066084317318 chr5 180915260 8475810 0.04684961345991488 0.27291865221312483 chr6 171115067 9299781 0.05434811301567033 0.36163249614996684 chr7 159138663 8129482 0.05108426730969833 0.38168142180727677 chr8 146364022 8254735 0.056398661960792525 0.6303922304824126 chr9 141213431 6641657 0.04703275710367805 0.32301551674425694 chr10 135534747 7827813 0.05775502720346687 0.43317226975858036 chr11 135006516 6984704 0.05173605102141885 0.3133999924161489 chr12 133851895 7658055 0.05721289937658335 0.3036242221075919 chr13 115169878 5142801 0.0446540457392861 0.26793198830957315 chr14 107349540 4731064 0.044071581489776294 0.2702362413408578 chr15 102531392 4594766 0.04481326070360968 0.26705302532485264 chr16 90354753 4304853 0.04764390203136298 0.29079863319628485 chr17 81195210 3660444 0.04508201900087456 0.27325306463888394 chr18 78077248 4052175 0.051899562341131696 0.5054442008494067 chr19 59128983 2688358 0.04546599423162749 0.36343035998907475 chr20 63025520 3077017 0.04882176299378411 0.2833150689453607 chr21 48129895 2084267 0.04330503941469226 0.2752252248919041 chr22 51304566 1507342 0.029380269974411243 0.21355018753318916 chrMT 16571 101400 6.119123770442339 4.362978793226237 chrX 155270560 9094060 0.058569119606446965 0.31836076809158836 chrY 59373566 387067 0.006519180606399825 0.15587059398002678