BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818979.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,297,236 number of mapped reads = 2,263,881 (98.55%) number of supplementary alignments = 33,360 (1.45%) number of secondary alignments = 0 number of mapped bases = 209,674,504 bp number of sequenced bases = 209,547,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,078,468 duplication rate = 39.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2973 >>>>>>> ACTG content number of A's = 58,943,181 bp (28.13%) number of C's = 43,167,689 bp (20.6%) number of T's = 60,991,816 bp (29.11%) number of G's = 46,435,501 bp (22.16%) number of N's = 9,714 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,278,725 number of insertions = 29,407 mapped reads with insertion percentage = 1.26% number of deletions = 67,721 mapped reads with deletion percentage = 2.92% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.0677X std coverageData = 0.7812X There is a 2.93% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 20805122 0.08347069273701027 1.2435733885270368 chr2 243199373 17007503 0.06993234723512219 1.1004617093662743 chr3 198022430 11185557 0.056486313191894476 0.4565329106046814 chr4 191154276 11841090 0.061945200744554625 0.5625538839696069 chr5 180915260 11432063 0.06319015322422221 0.5086840097504846 chr6 171115067 8801468 0.05143596151004049 0.5036703234790283 chr7 159138663 10537335 0.06621480161612267 1.0074945588492286 chr8 146364022 19215479 0.13128553545761404 0.7871608387227962 chr9 141213431 9185000 0.0650433881179475 0.7118361801371392 chr10 135534747 10538531 0.07775519734433857 0.9895937438810425 chr11 135006516 6962968 0.051575051384927226 0.5218760391810803 chr12 133851895 9583306 0.0715963416132435 0.5383068987138087 chr13 115169878 4350168 0.03777175139492637 0.3745905335441798 chr14 107349540 4946646 0.046079806210627454 0.4361195989529141 chr15 102531392 5614572 0.05475954135100399 0.4587143883604033 chr16 90354753 6831899 0.0756119492684574 0.9135740300446399 chr17 81195210 7450858 0.09176474819142656 0.6774758639716613 chr18 78077248 4698221 0.060174008694568744 0.8645348676625387 chr19 59128983 4486385 0.07587455038758234 1.2629344788743309 chr20 63025520 6214154 0.09859742529692735 0.6573537135237995 chr21 48129895 2923387 0.06073952581862063 0.5232540970281854 chr22 51304566 1832169 0.03571161677890424 0.4311740344781746 chrMT 16571 22211 1.3403536298352543 2.3165611080635897 chrX 155270560 12438954 0.08011147766840024 0.6515244170951 chrY 59373566 769458 0.012959605626517363 0.8646142897223369