BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089379.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 28,698,848 number of mapped reads = 26,976,009 (94%) number of supplementary alignments = 132,638 (0.46%) number of secondary alignments = 0 number of mapped bases = 1,792,546,198 bp number of sequenced bases = 1,791,922,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,078,310 duplication rate = 14.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7715 >>>>>>> ACTG content number of A's = 468,129,255 bp (26.12%) number of C's = 343,602,662 bp (19.18%) number of T's = 548,404,201 bp (30.6%) number of G's = 431,591,237 bp (24.09%) number of N's = 194,735 bp (0.01%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,967,978 number of insertions = 115,625 mapped reads with insertion percentage = 0.42% number of deletions = 350,608 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.579X std coverageData = 3.5879X There is a 18.32% of reference with a coverageData >= 1X There is a 11.13% of reference with a coverageData >= 2X There is a 7.32% of reference with a coverageData >= 3X There is a 5.03% of reference with a coverageData >= 4X There is a 3.56% of reference with a coverageData >= 5X There is a 2.57% of reference with a coverageData >= 6X There is a 1.9% of reference with a coverageData >= 7X There is a 1.42% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 0.84% of reference with a coverageData >= 10X There is a 0.65% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 139317282 0.5589445733015846 6.036699988432497 chr2 243199373 157728268 0.6485554056095366 4.414985630636556 chr3 198022430 118458766 0.5982088291715236 1.9747702763884196 chr4 191154276 114977922 0.6014928067839822 2.7324774648289147 chr5 180915260 109999490 0.6080166482363069 1.9629031940278474 chr6 171115067 100613766 0.5879889349545122 2.480524971439183 chr7 159138663 93827507 0.5895959236505588 4.445018489229276 chr8 146364022 92122832 0.6294089950602751 3.235521274109725 chr9 141213431 71482457 0.5062015453756662 3.549797032304476 chr10 135534747 86098942 0.6352536445875389 4.608192678236111 chr11 135006516 83222272 0.6164315209793282 4.082518030733129 chr12 133851895 81945405 0.6122095245644449 2.072129878638775 chr13 115169878 54775088 0.4756025529522572 1.7033650035088823 chr14 107349540 54315398 0.5059676827679 1.9292669908422184 chr15 102531392 51248113 0.4998285110573745 1.8904990501277708 chr16 90354753 54977623 0.6084640948550875 2.577360129821083 chr17 81195210 47362788 0.5833199766340896 2.599968723951163 chr18 78077248 46584867 0.596650985956882 7.501570830374269 chr19 59128983 37295368 0.630745974440318 4.015554703037409 chr20 63025520 41400083 0.656878086844821 2.3657184658561867 chr21 48129895 22852622 0.4748113828214252 2.6122108317956187 chr22 51304566 22205064 0.4328087289540662 1.6682533863350115 chrMT 16571 257831 15.559169633697422 22.637541869974182 chrX 155270560 104501145 0.6730261357980547 2.7817050491279276 chrY 59373566 4975299 0.08379653329227353 2.0999448254836985