BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818779.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 = 1,064,506 number of mapped reads = 1,033,299 (97.07%) number of supplementary alignments = 9,223 (0.87%) number of secondary alignments = 0 number of mapped bases = 70,038,891 bp number of sequenced bases = 70,010,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,203 duplication rate = 35.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7958 >>>>>>> ACTG content number of A's = 20,453,287 bp (29.21%) number of C's = 15,375,065 bp (21.96%) number of T's = 19,861,670 bp (28.37%) number of G's = 14,316,502 bp (20.45%) number of N's = 4,380 bp (0.01%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 367,972 number of insertions = 7,841 mapped reads with insertion percentage = 0.75% number of deletions = 17,828 mapped reads with deletion percentage = 1.71% homopolymer indels = 42.31% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.3115X There is a 1.19% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 5740974 0.023032937598979945 0.4305161268308693 chr2 243199373 6103453 0.025096499734808115 0.45063873253699865 chr3 198022430 4706508 0.023767549968960588 0.2552659833623969 chr4 191154276 4697834 0.024576138699612452 0.28240804863224617 chr5 180915260 4328563 0.02392591426505426 0.25982590910389286 chr6 171115067 4151147 0.02425938915127795 0.2781925815986117 chr7 159138663 3874816 0.024348677605768247 0.3042965421614671 chr8 146364022 3625529 0.024770629765831387 0.29010744815859274 chr9 141213431 3022834 0.021406136644325283 0.2694911519245308 chr10 135534747 3443140 0.025404112791828946 0.32391459445321064 chr11 135006516 3282508 0.024313700532795024 0.2791013795404494 chr12 133851895 3215228 0.02402078805085277 0.26686691649022154 chr13 115169878 2306888 0.02003030688284657 0.23481163243276407 chr14 107349540 2193769 0.02043575594268965 0.2515229548432441 chr15 102531392 1993952 0.019447234267530474 0.23228269352470424 chr16 90354753 2050225 0.02269083730437512 0.32027734575745115 chr17 81195210 1857133 0.022872445308042187 0.2650115512648217 chr18 78077248 1975150 0.025297382407740602 0.35280536581283245 chr19 59128983 1327593 0.022452491699375247 0.3672057850930801 chr20 63025520 1446122 0.02294502290500737 0.26090481244970687 chr21 48129895 957559 0.019895306233267285 0.24489053338292713 chr22 51304566 798608 0.015566021940425341 0.2167580594049299 chrMT 16571 50841 3.068070725967051 3.398664532642005 chrX 155270560 2183322 0.014061403526850164 0.2086357235605788 chrY 59373566 705195 0.011877255275521097 0.44048121833175163