BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089712.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 = 21,431,281 number of mapped reads = 19,016,574 (88.73%) number of supplementary alignments = 135,440 (0.63%) number of secondary alignments = 0 number of mapped bases = 1,264,513,599 bp number of sequenced bases = 1,264,069,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,469,888 duplication rate = 14.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0825 >>>>>>> ACTG content number of A's = 336,909,295 bp (26.65%) number of C's = 236,055,617 bp (18.67%) number of T's = 395,878,632 bp (31.32%) number of G's = 294,526,256 bp (23.3%) number of N's = 699,280 bp (0.06%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 8,773,630 number of insertions = 85,626 mapped reads with insertion percentage = 0.45% number of deletions = 252,017 mapped reads with deletion percentage = 1.31% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.4085X std coverageData = 3.1031X There is a 11.17% of reference with a coverageData >= 1X There is a 7.25% of reference with a coverageData >= 2X There is a 5.13% of reference with a coverageData >= 3X There is a 3.77% of reference with a coverageData >= 4X There is a 2.83% of reference with a coverageData >= 5X There is a 2.15% of reference with a coverageData >= 6X There is a 1.65% of reference with a coverageData >= 7X There is a 1.27% of reference with a coverageData >= 8X There is a 0.99% of reference with a coverageData >= 9X There is a 0.77% of reference with a coverageData >= 10X There is a 0.61% of reference with a coverageData >= 11X There is a 0.48% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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% 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 99801463 0.40040607561816266 6.445256399217764 chr2 243199373 107976833 0.4439848329707659 3.2639164738228024 chr3 198022430 91292789 0.46102246599034263 1.8268929147175144 chr4 191154276 88245388 0.46164485486058393 2.1041827295221247 chr5 180915260 79300786 0.4383311059553517 1.7868684226815221 chr6 171115067 73794653 0.43125748242847606 2.1690747732606814 chr7 159138663 70248560 0.4414298742726021 3.620508165656626 chr8 146364022 60960377 0.4164983728036662 4.861327201719679 chr9 141213431 52772500 0.37370737065371634 2.375989901651902 chr10 135534747 59344319 0.4378531728103643 2.805369386209012 chr11 135006516 60596346 0.4488401582039196 2.3353036716352857 chr12 133851895 57611447 0.43041188920037327 1.956488378085039 chr13 115169878 41020875 0.3561771160337601 1.5886306639618075 chr14 107349540 36909217 0.3438227774427352 1.7271648177781376 chr15 102531392 35057269 0.3419174197888584 1.7939213156520726 chr16 90354753 32937008 0.36452988809564896 1.7843284825867174 chr17 81195210 30871074 0.3802080689242629 2.0359877914543425 chr18 78077248 31174980 0.3992837964780726 4.556676540525409 chr19 59128983 22462885 0.3798963530287676 3.7092897881703055 chr20 63025520 26623018 0.4224164751040531 1.924979705983633 chr21 48129895 15981697 0.3320534358115678 1.8767020472181626 chr22 51304566 12605465 0.24569869668130512 1.3865693269579296 chrMT 16571 110062 6.64184418562549 9.838815483349146 chrX 155270560 73278200 0.4719387886538182 1.9899969565555269 chrY 59373566 3536388 0.05956165745544069 1.7597465817622902