BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083609.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 = 1,978,361 number of mapped reads = 1,783,843 (90.17%) number of supplementary alignments = 18,149 (0.92%) number of secondary alignments = 0 number of mapped bases = 118,327,598 bp number of sequenced bases = 118,284,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,416 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4345 >>>>>>> ACTG content number of A's = 31,775,466 bp (26.86%) number of C's = 22,242,955 bp (18.8%) number of T's = 37,033,576 bp (31.31%) number of G's = 27,226,397 bp (23.02%) number of N's = 5,664 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 804,355 number of insertions = 8,711 mapped reads with insertion percentage = 0.48% number of deletions = 27,043 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.98% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.3007X There is a 3.16% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 13040349 0.05231822070365073 0.462219902727042 chr2 243199373 10833471 0.044545637048167885 0.45653914948941243 chr3 198022430 9588649 0.04842203481696493 0.2626659992643597 chr4 191154276 5200471 0.02720562212272981 0.19930012142762837 chr5 180915260 5448578 0.030116740843199187 0.20351608899460902 chr6 171115067 8442852 0.04934020216933907 0.3039646407008885 chr7 159138663 9699122 0.06094761522534596 0.4822085830445776 chr8 146364022 7508516 0.05130028471067842 0.3111165277076508 chr9 141213431 4769433 0.033774641450358925 0.2362612824143824 chr10 135534747 4175679 0.030808918690053703 0.22833821072744837 chr11 135006516 3699826 0.02740479578037552 0.20574193005169364 chr12 133851895 4615970 0.03448565296740849 0.21826169854215965 chr13 115169878 3909591 0.033946298006845156 0.21769754648199038 chr14 107349540 2037730 0.018982195918119445 0.16210444205063151 chr15 102531392 2941679 0.028690520460309364 0.2081868623284607 chr16 90354753 3301296 0.036537048582269936 0.23237409832981037 chr17 81195210 2753141 0.03390767755881166 0.22094080839002864 chr18 78077248 3101158 0.039719099730564277 0.31602615543806134 chr19 59128983 3512860 0.059410120414213785 0.39556980872580005 chr20 63025520 2787961 0.04423543034631051 0.25143026154129183 chr21 48129895 1961463 0.04075352751133157 0.24439183043528942 chr22 51304566 1003801 0.019565529508621123 0.16245205530655832 chrMT 16571 2285 0.13789149719389296 0.4101716443140422 chrX 155270560 3806822 0.024517345722202585 0.1892384170647312 chrY 59373566 184895 0.003114096262973324 0.07451606149274584