BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514732.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 48,556,393 number of mapped reads = 46,691,869 (96.16%) number of supplementary alignments = 1,435,463 (2.96%) number of secondary alignments = 0 number of mapped bases = 4,389,431,240 bp number of sequenced bases = 4,386,884,303 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,566,403 duplication rate = 44.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.994 >>>>>>> ACTG content number of A's = 1,135,177,224 bp (25.88%) number of C's = 1,034,697,208 bp (23.59%) number of T's = 1,147,832,325 bp (26.17%) number of G's = 1,039,718,387 bp (23.7%) number of N's = 29,459,159 bp (0.67%) GC percentage = 47.29% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 41,685,057 number of insertions = 1,640,082 mapped reads with insertion percentage = 3.34% number of deletions = 1,268,308 mapped reads with deletion percentage = 2.63% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 1.4179X std coverageData = 55.6473X There is a 3.98% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 2.06% of reference with a coverageData >= 3X There is a 1.8% of reference with a coverageData >= 4X There is a 1.62% of reference with a coverageData >= 5X There is a 1.49% of reference with a coverageData >= 6X There is a 1.38% of reference with a coverageData >= 7X There is a 1.29% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 1.14% of reference with a coverageData >= 10X There is a 1.09% of reference with a coverageData >= 11X There is a 1.03% of reference with a coverageData >= 12X There is a 0.99% of reference with a coverageData >= 13X There is a 0.95% of reference with a coverageData >= 14X There is a 0.91% of reference with a coverageData >= 15X There is a 0.87% of reference with a coverageData >= 16X There is a 0.84% of reference with a coverageData >= 17X There is a 0.81% of reference with a coverageData >= 18X There is a 0.78% of reference with a coverageData >= 19X There is a 0.76% of reference with a coverageData >= 20X There is a 0.73% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.69% of reference with a coverageData >= 23X There is a 0.67% of reference with a coverageData >= 24X There is a 0.65% of reference with a coverageData >= 25X There is a 0.64% of reference with a coverageData >= 26X There is a 0.62% of reference with a coverageData >= 27X There is a 0.6% of reference with a coverageData >= 28X There is a 0.59% of reference with a coverageData >= 29X There is a 0.58% of reference with a coverageData >= 30X There is a 0.56% of reference with a coverageData >= 31X There is a 0.55% of reference with a coverageData >= 32X There is a 0.54% of reference with a coverageData >= 33X There is a 0.53% of reference with a coverageData >= 34X There is a 0.52% of reference with a coverageData >= 35X There is a 0.51% of reference with a coverageData >= 36X There is a 0.5% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.48% of reference with a coverageData >= 39X There is a 0.47% of reference with a coverageData >= 40X There is a 0.46% of reference with a coverageData >= 41X There is a 0.45% of reference with a coverageData >= 42X There is a 0.44% of reference with a coverageData >= 43X There is a 0.44% of reference with a coverageData >= 44X There is a 0.43% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.42% of reference with a coverageData >= 47X There is a 0.41% of reference with a coverageData >= 48X There is a 0.4% of reference with a coverageData >= 49X There is a 0.4% of reference with a coverageData >= 50X There is a 0.39% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175981268 0.7060414425206186 12.677399986303417 chr2 243199373 308647320 1.2691123179828263 45.86073220233806 chr3 198022430 773284444 3.9050346165330865 56.60414403426402 chr4 191154276 58318339 0.3050851920257332 24.637229287487823 chr5 180915260 327233927 1.808769072327011 52.789920420736344 chr6 171115067 157675346 0.9214579917734538 121.66538125438645 chr7 159138663 264833709 1.6641694985209219 52.49613445109822 chr8 146364022 66485318 0.454246317445417 12.733547559680353 chr9 141213431 67640023 0.4789914282303643 51.86806495285174 chr10 135534747 811887084 5.990250485360776 146.48302078909262 chr11 135006516 144272602 1.0686343613222342 33.65281594501007 chr12 133851895 64629943 0.4828466791598281 19.671387806546072 chr13 115169878 64321296 0.5584906150547455 16.369542477669018 chr14 107349540 237980087 2.2168710457445835 58.065485761240524 chr15 102531392 37880094 0.3694487440490421 15.452841829089136 chr16 90354753 84937879 0.9400488206746578 23.959692345329955 chr17 81195210 141614953 1.7441294012294568 50.26733610910934 chr18 78077248 85212656 1.0913890817463239 15.915486359843632 chr19 59128983 47795875 0.8083324382562102 15.542291051129643 chr20 63025520 65800049 1.044022310327626 11.592905906118936 chr21 48129895 6978080 0.144984317958724 6.431317732041566 chr22 51304566 275164147 5.363346159092351 99.24272382140158 chrMT 16571 2925132 176.52115140908816 109.8391684953598 chrX 155270560 113221850 0.7291907107181168 19.451769163275035 chrY 59373566 4709819 0.07932518319684555 5.898302814279013