BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514749.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 = 64,795,530 number of mapped reads = 59,654,413 (92.07%) number of supplementary alignments = 8,260,520 (12.75%) number of secondary alignments = 0 number of mapped bases = 5,626,414,833 bp number of sequenced bases = 5,622,396,309 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,471,326 duplication rate = 44.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0428 >>>>>>> ACTG content number of A's = 1,741,836,236 bp (30.98%) number of C's = 1,057,294,169 bp (18.81%) number of T's = 1,720,662,070 bp (30.6%) number of G's = 1,102,213,221 bp (19.6%) number of N's = 390,613 bp (0.01%) GC percentage = 38.41% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 30,322,181 number of insertions = 3,968,927 mapped reads with insertion percentage = 6.38% number of deletions = 1,426,959 mapped reads with deletion percentage = 2.25% homopolymer indels = 54.99% >>>>>>> Coverage mean coverageData = 1.8175X std coverageData = 102.9656X There is a 6.08% of reference with a coverageData >= 1X There is a 4.02% of reference with a coverageData >= 2X There is a 3.24% of reference with a coverageData >= 3X There is a 2.81% of reference with a coverageData >= 4X There is a 2.52% of reference with a coverageData >= 5X There is a 2.31% of reference with a coverageData >= 6X There is a 2.14% of reference with a coverageData >= 7X There is a 2% of reference with a coverageData >= 8X There is a 1.89% of reference with a coverageData >= 9X There is a 1.79% of reference with a coverageData >= 10X There is a 1.7% of reference with a coverageData >= 11X There is a 1.62% of reference with a coverageData >= 12X There is a 1.56% of reference with a coverageData >= 13X There is a 1.49% of reference with a coverageData >= 14X There is a 1.44% of reference with a coverageData >= 15X There is a 1.39% of reference with a coverageData >= 16X There is a 1.34% of reference with a coverageData >= 17X There is a 1.29% of reference with a coverageData >= 18X There is a 1.25% of reference with a coverageData >= 19X There is a 1.22% of reference with a coverageData >= 20X There is a 1.18% of reference with a coverageData >= 21X There is a 1.15% of reference with a coverageData >= 22X There is a 1.12% of reference with a coverageData >= 23X There is a 1.09% of reference with a coverageData >= 24X There is a 1.06% of reference with a coverageData >= 25X There is a 1.03% of reference with a coverageData >= 26X There is a 1.01% of reference with a coverageData >= 27X There is a 0.99% of reference with a coverageData >= 28X There is a 0.96% of reference with a coverageData >= 29X There is a 0.94% of reference with a coverageData >= 30X There is a 0.92% of reference with a coverageData >= 31X There is a 0.9% of reference with a coverageData >= 32X There is a 0.88% of reference with a coverageData >= 33X There is a 0.87% of reference with a coverageData >= 34X There is a 0.85% of reference with a coverageData >= 35X There is a 0.83% of reference with a coverageData >= 36X There is a 0.82% of reference with a coverageData >= 37X There is a 0.8% of reference with a coverageData >= 38X There is a 0.79% of reference with a coverageData >= 39X There is a 0.77% of reference with a coverageData >= 40X There is a 0.76% of reference with a coverageData >= 41X There is a 0.75% of reference with a coverageData >= 42X There is a 0.73% of reference with a coverageData >= 43X There is a 0.72% of reference with a coverageData >= 44X There is a 0.71% of reference with a coverageData >= 45X There is a 0.7% of reference with a coverageData >= 46X There is a 0.69% of reference with a coverageData >= 47X There is a 0.68% of reference with a coverageData >= 48X There is a 0.67% of reference with a coverageData >= 49X There is a 0.66% of reference with a coverageData >= 50X There is a 0.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 519152716 2.0828542529488825 34.078770000190346 chr2 243199373 422627734 1.7377829917349334 57.20388759016383 chr3 198022430 346043369 1.7474958215592042 111.99078640039971 chr4 191154276 386791665 2.0234528522919364 32.16234325007204 chr5 180915260 427534282 2.3631742396965296 34.812999514163174 chr6 171115067 397997046 2.3259029901791175 374.73655996110324 chr7 159138663 387529927 2.435171439136698 39.19505382392245 chr8 146364022 365782719 2.4991300047767204 42.18485045643964 chr9 141213431 221743730 1.5702736519446228 78.94789540342173 chr10 135534747 312204649 2.3035026508737277 66.68778931850693 chr11 135006516 226564502 1.6781745704777686 29.821867199317776 chr12 133851895 250401480 1.870735412449708 33.694436776585896 chr13 115169878 123453257 1.071923137749612 19.908486875882254 chr14 107349540 133510798 1.2437016311388014 27.09887426824103 chr15 102531392 166136110 1.6203438455219645 24.518389358393378 chr16 90354753 119886665 1.3268440344250623 24.924408034410057 chr17 81195210 63124670 0.7774432752868057 16.593495274753575 chr18 78077248 206158515 2.640442898294776 59.241897424357724 chr19 59128983 71778097 1.2139240920142327 31.166699446702438 chr20 63025520 53020958 0.8412617301689855 20.120673001930463 chr21 48129895 44150143 0.9173122650693504 24.240312596698022 chr22 51304566 37318019 0.7273820228788214 105.07637746408525 chrMT 16571 85282378 5146.483495262809 5302.355736623063 chrX 155270560 195088932 1.2564450852756632 44.53545433946855 chrY 59373566 63132472 1.0633094195487602 44.18332359117582