BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084411.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 = 2,195,485 number of mapped reads = 2,022,632 (92.13%) number of supplementary alignments = 15,246 (0.69%) number of secondary alignments = 0 number of mapped bases = 136,519,582 bp number of sequenced bases = 136,471,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,937 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0752 >>>>>>> ACTG content number of A's = 38,776,732 bp (28.41%) number of C's = 25,842,082 bp (18.94%) number of T's = 42,508,668 bp (31.15%) number of G's = 29,164,651 bp (21.37%) number of N's = 179,657 bp (0.13%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,360,839 number of insertions = 9,694 mapped reads with insertion percentage = 0.47% number of deletions = 27,847 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.316X There is a 3.79% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.07% 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 13684010 0.05490060544322575 0.519389660078109 chr2 243199373 13157002 0.05409965427830277 0.3529141054533367 chr3 198022430 9459051 0.04776757360264693 0.24843918591947076 chr4 191154276 6696842 0.03503370230650765 0.21829720919548606 chr5 180915260 6645043 0.036730140951072895 0.21535646205152129 chr6 171115067 6638322 0.0387944914283907 0.24664852245061275 chr7 159138663 7681233 0.04826754765433715 0.42282160491469006 chr8 146364022 6792207 0.04640626095940435 0.34636077798150827 chr9 141213431 5122482 0.036274750664474685 0.2632932672134056 chr10 135534747 9690775 0.07150029947670909 0.4511718481466617 chr11 135006516 7691197 0.05696907992203873 0.3214577289891393 chr12 133851895 4986288 0.03725227797484675 0.2190462713867302 chr13 115169878 3436428 0.029837906053872872 0.19404684040284845 chr14 107349540 3854774 0.035908621499449365 0.21959571242455933 chr15 102531392 3077345 0.030013685954834203 0.19723801959545229 chr16 90354753 2938413 0.032520845914990215 0.22053373493872946 chr17 81195210 3604281 0.044390315635614463 0.2553587307410633 chr18 78077248 3864744 0.04949897824267577 0.4263907010464254 chr19 59128983 2768980 0.04682948800252492 0.3655641186907285 chr20 63025520 2919553 0.04632334647933091 0.24477161002979542 chr21 48129895 1433405 0.02978200970519466 0.20565430382908045 chr22 51304566 1149757 0.022410422495338915 0.16552079938286796 chrMT 16571 37411 2.2576187315189187 2.0911544374220408 chrX 155270560 8888587 0.05724579727154974 0.29893833329114633 chrY 59373566 301452 0.005077208938401982 0.10477219798137266