BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081743.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 = 2,349,272 number of mapped reads = 2,119,424 (90.22%) number of supplementary alignments = 14,025 (0.6%) number of secondary alignments = 0 number of mapped bases = 141,617,852 bp number of sequenced bases = 141,566,043 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,944 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7479 >>>>>>> ACTG content number of A's = 39,576,959 bp (27.96%) number of C's = 26,810,859 bp (18.94%) number of T's = 43,820,655 bp (30.95%) number of G's = 31,356,063 bp (22.15%) number of N's = 1,507 bp (0%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,105,135 number of insertions = 10,272 mapped reads with insertion percentage = 0.48% number of deletions = 29,520 mapped reads with deletion percentage = 1.38% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.3312X There is a 3.9% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% 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 11109382 0.044571130677343425 0.4782816476467834 chr2 243199373 12207325 0.050194722335900104 0.40781677683386447 chr3 198022430 9536687 0.048159630199467805 0.2502316809882644 chr4 191154276 9525232 0.04983007547265121 0.27182653913594923 chr5 180915260 8804132 0.04866439680102165 0.2514376942511285 chr6 171115067 8291598 0.048456270656750525 0.27509833654685467 chr7 159138663 7612940 0.047838406182914836 0.38592481022996794 chr8 146364022 7221508 0.04933936565367136 0.42934716124587685 chr9 141213431 5967998 0.04226225478509902 0.33029877749494985 chr10 135534747 6691724 0.04937275605052039 0.3931812135128245 chr11 135006516 6388753 0.04732181223015932 0.2990626675014106 chr12 133851895 6387541 0.047720960543741274 0.25029112378392354 chr13 115169878 4567804 0.03966144689325798 0.2266965252315772 chr14 107349540 4332368 0.04035758327422735 0.2412542631886332 chr15 102531392 4044921 0.03945056163872231 0.2317288926587556 chr16 90354753 3969481 0.04393217698243279 0.2677863588481322 chr17 81195210 3568928 0.04395490817746515 0.2531646866153173 chr18 78077248 3766245 0.04823741994594891 0.5324563112551032 chr19 59128983 2568452 0.043438122384076856 0.3938442822783557 chr20 63025520 2864498 0.04544981144146054 0.24907461257704397 chr21 48129895 1839310 0.038215541504921215 0.24051268873062454 chr22 51304566 1467457 0.02860285378888109 0.1899644342870365 chrMT 16571 9647 0.5821616076277835 0.8497455287868431 chrX 155270560 8501471 0.054752626640877704 0.2902727413052532 chrY 59373566 372450 0.006272993607963517 0.14918147718949168