BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094011.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 420,380 number of mapped reads = 293,347 (69.78%) number of supplementary alignments = 4,722 (1.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 146,804 number of mapped paired reads (second in pair) = 146,543 number of mapped paired reads (both in pair) = 290,332 number of mapped paired reads (singletons) = 3,015 number of mapped bases = 40,426,328 bp number of sequenced bases = 39,952,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,294 duplication rate = 48.51% >>>>>>> Insert size mean insert size = 54,588.1947 std insert size = 2,661,026.6313 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 30.2703 >>>>>>> ACTG content number of A's = 11,266,955 bp (28.2%) number of C's = 8,542,964 bp (21.38%) number of T's = 11,212,890 bp (28.07%) number of G's = 8,929,135 bp (22.35%) number of N's = 605 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.0279 number of mismatches = 1,091,328 number of insertions = 14,842 mapped reads with insertion percentage = 4.98% number of deletions = 69,228 mapped reads with deletion percentage = 21.79% homopolymer indels = 34.84% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 15.0708X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 103641 4.158103983219364E-4 0.2721257155347394 chr2 243199373 2488961 0.010234241023310532 7.364888812661854 chr3 198022430 834113 0.004212214747591978 2.832306921557597 chr4 191154276 887292 0.004641758576198421 4.554768362342151 chr5 180915260 439494 0.0024292809793933358 1.1106722962226359 chr6 171115067 1252661 0.007320576860715603 6.727013422159101 chr7 159138663 595737 0.0037435088919906285 1.7235717223398501 chr8 146364022 105138 7.18332268841314E-4 0.5829926990085397 chr9 141213431 304670 0.0021575143231241226 0.8725684887435711 chr10 135534747 21796 1.6081484993659965E-4 0.07593948818408434 chr11 135006516 1482417 0.010980336682416129 5.756503777293964 chr12 133851895 191739 0.001432471314657144 1.1222941685526853 chr13 115169878 594936 0.0051657257117177805 4.323129101944417 chr14 107349540 152023 0.0014161495242550643 1.0166954538567043 chr15 102531392 462694 0.004512705728212487 2.661120138446161 chr16 90354753 376025 0.004161651573548101 2.1982265129217913 chr17 81195210 952873 0.011735581446245412 6.151255640592328 chr18 78077248 95613 0.0012245949037548046 0.773736492099331 chr19 59128983 38944 6.58627935474554E-4 0.2538002014530952 chr20 63025520 3054 4.8456561722933824E-5 0.00912586394132717 chr21 48129895 90800 0.0018865613565124128 0.6853284249628616 chr22 51304566 66615 0.0012984224445052317 0.6817413484246654 chrMT 16571 18219964 1099.5090217850461 5864.708588560227 chrX 155270560 10545832 0.06791906978373749 21.898006415089558 chrY 59373566 119296 0.002009244315896404 1.3014164290798276