BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714207.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 92,190 number of mapped reads = 26,639 (28.9%) number of supplementary alignments = 923 (1%) number of secondary alignments = 0 number of mapped bases = 3,296,934 bp number of sequenced bases = 3,234,495 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,402 duplication rate = 37.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5405 >>>>>>> ACTG content number of A's = 867,085 bp (26.81%) number of C's = 588,385 bp (18.19%) number of T's = 810,661 bp (25.06%) number of G's = 968,335 bp (29.94%) number of N's = 29 bp (0%) GC percentage = 48.13% >>>>>>> Mismatches and indels general error rate = 0.0408 number of mismatches = 121,435 number of insertions = 3,441 mapped reads with insertion percentage = 12.38% number of deletions = 10,293 mapped reads with deletion percentage = 36.69% homopolymer indels = 26.16% >>>>>>> Coverage mean coverageData = 0.0011X std coverageData = 0.4895X There is a 0.01% 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 216101 8.670028549296974E-4 0.19116555516715397 chr2 243199373 622461 0.002559467947312512 1.5815707518950493 chr3 198022430 202845 0.0010243536552904638 0.2528109483827617 chr4 191154276 127112 6.649707380859218E-4 0.1407665363212349 chr5 180915260 229894 0.0012707275218243061 0.24251914025141877 chr6 171115067 153347 8.9616304799156E-4 0.18311276923104228 chr7 159138663 84053 5.281746020450103E-4 0.13365954147362438 chr8 146364022 127720 8.726188188515345E-4 0.20531090553206532 chr9 141213431 154785 0.0010961067860464349 0.2286415349775392 chr10 135534747 111735 8.244011404691669E-4 0.18813861497172674 chr11 135006516 103570 7.671481575007832E-4 0.14852304024386848 chr12 133851895 114665 8.56655783618155E-4 0.15476257228075438 chr13 115169878 95792 8.317452589469618E-4 0.2305846187527096 chr14 107349540 75518 7.034776301789462E-4 0.16057435182664875 chr15 102531392 127795 0.0012463987614641963 0.25866166585727784 chr16 90354753 42830 4.740204425106447E-4 0.13405921677763455 chr17 81195210 68798 8.473159931478716E-4 0.1985650385253612 chr18 78077248 46100 5.904408925888372E-4 0.15989719244355105 chr19 59128983 57494 9.72348873309727E-4 0.22339264366366424 chr20 63025520 104294 0.0016547899961793255 0.4782659669434304 chr21 48129895 11351 2.358409466715022E-4 0.08041576330923106 chr22 51304566 9244 1.801788947985643E-4 0.06908432077524149 chrMT 16571 43566 2.629050751312534 22.442231012315446 chrX 155270560 365108 0.0023514309473734105 0.3119525748997671 chrY 59373566 756 1.2732939099531263E-5 0.004124412082835937