BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714142.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 = 896,214 number of mapped reads = 433,493 (48.37%) number of supplementary alignments = 29,443 (3.29%) number of secondary alignments = 0 number of mapped bases = 52,692,012 bp number of sequenced bases = 51,806,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 375,799 duplication rate = 43.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.53 >>>>>>> ACTG content number of A's = 13,820,645 bp (26.68%) number of C's = 9,354,758 bp (18.06%) number of T's = 12,909,678 bp (24.92%) number of G's = 15,720,614 bp (30.34%) number of N's = 602 bp (0%) GC percentage = 48.4% >>>>>>> Mismatches and indels general error rate = 0.0397 number of mismatches = 1,839,013 number of insertions = 61,615 mapped reads with insertion percentage = 13.02% number of deletions = 144,877 mapped reads with deletion percentage = 31.9% homopolymer indels = 30.93% >>>>>>> Coverage mean coverageData = 0.017X std coverageData = 7.8874X There is a 0.07% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2878614 0.01154907453570597 1.5353025569728946 chr2 243199373 10764926 0.044263790104425965 26.33987226466278 chr3 198022430 2449850 0.01237157831059845 1.6764343913463104 chr4 191154276 2126871 0.011126463108782353 1.6187226555296537 chr5 180915260 2163431 0.011958256036555457 1.3026295969217618 chr6 171115067 2615471 0.01528486676161603 2.150118663523583 chr7 159138663 1809767 0.011372264702261574 1.6690997001848518 chr8 146364022 2516540 0.01719370625111682 5.428889535286831 chr9 141213431 1760938 0.012470046138883206 1.8382235415607209 chr10 135534747 2426734 0.017904884568087916 1.9854330485273788 chr11 135006516 2333054 0.017281047382927798 2.270105355938581 chr12 133851895 1940572 0.014497904568329048 2.0565110355688874 chr13 115169878 1094596 0.0095041865026548 1.1806523378932514 chr14 107349540 1194651 0.011128608469118732 1.2739943054126353 chr15 102531392 1142924 0.01114706411086275 1.5135675005472626 chr16 90354753 1808139 0.020011553791752384 4.602504157333941 chr17 81195210 1095524 0.013492470799693726 1.7141412996769698 chr18 78077248 998960 0.012794508331031339 1.313974765736392 chr19 59128983 856664 0.014488055713726718 2.614137388578684 chr20 63025520 1329983 0.021102293166323737 5.819935126623288 chr21 48129895 369129 0.007669432896124124 0.7728997403353917 chr22 51304566 465837 0.009079835116429989 0.9220166598276986 chrMT 16571 1227626 74.0827952447046 592.3591484906095 chrX 155270560 4871049 0.03137136234969462 4.110799683641553 chrY 59373566 450162 0.007581858903337556 1.219201994905364