BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094012.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 = 449,254 number of mapped reads = 400,384 (89.12%) number of supplementary alignments = 3,633 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 200,809 number of mapped paired reads (second in pair) = 199,575 number of mapped paired reads (both in pair) = 397,852 number of mapped paired reads (singletons) = 2,532 number of mapped bases = 54,441,161 bp number of sequenced bases = 53,439,653 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 391,613 duplication rate = 46.11% >>>>>>> Insert size mean insert size = 76,458.3885 std insert size = 2,556,108.2733 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 34.7412 >>>>>>> ACTG content number of A's = 15,091,905 bp (28.24%) number of C's = 11,578,258 bp (21.67%) number of T's = 14,799,189 bp (27.69%) number of G's = 11,969,676 bp (22.4%) number of N's = 625 bp (0%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0349 number of mismatches = 1,844,428 number of insertions = 19,156 mapped reads with insertion percentage = 4.67% number of deletions = 138,285 mapped reads with deletion percentage = 33.13% homopolymer indels = 29.12% >>>>>>> Coverage mean coverageData = 0.0176X std coverageData = 15.9876X 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 1166846 0.004681416621224788 2.8181152119084034 chr2 243199373 3021604 0.012424390584263555 12.369913182669485 chr3 198022430 337001 0.0017018324641304523 1.0819386993080888 chr4 191154276 1313843 0.006873207481898024 3.6735806752184326 chr5 180915260 1961634 0.010842833269012244 5.951694631161006 chr6 171115067 822534 0.004806905753074333 3.329476720808714 chr7 159138663 1716875 0.010788547343771514 6.412131427251408 chr8 146364022 235394 0.0016082777501153938 0.7099574310272627 chr9 141213431 859066 0.0060834581662419914 3.0473399676789956 chr10 135534747 356572 0.0026308530313632417 1.4273520823168135 chr11 135006516 2413323 0.017875603870853168 6.6809901945132735 chr12 133851895 338755 0.0025308196047579305 1.4127132558072835 chr13 115169878 195999 0.001701825194257825 1.0484677803367317 chr14 107349540 85885 8.000500048719352E-4 0.32508887229300065 chr15 102531392 231180 0.002254724094646057 1.1216932434592004 chr16 90354753 561087 0.0062098227416990445 4.232233056638683 chr17 81195210 895807 0.01103275673528032 4.841410177383941 chr18 78077248 141800 0.0018161500774207615 1.008468970044877 chr19 59128983 96772 0.0016366254768833079 0.48293179569953487 chr20 63025520 25363 4.0242428781230206E-4 0.1064971390533895 chr21 48129895 277418 0.005763943594724236 2.7412946878519406 chr22 51304566 137681 0.0026836012997361676 0.8693391157090857 chrMT 16571 18711894 1129.195220566049 6117.629184748975 chrX 155270560 18503813 0.11917141923105062 22.824984016681615 chrY 59373566 33015 5.560555348823077E-4 0.26740538602220515