BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094041.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 = 358,778 number of mapped reads = 344,315 (95.97%) number of supplementary alignments = 15,543 (4.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 172,950 number of mapped paired reads (second in pair) = 171,365 number of mapped paired reads (both in pair) = 341,700 number of mapped paired reads (singletons) = 2,615 number of mapped bases = 45,393,851 bp number of sequenced bases = 44,339,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 319,665 duplication rate = 49.76% >>>>>>> Insert size mean insert size = 796,837.9978 std insert size = 8,009,607.0391 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 43.6033 >>>>>>> ACTG content number of A's = 12,179,072 bp (27.47%) number of C's = 10,039,111 bp (22.64%) number of T's = 11,719,196 bp (26.43%) number of G's = 10,401,333 bp (23.46%) number of N's = 422 bp (0%) GC percentage = 46.1% >>>>>>> Mismatches and indels general error rate = 0.0422 number of mismatches = 1,820,793 number of insertions = 28,954 mapped reads with insertion percentage = 8.27% number of deletions = 149,457 mapped reads with deletion percentage = 40.58% homopolymer indels = 29.8% >>>>>>> Coverage mean coverageData = 0.0147X std coverageData = 3.0381X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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% 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 824344 0.0033072896536534605 1.2983761364969049 chr2 243199373 2171883 0.008930462990955162 2.351112761460121 chr3 198022430 932291 0.004708007067684201 1.434216788038405 chr4 191154276 1318781 0.006899040019382041 2.6257760739250906 chr5 180915260 342910 0.0018954177773616223 0.5117022656906968 chr6 171115067 1134582 0.006630520736084567 2.387004726606069 chr7 159138663 1084566 0.006815226291049083 1.7643447545428275 chr8 146364022 831806 0.005683131610034603 1.7023010123783882 chr9 141213431 571234 0.004045181792941495 1.4584778556409692 chr10 135534747 1143536 0.008437216472614214 2.552279430356354 chr11 135006516 1401300 0.01037949901618082 2.501796918628927 chr12 133851895 1454049 0.010863118523648843 2.9851046735124744 chr13 115169878 919889 0.00798723603753405 2.0433862619392196 chr14 107349540 206023 0.0019191791599665914 0.7438703785489114 chr15 102531392 558387 0.0054460101351203735 1.2703685905888606 chr16 90354753 279635 0.003094856559455151 1.1058104688136308 chr17 81195210 1099314 0.01353914843006133 2.9297378190184684 chr18 78077248 232623 0.0029793954827916067 0.8450070253811062 chr19 59128983 187444 0.0031700866561496584 0.8136854549735547 chr20 63025520 398667 0.006325485295480307 1.5796280227237547 chr21 48129895 364496 0.0075731725573056 2.9421228025108928 chr22 51304566 97984 0.0019098495054026966 0.4193369486451038 chrMT 16571 1951510 117.76658017017681 491.8502892761782 chrX 155270560 25558067 0.1646034315841973 9.289245524420677 chrY 59373566 328530 0.005533270479324082 1.2309621081773905