BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094130.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 = 527,278 number of mapped reads = 506,263 (96.01%) number of supplementary alignments = 3,178 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 254,032 number of mapped paired reads (second in pair) = 252,231 number of mapped paired reads (both in pair) = 503,426 number of mapped paired reads (singletons) = 2,837 number of mapped bases = 72,703,403 bp number of sequenced bases = 72,338,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 502,068 duplication rate = 44.19% >>>>>>> Insert size mean insert size = 21,717.1914 std insert size = 1,367,101.3794 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 26.6374 >>>>>>> ACTG content number of A's = 19,865,929 bp (27.46%) number of C's = 15,731,448 bp (21.75%) number of T's = 20,720,462 bp (28.64%) number of G's = 16,020,169 bp (22.15%) number of N's = 828 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0198 number of mismatches = 1,373,761 number of insertions = 36,108 mapped reads with insertion percentage = 7.04% number of deletions = 94,462 mapped reads with deletion percentage = 18.21% homopolymer indels = 49.53% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 32.5518X 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 390978 0.0015686139453991571 1.7753176988839234 chr2 243199373 280257 0.0011523755038628327 0.9279809172542551 chr3 198022430 6030435 0.030453292589127403 28.528787907876346 chr4 191154276 28666 1.4996264064738997E-4 0.09643089189853322 chr5 180915260 236561 0.0013075790289884888 0.7190365547453438 chr6 171115067 89131 5.208834123297863E-4 0.2706079198204909 chr7 159138663 2035423 0.012790248212654646 11.661633711671072 chr8 146364022 132457 9.049833298513756E-4 0.4133024339710937 chr9 141213431 268686 0.0019026943690646535 0.8964164943743963 chr10 135534747 124078 9.154700381002667E-4 0.31826977550154234 chr11 135006516 891022 0.006599844410472751 5.187390837301128 chr12 133851895 166505 0.001243949515993031 0.7391819636802704 chr13 115169878 44841 3.893465963383238E-4 0.13143515628447297 chr14 107349540 170577 0.0015889867809400953 0.6816709916689346 chr15 102531392 25518 2.4887987476069766E-4 0.08899148352022632 chr16 90354753 41608 4.6049597412988337E-4 0.15527102659956937 chr17 81195210 18657 2.2977956458268905E-4 0.06452294604444309 chr18 78077248 29592 3.7900926016244836E-4 0.15854054818952365 chr19 59128983 15342 2.5946666459661583E-4 0.04714105436791692 chr20 63025520 2098773 0.03330036785099116 19.944371941316177 chr21 48129895 10233 2.1261214054175685E-4 0.04424659723034202 chr22 51304566 17939 3.4965698764511527E-4 0.11090814443258895 chrMT 16571 52645692 3176.977370104399 13084.959119696598 chrX 155270560 6906477 0.04448027365908901 20.16614142086615 chrY 59373566 3955 6.661213510402929E-5 0.015440799997809463