BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094009.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 = 518,730 number of mapped reads = 403,090 (77.71%) number of supplementary alignments = 12,067 (2.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 202,028 number of mapped paired reads (second in pair) = 201,062 number of mapped paired reads (both in pair) = 399,292 number of mapped paired reads (singletons) = 3,798 number of mapped bases = 53,732,792 bp number of sequenced bases = 52,976,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 397,630 duplication rate = 46.39% >>>>>>> Insert size mean insert size = 271,980.3311 std insert size = 4,918,453.0809 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 36.1407 >>>>>>> ACTG content number of A's = 15,127,581 bp (28.56%) number of C's = 11,201,096 bp (21.14%) number of T's = 14,602,186 bp (27.56%) number of G's = 12,045,224 bp (22.74%) number of N's = 540 bp (0%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0304 number of mismatches = 1,572,381 number of insertions = 17,726 mapped reads with insertion percentage = 4.32% number of deletions = 107,453 mapped reads with deletion percentage = 25.67% homopolymer indels = 32.21% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 16.1746X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% 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 733068 0.0029410879582121483 1.6133997529495152 chr2 243199373 1656248 0.006810247820828058 4.077678260962783 chr3 198022430 750341 0.0037891717620069606 1.5353668837111993 chr4 191154276 1036189 0.0054206948527795425 4.350563688496483 chr5 180915260 482824 0.0026687853749871623 2.2238755109873187 chr6 171115067 2185101 0.012769775556935615 9.589358700272461 chr7 159138663 393552 0.0024730131105852008 1.039399414215764 chr8 146364022 329230 0.002249391588870112 1.7528442085422795 chr9 141213431 909586 0.006441214504589156 2.7207708957242347 chr10 135534747 159394 0.0011760379056154507 0.8740600084532424 chr11 135006516 601097 0.004452355470013018 2.3501241842141978 chr12 133851895 528274 0.003946705423931428 1.8243153499014537 chr13 115169878 431717 0.003748523550576306 2.005081809175833 chr14 107349540 305851 0.002849113279851968 1.1000650760091049 chr15 102531392 415682 0.004054192495504206 2.3974936012434083 chr16 90354753 347129 0.0038418454865346155 1.7786258425836456 chr17 81195210 763838 0.009407426866683392 4.665044402862772 chr18 78077248 372516 0.004771121031315038 1.7586372755723114 chr19 59128983 173772 0.0029388633320481766 0.890813968478365 chr20 63025520 15253 2.4201307660769796E-4 0.0752171447633869 chr21 48129895 213051 0.004426583519452931 1.9680833071484953 chr22 51304566 137894 0.0026877529769962385 0.6888929708493983 chrMT 16571 17918045 1081.28930058536 6064.177355200744 chrX 155270560 22323415 0.1437710728936638 30.914915754544687 chrY 59373566 549725 0.009258749929219344 3.293688501906116