BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094000.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 = 381,092 number of mapped reads = 362,395 (95.09%) number of supplementary alignments = 22,250 (5.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,375 number of mapped paired reads (second in pair) = 180,020 number of mapped paired reads (both in pair) = 358,768 number of mapped paired reads (singletons) = 3,627 number of mapped bases = 46,759,412 bp number of sequenced bases = 45,972,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 344,708 duplication rate = 51.37% >>>>>>> Insert size mean insert size = 1,044,940.8884 std insert size = 9,300,268.8547 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 41.041 >>>>>>> ACTG content number of A's = 11,768,905 bp (25.6%) number of C's = 11,187,155 bp (24.33%) number of T's = 11,118,075 bp (24.18%) number of G's = 11,898,057 bp (25.88%) number of N's = 417 bp (0%) GC percentage = 50.22% >>>>>>> Mismatches and indels general error rate = 0.0334 number of mismatches = 1,489,029 number of insertions = 23,114 mapped reads with insertion percentage = 6.26% number of deletions = 119,378 mapped reads with deletion percentage = 31.63% homopolymer indels = 30.24% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 3.2812X 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% 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 875964 0.00351439044157888 1.1115464429369115 chr2 243199373 3015615 0.01239976469840652 4.158057053135173 chr3 198022430 925872 0.004675591547886772 1.8252248111536515 chr4 191154276 1015146 0.005310610995696481 1.7720969625934981 chr5 180915260 443399 0.0024508656704802017 1.3191265992434293 chr6 171115067 771684 0.004509737298586337 1.3767855270385698 chr7 159138663 978354 0.0061478083424642066 1.706241632524057 chr8 146364022 650208 0.0044424032020656005 1.6726032128985004 chr9 141213431 574267 0.00406665991990521 1.2057729927223386 chr10 135534747 590697 0.004358269839098899 1.4341576398980944 chr11 135006516 1209474 0.008958634263252893 2.5734069612019423 chr12 133851895 1105202 0.008256902152935527 2.120527088646704 chr13 115169878 921524 0.008001432457886254 2.6399802335595655 chr14 107349540 182709 0.0017020007724299518 0.6297561365852669 chr15 102531392 891934 0.008699130896418533 2.399881524516074 chr16 90354753 305551 0.003381681536996731 0.9767365392092355 chr17 81195210 1083120 0.013339703167218855 3.2871867890498137 chr18 78077248 176618 0.0022620930491812417 0.6173238553002557 chr19 59128983 152294 0.0025756235313568643 0.6555532353779097 chr20 63025520 440894 0.006995483734207985 2.6233726764911505 chr21 48129895 96481 0.002004596103939142 0.4084384553085483 chr22 51304566 180895 0.0035259044974671454 1.1285586299946462 chrMT 16571 1333373 80.46424476495082 377.36020072620016 chrX 155270560 28247245 0.1819227353852527 10.90373682878415 chrY 59373566 590892 0.009952105622222523 1.6933354250371528