BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093976.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 = 479,620 number of mapped reads = 225,380 (46.99%) number of supplementary alignments = 9,274 (1.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 111,118 number of mapped paired reads (second in pair) = 114,262 number of mapped paired reads (both in pair) = 214,252 number of mapped paired reads (singletons) = 11,128 number of mapped bases = 28,528,132 bp number of sequenced bases = 28,488,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 203,963 duplication rate = 29.85% >>>>>>> Insert size mean insert size = 390,089.7868 std insert size = 6,394,608.6761 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 27.0027 >>>>>>> ACTG content number of A's = 7,363,634 bp (25.85%) number of C's = 6,076,912 bp (21.33%) number of T's = 7,935,383 bp (27.85%) number of G's = 7,112,517 bp (24.97%) number of N's = 302 bp (0%) GC percentage = 46.3% >>>>>>> Mismatches and indels general error rate = 0.0263 number of mismatches = 730,727 number of insertions = 9,130 mapped reads with insertion percentage = 3.82% number of deletions = 18,556 mapped reads with deletion percentage = 8.01% homopolymer indels = 49.18% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 20.1716X There is a 0.04% of reference with a coverageData >= 1X There is a 0.02% 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% 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 983475 0.003945727380956054 1.9035627802386226 chr2 243199373 1796328 0.007386236147903227 4.650967859147486 chr3 198022430 507876 0.002564739762056248 0.9821202904490901 chr4 191154276 514451 0.0026912869058707324 1.184214794064639 chr5 180915260 470764 0.002602124331579326 1.3930411315370872 chr6 171115067 362792 0.002120163971300084 1.3223505661701667 chr7 159138663 291768 0.0018334199527615738 0.32625298847769146 chr8 146364022 284096 0.0019410234572537232 0.4321160875775812 chr9 141213431 210294 0.0014891926250272893 0.2616469373387865 chr10 135534747 309731 0.002285251618907733 0.7403281882844223 chr11 135006516 365775 0.0027093136749044024 0.6444567527536096 chr12 133851895 261676 0.0019549667189993837 0.4051231868512146 chr13 115169878 218992 0.001901469410256734 0.5528836513590274 chr14 107349540 133922 0.0012475321272918357 0.19556928040841734 chr15 102531392 1067042 0.010406978576863561 6.1083498914541305 chr16 90354753 439692 0.004866285230174887 0.9377333158081574 chr17 81195210 270326 0.003329334328958568 0.7031155397107038 chr18 78077248 305094 0.003907591620032509 1.3331526630493227 chr19 59128983 2778040 0.04698271235275601 19.49827058190803 chr20 63025520 243169 0.0038582624943038946 0.8835374469642931 chr21 48129895 31832 6.613768843667746E-4 0.11492068216801891 chr22 51304566 117845 0.0022969690456011264 0.5845057730267097 chrMT 16571 16205126 977.9208255385915 8543.711623649657 chrX 155270560 331627 0.00213580088846205 0.3522981714340455 chrY 59373566 26399 4.4462547524937277E-4 0.12568900538160171