BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094113.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 = 423,540 number of mapped reads = 407,198 (96.14%) number of supplementary alignments = 32,438 (7.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 204,450 number of mapped paired reads (second in pair) = 202,748 number of mapped paired reads (both in pair) = 404,412 number of mapped paired reads (singletons) = 2,786 number of mapped bases = 50,802,366 bp number of sequenced bases = 49,893,782 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 390,225 duplication rate = 51.18% >>>>>>> Insert size mean insert size = 1,815,746.8273 std insert size = 11,688,662.506 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 40.3764 >>>>>>> ACTG content number of A's = 14,245,801 bp (28.55%) number of C's = 10,888,939 bp (21.82%) number of T's = 13,319,614 bp (26.7%) number of G's = 11,438,988 bp (22.93%) number of N's = 440 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0343 number of mismatches = 1,633,599 number of insertions = 34,816 mapped reads with insertion percentage = 8.44% number of deletions = 132,184 mapped reads with deletion percentage = 31.46% homopolymer indels = 28.31% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 3.3973X 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1258456 0.005048958333387663 1.9925457588373885 chr2 243199373 2410001 0.009909569133634239 3.319807806039399 chr3 198022430 759376 0.003834797906479584 0.9761333044851872 chr4 191154276 3114592 0.01629360360215013 5.175403526812458 chr5 180915260 1026768 0.005675408475769263 2.722231722793106 chr6 171115067 1193696 0.006975984177945008 2.3476741895201587 chr7 159138663 995427 0.006255092139362765 1.7105633729837577 chr8 146364022 1087478 0.007429954336729008 1.9582926070733453 chr9 141213431 891767 0.0063150296234924 2.272715390078365 chr10 135534747 540734 0.003989633743146324 0.9444754117596259 chr11 135006516 1353287 0.010023864329629838 2.6097737180446665 chr12 133851895 1099937 0.008217567633241203 1.8354957533200928 chr13 115169878 772049 0.006703567055962324 1.559108343200316 chr14 107349540 193421 0.0018017869475733198 0.798096081085657 chr15 102531392 442443 0.004315195486666172 1.0926260509441388 chr16 90354753 95532 0.001057299110761777 0.303859601838378 chr17 81195210 339063 0.004175899046261473 1.0928095132316078 chr18 78077248 394797 0.005056492257513995 1.63375956781153 chr19 59128983 113454 0.0019187544625957798 0.7598569606507038 chr20 63025520 146243 0.0023203775232635924 0.6021806954559277 chr21 48129895 236652 0.004916944032394004 1.8547035858046466 chr22 51304566 54905 0.0010701776524140172 0.37599087945203685 chrMT 16571 162259 9.791744614084847 54.1515638137004 chrX 155270560 31098213 0.2002840267981258 11.228712687266608 chrY 59373566 1021816 0.017209948279003486 3.104194087646823