BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231873.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,076,784 number of mapped reads = 4,444,067 (87.54%) number of supplementary alignments = 31,792 (0.63%) number of secondary alignments = 0 number of mapped bases = 290,654,735 bp number of sequenced bases = 290,539,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 394,503 duplication rate = 6.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1009 >>>>>>> ACTG content number of A's = 76,672,920 bp (26.39%) number of C's = 53,395,634 bp (18.38%) number of T's = 92,371,838 bp (31.79%) number of G's = 67,985,930 bp (23.4%) number of N's = 112,787 bp (0.04%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,932,508 number of insertions = 21,309 mapped reads with insertion percentage = 0.48% number of deletions = 65,648 mapped reads with deletion percentage = 1.46% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.0939X std coverageData = 1.2859X There is a 7.42% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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% 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 29255804 0.11737504958914426 3.144609566162865 chr2 243199373 18693565 0.07686518583253091 1.4477387099444448 chr3 198022430 33493735 0.16914111699366582 0.5100539714584351 chr4 191154276 8630392 0.045148830466130926 0.3926697948087803 chr5 180915260 16593809 0.09172144461445651 0.392056137840664 chr6 171115067 21621569 0.12635689760738603 0.655087970664372 chr7 159138663 15787806 0.09920785874643172 1.706591511720616 chr8 146364022 18419552 0.1258475392265457 1.4924073299391645 chr9 141213431 11187387 0.0792232503719848 0.8983770457359572 chr10 135534747 12851151 0.09481812807751801 0.9865505112657648 chr11 135006516 12914332 0.09565710146908761 0.9021900529477089 chr12 133851895 11143943 0.0832557731065369 0.392258612053244 chr13 115169878 11550823 0.10029378515100972 0.40694655368039395 chr14 107349540 12655401 0.11788966212617213 0.5515212574124566 chr15 102531392 5021527 0.04897550791078697 0.3779427571421087 chr16 90354753 7592938 0.08403473805080293 0.5852405332528542 chr17 81195210 6532481 0.08045401939350856 0.4603066891493004 chr18 78077248 5875174 0.0752482208389312 2.3395773910410096 chr19 59128983 7924080 0.13401346679681603 1.69438497187924 chr20 63025520 5977723 0.09484607187691589 0.5353813590298356 chr21 48129895 5769838 0.11988054409842365 0.46715417447692326 chr22 51304566 2233762 0.04353924366108077 0.24560383072963546 chrMT 16571 246398 14.86922937662181 8.948549546772432 chrX 155270560 8019897 0.05165111145345261 0.5182390810826312 chrY 59373566 661648 0.011143814403871244 0.23116107420172127