BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080759.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,658,864 number of mapped reads = 3,425,381 (73.52%) number of supplementary alignments = 23,388 (0.5%) number of secondary alignments = 0 number of mapped bases = 218,919,105 bp number of sequenced bases = 218,849,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 543,262 duplication rate = 11.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.981 >>>>>>> ACTG content number of A's = 64,052,708 bp (29.27%) number of C's = 45,199,510 bp (20.65%) number of T's = 60,550,090 bp (27.67%) number of G's = 48,978,263 bp (22.38%) number of N's = 68,632 bp (0.03%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,776,017 number of insertions = 15,397 mapped reads with insertion percentage = 0.45% number of deletions = 38,191 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.55% >>>>>>> Coverage mean coverageData = 0.0707X std coverageData = 0.5188X There is a 4.43% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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% 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 27649099 0.11092890717411694 0.7865866587981779 chr2 243199373 16212356 0.06666281989139833 0.47485584190750896 chr3 198022430 12869051 0.06498784506381423 0.38407881155622386 chr4 191154276 12429018 0.06502087350638183 0.43610704842160836 chr5 180915260 16781298 0.09275778063166147 0.4671005678876936 chr6 171115067 14768209 0.08630571964770349 0.5615731714191224 chr7 159138663 14802260 0.09301485711237878 0.7911852246033597 chr8 146364022 9704342 0.06630278307055541 0.547041299264767 chr9 141213431 7645377 0.05414057958835374 0.41777097861893864 chr10 135534747 9337310 0.06889237045611632 0.5571299021666393 chr11 135006516 8783783 0.06506191893730522 0.4680805098211658 chr12 133851895 8524323 0.06368473901695601 0.39418171509154154 chr13 115169878 8678632 0.07535505073644343 0.4220337354834036 chr14 107349540 5898796 0.05494942968549283 0.414103738073727 chr15 102531392 5612037 0.054734817215785 0.3616485439378872 chr16 90354753 5609267 0.062080486236291296 0.4203589368285702 chr17 81195210 6017150 0.07410720410723735 0.45279761703679705 chr18 78077248 2962276 0.03794032289662668 0.5984235251028437 chr19 59128983 3849013 0.06509520043664542 0.6648100524519471 chr20 63025520 4325817 0.06863595889411146 0.4521901477675321 chr21 48129895 3496514 0.07264744708044761 0.4973799361434931 chr22 51304566 1419890 0.02767570434179289 0.27475282580256233 chrMT 16571 34407 2.0763381811598576 2.492116223730129 chrX 155270560 10874560 0.07003620003689044 0.43444477929408276 chrY 59373566 634320 0.01068354223494004 0.3255128395097869