BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975247.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,920,610 number of mapped reads = 2,889,821 (98.95%) number of supplementary alignments = 117,719 (4.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,447,602 number of mapped paired reads (second in pair) = 1,442,219 number of mapped paired reads (both in pair) = 2,881,502 number of mapped paired reads (singletons) = 8,319 number of mapped bases = 393,969,872 bp number of sequenced bases = 393,793,995 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 651,187 duplication rate = 24.16% >>>>>>> Insert size mean insert size = 164,081.7145 std insert size = 3,854,047.9144 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 53.5266 >>>>>>> ACTG content number of A's = 112,011,695 bp (28.44%) number of C's = 84,540,765 bp (21.47%) number of T's = 110,650,553 bp (28.1%) number of G's = 86,555,098 bp (21.98%) number of N's = 35,884 bp (0.01%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 3,516,372 number of insertions = 66,097 mapped reads with insertion percentage = 2.18% number of deletions = 68,258 mapped reads with deletion percentage = 2.26% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.1273X std coverageData = 2.4055X There is a 6.77% of reference with a coverageData >= 1X There is a 4.77% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.22% 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 0.01% 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% 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 29038546 0.11650340482000243 7.392290819616206 chr2 243199373 35403499 0.1455739731697417 1.4311357097910322 chr3 198022430 22085578 0.11153068872046465 0.4771033938106879 chr4 191154276 23497072 0.12292203183568857 1.186643256832452 chr5 180915260 20898325 0.11551444029652336 0.4833352745909508 chr6 171115067 17994218 0.10515858314218467 0.5751444233982563 chr7 159138663 18725703 0.11766909842644588 1.1815918832228989 chr8 146364022 28548886 0.1950539866962661 1.22277248008804 chr9 141213431 19496619 0.13806490545506256 2.034804662901879 chr10 135534747 18589251 0.13715487291240525 2.620807126189882 chr11 135006516 20816530 0.15418907632576787 0.8254353052911154 chr12 133851895 19921384 0.14883154250449723 0.5353444690405909 chr13 115169878 9144153 0.07939708853386127 0.39029979163363976 chr14 107349540 13011048 0.12120264325305911 0.49079239218923826 chr15 102531392 8297836 0.08092971175110936 0.3905503854655058 chr16 90354753 10267507 0.1136354940840799 0.8166785143656446 chr17 81195210 12937127 0.1593336232519135 1.1137137961157233 chr18 78077248 11569517 0.14818038924732593 1.7564584225222353 chr19 59128983 11911005 0.20144105979296142 3.002679138545051 chr20 63025520 18610706 0.2952884165017599 0.8602012575480379 chr21 48129895 4090874 0.0849965286647727 0.8508119132337353 chr22 51304566 4727196 0.09213986918825119 0.7032380988474277 chrMT 16571 445954 26.911713233962946 8.407143263022613 chrX 155270560 8995644 0.05793528406157613 0.4310711040824888 chrY 59373566 4945694 0.08329791072343541 1.5727441895192298