BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080982.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 = 4,171,717 number of mapped reads = 3,516,204 (84.29%) number of supplementary alignments = 23,049 (0.55%) number of secondary alignments = 0 number of mapped bases = 236,247,642 bp number of sequenced bases = 236,163,743 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 238,269 duplication rate = 5.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2013 >>>>>>> ACTG content number of A's = 66,336,179 bp (28.09%) number of C's = 41,473,877 bp (17.56%) number of T's = 77,287,975 bp (32.73%) number of G's = 50,598,380 bp (21.43%) number of N's = 467,332 bp (0.2%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 2,292,663 number of insertions = 17,919 mapped reads with insertion percentage = 0.51% number of deletions = 47,602 mapped reads with deletion percentage = 1.34% homopolymer indels = 49.51% >>>>>>> Coverage mean coverageData = 0.0763X std coverageData = 0.5804X There is a 5.54% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% 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% 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 19674705 0.07893543021503646 0.8492519925998129 chr2 243199373 14526216 0.059729660569478524 0.5143116250891271 chr3 198022430 20840503 0.10524314341562216 0.42417468085979815 chr4 191154276 15112608 0.0790597433457361 0.39090797098323987 chr5 180915260 13435421 0.07426361380460664 0.35656379326181764 chr6 171115067 20583839 0.12029238196774338 0.6814460052328992 chr7 159138663 11765710 0.07393369894027575 0.6036288757615942 chr8 146364022 18545466 0.1267078189474733 1.1472181143849578 chr9 141213431 12350815 0.08746204176570145 0.712239730232261 chr10 135534747 10527808 0.07767608110118064 0.4788651569515255 chr11 135006516 10484811 0.07766151820405469 0.447684818078747 chr12 133851895 12209308 0.0912150552668679 0.4132762990373424 chr13 115169878 6341587 0.05506289587282536 0.30313460780635354 chr14 107349540 6300405 0.058690563555279324 0.39967236751276397 chr15 102531392 5707108 0.05566205518793698 0.3044661897166074 chr16 90354753 5256231 0.05817326510759207 0.38127037523765317 chr17 81195210 4901380 0.06036538362299944 0.32991383400075197 chr18 78077248 5991404 0.07673687474230649 1.1623298473559749 chr19 59128983 4041066 0.06834323533012567 0.6174861199085887 chr20 63025520 3633249 0.05764726732917079 0.33573910370164645 chr21 48129895 4458493 0.09263458812864644 0.4867781093882484 chr22 51304566 1929109 0.037601117218299826 0.24562980049252503 chrMT 16571 24991 1.508116589222135 1.4149335799442568 chrX 155270560 7070447 0.04553630127952137 0.3146049531224664 chrY 59373566 534962 0.009010103924025719 0.19085728951196956