BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237794.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 = 3,909,964 number of mapped reads = 3,670,133 (93.87%) number of supplementary alignments = 25,495 (0.65%) number of secondary alignments = 0 number of mapped bases = 268,527,563 bp number of sequenced bases = 268,420,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,214 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.3542 >>>>>>> ACTG content number of A's = 79,899,482 bp (29.77%) number of C's = 53,394,561 bp (19.89%) number of T's = 80,104,890 bp (29.84%) number of G's = 54,514,740 bp (20.31%) number of N's = 507,057 bp (0.19%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,198,237 number of insertions = 20,532 mapped reads with insertion percentage = 0.55% number of deletions = 57,597 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.0867X std coverageData = 0.9411X There is a 4.77% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% 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 21681569 0.08698702098720147 2.338021558869162 chr2 243199373 24551038 0.10095025203868432 0.8179936726222835 chr3 198022430 18796083 0.09491895943302989 0.5173052543079265 chr4 191154276 16973031 0.08879231663120107 0.5348657250589738 chr5 180915260 15764569 0.08713786222345202 0.48143393366672915 chr6 171115067 16935067 0.09896888273432988 0.696245512701887 chr7 159138663 14200746 0.08923504654553997 0.8808509935572557 chr8 146364022 12955707 0.08851701957192731 0.8437393046935098 chr9 141213431 10910384 0.07726165933890523 0.7310567028311867 chr10 135534747 12661936 0.09342206541323311 0.9499914066783344 chr11 135006516 12750657 0.09444475257772003 0.6432006905910115 chr12 133851895 12525288 0.09357572412404024 0.5049754997973449 chr13 115169878 9198636 0.07987015493756101 0.45698715949154595 chr14 107349540 8692894 0.0809774685573874 0.5077613355306251 chr15 102531392 6682304 0.06517324957414018 0.40678239074498446 chr16 90354753 7122953 0.0788331854551138 0.5851174583193219 chr17 81195210 7326762 0.09023638217082018 0.5867886468801059 chr18 78077248 7821239 0.10017308755554499 1.3767113882342112 chr19 59128983 4785228 0.08092863697655682 1.3581315009485595 chr20 63025520 4969331 0.07884633081964258 0.48167470801995454 chr21 48129895 3879855 0.08061216422765934 0.5060241281781902 chr22 51304566 3010961 0.05868797330826266 0.38349739241934744 chrMT 16571 23026 1.389535936274214 2.036025799321153 chrX 155270560 13616920 0.08769801564443382 0.5284900994032616 chrY 59373566 691379 0.011644559129225959 0.3002377307707673