BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231810.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 = 5,667,232 number of mapped reads = 4,904,572 (86.54%) number of supplementary alignments = 36,451 (0.64%) number of secondary alignments = 0 number of mapped bases = 314,838,120 bp number of sequenced bases = 314,721,126 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 666,779 duplication rate = 11.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4625 >>>>>>> ACTG content number of A's = 82,105,741 bp (26.09%) number of C's = 55,844,073 bp (17.74%) number of T's = 103,551,779 bp (32.9%) number of G's = 73,097,983 bp (23.23%) number of N's = 121,550 bp (0.04%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,896,429 number of insertions = 20,301 mapped reads with insertion percentage = 0.41% number of deletions = 67,431 mapped reads with deletion percentage = 1.36% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.1017X std coverageData = 0.9087X There is a 7.21% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 21479315 0.08617557265785107 1.545452662838446 chr2 243199373 16850021 0.06928480444725489 1.6178704298078699 chr3 198022430 26093126 0.13176853753385412 0.4842078480227336 chr4 191154276 21561429 0.11279595440491219 0.48312482844790483 chr5 180915260 33472754 0.18501896412718308 0.5831771948462543 chr6 171115067 24150001 0.14113310664805456 0.7664354440215392 chr7 159138663 19011811 0.11946695191224524 1.1787448157549423 chr8 146364022 22859705 0.15618390836513088 1.4653935187283857 chr9 141213431 12175138 0.08621798871241929 0.5757080529046469 chr10 135534747 16609076 0.12254478181893828 0.6573711869861305 chr11 135006516 11178964 0.08280314410898508 0.5771839595158501 chr12 133851895 10994646 0.08214038359337386 0.4067907776886035 chr13 115169878 11244454 0.09763363646178387 0.4628436628924817 chr14 107349540 15398394 0.14344163934004747 0.5393445665215773 chr15 102531392 7642368 0.07453685989165153 0.41238262339279075 chr16 90354753 5561803 0.0615551790618032 0.3929156519422388 chr17 81195210 5664392 0.06976263747578212 0.39557508421384935 chr18 78077248 4574543 0.05858996208472922 1.3304432300577518 chr19 59128983 6965004 0.11779340091136017 0.9909360812054736 chr20 63025520 3399368 0.05393637371020501 0.3557363070746493 chr21 48129895 7049645 0.14647123165342454 0.5375330393355677 chr22 51304566 2057306 0.040099861677028906 0.2539243518733505 chrMT 16571 347070 20.94442097640456 12.35257514562503 chrX 155270560 7804543 0.05026415181345388 0.38251535302203343 chrY 59373566 693244 0.011675970414173877 0.28345949744045096