BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080723.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 = 2,592,100 number of mapped reads = 2,420,075 (93.36%) number of supplementary alignments = 13,567 (0.52%) number of secondary alignments = 0 number of mapped bases = 169,129,241 bp number of sequenced bases = 169,064,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,463 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9964 >>>>>>> ACTG content number of A's = 49,257,460 bp (29.14%) number of C's = 31,487,910 bp (18.62%) number of T's = 53,557,016 bp (31.68%) number of G's = 34,759,634 bp (20.56%) number of N's = 2,449 bp (0%) GC percentage = 39.18% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,325,484 number of insertions = 12,371 mapped reads with insertion percentage = 0.51% number of deletions = 36,491 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.41% >>>>>>> Coverage mean coverageData = 0.0546X std coverageData = 0.426X There is a 4.5% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 21718744 0.08713616805793234 0.7996110230257932 chr2 243199373 10761529 0.04424982214078323 0.4202298333918835 chr3 198022430 11546003 0.05830654133473668 0.2811511741870038 chr4 191154276 11561035 0.060480127580300636 0.29479376597061896 chr5 180915260 5670925 0.03134575270212142 0.20464987221496236 chr6 171115067 5186011 0.03030715582748771 0.2599682724538294 chr7 159138663 7163303 0.045012964574171394 0.5466476806119801 chr8 146364022 17055048 0.11652486565311795 0.7646168924748098 chr9 141213431 4515781 0.031978410042313894 0.31843301913699734 chr10 135534747 7230074 0.053344800208318534 0.4412746446533803 chr11 135006516 9392243 0.06956881251568628 0.3764198663408546 chr12 133851895 7028464 0.05250926032836517 0.2681010315438723 chr13 115169878 2867758 0.02490024344733612 0.18010354319677746 chr14 107349540 5224934 0.04867216012290318 0.2676732005593803 chr15 102531392 3397346 0.033134691080757006 0.20827070054021773 chr16 90354753 4320942 0.04782196682005207 0.26854057442722956 chr17 81195210 4031422 0.049650983106023124 0.28370126386985006 chr18 78077248 7694646 0.09855170612570771 0.5968751207308036 chr19 59128983 2120150 0.03585635829386749 0.5072790513732842 chr20 63025520 4499410 0.0713902876168257 0.31804232572294966 chr21 48129895 3477186 0.07224586714764285 0.3247316989818762 chr22 51304566 1261744 0.024593210670566825 0.17787028179150605 chrMT 16571 52635 3.176332146521031 2.362457663357015 chrX 155270560 10987377 0.07076278336343993 0.334848735258728 chrY 59373566 364531 0.006139617755147131 0.1253545020565707