BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240251.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 = 1,965,707 number of mapped reads = 1,289,076 (65.58%) number of supplementary alignments = 10,221 (0.52%) number of secondary alignments = 0 number of mapped bases = 83,617,976 bp number of sequenced bases = 83,578,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 170,115 duplication rate = 10.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4897 >>>>>>> ACTG content number of A's = 23,319,547 bp (27.9%) number of C's = 15,261,303 bp (18.26%) number of T's = 26,836,040 bp (32.11%) number of G's = 18,154,441 bp (21.72%) number of N's = 7,515 bp (0.01%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 703,265 number of insertions = 5,879 mapped reads with insertion percentage = 0.45% number of deletions = 22,562 mapped reads with deletion percentage = 1.73% homopolymer indels = 48.16% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.3282X There is a 1.45% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% 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% 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 6530242 0.0261995014247126 0.45399563881422483 chr2 243199373 8768886 0.03605636762887542 0.3775938012401652 chr3 198022430 5190308 0.02621070754459482 0.2741365178999758 chr4 191154276 5492841 0.028735119689396852 0.28820814632785013 chr5 180915260 4260736 0.02355100393410705 0.25535976696955787 chr6 171115067 4286684 0.025051470189939497 0.28581108676389955 chr7 159138663 4881295 0.030673218613128602 0.43104145627282 chr8 146364022 5436130 0.03714116301067485 0.4595800551956566 chr9 141213431 3051355 0.021608107517761536 0.2838426914815031 chr10 135534747 3933225 0.029020049006326033 0.3247353407563406 chr11 135006516 3615656 0.026781344390814442 0.3030553302717238 chr12 133851895 4107999 0.03069063011771331 0.2945570350741575 chr13 115169878 2168131 0.01882550400895623 0.23200776349987579 chr14 107349540 2737559 0.025501357527940968 0.27346335247479364 chr15 102531392 2308750 0.022517493959313455 0.2585068742148518 chr16 90354753 2457917 0.02720296296975102 0.2760213244840893 chr17 81195210 1997159 0.024597005168162014 0.2723934571200246 chr18 78077248 2383551 0.03052811236379643 0.4351891832274785 chr19 59128983 1449643 0.02451662326071125 0.35050570033223744 chr20 63025520 1649526 0.026172350501828465 0.2712581015370403 chr21 48129895 1387723 0.02883286988263739 0.28446712814056885 chr22 51304566 738298 0.01439049304110671 0.18777996740492148 chrMT 16571 18385 1.109468348319353 1.8253318818123472 chrX 155270560 4535924 0.029213033043739907 0.2960958356952156 chrY 59373566 230053 0.0038746704215138436 0.10126454316397232