BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084998.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 = 2,531,714 number of mapped reads = 2,363,613 (93.36%) number of supplementary alignments = 25,744 (1.02%) number of secondary alignments = 0 number of mapped bases = 163,322,163 bp number of sequenced bases = 163,261,010 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,795 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4669 >>>>>>> ACTG content number of A's = 47,568,458 bp (29.14%) number of C's = 30,210,784 bp (18.5%) number of T's = 51,736,120 bp (31.69%) number of G's = 33,721,357 bp (20.65%) number of N's = 24,291 bp (0.01%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,294,102 number of insertions = 13,200 mapped reads with insertion percentage = 0.55% number of deletions = 37,633 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.0528X std coverageData = 0.4539X There is a 4.29% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.14% 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 13171126 0.0528429014425605 0.8097967161758302 chr2 243199373 13480512 0.05542987974726399 0.42353368160870974 chr3 198022430 11482686 0.057986794728253764 0.2845267880314371 chr4 191154276 11711447 0.06126698939237959 0.30108486731071016 chr5 180915260 10540961 0.05826463173974379 0.28490490306536076 chr6 171115067 9162960 0.05354852825438218 0.3292586051769395 chr7 159138663 8437417 0.05301927791111328 0.3576132209518907 chr8 146364022 8132372 0.05556264366662458 1.0171117228988362 chr9 141213431 6513371 0.04612430243975872 0.36550510393501323 chr10 135534747 7029928 0.05186808663906681 0.4003436686130472 chr11 135006516 7710286 0.05711047309746146 0.36425306276549807 chr12 133851895 7140042 0.05334285330812836 0.2748434455708238 chr13 115169878 4881136 0.042382054099249805 0.24192402548971786 chr14 107349540 4287791 0.03994233230994749 0.25579574893528456 chr15 102531392 4984363 0.048613043310676986 0.25850213024399 chr16 90354753 4580182 0.050691101994379865 0.3061016285734009 chr17 81195210 3514515 0.04328475780775738 0.26562392878818414 chr18 78077248 4254788 0.05449459489145929 0.7237430952850162 chr19 59128983 2356086 0.03984655037953215 0.5163899727640539 chr20 63025520 3324034 0.05274108012119535 0.28021656381081894 chr21 48129895 2180439 0.04530321539242917 0.2670901574299903 chr22 51304566 1258929 0.02453834225982927 0.18008013981057094 chrMT 16571 24190 1.4597791322189366 1.4854655896413091 chrX 155270560 12761276 0.08218735090541311 0.36643775324896777 chrY 59373566 401326 0.006759337985527095 0.12837843714514505