BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080640.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 = 5,104,241 number of mapped reads = 4,309,406 (84.43%) number of supplementary alignments = 25,371 (0.5%) number of secondary alignments = 0 number of mapped bases = 285,980,821 bp number of sequenced bases = 285,868,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,564 duplication rate = 3.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3978 >>>>>>> ACTG content number of A's = 78,239,250 bp (27.37%) number of C's = 50,757,110 bp (17.76%) number of T's = 92,797,883 bp (32.46%) number of G's = 63,839,637 bp (22.33%) number of N's = 234,207 bp (0.08%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 2,543,584 number of insertions = 24,010 mapped reads with insertion percentage = 0.55% number of deletions = 69,226 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.0924X std coverageData = 0.6383X There is a 7.46% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 34275982 0.13751613481436423 0.8626311815135874 chr2 243199373 18907778 0.07774599813626987 0.7001350266055 chr3 198022430 17137179 0.08654160541308376 0.3430707337934131 chr4 191154276 12496615 0.0653744988681289 0.31470967966846963 chr5 180915260 13549221 0.07489263758071044 0.31774354553965567 chr6 171115067 17009491 0.09940381813367727 0.6230546999223251 chr7 159138663 17488275 0.1098933136066375 1.622638275176932 chr8 146364022 32151568 0.21966851935785148 0.8595564847223632 chr9 141213431 9032188 0.06396125309072052 0.5083709341041007 chr10 135534747 13776513 0.10164561711986668 0.520834499548294 chr11 135006516 12142869 0.0899428365368676 0.43849442343998557 chr12 133851895 9212099 0.06882307493666788 0.31360732103211353 chr13 115169878 5963372 0.05177892087373749 0.26203642645855013 chr14 107349540 5705575 0.05314950581064437 0.3119626450391098 chr15 102531392 6873450 0.06703751764142635 0.30406387959277414 chr16 90354753 7292912 0.08071420437616603 0.36550233202689436 chr17 81195210 4588751 0.05651504565355518 0.3037773585813055 chr18 78077248 9139343 0.11705513749664948 0.8483266915593514 chr19 59128983 4969471 0.08404458774472749 0.5847716819083998 chr20 63025520 7370713 0.11694807119401791 0.41800673540581146 chr21 48129895 4066981 0.08450010123645606 0.36708432115279027 chr22 51304566 2627238 0.05120865850419629 0.2598649707368272 chrMT 16571 146219 8.823788546255507 11.726703969290275 chrX 155270560 19433673 0.1251600625385778 0.47641172120706454 chrY 59373566 623345 0.010498695665340363 0.18286155075689017