BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080686.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 = 1,107,910 number of mapped reads = 992,737 (89.6%) number of supplementary alignments = 10,745 (0.97%) number of secondary alignments = 0 number of mapped bases = 65,268,543 bp number of sequenced bases = 65,246,343 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,713 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9575 >>>>>>> ACTG content number of A's = 17,936,600 bp (27.49%) number of C's = 12,363,671 bp (18.95%) number of T's = 19,593,955 bp (30.03%) number of G's = 15,349,480 bp (23.53%) number of N's = 2,637 bp (0%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 476,589 number of insertions = 5,606 mapped reads with insertion percentage = 0.56% number of deletions = 13,421 mapped reads with deletion percentage = 1.34% homopolymer indels = 42.74% >>>>>>> Coverage mean coverageData = 0.0211X std coverageData = 0.3125X There is a 1.94% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 7780382 0.031215095748949005 0.4484231940006947 chr2 243199373 4447230 0.01828635471029771 0.3248165008807133 chr3 198022430 3906751 0.019728830718823115 0.14910242129262788 chr4 191154276 2720750 0.014233267792555161 0.13027752888235344 chr5 180915260 2916312 0.01611976789575407 0.13433328457734361 chr6 171115067 3826745 0.022363577136080014 0.24715790887550185 chr7 159138663 4360449 0.027400311890266416 0.9062575018702169 chr8 146364022 7438203 0.050819886597541025 0.3279240019761418 chr9 141213431 2117045 0.014991810516947215 0.2213033977901213 chr10 135534747 3131918 0.02310786030389683 0.2343598605571054 chr11 135006516 2738199 0.020281976612151077 0.20789234591636868 chr12 133851895 2110818 0.015769802885495197 0.13662151350334045 chr13 115169878 1303245 0.011315849444591753 0.11016871539038617 chr14 107349540 1306732 0.012172683739492502 0.13103492550915127 chr15 102531392 1200353 0.01170717549606661 0.12001312055271418 chr16 90354753 1729379 0.019139878562890875 0.16393429701200102 chr17 81195210 1136830 0.014001195390713319 0.13972228709683085 chr18 78077248 2007150 0.02570723291886517 0.36881169183460843 chr19 59128983 1276177 0.021582935055723857 0.31165349886438687 chr20 63025520 1663529 0.026394530342629462 0.17705676631014197 chr21 48129895 950151 0.01974138942127341 0.15528413384808915 chr22 51304566 675412 0.013164754185816521 0.11922099088550998 chrMT 16571 14534 0.8770744070967352 1.0886042761078711 chrX 155270560 4354794 0.02804648865824919 0.2072203061205171 chrY 59373566 155455 0.002618252708621207 0.06017205406396523