BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013316.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 = 1,580,146 number of mapped reads = 1,400,906 (88.66%) number of supplementary alignments = 7,474 (0.47%) number of secondary alignments = 0 number of mapped bases = 92,479,011 bp number of sequenced bases = 92,438,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,294 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6408 >>>>>>> ACTG content number of A's = 25,468,059 bp (27.55%) number of C's = 16,853,394 bp (18.23%) number of T's = 29,382,619 bp (31.79%) number of G's = 20,732,561 bp (22.43%) number of N's = 1,367 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 645,021 number of insertions = 6,003 mapped reads with insertion percentage = 0.43% number of deletions = 23,289 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 0.0299X std coverageData = 0.2878X There is a 2.63% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 5414522 0.021723203650513674 0.4708279035102701 chr2 243199373 10639905 0.04374972216725246 0.31467945430640093 chr3 198022430 5680240 0.02868483130926128 0.18720638950349267 chr4 191154276 5593631 0.029262390133506615 0.19438067054910368 chr5 180915260 4153886 0.022960395933433145 0.16885380899774652 chr6 171115067 4582957 0.026782895745819976 0.24050853201674632 chr7 159138663 6548514 0.04114973618950161 0.549124186845131 chr8 146364022 5579673 0.03812188899810365 0.29833849298066023 chr9 141213431 3001304 0.021253672393244237 0.24302770200801882 chr10 135534747 3438438 0.025369420581129648 0.2690950894834026 chr11 135006516 4517366 0.03346035535055212 0.26311016657328723 chr12 133851895 5112400 0.038194453653420446 0.21772965087149151 chr13 115169878 2540747 0.02206086386581047 0.16099619727796427 chr14 107349540 3068388 0.02858314996040039 0.1968224334923523 chr15 102531392 2105351 0.020533721028580202 0.1610274874334893 chr16 90354753 3900323 0.04316677175798378 0.24470129148020656 chr17 81195210 2410596 0.02968889420939979 0.23219999525599044 chr18 78077248 2023842 0.02592102119173053 0.3921375985391578 chr19 59128983 1829055 0.030933307275046486 0.33915597560156174 chr20 63025520 2510702 0.03983627584508624 0.2225643179899626 chr21 48129895 2339100 0.04859973203764521 0.2533328125533637 chr22 51304566 647901 0.012628525110221184 0.12432346227770893 chrMT 16571 22924 1.3833806046708104 1.419594493036943 chrX 155270560 4624722 0.0297849251010623 0.2107270259389044 chrY 59373566 192524 0.0032425877872991494 0.07810747002799914