BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472486.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,934,302 number of mapped reads = 17,748,460 (98.96%) number of supplementary alignments = 73,889 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,898,622 number of mapped paired reads (second in pair) = 8,849,838 number of mapped paired reads (both in pair) = 17,651,930 number of mapped paired reads (singletons) = 96,530 number of mapped bases = 1,748,556,630 bp number of sequenced bases = 1,748,364,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,721,037 duplication rate = 46.28% >>>>>>> Insert size mean insert size = 29,688.7289 std insert size = 1,690,879.698 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.1014 >>>>>>> ACTG content number of A's = 467,956,227 bp (26.77%) number of C's = 409,199,789 bp (23.4%) number of T's = 465,650,025 bp (26.63%) number of G's = 405,284,456 bp (23.18%) number of N's = 273,799 bp (0.02%) GC percentage = 46.59% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 10,079,178 number of insertions = 93,371 mapped reads with insertion percentage = 0.52% number of deletions = 78,294 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 0.5648X std coverageData = 23.6796X There is a 5.19% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 121911601 0.48911252662435695 15.46893402819697 chr2 243199373 119015108 0.48937259390056076 15.333701319953645 chr3 198022430 170680849 0.8619268483878316 22.403350984365396 chr4 191154276 68059572 0.3560452500680654 12.210503781580437 chr5 180915260 72663824 0.4016456323253218 13.143925814174265 chr6 171115067 110817274 0.6476184472989746 21.711940686528603 chr7 159138663 73794852 0.4637141635405093 13.99196232434858 chr8 146364022 84431633 0.5768605689176811 19.889691401046765 chr9 141213431 95669750 0.6774833620464897 20.439451285912437 chr10 135534747 50159884 0.37008874189288155 17.25148017935899 chr11 135006516 60000326 0.4444254083262174 14.747772648818055 chr12 133851895 119180836 0.8903933410879241 45.0706092221228 chr13 115169878 28722561 0.24939299666532597 9.572279011423653 chr14 107349540 40930903 0.38128624491544166 19.338981296596153 chr15 102531392 61493743 0.5997552729997072 23.641641347002256 chr16 90354753 75241430 0.8327335032391711 27.136557988130008 chr17 81195210 71660854 0.8825748957358445 26.702048341113947 chr18 78077248 31658195 0.4054727313134807 15.066266991777812 chr19 59128983 52420210 0.8865400238661301 36.635684605353646 chr20 63025520 56956316 0.9037024367272178 41.37508589649765 chr21 48129895 4675512 0.09714361521046327 3.955348383966471 chr22 51304566 22598118 0.4404699184084317 14.18768294555161 chrMT 16571 2347 0.14163297326655 0.5653582231187372 chrX 155270560 153820151 0.9906588280482791 53.27777288444366 chrY 59373566 1990781 0.0335297529543703 1.599686364858929