BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082758.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 = 4,408,153 number of mapped reads = 3,801,238 (86.23%) number of supplementary alignments = 29,747 (0.67%) number of secondary alignments = 0 number of mapped bases = 256,444,095 bp number of sequenced bases = 256,346,093 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,295 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0828 >>>>>>> ACTG content number of A's = 72,648,095 bp (28.34%) number of C's = 46,094,117 bp (17.98%) number of T's = 83,728,849 bp (32.66%) number of G's = 53,860,705 bp (21.01%) number of N's = 14,327 bp (0.01%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,257,616 number of insertions = 20,480 mapped reads with insertion percentage = 0.53% number of deletions = 57,833 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.0828X std coverageData = 0.5948X There is a 6.36% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% 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% 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 27548198 0.11052408972734315 1.1245462949306329 chr2 243199373 23013337 0.09462745202061026 0.7191609569962073 chr3 198022430 22574331 0.11399885861414791 0.4193942748835565 chr4 191154276 13889892 0.07266325551618841 0.34149822565666726 chr5 180915260 16179468 0.08943119557742116 0.37488869731888264 chr6 171115067 18089732 0.10571676893888017 0.5886753383096265 chr7 159138663 10302271 0.06473769985110407 0.47182846814908364 chr8 146364022 18994448 0.1297753897470787 0.8207477217593744 chr9 141213431 7523787 0.05327954251037212 0.5396955863176576 chr10 135534747 10954258 0.08082250671851698 0.49305107227787986 chr11 135006516 11824094 0.08758165420697175 0.5338300150697067 chr12 133851895 8132653 0.06075859441511829 0.3125325635326866 chr13 115169878 6176021 0.0536253151192884 0.28544221116985335 chr14 107349540 6573774 0.06123709519388718 0.34005336101049427 chr15 102531392 5050443 0.04925752885516272 0.271427379883888 chr16 90354753 8615462 0.09535150851444417 0.4455855827255745 chr17 81195210 6052532 0.07454296872931297 0.45745298960548775 chr18 78077248 6793892 0.08701500339766073 1.175058027909435 chr19 59128983 3665633 0.061993844879760576 0.7238900271298075 chr20 63025520 5499423 0.08725708252783952 0.37824126774740646 chr21 48129895 4472214 0.09291967081997582 0.3920951958329834 chr22 51304566 3673224 0.07159643451617932 0.32633090233139894 chrMT 16571 162851 9.827469675939895 5.835843998126328 chrX 155270560 10262629 0.06609513741690634 0.3812782018136982 chrY 59373566 419528 0.007065905389613957 0.1373324485402117