BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082755.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 = 5,068,466 number of mapped reads = 4,428,631 (87.38%) number of supplementary alignments = 32,415 (0.64%) number of secondary alignments = 0 number of mapped bases = 303,384,935 bp number of sequenced bases = 303,270,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 257,675 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6754 >>>>>>> ACTG content number of A's = 87,582,136 bp (28.88%) number of C's = 54,687,769 bp (18.03%) number of T's = 98,824,125 bp (32.59%) number of G's = 62,159,331 bp (20.5%) number of N's = 17,275 bp (0.01%) GC percentage = 38.53% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,624,024 number of insertions = 24,109 mapped reads with insertion percentage = 0.54% number of deletions = 66,884 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.098X std coverageData = 0.7191X There is a 7.12% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 29202317 0.11716045834846686 1.4638252860560037 chr2 243199373 31823328 0.1308528373549713 0.7831291004096395 chr3 198022430 21814412 0.11016131859406028 0.42638798397820293 chr4 191154276 18732973 0.09799923596791525 0.4137106060945766 chr5 180915260 17240335 0.09529508456058378 0.40100793905369464 chr6 171115067 22582398 0.13197200220831518 0.7189985519478206 chr7 159138663 15956436 0.10026750067643839 0.7043701849388088 chr8 146364022 23516316 0.16067005865690134 1.063061561968534 chr9 141213431 9035467 0.06398447326161207 0.6078863047268307 chr10 135534747 11125919 0.08208905277994874 0.5534049427786422 chr11 135006516 12393262 0.09179750998092566 0.5133036832183634 chr12 133851895 9679040 0.07231156495767206 0.35474429872465896 chr13 115169878 7479946 0.06494706888549452 0.32757257061413925 chr14 107349540 6649117 0.06193894263543188 0.3763814625955565 chr15 102531392 5918975 0.05772841745872328 0.304973175633349 chr16 90354753 11939158 0.13213646879207339 0.5487041614144181 chr17 81195210 6857974 0.08446279035425858 0.465415794017274 chr18 78077248 9211851 0.11798380752354386 1.3456932075844374 chr19 59128983 3828361 0.06474593009658225 0.8628129660099721 chr20 63025520 5602910 0.08889906818698204 0.4100583373189985 chr21 48129895 5941820 0.12345383259198882 0.462767227672908 chr22 51304566 3542727 0.0690528597396185 0.3295249103280115 chrMT 16571 444831 26.84394423993724 15.63218142022818 chrX 155270560 12383577 0.07975482924773376 0.4191112638473838 chrY 59373566 481485 0.008109416907854246 0.14359210985034368