BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230359.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 = 1,656,057 number of mapped reads = 1,498,698 (90.5%) number of supplementary alignments = 11,599 (0.7%) number of secondary alignments = 0 number of mapped bases = 101,221,408 bp number of sequenced bases = 101,176,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,915 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0708 >>>>>>> ACTG content number of A's = 29,449,910 bp (29.11%) number of C's = 18,639,133 bp (18.42%) number of T's = 32,051,073 bp (31.68%) number of G's = 20,985,510 bp (20.74%) number of N's = 50,543 bp (0.05%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 867,401 number of insertions = 8,664 mapped reads with insertion percentage = 0.57% number of deletions = 27,184 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.301X There is a 2.77% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8437695 0.0338522526690114 0.5080647511833425 chr2 243199373 8677805 0.03568185597254809 0.32200355471434444 chr3 198022430 7051540 0.035609804404480846 0.21584863490006445 chr4 191154276 4259009 0.022280479877939012 0.19435981381266157 chr5 180915260 6143717 0.03395908670169669 0.21047046708386652 chr6 171115067 5805253 0.033926018916849675 0.22141354351509115 chr7 159138663 4520661 0.028407056555451896 0.30025760729780043 chr8 146364022 6997447 0.04780851813432675 0.44917054915443355 chr9 141213431 5692425 0.04031079026753482 0.2989496775485695 chr10 135534747 3884120 0.028657743390335173 0.29142908901872094 chr11 135006516 6055780 0.04485546460587132 0.31678426022472417 chr12 133851895 3728430 0.027854891408149285 0.19316908307914735 chr13 115169878 2923775 0.02538662930597183 0.1810750704705342 chr14 107349540 4018145 0.03743048177011285 0.22891455415423992 chr15 102531392 2627869 0.02562989684173994 0.1812613388407424 chr16 90354753 3019620 0.03341960328307245 0.2588754029956803 chr17 81195210 2046957 0.025210317209598942 0.1956713719888364 chr18 78077248 3341779 0.04280093222548008 0.565291223064045 chr19 59128983 1696860 0.028697601648247528 0.37579725870343084 chr20 63025520 1359164 0.02156529608958403 0.1791490964728843 chr21 48129895 1993059 0.04141000099834001 0.2503621711231257 chr22 51304566 1206609 0.023518549986369635 0.17311816736311403 chrMT 16571 4229 0.2552048759881721 0.5144258334851589 chrX 155270560 5436175 0.03501098340857404 0.23351754724612747 chrY 59373566 293285 0.004939656142600564 0.1346253277983791