BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013264.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 = 2,173,721 number of mapped reads = 1,889,805 (86.94%) number of supplementary alignments = 11,245 (0.52%) number of secondary alignments = 0 number of mapped bases = 126,788,283 bp number of sequenced bases = 126,733,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,746 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7427 >>>>>>> ACTG content number of A's = 34,628,514 bp (27.32%) number of C's = 23,470,018 bp (18.52%) number of T's = 40,361,252 bp (31.85%) number of G's = 28,246,535 bp (22.29%) number of N's = 27,196 bp (0.02%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,041,654 number of insertions = 9,522 mapped reads with insertion percentage = 0.5% number of deletions = 32,543 mapped reads with deletion percentage = 1.7% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.041X std coverageData = 0.4034X There is a 3.37% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 7679770 0.030811437777721724 0.47346767193407463 chr2 243199373 15966306 0.06565109853305419 0.631932566983094 chr3 198022430 11676416 0.05896511824443322 0.28370137179169713 chr4 191154276 11213993 0.05866462019400497 0.29987851917462405 chr5 180915260 4493333 0.024836672152476248 0.18247281422030576 chr6 171115067 4914721 0.028721731441685376 0.24687817663725325 chr7 159138663 10463690 0.06575202909678837 0.9444846849156918 chr8 146364022 6691834 0.04572048450540667 0.43057417253908203 chr9 141213431 7583891 0.0537051677471104 0.36862712773790635 chr10 135534747 4713471 0.0347768458224222 0.39378227643353203 chr11 135006516 4839039 0.035843003311040185 0.2577563776246474 chr12 133851895 5110907 0.0381832995341605 0.2366514449813872 chr13 115169878 2607025 0.022636344201041873 0.17901225871376328 chr14 107349540 4147153 0.03863223820055493 0.25198549521375296 chr15 102531392 1291065 0.012591899659374566 0.13110742533884756 chr16 90354753 3420893 0.03786068675324695 0.24292439469233804 chr17 81195210 4302634 0.0529912294087299 0.2785415763887379 chr18 78077248 3058326 0.039170514821424036 0.5394432360336978 chr19 59128983 2606757 0.04408594343657154 0.4420512184753106 chr20 63025520 3429920 0.05442112972649809 0.28070401223369207 chr21 48129895 2542581 0.05282747863879612 0.28607463284145146 chr22 51304566 1489027 0.029023284204372765 0.19895032474650318 chrMT 16571 84477 5.09788184177177 4.193174215112504 chrX 155270560 2277613 0.014668672541658895 0.15847662022251224 chrY 59373566 183441 0.0030896072504723736 0.11651946153792073