BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003995.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 = 3,357,109 number of mapped reads = 3,030,829 (90.28%) number of supplementary alignments = 22,457 (0.67%) number of secondary alignments = 0 number of mapped bases = 197,806,744 bp number of sequenced bases = 197,724,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,848 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9703 >>>>>>> ACTG content number of A's = 53,429,343 bp (27.02%) number of C's = 38,532,442 bp (19.49%) number of T's = 59,171,822 bp (29.93%) number of G's = 46,551,650 bp (23.54%) number of N's = 39,292 bp (0.02%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,646,780 number of insertions = 16,207 mapped reads with insertion percentage = 0.53% number of deletions = 49,581 mapped reads with deletion percentage = 1.62% homopolymer indels = 44.73% >>>>>>> Coverage mean coverageData = 0.0639X std coverageData = 0.546X There is a 5.39% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 17793944 0.07138976797173155 0.9229498428183155 chr2 243199373 17810630 0.073234687163441 0.8067670530728698 chr3 198022430 12720987 0.06424013178709098 0.2949866482579411 chr4 191154276 10094604 0.05280867481091556 0.29330799583256717 chr5 180915260 9360386 0.05173906280763712 0.26051883200568576 chr6 171115067 11849366 0.06924794062699341 0.3633202846538219 chr7 159138663 12695415 0.07977580533022324 0.9699026365009502 chr8 146364022 14709616 0.10050021719135321 0.5260712307747908 chr9 141213431 6186895 0.043812369377244295 0.44983458268096127 chr10 135534747 9445349 0.06968950183675039 0.555632739117494 chr11 135006516 8180405 0.060592667986484446 0.4163143135748261 chr12 133851895 8810174 0.06582031580501718 0.2960377555143926 chr13 115169878 4413336 0.038320228141597926 0.22651832713446474 chr14 107349540 4789843 0.04461912924824829 0.28965907051879797 chr15 102531392 7697332 0.0750729298593742 0.33576065678819217 chr16 90354753 5132025 0.056798616891797604 0.33795812696158356 chr17 81195210 6058885 0.07462121226116664 0.3449851911103431 chr18 78077248 6078121 0.07784753120396866 0.9804614973699316 chr19 59128983 3764275 0.06366209613312646 0.7271289352007568 chr20 63025520 4328559 0.06867946508017704 0.3192584908209785 chr21 48129895 2603177 0.054086488241871296 0.2906177717487131 chr22 51304566 2421629 0.047201042495905725 0.24990026685653735 chrMT 16571 12636 0.7625369621628145 1.1461506929752574 chrX 155270560 10322324 0.06647959535922328 0.3487898983792964 chrY 59373566 526831 0.008873157458657611 0.17932483341579505