BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085021.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 = 2,394,338 number of mapped reads = 2,170,548 (90.65%) number of supplementary alignments = 17,642 (0.74%) number of secondary alignments = 0 number of mapped bases = 145,075,580 bp number of sequenced bases = 145,024,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,625 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8032 >>>>>>> ACTG content number of A's = 40,711,572 bp (28.07%) number of C's = 27,787,305 bp (19.16%) number of T's = 44,836,871 bp (30.92%) number of G's = 31,684,831 bp (21.85%) number of N's = 3,753 bp (0%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,207,813 number of insertions = 10,035 mapped reads with insertion percentage = 0.46% number of deletions = 29,826 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.0469X std coverageData = 0.3573X There is a 3.89% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15549850 0.062386404244906574 0.5171893967306416 chr2 243199373 13667453 0.05619855360400127 0.48090510021183946 chr3 198022430 9781741 0.04939713647590326 0.2663826167198359 chr4 191154276 10433150 0.05457973642190458 0.2753767429032378 chr5 180915260 7407469 0.04094441231767845 0.2348012118374397 chr6 171115067 9549106 0.055805173485979465 0.32062731970052444 chr7 159138663 9025420 0.056714187676693 0.3175235970903629 chr8 146364022 7954644 0.05434835618277831 0.604577170783126 chr9 141213431 3440407 0.024363171234045012 0.293771291540833 chr10 135534747 9221896 0.06804082498490222 0.46697644586006287 chr11 135006516 6729118 0.049842912767262285 0.35414257216848033 chr12 133851895 6034023 0.045079847394017096 0.2530322635987747 chr13 115169878 2849589 0.024742485183495637 0.1801234350801231 chr14 107349540 4822327 0.044921729520219646 0.2572479243073464 chr15 102531392 3080983 0.030049167770978862 0.20343302192788315 chr16 90354753 3253590 0.036009063076073045 0.23682909505158037 chr17 81195210 2743505 0.03378900060730183 0.2344953167098442 chr18 78077248 5824972 0.07460524223394759 0.5866544159176366 chr19 59128983 2223234 0.03759973345051445 0.39312193883023844 chr20 63025520 3018001 0.047885380398289455 0.25815471533944007 chr21 48129895 1696102 0.03524009350113895 0.22481035805664648 chr22 51304566 1056790 0.02059836155713704 0.16302752579873406 chrMT 16571 19869 1.1990223885100477 1.319462896951869 chrX 155270560 5410450 0.03484530486655036 0.24622346086069105 chrY 59373566 281891 0.004747752560457628 0.10120631005045916