BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438268.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 646,716,700 number of mapped reads = 644,728,361 (99.69%) number of supplementary alignments = 10,637,362 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 322,558,010 number of mapped paired reads (second in pair) = 322,170,351 number of mapped paired reads (both in pair) = 643,342,874 number of mapped paired reads (singletons) = 1,385,487 number of mapped bases = 92,651,631,698 bp number of sequenced bases = 92,626,650,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 246,900,318 duplication rate = 35.56% >>>>>>> Insert size mean insert size = 37,251.9474 std insert size = 1,861,359.6443 median insert size = 253 >>>>>>> Mapping quality mean mapping quality = 55.0337 >>>>>>> ACTG content number of A's = 28,042,769,798 bp (30.28%) number of C's = 18,499,241,462 bp (19.97%) number of T's = 26,738,459,560 bp (28.87%) number of G's = 19,345,478,594 bp (20.89%) number of N's = 701,362 bp (0%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 476,017,848 number of insertions = 11,346,463 mapped reads with insertion percentage = 1.73% number of deletions = 10,095,788 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 29.9292X std coverageData = 101.0006X There is a 91.37% of reference with a coverageData >= 1X There is a 90.67% of reference with a coverageData >= 2X There is a 89.85% of reference with a coverageData >= 3X There is a 88.94% of reference with a coverageData >= 4X There is a 87.91% of reference with a coverageData >= 5X There is a 86.76% of reference with a coverageData >= 6X There is a 85.48% of reference with a coverageData >= 7X There is a 84.09% of reference with a coverageData >= 8X There is a 82.58% of reference with a coverageData >= 9X There is a 80.97% of reference with a coverageData >= 10X There is a 79.27% of reference with a coverageData >= 11X There is a 77.48% of reference with a coverageData >= 12X There is a 75.61% of reference with a coverageData >= 13X There is a 73.68% of reference with a coverageData >= 14X There is a 71.7% of reference with a coverageData >= 15X There is a 69.67% of reference with a coverageData >= 16X There is a 67.61% of reference with a coverageData >= 17X There is a 65.53% of reference with a coverageData >= 18X There is a 63.44% of reference with a coverageData >= 19X There is a 61.35% of reference with a coverageData >= 20X There is a 59.27% of reference with a coverageData >= 21X There is a 57.2% of reference with a coverageData >= 22X There is a 55.14% of reference with a coverageData >= 23X There is a 53.11% of reference with a coverageData >= 24X There is a 51.12% of reference with a coverageData >= 25X There is a 49.16% of reference with a coverageData >= 26X There is a 47.24% of reference with a coverageData >= 27X There is a 45.36% of reference with a coverageData >= 28X There is a 43.53% of reference with a coverageData >= 29X There is a 41.75% of reference with a coverageData >= 30X There is a 40.02% of reference with a coverageData >= 31X There is a 38.34% of reference with a coverageData >= 32X There is a 36.72% of reference with a coverageData >= 33X There is a 35.14% of reference with a coverageData >= 34X There is a 33.62% of reference with a coverageData >= 35X There is a 32.15% of reference with a coverageData >= 36X There is a 30.74% of reference with a coverageData >= 37X There is a 29.37% of reference with a coverageData >= 38X There is a 28.06% of reference with a coverageData >= 39X There is a 26.8% of reference with a coverageData >= 40X There is a 25.59% of reference with a coverageData >= 41X There is a 24.43% of reference with a coverageData >= 42X There is a 23.32% of reference with a coverageData >= 43X There is a 22.25% of reference with a coverageData >= 44X There is a 21.23% of reference with a coverageData >= 45X There is a 20.25% of reference with a coverageData >= 46X There is a 19.31% of reference with a coverageData >= 47X There is a 18.41% of reference with a coverageData >= 48X There is a 17.56% of reference with a coverageData >= 49X There is a 16.74% of reference with a coverageData >= 50X There is a 15.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7425253009 29.790308963763824 29.106641688438422 chr2 243199373 8256244492 33.948461256929306 96.27551886824273 chr3 198022430 6759200746 34.13351076441189 210.09996105940473 chr4 191154276 6277452092 32.83971576968543 25.683420838176332 chr5 180915260 5943330060 32.851457969880485 29.150819594206062 chr6 171115067 5646976150 33.001045723226696 25.942555210438478 chr7 159138663 5038885623 31.663490995899593 29.04249642002469 chr8 146364022 4905031436 33.51254884209181 26.319339411479525 chr9 141213431 3936530556 27.876459966474435 31.19256660441797 chr10 135534747 4432160793 32.701287980417305 36.891633260515846 chr11 135006516 4349255641 32.21515353377462 25.069532251378835 chr12 133851895 4388855984 32.78889689234508 25.020208679982616 chr13 115169878 3187497027 27.6764817533279 24.514002956611314 chr14 107349540 2930595229 27.299560193737207 27.813372028583238 chr15 102531392 2629798408 25.648714571240777 26.677131624270583 chr16 90354753 2431651981 26.91227522917361 42.927408660277216 chr17 81195210 2197881759 27.069106157863253 31.627285527182 chr18 78077248 2622924626 33.593968706479 26.27974533211781 chr19 59128983 1413920599 23.912479587210218 262.1508520086829 chr20 63025520 1994474092 31.645499981594757 27.599689144178573 chr21 48129895 1168276291 24.273402030068837 121.98103256117244 chr22 51304566 1028159508 20.0403119675547 25.923195033194396 chrMT 16571 442457900 26700.73622593688 10187.070163195885 chrX 155270560 2756559267 17.753264153874373 39.40304349931221 chrY 59373566 488258429 8.223498467314561 23.610443654070078