BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365342.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 472,923,614 number of mapped reads = 436,182,504 (92.23%) number of supplementary alignments = 1,769,479 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 218,705,325 number of mapped paired reads (second in pair) = 217,477,179 number of mapped paired reads (both in pair) = 433,222,310 number of mapped paired reads (singletons) = 2,960,194 number of mapped bases = 44,568,998,684 bp number of sequenced bases = 44,554,553,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 312,588,658 duplication rate = 41.63% >>>>>>> Insert size mean insert size = 70,722.3711 std insert size = 2,596,600.6144 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.7872 >>>>>>> ACTG content number of A's = 13,293,320,051 bp (29.84%) number of C's = 8,761,572,040 bp (19.66%) number of T's = 12,906,032,396 bp (28.97%) number of G's = 9,575,428,652 bp (21.49%) number of N's = 18,200,515 bp (0.04%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 261,962,608 number of insertions = 13,276,812 mapped reads with insertion percentage = 2.98% number of deletions = 6,947,627 mapped reads with deletion percentage = 1.55% homopolymer indels = 50.11% >>>>>>> Coverage mean coverageData = 14.3971X std coverageData = 122.4247X There is a 78.34% of reference with a coverageData >= 1X There is a 72.28% of reference with a coverageData >= 2X There is a 67.13% of reference with a coverageData >= 3X There is a 63.24% of reference with a coverageData >= 4X There is a 59.55% of reference with a coverageData >= 5X There is a 56.49% of reference with a coverageData >= 6X There is a 53.41% of reference with a coverageData >= 7X There is a 50.74% of reference with a coverageData >= 8X There is a 48.02% of reference with a coverageData >= 9X There is a 45.61% of reference with a coverageData >= 10X There is a 43.16% of reference with a coverageData >= 11X There is a 40.95% of reference with a coverageData >= 12X There is a 38.72% of reference with a coverageData >= 13X There is a 36.7% of reference with a coverageData >= 14X There is a 34.68% of reference with a coverageData >= 15X There is a 32.83% of reference with a coverageData >= 16X There is a 30.99% of reference with a coverageData >= 17X There is a 29.31% of reference with a coverageData >= 18X There is a 27.65% of reference with a coverageData >= 19X There is a 26.12% of reference with a coverageData >= 20X There is a 24.62% of reference with a coverageData >= 21X There is a 23.25% of reference with a coverageData >= 22X There is a 21.9% of reference with a coverageData >= 23X There is a 20.67% of reference with a coverageData >= 24X There is a 19.47% of reference with a coverageData >= 25X There is a 18.37% of reference with a coverageData >= 26X There is a 17.3% of reference with a coverageData >= 27X There is a 16.32% of reference with a coverageData >= 28X There is a 15.38% of reference with a coverageData >= 29X There is a 14.51% of reference with a coverageData >= 30X There is a 13.67% of reference with a coverageData >= 31X There is a 12.9% of reference with a coverageData >= 32X There is a 12.16% of reference with a coverageData >= 33X There is a 11.48% of reference with a coverageData >= 34X There is a 10.82% of reference with a coverageData >= 35X There is a 10.22% of reference with a coverageData >= 36X There is a 9.64% of reference with a coverageData >= 37X There is a 9.11% of reference with a coverageData >= 38X There is a 8.59% of reference with a coverageData >= 39X There is a 8.12% of reference with a coverageData >= 40X There is a 7.67% of reference with a coverageData >= 41X There is a 7.25% of reference with a coverageData >= 42X There is a 6.85% of reference with a coverageData >= 43X There is a 6.48% of reference with a coverageData >= 44X There is a 6.13% of reference with a coverageData >= 45X There is a 5.8% of reference with a coverageData >= 46X There is a 5.49% of reference with a coverageData >= 47X There is a 5.2% of reference with a coverageData >= 48X There is a 4.92% of reference with a coverageData >= 49X There is a 4.66% of reference with a coverageData >= 50X There is a 4.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3717349044 14.914101433673057 338.5265339261277 chr2 243199373 3803483956 15.63936579721363 67.95077601541875 chr3 198022430 3016529400 15.23327130163992 22.959123379427574 chr4 191154276 3051017225 15.961020014012137 74.25051804279575 chr5 180915260 2643432790 14.611441787718736 19.992717781372395 chr6 171115067 2543259423 14.86286080816016 66.431646160458 chr7 159138663 2521469276 15.844479452488551 76.00858517895453 chr8 146364022 2205232090 15.066763401732702 45.55061502793522 chr9 141213431 1885433677 13.351659708629274 91.63753759268268 chr10 135534747 2277052581 16.800507850580928 207.35604502850973 chr11 135006516 2094716048 15.51566628087788 72.13149341184703 chr12 133851895 2023804192 15.119727606396607 33.794590280335555 chr13 115169878 1371466573 11.908205485812879 17.018271678328304 chr14 107349540 1355817028 12.629928623820838 18.992275319640996 chr15 102531392 1325058715 12.923444119436123 22.34309005964133 chr16 90354753 1286326321 14.236399063588829 42.36892911812326 chr17 81195210 1633248058 20.11507893138031 75.76756530185176 chr18 78077248 1216369341 15.579049878909666 120.21353712814923 chr19 59128983 876210072 14.818622400456304 168.92353243985855 chr20 63025520 905078595 14.36050975858668 25.965993645964037 chr21 48129895 588874556 12.235109924922961 43.8308364796486 chr22 51304566 549996815 10.720231314304462 34.838772875759766 chrMT 16571 102131940 6163.293705871703 1158.1632559467694 chrX 155270560 1220347002 7.859487349050586 29.304021428452593 chrY 59373566 355293966 5.984042898821337 134.1388895266033