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  (1) Mammalia (2) Rodentia (3) Primates (4) All  
(1) Nuclear (2) Mitochondrial (3) Both


NUCLEAR STATISTICS FOR THE RODENTIA ORDER
Sat Feb 6 15:09:00 2010

Contents of the Secondary Database
  • Total number of nuclear Polymorphic sets analyzed: 687
  • Number of Sequences analyzed: 5036
    • Number of different Species analyzed: 148
    • Number of different Genes analyzed: 441
    • Total number of Analysis units: 1710 [Phylogeny]
      (average number of analysis units per polymorphic set: 2.5)
      • CDS: 880
      • exon: 500
      • intron: 251
      • 5ŽUTR: 25
      • 3ŽUTR: 19
      • promoter: 35

      •  

QUALITY OF THE ALIGNMENTS:

  • Number of Analysis units according to the "Number of sequences":
    • Low quality (2-5): 1462
    • Medium quality (6-10): 113
    • High quality (>10): 135
       
  • Number of Analysis units according to the "Percentage of gaps or ambiguous bases":
    • Low quality (≥30% =  ! ): 29
    • Medium quality (≥10%-<30% =    K ): 85
    • High quality (<10% =   J ): 1596
       
  • Number of Analysis units according to the "Percentage of difference in size between the longest and the shortest sequences":
    • Low quality (≥30% =  ! ): 334
    • Medium quality (≥10%-<30% =    K ): 172
    • High quality (<10% =   J ): 1204
       

SET CONFIDENCE:

  • Existence in NCBI PopSet*: 20.5% (351/1710)
  • Consecutive GenBank accession numbers**: 29.1% (498/1710)
  • One or more shared references**: 50.2% (859/1710)
  • Journals* (Genetics, Mol.Biol.Evol., J.Mol.Evol., Mol.Phylogenet.Evol.): 6.5% (111/1710)

* At least one sequence in the set
** All the sequences in the set


AVERAGES BY GENE REGIONS:

  #Aligns #Polym. sets G+C Num. seqs. Align. length. Analyzed sites θ (Theta) π (Pi)
3ŽUTR 191652.5210.91101.21064.20.005360.00464
5ŽUTR 252356.7114.9196.2144.60.004040.00364
CDS 88055352.364.1684.2477.10.014980.01462
exon 50024154.284.4330.2287.80.005960.00594
intron 25113448.3712.1700.1507.40.005540.00546
promoter 353447.382.61986.4894.50.007270.00745


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Contents of the Primary the Database

  • Total number of Sequences: 31266
    • Number of different Species: 1139
    • Number of different Genes: 8502
       
  • Total number of References 13175
    • Published: 5015
    • Submitted: 5784
    • In press: 132
    • Published Only in Database: 54
    • Unpublished: 1624
    • Thesis: 25
    • Number of different Journals: 348

 




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