Protein: protease
Residue: Lys 45
wt codon: aaa
Dataset:

Group by: position amino acid codon

Show 95% confidence interval for Ka/Ks


Observed Expected

Ka/Ks

LOD

freq(%)

Na

Ns

Na

Ns
1.5 6.67 0.015 721 182 4328 1641

Mutant codon positions selected for by mutations at this codon position
10 View details for this pair
30 View details for this pair
88 View details for this pair

Mutant codon positions which select for mutations at this codon position
30 View details for this pair
77 View details for this pair
88 View details for this pair
93 View details for this pair

Query the Stanford HIV database for this codon position
Query the Los Alamos HIV database for this codon position


Brief Tutorial
Grouping options Clicking on the radio buttons corresponding to each grouping option will group the rows accordingly. For example, grouping by amino acid will group all the codons that translate to the same amino acid into one row.
Description of Fields
  • Ka/Ks: A measure of selection pressure (see FAQ for a more detailed explanation of Ka/Ks.)
  • Ka/Ks lower/upper: The lower and upper bounds of the 95% confidence interval surrounding the Ka/Ks value. These were calculated using Fisher's exact test using the quartet of Observed Na, Observed Ns, Expected Na and Expected Ns values.
  • LOD: Log (base 10) of p-value calculated by one-sided Fisher's exact test. The null hypothesis is Ka/Ks=1.
  • freq: The frequency of the mutation(s) in the dataset. When grouped by position, it is the frequency of all amino acid mutations at the given codon position; when grouped by amino acid, it is the frequency of the specified amino acid mutation; when grouped by codon, it is the frequency of the specific codon mutation.
  • Observed Na: The number of samples with the specified mutation at the given codon position.
  • Observed Ns: The number of samples with synonymous mutations (mutations which don't change the amino acid) at the given codon position.
  • Expected Na: The number of samples expected to have the specified amino acid mutation at the given codon position.
  • Expected Ns: The number of samples expected to have a synonymous mutation at the given codon position.