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Description of Fields
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- 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.
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