Transition-transversion ratio

An observed transition-transversion ratio compares the number of nucleotide transitions with the number of nucleotide transversions in a specified set of sequence alignment differences:Six transition differences and two transversion differences give $R=3$. If no transversion is observed, this ordinary finite ratio is undefined; the raw counts should remain explicit.

The instantaneous rate parameter can use a different convention. In the Kimura two-parameter model, let $\alpha$ be the rate to the one transition target and $\beta$ the rate to each of the two transversion targets from a base. ThenThus $\kappa =4$ corresponds to twice as many instantaneous transition events as total transversion events, not four times as many.^[ref]

Observed endpoint differences can hide repeated nucleotide substitutions. Under independent uniform endpoint bases, the four directed transition mismatches and eight transversion mismatches give a limiting ratio $1/2$, even when short-time event rates differ. Always state whether the ratio describes scored differences, total events or rates per possible target.