What is the difference between the transition/transversion ratio and the transition/transversion rate ratio?
The transition/transversion rate ratio is simply the instantaneous rate of transitions divided by the instantaneous rate of transversions. I will refer to this quantity as k. If k is 1.0, this means that transitions are occurring at the same rate as transversions. The transition/transversion ratio, however, is the probability of any transition (over a single unit of time) divided by the probability of any transversion (over a single unit of time). To find the probability of any transition during a single unit of time, one must consider each of the ways a transition can occur (i.e., A to G, G to A, C to T, and T to C) and add together the probabilities of each (note that this will be a sum of four terms). Likewise, finding the probability of any transversion during a single unit of time involves a sum of eight terms (i.e., A to C, A to T, G to C, G to T, C to A, C to G, T to A, and T to G). The probability of the specific transition A to G can be determined as follows: it is the probabi
