Table 9.6.

Transition probability matrix for the six synonymous arginine codons, with α for transitions (C↔T and A↔G), β for transversions, and k modeling AT-biased mutation (0 ≤ k ≤ 1) or GC-biased mutation (k > 1)

	CGT	CGC	CGA	CGG	AGA	AGG
CGT		kα	β	kβ	0	0
CGC	α		β	β	0	0
CGA	β	kβ		kα	β	0
CGG	β	β	α		0	β
AGA	0	0	kβ	0		kα
AGG	0	0	0	kβ	α

We ignore nonsynonymous substitutions because nonsynonymous substitution rate is often negligibly low compared to synonymous rate. The diagonal is constrained by the row sum equal to 1