. 2021 Apr 19;7(1):veab038. doi: 10.1093/ve/veab038

Table 2.

Nucleotide-level statistics of mutations.

Strand	N	M	$N_{n}$	$N_{v}$	r	α	$(n_{1}, n_{2}, n_{3})$	$(z_{1} : z_{2} : z_{3})$
CxNV1-RdRp	1033	46	606	362	0.0068	3.35	(181, 140, 645)	(0.56:0.44:2.00)
ZJMV3-RdRp	1075	12	210	39	0.0064	10.80	(47, 29, 173)	(0.57:0.35:2.08)
CxNV1-Robin	272	46	213	146	0.0096	2.92	(107, 100, 152)	(0.89:0.84:1.27)
ZJMV3-Robin	304	10	84	48	0.0145	3.50	(35, 31, 66)	(0.80:0.70:1.50)

The consensus sequence has N codons. Among the mutations observed in M polymorphs, there are $N_{n}$ transitions, $N_{v}$ transversions, with overall rate r and transition/transversion rate ratio α. The numbers total mutations at each base position is $(n_{1} : n_{2} : n_{3})$ , and normalising these to ratios via Equation (6) yields $(z_{1} : z_{2} : z_{3})$ .