Table 1.

For each amino acid (AA) that can have double-synonym single-nucleotide mutations, we list all of the possible codons which do not code for stop on the complementary strand, indicating their reverse complement (Comp. AA).

AA	Codon	$S^{(\mathrm{n})}+S^{(\mathrm{v})}$	$D^{(\mathrm{n})}+D^{(\mathrm{v})}$	Comp. AA
Leu	UUG*	1 + 0	1 + 0	Gln
	CUU	1 + 1	0 + 0	Lys
	CUC	1 + 1	0 + 0	Glu
	CUG*	1 + 2	1 + 0	Gln
Pro	CCU*	1 + 2	0 + 1	Arg
	CCC	1 + 2	0 + 0	Gly
	CCA	1 + 2	0 + 0	Trp
	CCG*	1 + 2	0 + 1	Arg
Gln	CAA*	1 + 0	1 + 0	Leu
	CAG*	1 + 0	1 + 0	Leu
Arg	CGU	1 + 2	0 + 0	Thr
	CGC	1 + 2	0 + 0	Ala
	CGA*	1 + 3	0 + 1	Ser
	CGG*	1 + 3	0 + 1	Pro
	AGA*	1 + 1	0 + 1	Ser
	AGG*	1 + 1	0 + 1	Pro
Ser	UCU*	1 + 1	0 + 1	Arg
	UCC	1 + 1	0 + 0	Gly
	UCG*	1 + 2	0 + 1	Arg
	AGU	1 + 0	0 + 0	Thr
	AGC	1 + 0	0 + 0	Ala

The codons that have a double synonym are marked with an asterisk. For each of these codons, we list the number of mutations which are synonymous, and the number of double synonym mutations. In each case the numbers of single (double) mutations are written $S^{(\mathrm{n})}+S^{(\mathrm{v})}$ ($D^{(\mathrm{n})}+D^{(\mathrm{v})}$), where the superscript n denotes transitions, and superscript v transversions. Also, double synonyms are counted in the list of single synonyms.