Table 3.

Summary of potential forces affecting codon bias in N₁N₂Y₃ codon-pairs

Amino acid	Codon pair	Preferred codona	Watson–Crickb	GCc	tRNA poold	Error minimizatione	Stabilityf	Extended stabilityg
Asn	AAY	C	+	− −	NR	+	+	+
Tyr	UAY	C	+	− −	NR	NR	+	+
Ser	AGY	C	+	−	NR	+	NR	+
Ile	AUY	C	+	−	NR	NR	+	+
His	CAY	C	+	− −	NR	+	NR	+
Asp	GAY	C	+	− −	NR	+	NR	+
Cys	UGY	C	+	+	NR	NR	NR	+
Phe	UUY	C	+	−	NR	+	+	+
Arg	CGY	U	NR	−	−	NR	+	+
Thr	ACY	U	−	++	+	NR	NR	+
Leu	CUY	C/U	NR	++	+	NR	NR	NR
Gly	GGY	U	−	−	++	NR	+	+
Val	GUY	U	−	+	+	NR	NR	+
Ser	UCY	U	−	++	++	NR	NR	+
Pro	CCY	U	−	+	++	NR	+	+
Ala	GCY	U	−	+	+	NR	+	+

^aCodon preference is determined by bias direction observed in organisms with high ENC’_diff as seen in Supplementary Figure S2.

^bAgreement with a prefect Watson–Crick base pairing. (+) The preferred codon forms a perfect Watson–Crick pairing with the available tRNA, (−) the preferred codon forms a wobble pairing with the tRNA, (NR) both codons form wobble pairing (due to A to I modification) or there is no preferred codon.

^cGC effect on bias direction as seen in Supplementary Figure S5: (−) no effect, (− −) opposite effect, (+) weak effect, (++) strong effect.

^dtRNA pool size effect on bias direction: (−) no effect, (+) weak effect, (++) strong effect, (NR) not relevant.

^eIndication of error minimization: (+) observed, (NR) not relevant.

^fAgreement with Grosjean’s stability model (56): (+) the preferred codon forms moderate interaction with the tRNA compared to its synonym, (NR) not relevant to SWY and WSY codon-pairs.

^gAgreement with the Extended Stability model: (+) the preferred codon forms a moderate interaction with the tRNA compared to its synonym, (NR) there is no distinctly preferred codon.