Compositional Constraint Is the Key Force in Shaping Codon Usage Bias in Hemagglutinin Gene in H1N1 Subtype of Influenza A Virus

Table 3

Synonymous codon usage pattern in 32 coding sequences.

AA	Codon	RSCU*	Fop*	𝑁^∗
Ala	GCA	2.06	0.53	18
	GCC	1.01	0.26	9
	GCG	0.24	0.06	2
	GCT	0.62	0.16	5
Arg	CGT	0.00	0.00	0
	CGC	0.00	0.00	0
	CGA	0.00	0.00	0
	CGG	0.05	0.01	0
	AGA	4.61	0.77	14
	AGG	1.32	0.22	4
Asn	AAT	1.30	0.66	27
	AAC	0.69	0.34	14
Asp	GAT	1.00	0.50	13
	GAC	1.00	0.50	13
Cys	TGT	1.20	0.60	9
	TGC	0.81	0.40	6
Gln	CAA	0.87	0.40	6
	CAG	1.19	0.59	9
Glu	GAA	1.38	0.69	24
	GAG	0.66	0.31	11
Gly	GGT	0.87	0.22	9
	GGC	0.51	0.12	5
	GGA	1.31	0.33	13
	GGG	1.37	0.34	14
His	CAT	1.08	0.54	8
	CAC	0.92	0.46	7
Ile	ATT	1.50	0.50	18
	ATC	0.52	0.17	6
	ATA	0.98	0.33	12
Leu	TTA	0.77	0.12	6
	TTG	1.35	0.22	10
	CTT	0.12	0.02	1
	CTC	0.64	0.11	5
	CTA	1.79	0.30	14
	CTG	1.33	0.22	10
Lys	AAA	1.28	0.64	27
	AAG	0.72	0.36	15
Phe	TTT	0.86	0.44	9
	TTC	1.13	0.56	11
Pro	CCT	0.23	0.06	1
	CCC	0.87	0.22	4
	CCA	1.86	0.47	9
	CCG	1.02	0.26	5
Ser	TCT	1.16	0.19	9
	TCC	0.54	0.09	4
	TCA	2.25	0.37	17
	TCG	0.12	0.02	1
	AGT	0.87	0.14	7
	AGC	1.08	0.18	8
Thr	ACT	1.00	0.25	9
	ACC	0.21	0.05	2
	ACA	2.49	0.62	24
	ACG	0.31	0.08	3
Tyr	TAT	0.96	0.48	13
	TAC	1.04	0.52	14
Val	GTT	0.76	0.19	7
	GTC	0.64	0.16	6
	GTA	1.83	0.46	17
	GTG	0.78	0.19	7

Note: *All values are mean values; 𝑁 represents the number of codons; the preferentially used codons for each amino acid are described in bold.