Gene-wise codon usage and bias analysis of SARS-CoV-2 (2019-nCoV)

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No	codon	AA	ORF1ab	ORF1a	S	E	M	N	ORF3a	ORF6	ORF7a	ORF7b	ORF8	ORF10
1	TTT	F	254	156	59	2	5	3	8	3	7	3	4	3
2	TTC	F	95	52	18	3	6	10	6	0	3	3	4	1
3	TTA	L	201	117	28	1	4	2	3	3	2	3	6	0
4	TTG	L	116	87	20	2	4	9	9	0	1	1	2	1
5	CTT	L	185	129	36	7	12	8	10	1	6	4	2	0
6	CTC	L	61	39	12	0	6	2	5	2	2	0	0	2
7	CTA	L	77	45	9	2	5	3	1	2	1	1	0	1
8	CTG	L	28	18	3	2	4	3	2	0	3	2	0	0
9	ATT	I	169	109	44	1	11	9	9	5	4	4	5	0
10	ATC	I	57	38	14	1	6	4	5	1	1	1	5	0
11	ATA	I	117	68	18	1	3	1	7	4	3	0	0	3
12	GTT	V	292	193	48	7	3	2	14	3	4	1	6	2
13	GTC	V	81	43	21	1	0	3	3	0	1	0	0	0
14	GTA	V	137	78	15	3	6	1	7	0	2	0	4	2
15	GTG	V	88	57	13	2	3	2	1	0	1	0	2	0
16	TCT	S	154	98	37	4	2	8	3	2	3	0	2	1
17	TCC	S	27	21	12	0	3	3	4	1	0	0	1	0
18	TCA	S	128	82	26	1	3	9	8	1	3	2	3	0
19	TCG	S	5	5	2	1	1	2	0	0	0	0	1	0
20	AGT	S	119	76	17	1	4	9	5	0	0	0	2	1
21	AGC	S	23	12	5	1	2	6	2	0	1	0	0	0
22	CCT	P	136	86	29	2	1	8	7	0	4	0	4	0
23	CCC	P	17	11	4	0	0	7	0	0	0	0	1	0
24	CCA	P	111	63	25	0	3	11	3	1	2	0	1	0
25	CCG	P	10	4	0	0	1	2	2	0	0	0	1	1
26	ACT	T	232	158	44	1	5	16	13	3	3	1	2	0
27	ACC	T	47	33	10	0	3	6	2	0	0	0	0	0
28	ACA	T	224	142	40	2	3	8	6	0	7	0	3	1
29	ACG	T	24	12	3	1	2	2	3	0	0	0	0	1
30	GCT	A	269	166	42	1	12	19	7	0	4	0	3	1
31	GCC	A	71	47	8	1	2	7	3	0	1	2	0	0
32	GCA	A	131	83	27	0	4	8	3	1	3	0	2	1
33	GCG	A	16	13	2	2	1	3	0	0	1	0	0	0
34	TAT	Y	208	112	40	0	4	2	8	1	2	1	6	2
35	TAC	Y	127	83	14	4	5	9	9	1	3	0	1	1
36	CAT	H	102	53	13	0	4	3	4	1	1	1	2	0
37	CAC	H	43	22	4	0	1	1	4	0	2	1	2	0
38	CAA	Q	163	97	46	0	2	27	5	2	4	1	3	1
39	CAG	Q	76	54	16	0	2	8	4	1	1	0	3	0
40	AAT	N	268	161	54	4	4	16	4	3	1	1	2	2
41	AAC	N	116	72	34	1	7	6	4	1	1	0	0	3
42	AAA	K	281	174	38	2	4	21	7	3	6	0	5	0
43	AAG	K	153	102	23	0	3	10	4	1	1	0	0	0
44	GAT	D	251	133	43	1	1	14	7	3	1	1	4	1
45	GAC	D	138	78	19	0	5	10	6	1	1	1	3	0
46	GAA	E	248	176	34	1	6	8	10	1	4	3	4	0
47	GAG	E	92	63	14	1	1	4	1	4	4	0	2	0
48	TGT	C	184	113	28	1	4	0	3	0	3	1	5	0
49	TGC	C	42	25	12	2	0	0	4	0	3	1	2	1
50	CGT	R	59	34	9	1	5	6	1	0	1	0	2	1
51	CGC	R	25	12	1	0	2	5	1	0	0	0	0	0
52	CGA	R	10	7	0	1	1	5	0	0	0	0	0	0
53	CGG	R	7	3	2	0	0	2	0	0	0	0	0	0
54	AGA	R	112	55	20	1	3	10	3	0	4	0	2	1
55	AGG	R	31	20	10	0	3	1	1	1	0	0	0	0
56	GGT	G	263	172	47	1	5	10	7	0	1	0	3	0
57	GGC	G	63	42	15	0	3	16	3	0	2	0	0	1
58	GGA	G	76	44	17	0	6	13	4	0	1	0	2	0
59	GGG	G	10	6	3	0	0	4	0	0	0	0	0	0
60	ATG	M	168	105	14	1	4	7	4	3	1	2	1	2
61	TGG	W	78	46	12	0	7	5	6	1	0	1	1	0

Gene-wise Relative Synonymous Codon Usage (RSCU) of SARS-CoV-2 (2019-nCoV)

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No	codon	AA	ORF1ab	ORF1a	S	E	M	N	ORF3a	ORF6	ORF7a	ORF7b	ORF8	ORF10
1	TTT	F	1.46	1.5	1.532	0.8	0.909	0.462	1.143	2	1.4	1	1	1.5
2	TTC	F	0.54	0.5	0.468	1.2	1.091	1.538	0.857	0	0.6	1	1	0.5
3	TTA	L	1.81	1.614	1.556	0.429	0.686	0.444	0.6	2.25	0.8	1.636	3.6	0
4	TTG	L	1.04	1.2	1.111	0.857	0.686	2	1.8	0	0.4	0.545	1.2	1.5
5	CTT	L	1.66	1.779	2	3	2.057	1.778	2	0.75	2.4	2.182	1.2	0
6	CTC	L	0.55	0.538	0.667	0	1.029	0.444	1	1.5	0.8	0	0	3
7	CTA	L	0.69	0.621	0.5	0.857	0.857	0.667	0.2	1.5	0.4	0.545	0	1.5
8	CTG	L	0.25	0.248	0.167	0.857	0.686	0.667	0.4	0	1.2	1.091	0	0
9	ATT	I	1.48	1.521	1.737	1	1.65	1.929	1.286	1.5	1.5	2.4	1.5	0
10	ATC	I	0.5	0.53	0.553	1	0.9	0.857	0.714	0.3	0.375	0.6	1.5	0
11	ATA	I	1.02	0.949	0.711	1	0.45	0.214	1	1.2	1.125	0	0	3
12	GTT	V	1.95	2.081	1.979	2.154	1	1	2.24	4	2	4	2	2
13	GTC	V	0.54	0.464	0.866	0.308	0	1.5	0.48	0	0.5	0	0	0
14	GTA	V	0.92	0.841	0.619	0.923	2	0.5	1.12	0	1	0	1.333	2
15	GTG	V	0.59	0.615	0.536	0.615	1	1	0.16	0	0.5	0	0.667	0
16	TCT	S	2.03	2	2.242	3	0.8	1.297	0.818	3	2.571	0	1.333	3
17	TCC	S	0.36	0.429	0.727	0	1.2	0.486	1.091	1.5	0	0	0.667	0
18	TCA	S	1.68	1.673	1.576	0.75	1.2	1.459	2.182	1.5	2.571	6	2	0
19	TCG	S	0.07	0.102	0.121	0.75	0.4	0.324	0	0	0	0	0.667	0
20	AGT	S	1.57	1.551	1.03	0.75	1.6	1.459	1.364	0	0	0	1.333	3
21	AGC	S	0.3	0.245	0.303	0.75	0.8	0.973	0.545	0	0.857	0	0	0
22	CCT	P	1.99	2.098	2	4	0.8	1.143	2.333	0	2.667	0	2.286	0
23	CCC	P	0.25	0.268	0.276	0	0	1	0	0	0	0	0.571	0
24	CCA	P	1.62	1.537	1.724	0	2.4	1.571	1	4	1.333	0	0.571	0
25	CCG	P	0.15	0.098	0	0	0.8	0.286	0.667	0	0	0	0.571	4
26	ACT	T	1.76	1.832	1.814	1	1.538	2	2.167	4	1.2	4	1.6	0
27	ACC	T	0.36	0.383	0.412	0	0.923	0.75	0.333	0	0	0	0	0
28	ACA	T	1.7	1.646	1.649	2	0.923	1	1	0	2.8	0	2.4	2
29	ACG	T	0.18	0.139	0.124	1	0.615	0.25	0.5	0	0	0	0	2
30	GCT	A	2.21	2.149	2.127	1	2.526	2.054	2.154	0	1.778	0	2.4	2
31	GCC	A	0.58	0.608	0.405	1	0.421	0.757	0.923	0	0.444	4	0	0
32	GCA	A	1.08	1.074	1.367	0	0.842	0.865	0.923	4	1.333	0	1.6	2
33	GCG	A	0.13	0.168	0.101	2	0.211	0.324	0	0	0.444	0	0	0
34	TAT	Y	1.24	1.149	1.481	0	0.889	0.364	0.941	1	0.8	2	1.714	1.333
35	TAC	Y	0.76	0.851	0.519	2	1.111	1.636	1.059	1	1.2	0	0.286	0.667
36	CAT	H	1.41	1.413	1.529	0	1.6	1.5	1	2	0.667	1	1	0
37	CAC	H	0.59	0.587	0.471	0	0.4	0.5	1	0	1.333	1	1	0
38	CAA	Q	1.36	1.285	1.484	0	1	1.543	1.111	1.333	1.6	2	1	2
39	CAG	Q	0.64	0.715	0.516	0	1	0.457	0.889	0.667	0.4	0	1	0
40	AAT	N	1.4	1.382	1.227	1.6	0.727	1.455	1	1.5	1	2	2	0.8
41	AAC	N	0.6	0.618	0.773	0.4	1.273	0.545	1	0.5	1	0	0	1.2
42	AAA	K	1.29	1.261	1.246	2	1.143	1.355	1.273	1.5	1.714	0	2	0
43	AAG	K	0.71	0.739	0.754	0	0.857	0.645	0.727	0.5	0.286	0	0	0
44	GAT	D	1.29	1.261	1.387	2	0.333	1.167	1.077	1.5	1	1	1.143	2
45	GAC	D	0.71	0.739	0.613	0	1.667	0.833	0.923	0.5	1	1	0.857	0
46	GAA	E	1.46	1.473	1.417	1	1.714	1.333	1.818	0.4	1	2	1.333	0
47	GAG	E	0.54	0.527	0.583	1	0.286	0.667	0.182	1.6	1	0	0.667	0
48	TGT	C	1.63	1.638	1.4	0.667	2	0	0.857	0	1	1	1.429	0
49	TGC	C	0.37	0.362	0.6	1.333	0	0	1.143	0	1	1	0.571	2
50	CGT	R	1.45	1.557	1.286	2	2.143	1.241	1	0	1.2	0	3	3
51	CGC	R	0.61	0.55	0.143	0	0.857	1.034	1	0	0	0	0	0
52	CGA	R	0.25	0.321	0	2	0.429	1.034	0	0	0	0	0	0
53	CGG	R	0.17	0.137	0.286	0	0	0.414	0	0	0	0	0	0
54	AGA	R	2.75	2.519	2.857	2	1.286	2.069	3	0	4.8	0	3	3
55	AGG	R	0.76	0.916	1.429	0	1.286	0.207	1	6	0	0	0	0
56	GGT	G	2.55	2.606	2.293	4	1.429	0.93	2	0	1	0	2.4	0
57	GGC	G	0.61	0.636	0.732	0	0.857	1.488	0.857	0	2	0	0	4
58	GGA	G	0.74	0.667	0.829	0	1.714	1.209	1.143	0	1	0	1.6	0
59	GGG	G	0.1	0.091	0.146	0	0	0.372	0	0	0	0	0	0
60	ATG	M	1	1	1	1	1	1	1	1	1	1	1	1
61	TGG	W	1	1	1	1	1	1	1	1	1	1	1	1

Codon usage, Amino acids, RSCU, Rare codons and context details of SARS-CoV-2 (2019-nCoV) genes

Genes	Codons	Amino acids	RSCU	Rare codons	Codon context
ORF1ab
ORF1a
S
E
M
N
ORF3a
ORF6
ORF7a
ORF7b
ORF8
ORF10

Genome-wise Codon usage, Amino acids, RSCU, Rare codons and context details of different coronaviruses

Genome	Codons	Amino acids	RSCU	Rare codons	Codon context
2019-nCoV
SARS-CoV
MERS-CoV
HCoV-229E
HCoV-HKU1
HCoV-NL63
HCoV-OC43

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