Table 2.

Comparison of missense and synonymous mutation frequency profiles of SARS-CoV-2 omicron sublineage BA.2 isolates in the Thailand dataset (nt length 29,469 bp).

Lineage	Gene	nt Position	aa Position	Genome Count	Frequency
BA.2	5′ UTR	C241T		1274	87.26
(n = 1460)	ORF1ab	C6196T		194	13.29
		C7471T		610	41.78
		C854T	P197S	26	1.78
		C3653T	L1130F	26	1.78
		C3686T	H1141Y	64	4.38
		C4893T	T1543I	32	2.19
		A4916G	I1551V	10	0.68
		C6401T	P2046S	45	3.08
		G7798T	K2511N	12	0.82
		C10789T		16	1.10
		C11109T	A3615V	26	1.78
		G14188A	A241T	42	2.88
		C15240T		194	13.29
		G15451A	G662S	13	0.89
		C16362T		88	6.03
		A19133C	E1889A	15	1.03
	ORF3a	A25411G	I7V	17	1.16
		C25613T	S74F	21	1.44
	S	C22120A	F186L	15	1.03
		G22632A	R357K	17	1.16
		T22882G	N440K	1270	86.99
		C23280T	T573I	49	3.36
		C23854A	N764K	1418	97.12
		T25224C	I1221T	25	1.71
		C25416T		582	39.86
	N	G29468T	D399Y	44	3.01
BA.2.27	5′ UTR	C241T		222	84.73
(n = 262)	ORF1ab	C10198T		242	92.37
		C12403T		58	22.14
		C17745T		20	7.63
		C19610T	T2048I	12	4.58
	ORF3a	C25672T	L94F	15	5.73
	N	G28739T	A156S	10	3.82
BA.2.3	5′ UTR	C241T		402	88.55
(n = 454)	ORF1ab	C832T		98	21.59
		T7282C		144	31.72
		C14267T	T267M	39	8.59
		C18508T	L1681F	37	8.15
		A21222G		358	78.85
BA.2.9	5′ UTR	C241T		451	86.90
(n = 519)	ORF1ab	G1820A	G519S	78	15.03
		A2442C	E726A	36	6.94
		T4443C	V1393A	87	16.76
		C5051T	P1596S	58	11.18
		C5672T	P1803S	42	8.09
		C12789T	T4175I	32	6.17
		A14109G	I214M	38	7.32
		A15553G	N696D	13	2.50
		T16494C		36	6.94
		C18457T	P1664S	11	2.12
	ORF9b	A28389T	N36Y	28	5.39
	S	T21752A	W64R	59	11.37
		T22882G	N440K	448	86.32
		G24348T	S929I	10	1.93
BA.2.10	5′ UTR	C241T		871	94.16
(n = 925)	ORF1ab	C2676T	P804L	15	1.62
		A4457G	I1398V	21	2.27
		T7813C		262	28.32
		C17528T	T1354I	71	7.68
	ORF3a	C25961T	T190I	120	12.97