CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 89

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
ORF3a	89	T89I		nonsyn	aCa	aTa	8321	8313	0.999039	25657-25659
ORF3a	89	T89I		nonsyn	aCA	aTT	8321	5	0.000600889	25657-25659
ORF3a	89	T89I		nonsyn	aCA	aTC	8321	3	0.000360534	25657-25659
ORF3a	89	T89T		syn	acA	acG	332	222	0.668675	25657-25659
ORF3a	89	T89T		syn	acA	acT	332	81	0.243976	25657-25659
ORF3a	89	T89T		syn	acA	acC	332	29	0.0873494	25657-25659
ORF3a	89	T89A		nonsyn	Aca	Gca	250	244	0.976	25657-25659
ORF3a	89	T89A		nonsyn	AcA	GcG	250	3	0.012	25657-25659
ORF3a	89	T89A		nonsyn	AcA	GcC	250	2	0.008	25657-25659
ORF3a	89	T89A		nonsyn	AcA	GcT	250	1	0.004	25657-25659
ORF3a	89	T89del		del	ACA	---	174	174	1	25657-25659
ORF3a	89	T89S		nonsyn	Aca	Tca	39	31	0.794872	25657-25659
ORF3a	89	T89S		nonsyn	AcA	TcT	39	6	0.153846	25657-25659
ORF3a	89	T89S		nonsyn	aCA	aGT	39	1	0.025641	25657-25659
ORF3a	89	T89S		nonsyn	AcA	TcG	39	1	0.025641	25657-25659
ORF3a	89	T89P		nonsyn	Aca	Cca	26	25	0.961538	25657-25659
ORF3a	89	T89P		nonsyn	AcA	CcT	26	1	0.0384615	25657-25659
ORF3a	89	T89L		nonsyn	ACa	TTa	10	7	0.7	25657-25659
ORF3a	89	T89L		nonsyn	ACA	TTG	10	1	0.1	25657-25659
ORF3a	89	T89L		nonsyn	ACA	CTT	10	1	0.1	25657-25659
ORF3a	89	T89L		nonsyn	ACa	CTa	10	1	0.1	25657-25659
ORF3a	89	T89del1		del	Aca	-ca	6	4	0.666667	25657-25659
ORF3a	89	T89del1		del	ACA	-NN	6	1	0.166667	25657-25659
ORF3a	89	T89del1		del	acA	ac-	6	1	0.166667	25657-25659
ORF3a	89	T89R		nonsyn	aCa	aGa	5	4	0.8	25657-25659
ORF3a	89	T89R		nonsyn	aCA	aGG	5	1	0.2	25657-25659
ORF3a	89	T89F		nonsyn	ACA	TTT	4	4	1	25657-25659
ORF3a	89	T89K		nonsyn	aCa	aAa	3	2	0.666667	25657-25659
ORF3a	89	T89E		nonsyn	ACa	GAa	3	2	0.666667	25657-25659
ORF3a	89	T89V		nonsyn	ACa	GTa	3	2	0.666667	25657-25659
ORF3a	89	T89V		nonsyn	ACA	GTC	3	1	0.333333	25657-25659
ORF3a	89	T89E		nonsyn	ACA	GAG	3	1	0.333333	25657-25659
ORF3a	89	T89K		nonsyn	aCA	aAG	3	1	0.333333	25657-25659
ORF3a	89	T89del2		del	ACa	--a	2	2	1	25657-25659
ORF3a	89	T89G		nonsyn	ACa	GGa	2	1	0.5	25657-25659
ORF3a	89	T89G		nonsyn	ACA	GGG	2	1	0.5	25657-25659
ORF3a	89	T89M		nonsyn	aCA	aTG	1	1	1	25657-25659
ORF3a	89	T89C		nonsyn	ACA	TGT	1	1	1	25657-25659
ORF3a	89	T89X		nonsyn	ACa	TGa	1	1	1	25657-25659

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
ORF3a	89	T89I	aCa	aTa	8313	8321	All	0.00159
ORF3a	89	T89I	aCA	aTT	5	8321	All	0.000001
ORF3a	89	T89I	aCA	aTC	3	8321	All	0.000001
ORF3a	89	T89I	aCa	aTa	2204	2204	B.1.1.7	0.001973
ORF3a	89	T89I	aCa	aTa	933	933	AY.4	0.001452
ORF3a	89	T89I	aCa	aTa	501	501	B.1.617.2	0.001886
ORF3a	89	T89I	aCa	aTa	440	444	AY.25	0.002647
ORF3a	89	T89I	aCA	aTT	4	444	AY.25	0.000024
ORF3a	89	T89T	acA	acG	222	332	All	0.000042
ORF3a	89	T89T	acA	acT	81	332	All	0.000015
ORF3a	89	T89T	acA	acC	29	332	All	0.000006
ORF3a	89	T89A	Aca	Gca	244	250	All	0.000047
ORF3a	89	T89A	AcA	GcG	3	250	All	0.000001
ORF3a	89	T89A	AcA	GcC	2	250	All	0
ORF3a	89	T89A	AcA	GcT	1	250	All	0
ORF3a	89	T89I	aCa	aTa	238	239	AY.43	0.001054
ORF3a	89	T89I	aCA	aTC	1	239	AY.43	0.000004
ORF3a	89	T89I	aCa	aTa	234	235	B.1.525	0.02648
ORF3a	89	T89I	aCA	aTC	1	235	B.1.525	0.000113
ORF3a	89	T89I	aCa	aTa	192	192	B.1.2	0.001691
ORF3a	89	T89del	ACA	---	174	174	All	0.000033
ORF3a	89	T89I	aCa	aTa	172	172	B.1.429	0.004047
ORF3a	89	T89I	aCa	aTa	139	139	B.1.177	0.00183
ORF3a	89	T89I	aCa	aTa	124	124	AY.54	0.011823
ORF3a	89	T89I	aCa	aTa	122	122	B.1.451	1
ORF3a	89	T89I	aCa	aTa	120	120	B.1	0.001099
ORF3a	89	T89I	aCa	aTa	111	111	P.1	0.001749
ORF3a	89	T89I	aCa	aTa	108	108	AY.44	0.000657
ORF3a	89	T89I	aCa	aTa	103	103	AY.57	0.067585
ORF3a	89	T89A	Aca	Gca	98	101	B.1.1.7	0.000088
ORF3a	89	T89A	AcA	GcC	1	101	B.1.1.7	0.000001
ORF3a	89	T89A	AcA	GcG	1	101	B.1.1.7	0.000001
ORF3a	89	T89A	AcA	GcT	1	101	B.1.1.7	0.000001
ORF3a	89	T89I	aCa	aTa	97	97	AY.103	0.000602
ORF3a	89	T89I	aCa	aTa	93	93	AY.13	0.014971
ORF3a	89	T89I	aCa	aTa	87	87	AY.23	0.006068
ORF3a	89	T89I	aCa	aTa	85	85	B.1.1.317	0.034994
ORF3a	89	T89T	acA	acG	70	85	B.1.1.7	0.000063
ORF3a	89	T89T	acA	acC	13	85	B.1.1.7	0.000012
ORF3a	89	T89T	acA	acT	2	85	B.1.1.7	0.000002
ORF3a	89	T89I	aCa	aTa	82	82	B.1.1	0.001488
ORF3a	89	T89I	aCa	aTa	71	71	B.1.524	0.099859
ORF3a	89	T89I	aCa	aTa	68	68	B.1.232	0.036539
ORF3a	89	T89I	aCa	aTa	67	67	AY.106	0.022438
ORF3a	89	T89T	acA	acG	60	60	B.1.177	0.00079
ORF3a	89	T89I	aCa	aTa	54	54	AY.26	0.001529
ORF3a	89	T89I	aCa	aTa	54	54	B.1.1.519	0.002144
ORF3a	89	T89I	aCa	aTa	52	52	Q.3	0.007542
ORF3a	89	T89I	aCa	aTa	48	48	AY.102	0.001273
ORF3a	89	T89I	aCa	aTa	45	45	AY.20	0.001749
ORF3a	89	T89I	aCa	aTa	44	44	B.1.526	0.001034
ORF3a	89	T89I	aCa	aTa	43	43	B.1.258	0.002862
ORF3a	89	T89I	aCa	aTa	42	42	AY.39	0.001038
ORF3a	89	T89I	aCa	aTa	40	41	AY.3	0.000398
ORF3a	89	T89I	aCA	aTT	1	41	AY.3	0.00001
ORF3a	89	T89I	aCa	aTa	41	41	B.1.621	0.003629
ORF3a	89	T89I	aCa	aTa	40	40	B.1.1.368	0.123457
ORF3a	89	T89S	Aca	Tca	31	39	All	0.000006
ORF3a	89	T89S	AcA	TcT	6	39	All	0.000001
ORF3a	89	T89S	AcA	TcG	1	39	All	0
ORF3a	89	T89S	aCA	aGT	1	39	All	0
ORF3a	89	T89I	aCa	aTa	39	39	AY.29	0.000615
ORF3a	89	T89I	aCa	aTa	39	39	AY.48	0.01814
ORF3a	89	T89T	acA	acT	20	38	AY.4	0.000031
ORF3a	89	T89T	acA	acG	18	38	AY.4	0.000028
ORF3a	89	T89I	aCa	aTa	37	37	B.1.351	0.0011
ORF3a	89	T89I	aCa	aTa	36	36	AY.108	0.039691
ORF3a	89	T89del	ACA	---	35	35	B.1.1.7	0.000031
ORF3a	89	T89I	aCa	aTa	33	33	AY.6	0.001357
ORF3a	89	T89I	aCa	aTa	31	31	AY.98	0.002449
ORF3a	89	T89I	aCa	aTa	31	31	R.1	0.00279
ORF3a	89	T89A	Aca	Gca	30	30	AY.46.2	0.01906
ORF3a	89	T89I	aCa	aTa	27	27	B.1.1.284	0.0029
ORF3a	89	T89P	Aca	Cca	25	26	All	0.000005
ORF3a	89	T89P	AcA	CcT	1	26	All	0
ORF3a	89	T89I	aCa	aTa	25	25	AY.4.2	0.000542
ORF3a	89	T89I	aCa	aTa	24	24	AY.45	0.00292
ORF3a	89	T89I	aCa	aTa	24	24	B.1.1.214	0.001331
ORF3a	89	T89I	aCa	aTa	24	24	B.1.620	0.022706
ORF3a	89	T89I	aCa	aTa	22	22	B.1.139	0.016129
ORF3a	89	T89del	ACA	---	21	21	AY.4	0.000033
ORF3a	89	T89I	aCa	aTa	21	21	AY.75	0.001176
ORF3a	89	T89I	aCa	aTa	21	21	Q.7	0.023333
ORF3a	89	T89I	aCa	aTa	20	20	AY.119	0.000706
ORF3a	89	T89A	Aca	Gca	20	20	AY.4	0.000031
ORF3a	89	T89I	aCa	aTa	20	20	AY.5	0.000413
ORF3a	89	T89I	aCa	aTa	20	20	Q.8	0.003298
ORF3a	89	T89I	aCa	aTa	17	18	AY.120	0.000632
ORF3a	89	T89I	aCA	aTC	1	18	AY.120	0.000037
ORF3a	89	T89I	aCa	aTa	18	18	C.37	0.002089
ORF3a	89	T89T	acA	acT	15	17	B.1.160	0.000468
ORF3a	89	T89T	acA	acG	2	17	B.1.160	0.000062
ORF3a	89	T89I	aCa	aTa	16	16	AW.1	0.04878
ORF3a	89	T89I	aCa	aTa	15	15	AY.117	0.001268
ORF3a	89	T89I	aCa	aTa	15	15	AY.27	0.000971
ORF3a	89	T89I	aCa	aTa	15	15	B.1.1.306	0.006576
ORF3a	89	T89I	aCa	aTa	15	15	P.1.14	0.000717
ORF3a	89	T89A	Aca	Gca	14	14	AY.39.1	0.000555
ORF3a	89	T89I	aCa	aTa	14	14	AY.47	0.000435
ORF3a	89	T89T	acA	acG	14	14	B.1.221	0.000994
ORF3a	89	T89I	aCa	aTa	14	14	B.1.596	0.00122
ORF3a	89	T89S	Aca	Tca	7	13	AY.25	0.000042
ORF3a	89	T89S	AcA	TcT	5	13	AY.25	0.00003
ORF3a	89	T89S	aCA	aGT	1	13	AY.25	0.000006
ORF3a	89	T89S	Aca	Tca	13	13	AY.26	0.000368
ORF3a	89	T89I	aCa	aTa	13	13	AY.33	0.000868
ORF3a	89	T89I	aCa	aTa	12	12	AY.100	0.000552
ORF3a	89	T89I	aCa	aTa	12	12	AY.61	0.001257
ORF3a	89	T89I	aCa	aTa	12	12	B.1.623	0.006438
ORF3a	89	T89I	aCa	aTa	11	11	AY.39.1	0.000436
ORF3a	89	T89I	aCa	aTa	11	11	AY.58	0.009982
ORF3a	89	T89I	aCa	aTa	11	11	B.1.177.8	0.008277
ORF3a	89	T89I	aCa	aTa	11	11	B.1.243	0.000765
ORF3a	89	T89I	aCa	aTa	11	11	B.1.409	0.008594
ORF3a	89	T89I	aCa	aTa	11	11	P.1.15	0.002556
ORF3a	89	T89L	ACa	TTa	7	10	All	0.000001
ORF3a	89	T89L	ACa	CTa	1	10	All	0
ORF3a	89	T89L	ACA	CTT	1	10	All	0
ORF3a	89	T89L	ACA	TTG	1	10	All	0
ORF3a	89	T89T	acA	acG	8	10	AY.103	0.00005
ORF3a	89	T89T	acA	acT	1	10	AY.103	0.000006
ORF3a	89	T89T	acA	acC	1	10	AY.103	0.000006
ORF3a	89	T89I	aCa	aTa	10	10	AY.24	0.00431
ORF3a	89	T89I	aCa	aTa	10	10	AY.3.1	0.000853
ORF3a	89	T89T	acA	acG	9	10	AY.43	0.00004
ORF3a	89	T89T	acA	acT	1	10	AY.43	0.000004
ORF3a	89	T89I	aCa	aTa	10	10	B.1.1.348	0.007962
ORF3a	89	T89I	aCa	aTa	10	10	B.1.396	0.007057
ORF3a	89	T89I	aCa	aTa	10	10	B.1.497	0.003148
ORF3a	89	T89I	aCa	aTa	10	10	B.1.541	0.044248
ORF3a	89	T89I	aCa	aTa	9	9	AY.4.5	0.000967
ORF3a	89	T89T	acA	acC	4	9	AY.44	0.000024
ORF3a	89	T89T	acA	acG	3	9	AY.44	0.000018
ORF3a	89	T89T	acA	acT	2	9	AY.44	0.000012
ORF3a	89	T89I	aCa	aTa	9	9	AY.95	0.006849
ORF3a	89	T89A	Aca	Gca	9	9	B.1	0.000082
ORF3a	89	T89A	Aca	Gca	9	9	B.1.1.33	0.003788
ORF3a	89	T89I	aCa	aTa	9	9	B.1.160	0.000281
ORF3a	89	T89del	ACA	---	9	9	B.1.177	0.000119
ORF3a	89	T89T	acA	acT	9	9	B.1.416	0.011421
ORF3a	89	T89I	aCa	aTa	9	9	B.1.427	0.000454
ORF3a	89	T89A	Aca	Gca	8	8	AY.102	0.000212
ORF3a	89	T89T	acA	acG	4	8	AY.113	0.00057
ORF3a	89	T89T	acA	acC	4	8	AY.113	0.00057
ORF3a	89	T89T	acA	acT	7	8	AY.25	0.000042
ORF3a	89	T89T	acA	acG	1	8	AY.25	0.000006
ORF3a	89	T89I	aCa	aTa	8	8	AY.46.6	0.000578
ORF3a	89	T89T	acA	acG	5	8	B.1	0.000046
ORF3a	89	T89T	acA	acT	2	8	B.1	0.000018
ORF3a	89	T89T	acA	acC	1	8	B.1	0.000009
ORF3a	89	T89I	aCa	aTa	8	8	B.1.1.25	0.004548
ORF3a	89	T89I	aCa	aTa	8	8	B.1.160.27	0.121212
ORF3a	89	T89I	aCa	aTa	8	8	B.1.177.21	0.000612
ORF3a	89	T89I	aCa	aTa	8	8	B.1.177.58	0.010652
ORF3a	89	T89I	aCa	aTa	8	8	B.1.177.7	0.001319
ORF3a	89	T89I	aCa	aTa	8	8	B.1.240	0.001725
ORF3a	89	T89I	aCa	aTa	8	8	B.1.369	0.002282
ORF3a	89	T89I	aCa	aTa	8	8	B.1.466.2	0.00313
ORF3a	89	T89del	ACA	---	8	8	B.1.617.2	0.00003
ORF3a	89	T89I	aCa	aTa	7	7	AY.42	0.000282
ORF3a	89	T89P	Aca	Cca	7	7	AY.46.2	0.004447
ORF3a	89	T89A	Aca	Gca	7	7	B.1.177	0.000092
ORF3a	89	T89I	aCa	aTa	7	7	B.1.221	0.000497
ORF3a	89	T89I	aCa	aTa	7	7	B.1.311	0.001922
ORF3a	89	T89I	aCa	aTa	7	7	B.1.617.1	0.000903
ORF3a	89	T89A	Aca	Gca	7	7	B.1.617.2	0.000026
ORF3a	89	T89I	aCa	aTa	7	7	B.3	0.005814
ORF3a	89	T89I	aCa	aTa	7	7	P.1.9	0.033654
ORF3a	89	T89del1	Aca	-ca	4	6	All	0.000001
ORF3a	89	T89del1	ACA	-NN	1	6	All	0
ORF3a	89	T89del1	acA	ac-	1	6	All	0
ORF3a	89	T89I	aCa	aTa	6	6	AY.116	0.001721
ORF3a	89	T89I	aCa	aTa	6	6	AY.120.1	0.001926
ORF3a	89	T89L	ACa	TTa	4	6	AY.25	0.000024
ORF3a	89	T89L	ACa	CTa	1	6	AY.25	0.000006
ORF3a	89	T89L	ACA	CTT	1	6	AY.25	0.000006
ORF3a	89	T89I	aCa	aTa	6	6	AY.35	0.001398
ORF3a	89	T89del	ACA	---	6	6	AY.43	0.000027
ORF3a	89	T89del	ACA	---	6	6	AY.44	0.000037
ORF3a	89	T89I	aCa	aTa	6	6	AY.46.4	0.000987
ORF3a	89	T89I	aCa	aTa	6	6	AY.99.2	0.000553
ORF3a	89	T89A	Aca	Gca	6	6	B.1.1	0.000109
ORF3a	89	T89I	aCa	aTa	6	6	B.1.1.1	0.00196
ORF3a	89	T89I	aCa	aTa	6	6	B.1.1.51	0.010309
ORF3a	89	T89A	Aca	Gca	6	6	B.1.2	0.000053
ORF3a	89	T89del	ACA	---	6	6	B.1.525	0.000679
ORF3a	89	T89I	aCa	aTa	6	6	P.2	0.00112
ORF3a	89	T89R	aCa	aGa	4	5	All	0.000001
ORF3a	89	T89R	aCA	aGG	1	5	All	0
ORF3a	89	T89I	aCa	aTa	5	5	AY.113	0.000712
ORF3a	89	T89I	aCa	aTa	5	5	AY.16	0.001898
ORF3a	89	T89I	aCa	aTa	5	5	AY.46.2	0.003177
ORF3a	89	T89I	aCa	aTa	5	5	AY.75.1	0.000902
ORF3a	89	T89I	aCa	aTa	5	5	B.1.1.354	0.02193
ORF3a	89	T89I	aCa	aTa	5	5	B.1.351.2	0.001513
ORF3a	89	T89I	aCa	aTa	5	5	B.1.438.1	0.000536
ORF3a	89	T89I	aCa	aTa	5	5	P.1.17	0.000809
ORF3a	89	T89F	ACA	TTT	4	4	All	0.000001
ORF3a	89	T89T	acA	acG	2	4	AY.100	0.000092
ORF3a	89	T89T	acA	acT	2	4	AY.100	0.000092
ORF3a	89	T89del	ACA	---	4	4	AY.102	0.000106
ORF3a	89	T89I	aCa	aTa	4	4	AY.14	0.000352
ORF3a	89	T89del	ACA	---	4	4	AY.23	0.000279
ORF3a	89	T89del	ACA	---	4	4	AY.29	0.000063
ORF3a	89	T89I	aCa	aTa	4	4	AY.34.1	0.00204
ORF3a	89	T89I	aCa	aTa	4	4	AY.36	0.000593
ORF3a	89	T89T	acA	acT	4	4	AY.46	0.000416
ORF3a	89	T89T	acA	acG	2	4	AY.6	0.000082
ORF3a	89	T89T	acA	acC	2	4	AY.6	0.000082
ORF3a	89	T89I	aCa	aTa	4	4	AY.9	0.00027
ORF3a	89	T89I	aCa	aTa	4	4	AY.9.2	0.000147
ORF3a	89	T89I	aCa	aTa	4	4	AY.97	0.006803
ORF3a	89	T89I	aCa	aTa	4	4	B	0.000511
ORF3a	89	T89del	ACA	---	4	4	B.1	0.000037
ORF3a	89	T89I	aCa	aTa	4	4	B.1.1.198	0.005874
ORF3a	89	T89I	aCa	aTa	4	4	B.1.1.253	0.010025
ORF3a	89	T89I	aCa	aTa	4	4	B.1.1.28	0.001245
ORF3a	89	T89I	aCa	aTa	4	4	B.1.1.298	0.003448
ORF3a	89	T89I	aCa	aTa	4	4	B.1.1.398	0.012903
ORF3a	89	T89P	Aca	Cca	4	4	B.1.1.7	0.000004
ORF3a	89	T89I	aCa	aTa	4	4	B.1.1.87	0.266667
ORF3a	89	T89I	aCa	aTa	4	4	B.1.177.4	0.000844
ORF3a	89	T89I	aCa	aTa	4	4	B.1.177.54	0.002426
ORF3a	89	T89I	aCa	aTa	4	4	B.1.177.86	0.000734
ORF3a	89	T89T	acA	acT	3	4	B.1.2	0.000026
ORF3a	89	T89T	acA	acC	1	4	B.1.2	0.000009
ORF3a	89	T89I	aCa	aTa	4	4	B.1.234	0.000528
ORF3a	89	T89I	aCa	aTa	4	4	B.1.258.17	0.000416
ORF3a	89	T89I	aCa	aTa	4	4	B.1.499	0.004202
ORF3a	89	T89I	aCa	aTa	4	4	B.1.561	0.001588
ORF3a	89	T89I	aCa	aTa	4	4	B.1.595	0.001044
ORF3a	89	T89T	acA	acT	2	4	B.1.617.2	0.000008
ORF3a	89	T89T	acA	acG	2	4	B.1.617.2	0.000008
ORF3a	89	T89I	aCa	aTa	4	4	B.6	0.00364
ORF3a	89	T89I	aCa	aTa	4	4	C.36	0.003643
ORF3a	89	T89P	Aca	Cca	4	4	C.37	0.000464
ORF3a	89	T89I	aCa	aTa	4	4	Q.1	0.000505
ORF3a	89	T89K	aCa	aAa	2	3	All	0
ORF3a	89	T89V	ACa	GTa	2	3	All	0
ORF3a	89	T89E	ACa	GAa	2	3	All	0
ORF3a	89	T89E	ACA	GAG	1	3	All	0
ORF3a	89	T89K	aCA	aAG	1	3	All	0
ORF3a	89	T89V	ACA	GTC	1	3	All	0
ORF3a	89	T89del	ACA	---	3	3	AY.25	0.000018
ORF3a	89	T89F	ACA	TTT	3	3	AY.25	0.000018
ORF3a	89	T89T	acA	acG	2	3	AY.3	0.00002
ORF3a	89	T89T	acA	acT	1	3	AY.3	0.00001
ORF3a	89	T89I	aCa	aTa	3	3	AY.5.3	0.001012
ORF3a	89	T89I	aCa	aTa	3	3	AY.7.1	0.000338
ORF3a	89	T89I	aCa	aTa	3	3	AY.71	0.001425
ORF3a	89	T89I	aCa	aTa	3	3	AY.78	0.004622
ORF3a	89	T89P	Aca	Cca	3	3	AY.94	0.001328
ORF3a	89	T89I	aCa	aTa	3	3	AY.98.1	0.000145
ORF3a	89	T89I	aCa	aTa	3	3	AY.99	0.003148
ORF3a	89	T89I	aCa	aTa	3	3	B.1.1.157	0.00274
ORF3a	89	T89I	aCa	aTa	3	3	B.1.1.318	0.000905
ORF3a	89	T89I	aCa	aTa	3	3	B.1.1.39	0.001529
ORF3a	89	T89I	aCa	aTa	3	3	B.1.1.434	0.001046
ORF3a	89	T89I	aCa	aTa	3	3	B.1.1.45	0.042254
ORF3a	89	T89I	aCa	aTa	3	3	B.1.1.63	0.001157
ORF3a	89	T89S	Aca	Tca	2	3	B.1.1.7	0.000002
ORF3a	89	T89S	AcA	TcG	1	3	B.1.1.7	0.000001
ORF3a	89	T89I	aCa	aTa	3	3	B.1.160.25	0.033333
ORF3a	89	T89I	aCa	aTa	3	3	B.1.177.10	0.002634
ORF3a	89	T89I	aCa	aTa	3	3	B.1.177.44	0.001557
ORF3a	89	T89I	aCa	aTa	3	3	B.1.177.57	0.000843
ORF3a	89	T89I	aCa	aTa	3	3	B.1.177.77	0.002179
ORF3a	89	T89I	aCa	aTa	3	3	B.1.177.81	0.000568
ORF3a	89	T89I	aCa	aTa	3	3	B.1.265	0.003812
ORF3a	89	T89I	aCa	aTa	3	3	B.1.36	0.000438
ORF3a	89	T89I	aCa	aTa	3	3	B.1.36.29	0.001552
ORF3a	89	T89I	aCa	aTa	3	3	B.1.543	0.03
ORF3a	89	T89I	aCa	aTa	3	3	B.1.582	0.001472
ORF3a	89	T89I	aCa	aTa	3	3	Q.4	0.001364
ORF3a	89	T89del	ACA	---	2	2	A	0.000774
ORF3a	89	T89del2	ACa	--a	2	2	All	0
ORF3a	89	T89G	ACa	GGa	1	2	All	0
ORF3a	89	T89G	ACA	GGG	1	2	All	0
ORF3a	89	T89I	aCa	aTa	2	2	AY.1	0.000791
ORF3a	89	T89del	ACA	---	2	2	AY.100	0.000092
ORF3a	89	T89T	acA	acT	1	2	AY.102	0.000027
ORF3a	89	T89T	acA	acG	1	2	AY.102	0.000027
ORF3a	89	T89del	ACA	---	2	2	AY.103	0.000012
ORF3a	89	T89S	Aca	Tca	2	2	AY.103	0.000012
ORF3a	89	T89A	Aca	Gca	2	2	AY.103	0.000012
ORF3a	89	T89I	aCa	aTa	2	2	AY.110	0.000225
ORF3a	89	T89I	aCa	aTa	2	2	AY.111	0.000366
ORF3a	89	T89del	ACA	---	2	2	AY.117	0.000169
ORF3a	89	T89I	aCa	aTa	2	2	AY.12	0.000632
ORF3a	89	T89I	aCa	aTa	2	2	AY.120.2.1	0.000997
ORF3a	89	T89T	acA	acG	2	2	AY.121	0.000271
ORF3a	89	T89S	Aca	Tca	2	2	AY.23	0.000139
ORF3a	89	T89P	AcA	CcT	1	2	AY.25	0.000006
ORF3a	89	T89P	Aca	Cca	1	2	AY.25	0.000006
ORF3a	89	T89T	acA	acT	2	2	AY.29	0.000032
ORF3a	89	T89I	aCa	aTa	2	2	AY.29.1	0.000441
ORF3a	89	T89S	AcA	TcT	1	2	AY.3	0.00001
ORF3a	89	T89S	Aca	Tca	1	2	AY.3	0.00001
ORF3a	89	T89I	aCa	aTa	2	2	AY.30	0.000791
ORF3a	89	T89I	aCa	aTa	2	2	AY.39.1.1	0.001449
ORF3a	89	T89del1	Aca	-ca	1	2	AY.4	0.000002
ORF3a	89	T89del1	ACA	-NN	1	2	AY.4	0.000002
ORF3a	89	T89I	aCa	aTa	2	2	AY.4.4	0.000818
ORF3a	89	T89del	ACA	---	2	2	AY.4.5	0.000215
ORF3a	89	T89I	aCa	aTa	2	2	AY.46	0.000208
ORF3a	89	T89del	ACA	---	2	2	AY.46	0.000208
ORF3a	89	T89A	Aca	Gca	2	2	AY.5	0.000041
ORF3a	89	T89I	aCa	aTa	2	2	AY.5.4	0.000553
ORF3a	89	T89I	aCa	aTa	2	2	AY.53	0.000575
ORF3a	89	T89I	aCa	aTa	2	2	AY.59	0.001059
ORF3a	89	T89I	aCa	aTa	2	2	AY.66	0.002139
ORF3a	89	T89I	aCa	aTa	2	2	AY.68	0.000547
ORF3a	89	T89I	aCa	aTa	2	2	AY.69	0.000373
ORF3a	89	T89T	acA	acG	2	2	AY.7	0.000392
ORF3a	89	T89del	ACA	---	2	2	AY.75	0.000112
ORF3a	89	T89I	aCa	aTa	2	2	AY.85	0.000854
ORF3a	89	T89I	aCa	aTa	2	2	AY.9.1	0.000167
ORF3a	89	T89I	aCa	aTa	2	2	AY.92	0.000575
ORF3a	89	T89del	ACA	---	2	2	B.1.1	0.000036
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.170	0.002494
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.174	0.006757
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.205	0.007435
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.222	0.000408
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.229	0.011494
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.265	0.006309
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.294	0.002532
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.316	0.00185
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.37	0.000386
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.370	0.025316
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.372	0.001377
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.397	0.004505
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.464	0.002946
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.486	0.003155
ORF3a	89	T89I	aCa	aTa	2	2	B.1.1.523	0.003125
ORF3a	89	T89R	aCa	aGa	1	2	B.1.1.7	0.000001
ORF3a	89	T89L	ACA	TTG	1	2	B.1.1.7	0.000001
ORF3a	89	T89G	ACA	GGG	1	2	B.1.1.7	0.000001
ORF3a	89	T89G	ACa	GGa	1	2	B.1.1.7	0.000001
ORF3a	89	T89R	aCA	aGG	1	2	B.1.1.7	0.000001
ORF3a	89	T89L	ACa	TTa	1	2	B.1.1.7	0.000001
ORF3a	89	T89P	Aca	Cca	2	2	B.1.1.70	0.000682
ORF3a	89	T89I	aCa	aTa	2	2	B.1.127	0.004396
ORF3a	89	T89I	aCa	aTa	2	2	B.1.131	0.017544
ORF3a	89	T89A	Aca	Gca	2	2	B.1.160	0.000062
ORF3a	89	T89del	ACA	---	2	2	B.1.160	0.000062
ORF3a	89	T89I	aCa	aTa	2	2	B.1.177.19	0.002861
ORF3a	89	T89del	ACA	---	2	2	B.1.177.60	0.000437
ORF3a	89	T89I	aCa	aTa	2	2	B.1.177.66	0.083333
ORF3a	89	T89T	acA	acG	2	2	B.1.258	0.000133
ORF3a	89	T89I	aCa	aTa	2	2	B.1.340	0.008584
ORF3a	89	T89I	aCa	aTa	2	2	B.1.36.38	0.003284
ORF3a	89	T89I	aCa	aTa	2	2	B.1.404	0.002604
ORF3a	89	T89I	aCa	aTa	2	2	B.1.428	0.002041
ORF3a	89	T89I	aCa	aTa	2	2	B.1.459	0.008163
ORF3a	89	T89I	aCa	aTa	2	2	B.1.470	0.002809
ORF3a	89	T89I	aCa	aTa	2	2	B.1.523	0.004902
ORF3a	89	T89V	ACA	GTC	1	2	B.1.525	0.000113
ORF3a	89	T89A	AcA	GcC	1	2	B.1.525	0.000113
ORF3a	89	T89A	Aca	Gca	1	2	B.1.525	0.000113
ORF3a	89	T89V	ACa	GTa	1	2	B.1.525	0.000113
ORF3a	89	T89I	aCa	aTa	2	2	B.1.544	0.012048
ORF3a	89	T89I	aCa	aTa	2	2	B.1.568	0.002222
ORF3a	89	T89A	AcA	GcG	1	2	B.1.576	0.000907
ORF3a	89	T89A	Aca	Gca	1	2	B.1.576	0.000907
ORF3a	89	T89K	aCa	aAa	1	2	B.1.576	0.000907
ORF3a	89	T89K	aCA	aAG	1	2	B.1.576	0.000907
ORF3a	89	T89E	ACA	GAG	1	2	B.1.576	0.000907
ORF3a	89	T89E	ACa	GAa	1	2	B.1.576	0.000907
ORF3a	89	T89del	ACA	---	2	2	B.1.596	0.000174
ORF3a	89	T89I	aCa	aTa	2	2	B.1.617.3	0.00597
ORF3a	89	T89I	aCa	aTa	2	2	B.1.621.1	0.001012
ORF3a	89	T89I	aCa	aTa	2	2	B.1.628	0.000705
ORF3a	89	T89I	aCa	aTa	2	2	B.40	0.000729
ORF3a	89	T89I	aCa	aTa	2	2	C.36.3	0.001134
ORF3a	89	T89I	aCa	aTa	2	2	D.2	0.00015
ORF3a	89	T89del	ACA	---	2	2	P.1.15	0.000465
ORF3a	89	T89T	acA	acG	2	2	Q.8	0.00033
ORF3a	89	T89del	ACA	---	2	2	U.3	0.007722
ORF3a	89	T89K	aCa	aAa	1	1		0.055556
ORF3a	89	T89I	aCa	aTa	1	1	A	0.000387
ORF3a	89	T89I	aCa	aTa	1	1	A.1	0.000282
ORF3a	89	T89I	aCa	aTa	1	1	A.21	0.00277
ORF3a	89	T89del	ACA	---	1	1	AH.3	0.003802
ORF3a	89	T89M	aCA	aTG	1	1	All	0
ORF3a	89	T89C	ACA	TGT	1	1	All	0
ORF3a	89	T89X	ACa	TGa	1	1	All	0
ORF3a	89	T89del	ACA	---	1	1	AV.1	0.005051
ORF3a	89	T89I	aCa	aTa	1	1	AY.10	0.00053
ORF3a	89	T89L	ACa	TTa	1	1	AY.103	0.000006
ORF3a	89	T89T	acA	acT	1	1	AY.105	0.000643
ORF3a	89	T89I	aCa	aTa	1	1	AY.11	0.001339
ORF3a	89	T89T	acA	acC	1	1	AY.111	0.000183
ORF3a	89	T89del	ACA	---	1	1	AY.111	0.000183
ORF3a	89	T89del	ACA	---	1	1	AY.113	0.000142
ORF3a	89	T89I	aCa	aTa	1	1	AY.116.1	0.000311
ORF3a	89	T89T	acA	acG	1	1	AY.117	0.000085
ORF3a	89	T89I	aCa	aTa	1	1	AY.118	0.000063
ORF3a	89	T89del	ACA	---	1	1	AY.118	0.000063
ORF3a	89	T89T	acA	acT	1	1	AY.119	0.000035
ORF3a	89	T89del	ACA	---	1	1	AY.120	0.000037
ORF3a	89	T89I	aCa	aTa	1	1	AY.120.2	0.001285
ORF3a	89	T89S	Aca	Tca	1	1	AY.121	0.000135
ORF3a	89	T89T	acA	acG	1	1	AY.14	0.000088
ORF3a	89	T89A	Aca	Gca	1	1	AY.20	0.000039
ORF3a	89	T89C	ACA	TGT	1	1	AY.25	0.000006
ORF3a	89	T89V	ACa	GTa	1	1	AY.25	0.000006
ORF3a	89	T89X	ACa	TGa	1	1	AY.25	0.000006
ORF3a	89	T89R	aCa	aGa	1	1	AY.25	0.000006
ORF3a	89	T89A	Aca	Gca	1	1	AY.25	0.000006
ORF3a	89	T89T	acA	acG	1	1	AY.26	0.000028
ORF3a	89	T89I	aCa	aTa	1	1	AY.28	0.00189
ORF3a	89	T89A	Aca	Gca	1	1	AY.3	0.00001
ORF3a	89	T89F	ACA	TTT	1	1	AY.3	0.00001
ORF3a	89	T89L	ACa	TTa	1	1	AY.3	0.00001
ORF3a	89	T89del	ACA	---	1	1	AY.3.1	0.000085
ORF3a	89	T89I	aCa	aTa	1	1	AY.34	0.000097
ORF3a	89	T89del	ACA	---	1	1	AY.35	0.000233
ORF3a	89	T89del	ACA	---	1	1	AY.36	0.000148
ORF3a	89	T89del	ACA	---	1	1	AY.37	0.000316
ORF3a	89	T89T	acA	acT	1	1	AY.39	0.000025
ORF3a	89	T89del	ACA	---	1	1	AY.39	0.000025
ORF3a	89	T89P	Aca	Cca	1	1	AY.39	0.000025
ORF3a	89	T89T	acA	acT	1	1	AY.39.1	0.00004
ORF3a	89	T89del2	ACa	--a	1	1	AY.4	0.000002
ORF3a	89	T89R	aCa	aGa	1	1	AY.4	0.000002
ORF3a	89	T89A	Aca	Gca	1	1	AY.4.2	0.000022
ORF3a	89	T89del	ACA	---	1	1	AY.4.2	0.000022
ORF3a	89	T89I	aCa	aTa	1	1	AY.4.2.1	0.000149
ORF3a	89	T89I	aCa	aTa	1	1	AY.4.3	0.000842
ORF3a	89	T89I	aCa	aTa	1	1	AY.41	0.000294
ORF3a	89	T89A	Aca	Gca	1	1	AY.42	0.00004
ORF3a	89	T89A	Aca	Gca	1	1	AY.43	0.000004
ORF3a	89	T89del1	Aca	-ca	1	1	AY.43	0.000004
ORF3a	89	T89A	Aca	Gca	1	1	AY.44	0.000006
ORF3a	89	T89A	Aca	Gca	1	1	AY.46	0.000104
ORF3a	89	T89I	aCa	aTa	1	1	AY.46.1	0.001027
ORF3a	89	T89del	ACA	---	1	1	AY.46.2	0.000635
ORF3a	89	T89I	aCa	aTa	1	1	AY.46.3	0.000934
ORF3a	89	T89del	ACA	---	1	1	AY.46.4	0.000165
ORF3a	89	T89del	ACA	---	1	1	AY.47	0.000031
ORF3a	89	T89T	acA	acG	1	1	AY.5.3	0.000337
ORF3a	89	T89T	acA	acC	1	1	AY.50	0.000799
ORF3a	89	T89del	ACA	---	1	1	AY.54	0.000095
ORF3a	89	T89del	ACA	---	1	1	AY.58	0.000907
ORF3a	89	T89del	ACA	---	1	1	AY.6	0.000041
ORF3a	89	T89del	ACA	---	1	1	AY.62	0.000436
ORF3a	89	T89I	aCa	aTa	1	1	AY.64	0.000595
ORF3a	89	T89I	aCa	aTa	1	1	AY.65	0.000533
ORF3a	89	T89I	aCa	aTa	1	1	AY.70	0.000209
ORF3a	89	T89I	aCa	aTa	1	1	AY.72	0.001361
ORF3a	89	T89I	aCa	aTa	1	1	AY.74	0.000116
ORF3a	89	T89del	ACA	---	1	1	AY.74	0.000116
ORF3a	89	T89I	aCa	aTa	1	1	AY.77	0.001127
ORF3a	89	T89T	acA	acG	1	1	AY.79	0.001211
ORF3a	89	T89I	aCa	aTa	1	1	AY.81	0.001992
ORF3a	89	T89I	aCa	aTa	1	1	AY.84	0.000437
ORF3a	89	T89I	aCa	aTa	1	1	AY.86	0.00083
ORF3a	89	T89I	aCa	aTa	1	1	AY.87	0.000833
ORF3a	89	T89A	AcA	GcG	1	1	AY.9.2	0.000037
ORF3a	89	T89del	ACA	---	1	1	AY.9.2	0.000037
ORF3a	89	T89I	aCa	aTa	1	1	AY.90	0.000684
ORF3a	89	T89I	aCa	aTa	1	1	AY.94	0.000443
ORF3a	89	T89T	acA	acG	1	1	AY.95	0.000761
ORF3a	89	T89A	Aca	Gca	1	1	AY.99	0.001049
ORF3a	89	T89del	ACA	---	1	1	B	0.000128
ORF3a	89	T89S	Aca	Tca	1	1	B.1	0.000009
ORF3a	89	T89P	Aca	Cca	1	1	B.1	0.000009
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.10	0.001115
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.110	0.090909
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.163	0.007634
ORF3a	89	T89A	Aca	Gca	1	1	B.1.1.192	0.002309
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.216	0.00089
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.242	0.043478
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.257	0.009709
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.263	0.001558
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.296	0.018182
ORF3a	89	T89A	Aca	Gca	1	1	B.1.1.317	0.000412
ORF3a	89	T89A	Aca	Gca	1	1	B.1.1.318	0.000302
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.319	0.017544
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.33	0.000421
ORF3a	89	T89P	Aca	Cca	1	1	B.1.1.37	0.000193
ORF3a	89	T89T	acA	acT	1	1	B.1.1.375	0.011905
ORF3a	89	T89del	ACA	---	1	1	B.1.1.409	0.002833
ORF3a	89	T89del	ACA	---	1	1	B.1.1.420	0.001006
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.43	0.014925
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.432	0.001266
ORF3a	89	T89del	ACA	---	1	1	B.1.1.434	0.000349
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.462	0.008621
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.506	0.037037
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.517	0.006803
ORF3a	89	T89A	Aca	Gca	1	1	B.1.1.519	0.00004
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.525	0.005464
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.54	0.003021
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.61	0.008772
ORF3a	89	T89M	aCA	aTG	1	1	B.1.1.7	0.000001
ORF3a	89	T89del1	acA	ac-	1	1	B.1.1.7	0.000001
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.70	0.000341
ORF3a	89	T89del	ACA	---	1	1	B.1.1.70	0.000341
ORF3a	89	T89I	aCa	aTa	1	1	B.1.1.83	0.00271
ORF3a	89	T89I	aCa	aTa	1	1	B.1.108	0.005814
ORF3a	89	T89I	aCa	aTa	1	1	B.1.128	0.000635
ORF3a	89	T89I	aCa	aTa	1	1	B.1.13	0.002375
ORF3a	89	T89I	aCa	aTa	1	1	B.1.14	0.017544
ORF3a	89	T89del	ACA	---	1	1	B.1.140	0.018868
ORF3a	89	T89I	aCa	aTa	1	1	B.1.147	0.000756
ORF3a	89	T89I	aCa	aTa	1	1	B.1.157	0.002985
ORF3a	89	T89I	aCa	aTa	1	1	B.1.160.12	0.00641
ORF3a	89	T89del2	ACa	--a	1	1	B.1.177	0.000013
ORF3a	89	T89I	aCa	aTa	1	1	B.1.177.11	0.001698
ORF3a	89	T89I	aCa	aTa	1	1	B.1.177.23	0.003236
ORF3a	89	T89I	aCa	aTa	1	1	B.1.177.5	0.001242
ORF3a	89	T89I	aCa	aTa	1	1	B.1.177.60	0.000218
ORF3a	89	T89I	aCa	aTa	1	1	B.1.177.62	0.001192
ORF3a	89	T89del	ACA	---	1	1	B.1.177.62	0.001192
ORF3a	89	T89del	ACA	---	1	1	B.1.2	0.000009
ORF3a	89	T89S	Aca	Tca	1	1	B.1.2	0.000009
ORF3a	89	T89I	aCa	aTa	1	1	B.1.201	0.005682
ORF3a	89	T89I	aCa	aTa	1	1	B.1.210	0.002132
ORF3a	89	T89del	ACA	---	1	1	B.1.234	0.000132
ORF3a	89	T89T	acA	acG	1	1	B.1.243	0.00007
ORF3a	89	T89del	ACA	---	1	1	B.1.258	0.000067
ORF3a	89	T89A	Aca	Gca	1	1	B.1.258	0.000067
ORF3a	89	T89I	aCa	aTa	1	1	B.1.279	0.000514
ORF3a	89	T89I	aCa	aTa	1	1	B.1.320	0.001245
ORF3a	89	T89I	aCa	aTa	1	1	B.1.324	0.001605
ORF3a	89	T89I	aCa	aTa	1	1	B.1.325	0.006897
ORF3a	89	T89I	aCa	aTa	1	1	B.1.346	0.001311
ORF3a	89	T89I	aCa	aTa	1	1	B.1.349	0.000715
ORF3a	89	T89del	ACA	---	1	1	B.1.351.2	0.000303
ORF3a	89	T89A	Aca	Gca	1	1	B.1.351.2	0.000303
ORF3a	89	T89I	aCa	aTa	1	1	B.1.351.3	0.000876
ORF3a	89	T89I	aCa	aTa	1	1	B.1.354	0.043478
ORF3a	89	T89T	acA	acG	1	1	B.1.36	0.000146
ORF3a	89	T89I	aCa	aTa	1	1	B.1.36.10	0.004785
ORF3a	89	T89I	aCa	aTa	1	1	B.1.36.24	0.006173
ORF3a	89	T89I	aCa	aTa	1	1	B.1.36.27	0.000763
ORF3a	89	T89I	aCa	aTa	1	1	B.1.36.36	0.000602
ORF3a	89	T89I	aCa	aTa	1	1	B.1.361	0.001289
ORF3a	89	T89del	ACA	---	1	1	B.1.362	0.001541
ORF3a	89	T89I	aCa	aTa	1	1	B.1.367	0.000792
ORF3a	89	T89I	aCa	aTa	1	1	B.1.389	0.001002
ORF3a	89	T89I	aCa	aTa	1	1	B.1.391	0.001127
ORF3a	89	T89I	aCa	aTa	1	1	B.1.400	0.000429
ORF3a	89	T89I	aCa	aTa	1	1	B.1.408	0.00369
ORF3a	89	T89A	Aca	Gca	1	1	B.1.456	0.003268
ORF3a	89	T89I	aCa	aTa	1	1	B.1.462	0.007246
ORF3a	89	T89T	acA	acC	1	1	B.1.525	0.000113
ORF3a	89	T89P	Aca	Cca	1	1	B.1.526	0.000024
ORF3a	89	T89A	Aca	Gca	1	1	B.1.526	0.000024
ORF3a	89	T89I	aCa	aTa	1	1	B.1.538	0.008065
ORF3a	89	T89I	aCa	aTa	1	1	B.1.552	0.015152
ORF3a	89	T89I	aCa	aTa	1	1	B.1.556	0.007519
ORF3a	89	T89I	aCa	aTa	1	1	B.1.564.1	0.001577
ORF3a	89	T89I	aCa	aTa	1	1	B.1.565	0.00081
ORF3a	89	T89A	Aca	Gca	1	1	B.1.567	0.003333
ORF3a	89	T89S	Aca	Tca	1	1	B.1.575.1	0.002439
ORF3a	89	T89I	aCa	aTa	1	1	B.1.576	0.000907
ORF3a	89	T89T	acA	acG	1	1	B.1.576	0.000907
ORF3a	89	T89T	acA	acG	1	1	B.1.596	0.000087
ORF3a	89	T89I	aCa	aTa	1	1	B.1.600	0.005848
ORF3a	89	T89I	aCa	aTa	1	1	B.1.609	0.000479
ORF3a	89	T89del	ACA	---	1	1	B.1.617.1	0.000129
ORF3a	89	T89R	aCa	aGa	1	1	B.1.617.2	0.000004
ORF3a	89	T89del1	Aca	-ca	1	1	B.1.617.2	0.000004
ORF3a	89	T89T	acA	acT	1	1	B.1.621	0.000089
ORF3a	89	T89del	ACA	---	1	1	B.1.627	0.00202
ORF3a	89	T89del	ACA	---	1	1	B.1.631	0.003367
ORF3a	89	T89I	aCa	aTa	1	1	B.1.637	0.000073
ORF3a	89	T89del	ACA	---	1	1	B.1.638	0.052632
ORF3a	89	T89I	aCa	aTa	1	1	B.4.6	0.016667
ORF3a	89	T89E	ACa	GAa	1	1	B.45	0.003831
ORF3a	89	T89A	Aca	Gca	1	1	B.6.6	0.000889
ORF3a	89	T89I	aCa	aTa	1	1	C.11	0.010638
ORF3a	89	T89I	aCa	aTa	1	1	C.16	0.00106
ORF3a	89	T89I	aCa	aTa	1	1	C.25	0.125
ORF3a	89	T89I	aCa	aTa	1	1	C.30	0.001727
ORF3a	89	T89I	aCa	aTa	1	1	C.32	0.023256
ORF3a	89	T89I	aCa	aTa	1	1	C.35	0.000774
ORF3a	89	T89T	acA	acT	1	1	C.36	0.000911
ORF3a	89	T89A	Aca	Gca	1	1	C.37	0.000116
ORF3a	89	T89I	aCa	aTa	1	1	C.8	0.004464
ORF3a	89	T89del1	Aca	-ca	1	1	D.2	0.000075
ORF3a	89	T89A	Aca	Gca	1	1	D.2	0.000075
ORF3a	89	T89T	acA	acG	1	1	P.1	0.000016
ORF3a	89	T89I	aCa	aTa	1	1	P.1.2	0.001156
ORF3a	89	T89I	aCa	aTa	1	1	P.1.7	0.000319
ORF3a	89	T89del	ACA	---	1	1	Q.4	0.000455
ORF3a	89	T89A	Aca	Gca	1	1	R.1	0.00009

CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.