CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 65

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	65	L65L		syn	ctC	ctT	11370	9337	0.821196	25585-25587
ORF3a	65	L65L		syn	ctC	ctA	11370	1964	0.172735	25585-25587
ORF3a	65	L65L		syn	ctC	ctG	11370	69	0.0060686	25585-25587
ORF3a	65	L65F		nonsyn	Ctc	Ttc	2523	2517	0.997622	25585-25587
ORF3a	65	L65F		nonsyn	CtC	TtT	2523	6	0.00237812	25585-25587
ORF3a	65	L65P		nonsyn	cTc	cCc	753	750	0.996016	25585-25587
ORF3a	65	L65P		nonsyn	cTC	cCT	753	3	0.00398406	25585-25587
ORF3a	65	L65I		nonsyn	Ctc	Atc	467	467	1	25585-25587
ORF3a	65	L65V		nonsyn	Ctc	Gtc	162	160	0.987654	25585-25587
ORF3a	65	L65V		nonsyn	CtC	GtG	162	2	0.0123457	25585-25587
ORF3a	65	L65del		del	CTC	---	59	59	1	25585-25587
ORF3a	65	L65H		nonsyn	cTc	cAc	58	56	0.965517	25585-25587
ORF3a	65	L65H		nonsyn	cTC	cAT	58	2	0.0344828	25585-25587
ORF3a	65	L65R		nonsyn	cTc	cGc	38	38	1	25585-25587
ORF3a	65	L65Y		nonsyn	CTc	TAc	5	3	0.6	25585-25587
ORF3a	65	L65Y		nonsyn	CTC	TAT	5	2	0.4	25585-25587
ORF3a	65	L65Q		nonsyn	cTC	cAA	4	4	1	25585-25587
ORF3a	65	L65del1		del	ctC	ct-	3	2	0.666667	25585-25587
ORF3a	65	L65del1		del	Ctc	-tc	3	1	0.333333	25585-25587
ORF3a	65	L65del2		del	cTC	c--	2	2	1	25585-25587
ORF3a	65	L65K		nonsyn	CTC	AAA	2	2	1	25585-25587
ORF3a	65	L65S		nonsyn	CTC	TCA	1	1	1	25585-25587

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	65	L65L	ctC	ctT	9337	11370	All	0.001786
ORF3a	65	L65L	ctC	ctA	1964	11370	All	0.000376
ORF3a	65	L65L	ctC	ctG	69	11370	All	0.000013
ORF3a	65	L65F	Ctc	Ttc	2517	2523	All	0.000481
ORF3a	65	L65F	CtC	TtT	6	2523	All	0.000001
ORF3a	65	L65L	ctC	ctA	1396	2166	AY.4	0.002173
ORF3a	65	L65L	ctC	ctT	767	2166	AY.4	0.001194
ORF3a	65	L65L	ctC	ctG	3	2166	AY.4	0.000005
ORF3a	65	L65L	ctC	ctT	1725	1823	B.1.1.7	0.001544
ORF3a	65	L65L	ctC	ctA	96	1823	B.1.1.7	0.000086
ORF3a	65	L65L	ctC	ctG	2	1823	B.1.1.7	0.000002
ORF3a	65	L65L	ctC	ctT	992	999	AY.103	0.006159
ORF3a	65	L65L	ctC	ctA	6	999	AY.103	0.000037
ORF3a	65	L65L	ctC	ctG	1	999	AY.103	0.000006
ORF3a	65	L65P	cTc	cCc	750	753	All	0.000143
ORF3a	65	L65P	cTC	cCT	3	753	All	0.000001
ORF3a	65	L65L	ctC	ctT	588	631	B.1.2	0.005178
ORF3a	65	L65L	ctC	ctA	27	631	B.1.2	0.000238
ORF3a	65	L65L	ctC	ctG	16	631	B.1.2	0.000141
ORF3a	65	L65I	Ctc	Atc	467	467	All	0.000089
ORF3a	65	L65F	Ctc	Ttc	424	425	AY.4	0.00066
ORF3a	65	L65F	CtC	TtT	1	425	AY.4	0.000002
ORF3a	65	L65F	Ctc	Ttc	395	396	B.1.1.7	0.000354
ORF3a	65	L65F	CtC	TtT	1	396	B.1.1.7	0.000001
ORF3a	65	L65L	ctC	ctT	369	390	AY.43	0.001635
ORF3a	65	L65L	ctC	ctA	19	390	AY.43	0.000084
ORF3a	65	L65L	ctC	ctG	2	390	AY.43	0.000009
ORF3a	65	L65L	ctC	ctT	270	303	B.1.617.2	0.001017
ORF3a	65	L65L	ctC	ctA	33	303	B.1.617.2	0.000124
ORF3a	65	L65L	ctC	ctT	289	289	B.1.427	0.014594
ORF3a	65	L65L	ctC	ctT	277	278	B.1.526	0.006511
ORF3a	65	L65L	ctC	ctA	1	278	B.1.526	0.000024
ORF3a	65	L65F	Ctc	Ttc	276	276	B.1.2	0.00243
ORF3a	65	L65L	ctC	ctT	219	255	B.1.429	0.005153
ORF3a	65	L65L	ctC	ctA	36	255	B.1.429	0.000847
ORF3a	65	L65P	cTc	cCc	230	230	B.1.1.7	0.000206
ORF3a	65	L65L	ctC	ctT	217	219	AY.33	0.014491
ORF3a	65	L65L	ctC	ctA	2	219	AY.33	0.000134
ORF3a	65	L65L	ctC	ctT	194	194	B.1.160.15	0.960396
ORF3a	65	L65L	ctC	ctT	173	190	P.1	0.002725
ORF3a	65	L65L	ctC	ctA	17	190	P.1	0.000268
ORF3a	65	L65L	ctC	ctT	175	175	B.1.1.519	0.006949
ORF3a	65	L65V	Ctc	Gtc	160	162	All	0.000031
ORF3a	65	L65V	CtC	GtG	2	162	All	0
ORF3a	65	L65L	ctC	ctT	156	161	B.1.177	0.002054
ORF3a	65	L65L	ctC	ctA	4	161	B.1.177	0.000053
ORF3a	65	L65L	ctC	ctG	1	161	B.1.177	0.000013
ORF3a	65	L65P	cTc	cCc	154	154	AY.4	0.00024
ORF3a	65	L65L	ctC	ctT	79	152	AY.25	0.000475
ORF3a	65	L65L	ctC	ctA	72	152	AY.25	0.000433
ORF3a	65	L65L	ctC	ctG	1	152	AY.25	0.000006
ORF3a	65	L65L	ctC	ctT	152	152	AY.54	0.014493
ORF3a	65	L65L	ctC	ctT	147	148	AY.4.2	0.003188
ORF3a	65	L65L	ctC	ctA	1	148	AY.4.2	0.000022
ORF3a	65	L65I	Ctc	Atc	133	133	B.1.1.7	0.000119
ORF3a	65	L65L	ctC	ctT	115	120	B.1.160	0.003587
ORF3a	65	L65L	ctC	ctA	5	120	B.1.160	0.000156
ORF3a	65	L65L	ctC	ctT	107	114	B.1	0.00098
ORF3a	65	L65L	ctC	ctA	7	114	B.1	0.000064
ORF3a	65	L65L	ctC	ctT	98	113	AY.44	0.000597
ORF3a	65	L65L	ctC	ctA	14	113	AY.44	0.000085
ORF3a	65	L65L	ctC	ctG	1	113	AY.44	0.000006
ORF3a	65	L65L	ctC	ctT	110	112	B.1.1.222	0.02244
ORF3a	65	L65L	ctC	ctA	2	112	B.1.1.222	0.000408
ORF3a	65	L65F	Ctc	Ttc	110	110	B.1.160	0.003431
ORF3a	65	L65F	Ctc	Ttc	98	98	B.1.617.2	0.000369
ORF3a	65	L65L	ctC	ctT	93	93	AY.98.1	0.004504
ORF3a	65	L65F	Ctc	Ttc	84	84	AY.103	0.000522
ORF3a	65	L65L	ctC	ctT	83	84	AY.119	0.002931
ORF3a	65	L65L	ctC	ctA	1	84	AY.119	0.000035
ORF3a	65	L65L	ctC	ctT	75	82	AY.3	0.000746
ORF3a	65	L65L	ctC	ctA	7	82	AY.3	0.00007
ORF3a	65	L65L	ctC	ctT	79	82	B.1.1	0.001433
ORF3a	65	L65L	ctC	ctA	3	82	B.1.1	0.000054
ORF3a	65	L65I	Ctc	Atc	77	77	AY.27	0.004983
ORF3a	65	L65F	Ctc	Ttc	71	71	AY.43	0.000315
ORF3a	65	L65L	ctC	ctT	65	68	AY.47	0.002022
ORF3a	65	L65L	ctC	ctA	3	68	AY.47	0.000093
ORF3a	65	L65F	Ctc	Ttc	68	68	B.1	0.000623
ORF3a	65	L65L	ctC	ctT	54	61	AY.39	0.001334
ORF3a	65	L65L	ctC	ctA	7	61	AY.39	0.000173
ORF3a	65	L65del	CTC	---	59	59	All	0.000011
ORF3a	65	L65L	ctC	ctT	59	59	B.1.177.59	0.951613
ORF3a	65	L65H	cTc	cAc	56	58	All	0.000011
ORF3a	65	L65H	cTC	cAT	2	58	All	0
ORF3a	65	L65F	Ctc	Ttc	58	58	AY.44	0.000353
ORF3a	65	L65L	ctC	ctA	50	56	B.1.637	0.003654
ORF3a	65	L65L	ctC	ctT	6	56	B.1.637	0.000438
ORF3a	65	L65I	Ctc	Atc	55	55	AY.103	0.000341
ORF3a	65	L65P	cTc	cCc	52	52	B.1.617.2	0.000196
ORF3a	65	L65V	Ctc	Gtc	51	51	AY.43	0.000226
ORF3a	65	L65L	ctC	ctT	50	50	B.1.351	0.001486
ORF3a	65	L65P	cTc	cCc	49	49	AY.3	0.000487
ORF3a	65	L65L	ctC	ctT	47	47	AY.120	0.001747
ORF3a	65	L65F	Ctc	Ttc	46	46	B.1.177.86	0.008439
ORF3a	65	L65L	ctC	ctT	44	45	B.1.243	0.003062
ORF3a	65	L65L	ctC	ctA	1	45	B.1.243	0.00007
ORF3a	65	L65L	ctC	ctT	35	44	AY.29	0.000552
ORF3a	65	L65L	ctC	ctA	9	44	AY.29	0.000142
ORF3a	65	L65L	ctC	ctT	44	44	B.1.221	0.003125
ORF3a	65	L65L	ctC	ctT	41	44	C.37	0.004759
ORF3a	65	L65L	ctC	ctA	2	44	C.37	0.000232
ORF3a	65	L65L	ctC	ctG	1	44	C.37	0.000116
ORF3a	65	L65F	Ctc	Ttc	43	43	AY.3	0.000428
ORF3a	65	L65P	cTc	cCc	42	42	AY.100	0.001932
ORF3a	65	L65F	Ctc	Ttc	40	40	AY.25	0.000241
ORF3a	65	L65F	Ctc	Ttc	39	39	P.1	0.000614
ORF3a	65	L65R	cTc	cGc	38	38	All	0.000007
ORF3a	65	L65L	ctC	ctT	38	38	AY.3.1	0.00324
ORF3a	65	L65F	Ctc	Ttc	37	37	AY.12	0.011694
ORF3a	65	L65F	Ctc	Ttc	37	37	B.1.351	0.0011
ORF3a	65	L65L	ctC	ctA	31	36	AY.27	0.002006
ORF3a	65	L65L	ctC	ctT	5	36	AY.27	0.000324
ORF3a	65	L65L	ctC	ctT	35	36	AY.39.1	0.001386
ORF3a	65	L65L	ctC	ctA	1	36	AY.39.1	0.00004
ORF3a	65	L65F	Ctc	Ttc	36	36	B.1.1	0.000653
ORF3a	65	L65L	ctC	ctT	35	35	B.1.1.323	0.492958
ORF3a	65	L65I	Ctc	Atc	34	34	AY.4	0.000053
ORF3a	65	L65L	ctC	ctT	34	34	P.1.15	0.0079
ORF3a	65	L65L	ctC	ctT	33	33	B.1.1.219	0.165
ORF3a	65	L65V	Ctc	Gtc	32	32	B.1.1.7	0.000029
ORF3a	65	L65L	ctC	ctT	31	32	B.1.595	0.00809
ORF3a	65	L65L	ctC	ctA	1	32	B.1.595	0.000261
ORF3a	65	L65L	ctC	ctT	31	31	B.1.36	0.004523
ORF3a	65	L65L	ctC	ctT	31	31	B.1.628	0.010923
ORF3a	65	L65L	ctC	ctT	28	30	AY.102	0.000742
ORF3a	65	L65L	ctC	ctG	1	30	AY.102	0.000027
ORF3a	65	L65L	ctC	ctA	1	30	AY.102	0.000027
ORF3a	65	L65L	ctC	ctT	29	30	AY.9	0.00196
ORF3a	65	L65L	ctC	ctA	1	30	AY.9	0.000068
ORF3a	65	L65L	ctC	ctT	30	30	B.1.177.33	0.049342
ORF3a	65	L65I	Ctc	Atc	29	29	AY.26	0.000821
ORF3a	65	L65P	cTc	cCc	29	29	AY.44	0.000177
ORF3a	65	L65F	Ctc	Ttc	29	29	B.1.36	0.004231
ORF3a	65	L65V	Ctc	Gtc	28	28	AY.57	0.018373
ORF3a	65	L65F	Ctc	Ttc	28	28	B.1.177	0.000369
ORF3a	65	L65L	ctC	ctT	24	26	B.1.1.232	0.043557
ORF3a	65	L65L	ctC	ctA	2	26	B.1.1.232	0.00363
ORF3a	65	L65L	ctC	ctG	22	26	B.1.1.306	0.009645
ORF3a	65	L65L	ctC	ctT	4	26	B.1.1.306	0.001754
ORF3a	65	L65L	ctC	ctT	26	26	B.1.1.328	0.440678
ORF3a	65	L65L	ctC	ctT	24	24	AY.12	0.007585
ORF3a	65	L65F	Ctc	Ttc	24	24	AY.9.1	0.002009
ORF3a	65	L65L	ctC	ctT	24	24	B.1.517	0.010248
ORF3a	65	L65F	Ctc	Ttc	23	23	AY.20	0.000894
ORF3a	65	L65L	ctC	ctT	23	23	B.1.369	0.00656
ORF3a	65	L65P	cTc	cCc	23	23	B.1.621	0.002036
ORF3a	65	L65F	Ctc	Ttc	22	22	AY.39	0.000544
ORF3a	65	L65F	Ctc	Ttc	22	22	AY.7.2	0.012304
ORF3a	65	L65L	ctC	ctT	21	21	B.1.234	0.002771
ORF3a	65	L65L	ctC	ctT	21	21	P.1.14	0.001004
ORF3a	65	L65P	cTc	cCc	20	20	AY.25	0.00012
ORF3a	65	L65F	Ctc	Ttc	20	20	B.1.210	0.042644
ORF3a	65	L65F	Ctc	Ttc	20	20	B.1.577	0.013746
ORF3a	65	L65L	ctC	ctT	15	19	AY.23	0.001046
ORF3a	65	L65L	ctC	ctA	3	19	AY.23	0.000209
ORF3a	65	L65L	ctC	ctG	1	19	AY.23	0.00007
ORF3a	65	L65P	cTc	cCc	19	19	B.1.1.160	0.452381
ORF3a	65	L65L	ctC	ctT	19	19	B.1.177.81	0.003597
ORF3a	65	L65F	Ctc	Ttc	17	17	AY.102	0.000451
ORF3a	65	L65L	ctC	ctT	17	17	AY.5.3	0.005735
ORF3a	65	L65P	cTc	cCc	17	17	B.1.221	0.001208
ORF3a	65	L65L	ctC	ctT	15	16	B.1.258.17	0.00156
ORF3a	65	L65L	ctC	ctA	1	16	B.1.258.17	0.000104
ORF3a	65	L65F	Ctc	Ttc	16	16	B.1.632	0.107383
ORF3a	65	L65L	ctC	ctT	16	16	P.7	0.069869
ORF3a	65	L65P	cTc	cCc	15	15	AY.43	0.000066
ORF3a	65	L65L	ctC	ctT	8	15	AY.45	0.000973
ORF3a	65	L65L	ctC	ctA	7	15	AY.45	0.000852
ORF3a	65	L65L	ctC	ctT	14	15	B.1.1.28	0.004357
ORF3a	65	L65L	ctC	ctG	1	15	B.1.1.28	0.000311
ORF3a	65	L65L	ctC	ctA	15	15	B.1.1.420	0.015091
ORF3a	65	L65L	ctC	ctA	15	15	B.1.1.432	0.018987
ORF3a	65	L65L	ctC	ctT	15	15	C.16	0.015907
ORF3a	65	L65F	Ctc	Ttc	15	15	P.1.14	0.000717
ORF3a	65	L65L	ctC	ctT	15	15	Q.2	0.009202
ORF3a	65	L65L	ctC	ctT	13	14	AY.20	0.000505
ORF3a	65	L65L	ctC	ctA	1	14	AY.20	0.000039
ORF3a	65	L65L	ctC	ctT	13	14	AY.5	0.000268
ORF3a	65	L65L	ctC	ctA	1	14	AY.5	0.000021
ORF3a	65	L65L	ctC	ctT	13	14	B.1.258	0.000865
ORF3a	65	L65L	ctC	ctA	1	14	B.1.258	0.000067
ORF3a	65	L65L	ctC	ctT	14	14	B.1.527	0.051852
ORF3a	65	L65F	Ctc	Ttc	14	14	B.1.617.1	0.001806
ORF3a	65	L65I	Ctc	Atc	13	13	B.1	0.000119
ORF3a	65	L65del	CTC	---	13	13	B.1.1.7	0.000012
ORF3a	65	L65H	cTc	cAc	13	13	B.1.1.7	0.000012
ORF3a	65	L65F	Ctc	Ttc	12	12	AY.105	0.007717
ORF3a	65	L65L	ctC	ctT	12	12	AY.4.3	0.010101
ORF3a	65	L65L	ctC	ctT	12	12	AY.71	0.005701
ORF3a	65	L65L	ctC	ctT	12	12	B.1.1.294	0.01519
ORF3a	65	L65F	Ctc	Ttc	12	12	B.1.1.519	0.000477
ORF3a	65	L65L	ctC	ctT	10	12	B.1.617.1	0.00129
ORF3a	65	L65L	ctC	ctA	2	12	B.1.617.1	0.000258
ORF3a	65	L65F	Ctc	Ttc	12	12	C.37	0.001393
ORF3a	65	L65F	Ctc	Ttc	11	11	AY.23	0.000767
ORF3a	65	L65L	ctC	ctG	10	11	AY.74	0.001156
ORF3a	65	L65L	ctC	ctT	1	11	AY.74	0.000116
ORF3a	65	L65L	ctC	ctT	11	11	AY.95	0.008371
ORF3a	65	L65L	ctC	ctT	11	11	B.1.1.1	0.003594
ORF3a	65	L65L	ctC	ctT	11	11	B.1.1.291	0.008166
ORF3a	65	L65F	Ctc	Ttc	11	11	B.1.429	0.000259
ORF3a	65	L65L	ctC	ctT	10	11	B.1.525	0.001132
ORF3a	65	L65L	ctC	ctA	1	11	B.1.525	0.000113
ORF3a	65	L65L	ctC	ctT	11	11	B.1.596	0.000959
ORF3a	65	L65F	Ctc	Ttc	11	11	B.1.621	0.000974
ORF3a	65	L65L	ctC	ctT	10	10	AY.100	0.00046
ORF3a	65	L65L	ctC	ctT	9	10	AY.113	0.001282
ORF3a	65	L65L	ctC	ctA	1	10	AY.113	0.000142
ORF3a	65	L65F	Ctc	Ttc	10	10	AY.39.1	0.000396
ORF3a	65	L65V	Ctc	Gtc	10	10	AY.4	0.000016
ORF3a	65	L65F	Ctc	Ttc	10	10	B.1.1.317	0.004117
ORF3a	65	L65L	ctC	ctT	10	10	B.1.478	0.117647
ORF3a	65	L65H	cTc	cAc	10	10	B.1.617.2	0.000038
ORF3a	65	L65V	Ctc	Gtc	9	9	AY.25	0.000054
ORF3a	65	L65F	Ctc	Ttc	9	9	AY.6	0.00037
ORF3a	65	L65L	ctC	ctT	9	9	AY.62	0.003922
ORF3a	65	L65F	Ctc	Ttc	9	9	AY.99.2	0.000829
ORF3a	65	L65P	cTc	cCc	9	9	B.1.1	0.000163
ORF3a	65	L65L	ctC	ctT	8	9	P.2	0.001493
ORF3a	65	L65L	ctC	ctA	1	9	P.2	0.000187
ORF3a	65	L65L	ctC	ctT	9	9	Q.1	0.001137
ORF3a	65	L65L	ctC	ctT	8	8	AY.117	0.000676
ORF3a	65	L65R	cTc	cGc	8	8	AY.25	0.000048
ORF3a	65	L65L	ctC	ctT	8	8	AY.26	0.000226
ORF3a	65	L65I	Ctc	Atc	8	8	AY.33	0.000534
ORF3a	65	L65L	ctC	ctT	6	8	AY.42	0.000241
ORF3a	65	L65L	ctC	ctA	2	8	AY.42	0.00008
ORF3a	65	L65L	ctC	ctT	7	8	AY.61	0.000733
ORF3a	65	L65L	ctC	ctA	1	8	AY.61	0.000105
ORF3a	65	L65L	ctC	ctT	8	8	AY.76	0.038647
ORF3a	65	L65L	ctC	ctT	7	8	AY.9.2	0.000257
ORF3a	65	L65L	ctC	ctA	1	8	AY.9.2	0.000037
ORF3a	65	L65F	Ctc	Ttc	8	8	B.1.1.277	0.00607
ORF3a	65	L65L	ctC	ctT	8	8	B.1.1.37	0.001543
ORF3a	65	L65L	ctC	ctT	8	8	B.1.1.39	0.004077
ORF3a	65	L65F	Ctc	Ttc	8	8	B.1.258.17	0.000832
ORF3a	65	L65L	ctC	ctT	8	8	B.1.564.1	0.012618
ORF3a	65	L65P	cTc	cCc	5	7		0.277778
ORF3a	65	L65P	cTC	cCT	2	7		0.111111
ORF3a	65	L65F	Ctc	Ttc	7	7	AY.119	0.000247
ORF3a	65	L65L	ctC	ctA	4	7	AY.16	0.001519
ORF3a	65	L65L	ctC	ctT	3	7	AY.16	0.001139
ORF3a	65	L65F	Ctc	Ttc	7	7	AY.33	0.000467
ORF3a	65	L65I	Ctc	Atc	7	7	AY.43	0.000031
ORF3a	65	L65H	cTc	cAc	7	7	B.1	0.000064
ORF3a	65	L65L	ctC	ctT	5	7	B.1.1.214	0.000277
ORF3a	65	L65L	ctC	ctG	2	7	B.1.1.214	0.000111
ORF3a	65	L65I	Ctc	Atc	7	7	B.1.1.349	0.072165
ORF3a	65	L65F	Ctc	Ttc	7	7	B.1.36.8	0.007
ORF3a	65	L65L	ctC	ctT	7	7	B.1.404	0.009115
ORF3a	65	L65L	ctC	ctT	7	7	B.1.422	0.005686
ORF3a	65	L65I	Ctc	Atc	7	7	B.1.617.2	0.000026
ORF3a	65	L65V	Ctc	Gtc	7	7	B.1.617.2	0.000026
ORF3a	65	L65H	cTc	cAc	7	7	B.1.621	0.00062
ORF3a	65	L65L	ctC	ctT	4	7	B.1.621	0.000354
ORF3a	65	L65L	ctC	ctA	3	7	B.1.621	0.000266
ORF3a	65	L65P	cTc	cCc	7	7	P.1	0.00011
ORF3a	65	L65L	ctC	ctT	7	7	Q.8	0.001154
ORF3a	65	L65F	Ctc	Ttc	3	6		0.166667
ORF3a	65	L65F	CtC	TtT	3	6		0.166667
ORF3a	65	L65F	Ctc	Ttc	6	6	AY.100	0.000276
ORF3a	65	L65H	cTc	cAc	6	6	AY.103	0.000037
ORF3a	65	L65I	Ctc	Atc	6	6	AY.25	0.000036
ORF3a	65	L65I	Ctc	Atc	6	6	AY.39	0.000148
ORF3a	65	L65F	Ctc	Ttc	6	6	AY.47	0.000187
ORF3a	65	L65F	Ctc	Ttc	6	6	AY.5	0.000124
ORF3a	65	L65P	cTc	cCc	5	6	B.1	0.000046
ORF3a	65	L65P	cTC	cCT	1	6	B.1	0.000009
ORF3a	65	L65I	Ctc	Atc	6	6	B.1.1.207	0.007092
ORF3a	65	L65I	Ctc	Atc	6	6	B.1.1.294	0.007595
ORF3a	65	L65L	ctC	ctT	6	6	B.1.1.33	0.002525
ORF3a	65	L65F	Ctc	Ttc	6	6	B.1.1.434	0.002091
ORF3a	65	L65L	ctC	ctT	6	6	B.1.177.86	0.001101
ORF3a	65	L65L	ctC	ctT	6	6	B.1.240	0.001293
ORF3a	65	L65L	ctC	ctT	6	6	B.1.250	0.086957
ORF3a	65	L65F	Ctc	Ttc	6	6	B.1.258	0.000399
ORF3a	65	L65L	ctC	ctT	6	6	B.1.36.1	0.006842
ORF3a	65	L65F	Ctc	Ttc	6	6	B.1.427	0.000303
ORF3a	65	L65L	ctC	ctT	6	6	B.1.609	0.002876
ORF3a	65	L65P	cTc	cCc	6	6	P.1.14	0.000287
ORF3a	65	L65L	ctC	ctT	5	5		0.277778
ORF3a	65	L65L	ctC	ctT	5	5	A.2.5.2	0.007862
ORF3a	65	L65Y	CTc	TAc	3	5	All	0.000001
ORF3a	65	L65Y	CTC	TAT	2	5	All	0
ORF3a	65	L65F	Ctc	Ttc	5	5	AY.120	0.000186
ORF3a	65	L65del	CTC	---	5	5	AY.25	0.00003
ORF3a	65	L65F	Ctc	Ttc	5	5	AY.29	0.000079
ORF3a	65	L65L	ctC	ctT	5	5	AY.32	0.002662
ORF3a	65	L65P	cTc	cCc	5	5	AY.39.1	0.000198
ORF3a	65	L65del	CTC	---	5	5	AY.4	0.000008
ORF3a	65	L65L	ctC	ctT	5	5	AY.46.4	0.000823
ORF3a	65	L65L	ctC	ctT	5	5	AY.6	0.000206
ORF3a	65	L65L	ctC	ctT	5	5	AY.75	0.00028
ORF3a	65	L65L	ctC	ctT	4	5	AY.84	0.00175
ORF3a	65	L65L	ctC	ctG	1	5	AY.84	0.000437
ORF3a	65	L65L	ctC	ctT	4	5	AY.98	0.000316
ORF3a	65	L65L	ctC	ctA	1	5	AY.98	0.000079
ORF3a	65	L65L	ctC	ctT	5	5	B	0.000639
ORF3a	65	L65I	Ctc	Atc	5	5	B.1.1	0.000091
ORF3a	65	L65L	ctC	ctT	5	5	B.1.1.171	0.018382
ORF3a	65	L65F	Ctc	Ttc	5	5	B.1.1.416	0.004525
ORF3a	65	L65R	cTc	cGc	5	5	B.1.1.7	0.000004
ORF3a	65	L65del	CTC	---	5	5	B.1.177	0.000066
ORF3a	65	L65I	Ctc	Atc	5	5	B.1.206	0.004078
ORF3a	65	L65F	Ctc	Ttc	5	5	B.1.36.10	0.023923
ORF3a	65	L65F	Ctc	Ttc	5	5	B.1.466.2	0.001956
ORF3a	65	L65H	cTC	cAT	2	4		0.111111
ORF3a	65	L65Y	CTC	TAT	2	4		0.111111
ORF3a	65	L65Y	CTc	TAc	2	4		0.111111
ORF3a	65	L65H	cTc	cAc	2	4		0.111111
ORF3a	65	L65L	ctC	ctT	4	4	A	0.001548
ORF3a	65	L65L	ctC	ctT	4	4	A.27	0.006623
ORF3a	65	L65Q	cTC	cAA	4	4	All	0.000001
ORF3a	65	L65F	Ctc	Ttc	4	4	AY.113	0.00057
ORF3a	65	L65F	Ctc	Ttc	4	4	AY.117	0.000338
ORF3a	65	L65H	cTc	cAc	4	4	AY.119	0.000141
ORF3a	65	L65I	Ctc	Atc	4	4	AY.4.2	0.000087
ORF3a	65	L65R	cTc	cGc	4	4	AY.43	0.000018
ORF3a	65	L65F	Ctc	Ttc	4	4	AY.46	0.000416
ORF3a	65	L65L	ctC	ctA	4	4	AY.46.5	0.000794
ORF3a	65	L65F	Ctc	Ttc	4	4	AY.74	0.000463
ORF3a	65	L65L	ctC	ctT	3	4	AY.99.2	0.000276
ORF3a	65	L65L	ctC	ctA	1	4	AY.99.2	0.000092
ORF3a	65	L65F	Ctc	Ttc	4	4	B.1.1.222	0.000816
ORF3a	65	L65L	ctC	ctT	4	4	B.1.1.284	0.00043
ORF3a	65	L65P	cTc	cCc	4	4	B.1.1.284	0.00043
ORF3a	65	L65L	ctC	ctT	4	4	B.1.1.317	0.001647
ORF3a	65	L65P	cTc	cCc	4	4	B.1.177	0.000053
ORF3a	65	L65L	ctC	ctA	3	4	B.1.177.16	0.001993
ORF3a	65	L65L	ctC	ctG	1	4	B.1.177.16	0.000664
ORF3a	65	L65L	ctC	ctA	4	4	B.1.213	0.059701
ORF3a	65	L65F	Ctc	Ttc	4	4	B.1.243	0.000278
ORF3a	65	L65F	Ctc	Ttc	4	4	B.1.311	0.001098
ORF3a	65	L65L	ctC	ctT	4	4	B.1.351.2	0.00121
ORF3a	65	L65F	Ctc	Ttc	4	4	B.1.369	0.001141
ORF3a	65	L65F	Ctc	Ttc	4	4	B.1.456	0.013072
ORF3a	65	L65L	ctC	ctT	4	4	B.1.551	0.005161
ORF3a	65	L65R	cTc	cGc	4	4	B.1.617.2	0.000015
ORF3a	65	L65F	Ctc	Ttc	4	4	B.1.620	0.003784
ORF3a	65	L65L	ctC	ctA	2	4	C.26	0.014706
ORF3a	65	L65L	ctC	ctT	2	4	C.26	0.014706
ORF3a	65	L65L	ctC	ctT	4	4	D.2	0.0003
ORF3a	65	L65L	ctC	ctT	4	4	N.5	0.007067
ORF3a	65	L65L	ctC	ctT	3	4	P.1.1	0.000953
ORF3a	65	L65L	ctC	ctA	1	4	P.1.1	0.000318
ORF3a	65	L65F	Ctc	Ttc	4	4	P.1.17	0.000647
ORF3a	65	L65P	cTc	cCc	4	4	P.1.4	0.003906
ORF3a	65	L65L	ctC	ctT	4	4	R.1	0.00036
ORF3a	65	L65L	ctC	ctT	3	3	A.2.5	0.001497
ORF3a	65	L65L	ctC	ctT	3	3	A.23.1	0.002113
ORF3a	65	L65del1	ctC	ct-	2	3	All	0
ORF3a	65	L65del1	Ctc	-tc	1	3	All	0
ORF3a	65	L65V	Ctc	Gtc	3	3	AY.100	0.000138
ORF3a	65	L65I	Ctc	Atc	3	3	AY.102	0.00008
ORF3a	65	L65L	ctC	ctT	3	3	AY.109	0.002219
ORF3a	65	L65L	ctC	ctT	3	3	AY.111	0.000549
ORF3a	65	L65L	ctC	ctT	3	3	AY.13	0.000483
ORF3a	65	L65H	cTc	cAc	3	3	AY.23	0.000209
ORF3a	65	L65R	cTc	cGc	3	3	AY.3	0.00003
ORF3a	65	L65I	Ctc	Atc	3	3	AY.3.1	0.000256
ORF3a	65	L65L	ctC	ctT	3	3	AY.38	0.001498
ORF3a	65	L65R	cTc	cGc	3	3	AY.4	0.000005
ORF3a	65	L65L	ctC	ctT	3	3	AY.4.5	0.000322
ORF3a	65	L65F	Ctc	Ttc	3	3	AY.40	0.002893
ORF3a	65	L65del	CTC	---	3	3	AY.43	0.000013
ORF3a	65	L65I	Ctc	Atc	3	3	AY.44	0.000018
ORF3a	65	L65L	ctC	ctT	3	3	AY.46	0.000312
ORF3a	65	L65L	ctC	ctA	3	3	AY.46.2	0.001906
ORF3a	65	L65P	cTc	cCc	3	3	AY.51	0.002727
ORF3a	65	L65F	Ctc	Ttc	3	3	AY.55	0.002752
ORF3a	65	L65I	Ctc	Atc	3	3	AY.71	0.001425
ORF3a	65	L65L	ctC	ctT	3	3	AY.73	0.001996
ORF3a	65	L65I	Ctc	Atc	3	3	AY.75.1	0.000541
ORF3a	65	L65L	ctC	ctT	2	3	AY.75.1	0.000361
ORF3a	65	L65L	ctC	ctA	1	3	AY.75.1	0.00018
ORF3a	65	L65F	Ctc	Ttc	3	3	AY.88	0.002653
ORF3a	65	L65F	Ctc	Ttc	3	3	AY.9	0.000203
ORF3a	65	L65L	ctC	ctT	3	3	AY.92	0.000862
ORF3a	65	L65L	ctC	ctT	3	3	AY.93	0.000819
ORF3a	65	L65L	ctC	ctA	3	3	AY.94	0.001328
ORF3a	65	L65L	ctC	ctT	2	3	AZ.2	0.001642
ORF3a	65	L65L	ctC	ctA	1	3	AZ.2	0.000821
ORF3a	65	L65del	CTC	---	3	3	B.1	0.000027
ORF3a	65	L65F	Ctc	Ttc	3	3	B.1.1.214	0.000166
ORF3a	65	L65L	ctC	ctT	3	3	B.1.1.241	0.006211
ORF3a	65	L65F	Ctc	Ttc	3	3	B.1.1.37	0.000579
ORF3a	65	L65L	ctC	ctT	3	3	B.1.1.388	0.136364
ORF3a	65	L65L	ctC	ctT	3	3	B.1.177.10	0.002634
ORF3a	65	L65V	Ctc	Gtc	3	3	B.1.177.4	0.000633
ORF3a	65	L65L	ctC	ctT	2	3	B.1.177.73	0.001133
ORF3a	65	L65L	ctC	ctA	1	3	B.1.177.73	0.000566
ORF3a	65	L65I	Ctc	Atc	3	3	B.1.2	0.000026
ORF3a	65	L65F	Ctc	Ttc	3	3	B.1.221	0.000213
ORF3a	65	L65F	Ctc	Ttc	3	3	B.1.239	0.003663
ORF3a	65	L65F	Ctc	Ttc	2	3	B.1.258.14	0.001961
ORF3a	65	L65F	CtC	TtT	1	3	B.1.258.14	0.00098
ORF3a	65	L65I	Ctc	Atc	3	3	B.1.36	0.000438
ORF3a	65	L65P	cTc	cCc	3	3	B.1.36.17	0.001482
ORF3a	65	L65L	ctC	ctT	3	3	B.1.575	0.00091
ORF3a	65	L65del	CTC	---	3	3	B.1.617.2	0.000011
ORF3a	65	L65L	ctC	ctT	3	3	B.1.619	0.002613
ORF3a	65	L65L	ctC	ctT	3	3	C.28	0.12
ORF3a	65	L65F	Ctc	Ttc	3	3	C.35	0.002322
ORF3a	65	L65L	ctC	ctT	3	3	C.36.3	0.001702
ORF3a	65	L65L	ctC	ctT	3	3	P.1.10	0.000808
ORF3a	65	L65F	Ctc	Ttc	3	3	P.1.16	0.001122
ORF3a	65	L65F	Ctc	Ttc	3	3	P.1.7	0.000958
ORF3a	65	L65F	Ctc	Ttc	3	3	Q.1	0.000379
ORF3a	65	L65F	Ctc	Ttc	3	3	R.1	0.00027
ORF3a	65	L65del	CTC	---	3	3	U.3	0.011583
ORF3a	65	L65L	ctC	ctT	2	2	A.2	0.001324
ORF3a	65	L65K	CTC	AAA	2	2	All	0
ORF3a	65	L65del2	cTC	c--	2	2	All	0
ORF3a	65	L65I	Ctc	Atc	2	2	AY.100	0.000092
ORF3a	65	L65V	Ctc	Gtc	2	2	AY.102	0.000053
ORF3a	65	L65P	cTc	cCc	2	2	AY.103	0.000012
ORF3a	65	L65R	cTc	cGc	2	2	AY.103	0.000012
ORF3a	65	L65L	ctC	ctT	2	2	AY.106	0.00067
ORF3a	65	L65L	ctC	ctT	2	2	AY.107	0.000932
ORF3a	65	L65L	ctC	ctT	2	2	AY.108	0.002205
ORF3a	65	L65L	ctC	ctT	2	2	AY.110	0.000225
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.111	0.000366
ORF3a	65	L65L	ctC	ctA	2	2	AY.118	0.000125
ORF3a	65	L65I	Ctc	Atc	2	2	AY.120	0.000074
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.120.1	0.000642
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.121	0.000271
ORF3a	65	L65L	ctC	ctA	1	2	AY.121	0.000135
ORF3a	65	L65L	ctC	ctT	1	2	AY.121	0.000135
ORF3a	65	L65L	ctC	ctA	2	2	AY.19	0.002281
ORF3a	65	L65P	cTc	cCc	2	2	AY.20	0.000078
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.21	0.003795
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.26	0.000057
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.29.1	0.000441
ORF3a	65	L65V	Ctc	Gtc	2	2	AY.3	0.00002
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.3.1	0.000171
ORF3a	65	L65L	ctC	ctT	1	2	AY.34	0.000097
ORF3a	65	L65L	ctC	ctA	1	2	AY.34	0.000097
ORF3a	65	L65L	ctC	ctT	2	2	AY.34.1	0.00102
ORF3a	65	L65L	ctC	ctT	1	2	AY.35	0.000233
ORF3a	65	L65L	ctC	ctA	1	2	AY.35	0.000233
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.4.2	0.000043
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.4.2.1	0.000298
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.4.4	0.000818
ORF3a	65	L65del	CTC	---	2	2	AY.4.5	0.000215
ORF3a	65	L65V	Ctc	Gtc	2	2	AY.44	0.000012
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.45	0.000243
ORF3a	65	L65L	ctC	ctT	2	2	AY.46.6	0.000144
ORF3a	65	L65P	cTc	cCc	2	2	AY.46.6	0.000144
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.54	0.000191
ORF3a	65	L65L	ctC	ctT	2	2	AY.55	0.001835
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.57	0.001312
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.61	0.00021
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.62	0.000871
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.75	0.000112
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.75.1	0.000361
ORF3a	65	L65L	ctC	ctT	2	2	AY.9.1	0.000167
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.9.2	0.000073
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.92	0.000575
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.94	0.000885
ORF3a	65	L65F	Ctc	Ttc	2	2	AY.98.1	0.000097
ORF3a	65	L65F	Ctc	Ttc	2	2	B	0.000256
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.15	0.027027
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.170	0.002494
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.205	0.007435
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.225	0.014388
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.25	0.001137
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.277	0.001517
ORF3a	65	L65F	Ctc	Ttc	2	2	B.1.1.306	0.000877
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.312	0.003824
ORF3a	65	L65L	ctC	ctT	1	2	B.1.1.318	0.000302
ORF3a	65	L65L	ctC	ctA	1	2	B.1.1.318	0.000302
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.324	0.105263
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.348	0.001592
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.372	0.001377
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.416	0.00181
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.63	0.000772
ORF3a	65	L65L	ctC	ctT	2	2	B.1.1.70	0.000682
ORF3a	65	L65I	Ctc	Atc	2	2	B.1.177	0.000026
ORF3a	65	L65L	ctC	ctT	2	2	B.1.177.56	0.001335
ORF3a	65	L65P	cTc	cCc	2	2	B.1.2	0.000018
ORF3a	65	L65F	Ctc	Ttc	2	2	B.1.214.4	0.018182
ORF3a	65	L65L	ctC	ctT	2	2	B.1.243.1	0.044444
ORF3a	65	L65L	ctC	ctA	1	2	B.1.301	0.005917
ORF3a	65	L65L	ctC	ctT	1	2	B.1.301	0.005917
ORF3a	65	L65F	Ctc	Ttc	2	2	B.1.351.3	0.001753
ORF3a	65	L65I	Ctc	Atc	2	2	B.1.36.10	0.009569
ORF3a	65	L65L	ctC	ctT	2	2	B.1.36.22	0.002415
ORF3a	65	L65L	ctC	ctT	1	2	B.1.36.29	0.000517
ORF3a	65	L65L	ctC	ctA	1	2	B.1.36.29	0.000517
ORF3a	65	L65L	ctC	ctT	2	2	B.1.377	0.009132
ORF3a	65	L65P	cTc	cCc	2	2	B.1.427	0.000101
ORF3a	65	L65L	ctC	ctT	2	2	B.1.453	0.006472
ORF3a	65	L65L	ctC	ctT	2	2	B.1.470	0.002809
ORF3a	65	L65L	ctC	ctT	2	2	B.1.576	0.001813
ORF3a	65	L65L	ctC	ctT	2	2	B.1.621.1	0.001012
ORF3a	65	L65R	cTc	cGc	2	2	B.1.628	0.000705
ORF3a	65	L65I	Ctc	Atc	2	2	B.1.637	0.000146
ORF3a	65	L65L	ctC	ctT	2	2	B.12	0.012821
ORF3a	65	L65L	ctC	ctT	2	2	B.29	0.007018
ORF3a	65	L65L	ctC	ctT	2	2	B.3	0.001661
ORF3a	65	L65F	Ctc	Ttc	2	2	B.6	0.00182
ORF3a	65	L65L	ctC	ctT	2	2	B.6	0.00182
ORF3a	65	L65L	ctC	ctT	2	2	C.1.2	0.008511
ORF3a	65	L65L	ctC	ctT	2	2	C.23	0.011628
ORF3a	65	L65P	cTc	cCc	2	2	C.37	0.000232
ORF3a	65	L65L	ctC	ctT	2	2	L.3	0.007092
ORF3a	65	L65I	Ctc	Atc	2	2	P.1	0.000032
ORF3a	65	L65P	cTc	cCc	2	2	P.1.6	0.003891
ORF3a	65	L65F	Ctc	Ttc	2	2	P.2	0.000373
ORF3a	65	L65F	Ctc	Ttc	2	2	P.3	0.00319
ORF3a	65	L65L	ctC	ctT	2	2	P.6	0.006289
ORF3a	65	L65L	ctC	ctT	2	2	Q.3	0.00029
ORF3a	65	L65F	Ctc	Ttc	1	1	A	0.000387
ORF3a	65	L65L	ctC	ctT	1	1	A.1	0.000282
ORF3a	65	L65L	ctC	ctT	1	1	A.16	0.016129
ORF3a	65	L65L	ctC	ctT	1	1	A.2.4	0.003367
ORF3a	65	L65V	Ctc	Gtc	1	1	A.2.5.2	0.001572
ORF3a	65	L65L	ctC	ctT	1	1	A.28	0.002646
ORF3a	65	L65F	Ctc	Ttc	1	1	AA.5	0.016129
ORF3a	65	L65L	ctC	ctT	1	1	AD.2	0.000219
ORF3a	65	L65del2	cTC	c--	1	1	AD.2	0.000219
ORF3a	65	L65del	CTC	---	1	1	AH.3	0.003802
ORF3a	65	L65S	CTC	TCA	1	1	All	0
ORF3a	65	L65L	ctC	ctT	1	1	AY.101	0.00049
ORF3a	65	L65H	cTc	cAc	1	1	AY.102	0.000027
ORF3a	65	L65V	Ctc	Gtc	1	1	AY.103	0.000006
ORF3a	65	L65L	ctC	ctA	1	1	AY.105	0.000643
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.107	0.000466
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.110	0.000113
ORF3a	65	L65del	CTC	---	1	1	AY.111	0.000183
ORF3a	65	L65L	ctC	ctT	1	1	AY.114	0.000231
ORF3a	65	L65L	ctC	ctT	1	1	AY.116	0.000287
ORF3a	65	L65P	cTc	cCc	1	1	AY.116	0.000287
ORF3a	65	L65L	ctC	ctT	1	1	AY.116.1	0.000311
ORF3a	65	L65I	Ctc	Atc	1	1	AY.117	0.000085
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.118	0.000063
ORF3a	65	L65P	cTc	cCc	1	1	AY.119	0.000035
ORF3a	65	L65del	CTC	---	1	1	AY.120	0.000037
ORF3a	65	L65I	Ctc	Atc	1	1	AY.121	0.000135
ORF3a	65	L65I	Ctc	Atc	1	1	AY.13	0.000161
ORF3a	65	L65L	ctC	ctG	1	1	AY.14	0.000088
ORF3a	65	L65L	ctC	ctT	1	1	AY.16.1	0.00047
ORF3a	65	L65del	CTC	---	1	1	AY.23	0.00007
ORF3a	65	L65L	ctC	ctA	1	1	AY.23.1	0.000417
ORF3a	65	L65V	Ctc	Gtc	1	1	AY.26	0.000028
ORF3a	65	L65P	cTc	cCc	1	1	AY.28	0.00189
ORF3a	65	L65I	Ctc	Atc	1	1	AY.29	0.000016
ORF3a	65	L65P	cTc	cCc	1	1	AY.29	0.000016
ORF3a	65	L65L	ctC	ctT	1	1	AY.29.1	0.000221
ORF3a	65	L65L	ctC	ctA	1	1	AY.30	0.000396
ORF3a	65	L65P	cTc	cCc	1	1	AY.36	0.000148
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.36	0.000148
ORF3a	65	L65P	cTc	cCc	1	1	AY.39	0.000025
ORF3a	65	L65del	CTC	---	1	1	AY.39	0.000025
ORF3a	65	L65H	cTc	cAc	1	1	AY.39	0.000025
ORF3a	65	L65del1	ctC	ct-	1	1	AY.4	0.000002
ORF3a	65	L65H	cTc	cAc	1	1	AY.4	0.000002
ORF3a	65	L65P	cTc	cCc	1	1	AY.4.2	0.000022
ORF3a	65	L65del2	cTC	c--	1	1	AY.4.2	0.000022
ORF3a	65	L65L	ctC	ctT	1	1	AY.4.4	0.000409
ORF3a	65	L65L	ctC	ctT	1	1	AY.41	0.000294
ORF3a	65	L65P	cTc	cCc	1	1	AY.41	0.000294
ORF3a	65	L65Y	CTc	TAc	1	1	AY.43	0.000004
ORF3a	65	L65del1	Ctc	-tc	1	1	AY.44	0.000006
ORF3a	65	L65S	CTC	TCA	1	1	AY.44	0.000006
ORF3a	65	L65L	ctC	ctT	1	1	AY.46.1	0.001027
ORF3a	65	L65P	cTc	cCc	1	1	AY.46.2	0.000635
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.46.5	0.000198
ORF3a	65	L65L	ctC	ctT	1	1	AY.48	0.000465
ORF3a	65	L65P	cTc	cCc	1	1	AY.5	0.000021
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.5.3	0.000337
ORF3a	65	L65L	ctC	ctT	1	1	AY.5.4	0.000277
ORF3a	65	L65H	cTc	cAc	1	1	AY.5.4	0.000277
ORF3a	65	L65I	Ctc	Atc	1	1	AY.53	0.000288
ORF3a	65	L65P	cTc	cCc	1	1	AY.55	0.000917
ORF3a	65	L65L	ctC	ctT	1	1	AY.58	0.000907
ORF3a	65	L65I	Ctc	Atc	1	1	AY.61	0.000105
ORF3a	65	L65P	cTc	cCc	1	1	AY.62	0.000436
ORF3a	65	L65I	Ctc	Atc	1	1	AY.62	0.000436
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.64	0.000595
ORF3a	65	L65L	ctC	ctT	1	1	AY.64	0.000595
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.65	0.000533
ORF3a	65	L65L	ctC	ctT	1	1	AY.65	0.000533
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.67	0.000464
ORF3a	65	L65V	CtC	GtG	1	1	AY.67	0.000464
ORF3a	65	L65L	ctC	ctT	1	1	AY.68	0.000274
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.69	0.000187
ORF3a	65	L65P	cTc	cCc	1	1	AY.7.1	0.000113
ORF3a	65	L65L	ctC	ctT	1	1	AY.7.2	0.000559
ORF3a	65	L65P	cTc	cCc	1	1	AY.70	0.000209
ORF3a	65	L65L	ctC	ctT	1	1	AY.70	0.000209
ORF3a	65	L65L	ctC	ctT	1	1	AY.77	0.001127
ORF3a	65	L65P	cTc	cCc	1	1	AY.80	0.001129
ORF3a	65	L65L	ctC	ctT	1	1	AY.82	0.001357
ORF3a	65	L65L	ctC	ctT	1	1	AY.85	0.000427
ORF3a	65	L65del	CTC	---	1	1	AY.9	0.000068
ORF3a	65	L65V	Ctc	Gtc	1	1	AY.9.1	0.000084
ORF3a	65	L65V	Ctc	Gtc	1	1	AY.9.2	0.000037
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.93	0.000273
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.95	0.000761
ORF3a	65	L65F	Ctc	Ttc	1	1	AY.98	0.000079
ORF3a	65	L65P	cTc	cCc	1	1	AY.98.1	0.000048
ORF3a	65	L65V	CtC	GtG	1	1	AY.99	0.001049
ORF3a	65	L65I	Ctc	Atc	1	1	AY.99.1	0.001553
ORF3a	65	L65I	Ctc	Atc	1	1	AY.99.2	0.000092
ORF3a	65	L65K	CTC	AAA	1	1	B.1	0.000009
ORF3a	65	L65Q	cTC	cAA	1	1	B.1	0.000009
ORF3a	65	L65K	CTC	AAA	1	1	B.1.1	0.000018
ORF3a	65	L65V	Ctc	Gtc	1	1	B.1.1	0.000018
ORF3a	65	L65del	CTC	---	1	1	B.1.1	0.000018
ORF3a	65	L65Q	cTC	cAA	1	1	B.1.1	0.000018
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.1	0.000327
ORF3a	65	L65Q	cTC	cAA	1	1	B.1.1.139	0.022727
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.153	0.001095
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.161	0.003534
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.198	0.001468
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.207	0.001182
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.1.214	0.000055
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.1.220	0.001859
ORF3a	65	L65P	cTc	cCc	1	1	B.1.1.222	0.000204
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.231	0.003096
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.254	0.011236
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.261	0.008621
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.1.263	0.001558
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.269	0.001353
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.28	0.000311
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.284	0.000107
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.297	0.002237
ORF3a	65	L65P	cTc	cCc	1	1	B.1.1.306	0.000438
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.311	0.000358
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.316	0.000925
ORF3a	65	L65P	cTc	cCc	1	1	B.1.1.318	0.000302
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.318	0.000302
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.33	0.000421
ORF3a	65	L65P	cTc	cCc	1	1	B.1.1.34	0.013158
ORF3a	65	L65L	ctC	ctG	1	1	B.1.1.340	0.045455
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.345	0.043478
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.347	0.018182
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.369	0.000446
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.369	0.000446
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.389	0.006061
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.39	0.00051
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.396	0.045455
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.398	0.003226
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.4	0.002976
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.409	0.002833
ORF3a	65	L65del	CTC	---	1	1	B.1.1.409	0.002833
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.433	0.001425
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.434	0.000349
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.1.448	0.002033
ORF3a	65	L65L	ctC	ctA	1	1	B.1.1.448	0.002033
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.1.47	0.005348
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.50	0.000679
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.518	0.006329
ORF3a	65	L65P	cTc	cCc	1	1	B.1.1.519	0.00004
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.521	0.005348
ORF3a	65	L65L	ctC	ctA	1	1	B.1.1.526	0.003546
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.53	0.013699
ORF3a	65	L65L	ctC	ctT	1	1	B.1.1.57	0.011494
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.1.8	0.003584
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.127	0.002198
ORF3a	65	L65L	ctC	ctT	1	1	B.1.128	0.000635
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.13	0.002375
ORF3a	65	L65L	ctC	ctA	1	1	B.1.139	0.000733
ORF3a	65	L65L	ctC	ctT	1	1	B.1.140	0.018868
ORF3a	65	L65L	ctC	ctT	1	1	B.1.146	0.004237
ORF3a	65	L65P	cTc	cCc	1	1	B.1.160	0.000031
ORF3a	65	L65L	ctC	ctT	1	1	B.1.160.26	0.002421
ORF3a	65	L65del	CTC	---	1	1	B.1.160.7	0.002079
ORF3a	65	L65del	CTC	---	1	1	B.1.161	0.017241
ORF3a	65	L65Q	cTC	cAA	1	1	B.1.177	0.000013
ORF3a	65	L65R	cTc	cGc	1	1	B.1.177	0.000013
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.12	0.000152
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.177.12	0.000152
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.177.20	0.001517
ORF3a	65	L65L	ctC	ctA	1	1	B.1.177.21	0.000076
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.177.21	0.000076
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.23	0.003236
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.31	0.011494
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.177.4	0.000211
ORF3a	65	L65L	ctC	ctA	1	1	B.1.177.40	0.005155
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.41	0.0025
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.50	0.004695
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.54	0.000606
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.60	0.000218
ORF3a	65	L65P	cTc	cCc	1	1	B.1.177.69	0.001484
ORF3a	65	L65P	cTc	cCc	1	1	B.1.177.81	0.000189
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.177.87	0.000728
ORF3a	65	L65L	ctC	ctT	1	1	B.1.177.87	0.000728
ORF3a	65	L65L	ctC	ctT	1	1	B.1.189	0.004292
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.194	0.04
ORF3a	65	L65V	Ctc	Gtc	1	1	B.1.2	0.000009
ORF3a	65	L65del1	ctC	ct-	1	1	B.1.2	0.000009
ORF3a	65	L65L	ctC	ctT	1	1	B.1.206	0.000816
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.221	0.000071
ORF3a	65	L65L	ctC	ctT	1	1	B.1.232	0.000537
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.234	0.000132
ORF3a	65	L65V	Ctc	Gtc	1	1	B.1.234	0.000132
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.234	0.000132
ORF3a	65	L65V	Ctc	Gtc	1	1	B.1.240	0.000216
ORF3a	65	L65P	cTc	cCc	1	1	B.1.243	0.00007
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.258	0.000067
ORF3a	65	L65L	ctC	ctT	1	1	B.1.258.14	0.00098
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.258.22	0.002667
ORF3a	65	L65L	ctC	ctT	1	1	B.1.260	0.003344
ORF3a	65	L65L	ctC	ctT	1	1	B.1.311	0.000275
ORF3a	65	L65L	ctC	ctT	1	1	B.1.346	0.001311
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.351	0.00003
ORF3a	65	L65L	ctC	ctT	1	1	B.1.36.26	0.002857
ORF3a	65	L65P	cTc	cCc	1	1	B.1.36.29	0.000517
ORF3a	65	L65R	cTc	cGc	1	1	B.1.36.31	0.001751
ORF3a	65	L65L	ctC	ctT	1	1	B.1.36.36	0.000602
ORF3a	65	L65L	ctC	ctT	1	1	B.1.36.37	0.002778
ORF3a	65	L65P	cTc	cCc	1	1	B.1.36.8	0.001
ORF3a	65	L65L	ctC	ctT	1	1	B.1.36.8	0.001
ORF3a	65	L65L	ctC	ctT	1	1	B.1.36.9	0.003215
ORF3a	65	L65L	ctC	ctA	1	1	B.1.371	0.001122
ORF3a	65	L65L	ctC	ctT	1	1	B.1.396	0.000706
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.396	0.000706
ORF3a	65	L65L	ctC	ctT	1	1	B.1.400	0.000429
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.400	0.000429
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.409	0.000781
ORF3a	65	L65del	CTC	---	1	1	B.1.415	0.014286
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.426	0.001009
ORF3a	65	L65P	cTc	cCc	1	1	B.1.429	0.000024
ORF3a	65	L65del	CTC	---	1	1	B.1.429	0.000024
ORF3a	65	L65L	ctC	ctT	1	1	B.1.433	0.003195
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.438.1	0.000107
ORF3a	65	L65del	CTC	---	1	1	B.1.446	0.02
ORF3a	65	L65R	cTc	cGc	1	1	B.1.459	0.004082
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.465	0.003802
ORF3a	65	L65L	ctC	ctT	1	1	B.1.466	0.023256
ORF3a	65	L65L	ctC	ctT	1	1	B.1.466.2	0.000391
ORF3a	65	L65L	ctC	ctT	1	1	B.1.468	0.005714
ORF3a	65	L65P	cTc	cCc	1	1	B.1.470	0.001404
ORF3a	65	L65L	ctC	ctT	1	1	B.1.497	0.000315
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.497	0.000315
ORF3a	65	L65L	ctC	ctT	1	1	B.1.503	0.002488
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.525	0.000113
ORF3a	65	L65R	cTc	cGc	1	1	B.1.526	0.000024
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.526	0.000024
ORF3a	65	L65L	ctC	ctT	1	1	B.1.560	0.00463
ORF3a	65	L65del	CTC	---	1	1	B.1.561	0.000397
ORF3a	65	L65L	ctC	ctT	1	1	B.1.561	0.000397
ORF3a	65	L65R	cTc	cGc	1	1	B.1.564	0.000426
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.576	0.000907
ORF3a	65	L65L	ctC	ctT	1	1	B.1.581	0.009434
ORF3a	65	L65L	ctC	ctT	1	1	B.1.582	0.000491
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.595	0.000261
ORF3a	65	L65L	ctC	ctT	1	1	B.1.595.1	0.005848
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.596	0.000087
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.605	0.005952
ORF3a	65	L65L	ctC	ctT	1	1	B.1.606	0.006024
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.609	0.000479
ORF3a	65	L65P	cTc	cCc	1	1	B.1.617.1	0.000129
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.617.1	0.000129
ORF3a	65	L65L	ctC	ctT	1	1	B.1.620	0.000946
ORF3a	65	L65V	Ctc	Gtc	1	1	B.1.621	0.000089
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.621.1	0.000506
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.623	0.000536
ORF3a	65	L65L	ctC	ctT	1	1	B.1.625	0.002353
ORF3a	65	L65L	ctC	ctT	1	1	B.1.627	0.00202
ORF3a	65	L65I	Ctc	Atc	1	1	B.1.628	0.000352
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.630	0.005236
ORF3a	65	L65L	ctC	ctT	1	1	B.1.636	0.006711
ORF3a	65	L65R	cTc	cGc	1	1	B.1.637	0.000073
ORF3a	65	L65del	CTC	---	1	1	B.1.638	0.052632
ORF3a	65	L65L	ctC	ctT	1	1	B.1.78	0.008547
ORF3a	65	L65L	ctC	ctT	1	1	B.1.9.5	0.005682
ORF3a	65	L65F	Ctc	Ttc	1	1	B.1.93	0.000934
ORF3a	65	L65L	ctC	ctA	1	1	B.4	0.002208
ORF3a	65	L65del	CTC	---	1	1	B.40	0.000364
ORF3a	65	L65L	ctC	ctT	1	1	B.6.8	0.008264
ORF3a	65	L65L	ctC	ctT	1	1	C.36	0.000911
ORF3a	65	L65R	cTc	cGc	1	1	C.37	0.000116
ORF3a	65	L65F	Ctc	Ttc	1	1	D.2	0.000075
ORF3a	65	L65L	ctC	ctT	1	1	D.5	0.004975
ORF3a	65	L65L	ctC	ctT	1	1	N.6	0.007092
ORF3a	65	L65V	Ctc	Gtc	1	1	P.1	0.000016
ORF3a	65	L65F	Ctc	Ttc	1	1	P.1.1	0.000318
ORF3a	65	L65I	Ctc	Atc	1	1	P.1.1	0.000318
ORF3a	65	L65P	cTc	cCc	1	1	P.1.1	0.000318
ORF3a	65	L65F	Ctc	Ttc	1	1	P.1.12	0.000484
ORF3a	65	L65del	CTC	---	1	1	P.1.15	0.000232
ORF3a	65	L65I	Ctc	Atc	1	1	P.1.16	0.000374
ORF3a	65	L65L	ctC	ctT	1	1	P.3	0.001595
ORF3a	65	L65F	Ctc	Ttc	1	1	P.6	0.003145
ORF3a	65	L65I	Ctc	Atc	1	1	Q.4	0.000455
ORF3a	65	L65L	ctC	ctT	1	1	Q.6	0.006623
ORF3a	65	L65L	ctC	ctA	1	1	W.4	0.001351

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.