CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 180

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	180	S180P		nonsyn	Tct	Cct	5612	5609	0.999465	25930-25932
ORF3a	180	S180P		nonsyn	TcT	CcC	5612	3	0.000534569	25930-25932
ORF3a	180	S180F		nonsyn	tCt	tTt	1877	1875	0.998934	25930-25932
ORF3a	180	S180F		nonsyn	tCT	tTC	1877	2	0.00106553	25930-25932
ORF3a	180	S180Y		nonsyn	tCt	tAt	430	421	0.97907	25930-25932
ORF3a	180	S180Y		nonsyn	tCT	tAC	430	9	0.0209302	25930-25932
ORF3a	180	S180S		syn	tcT	tcC	237	134	0.565401	25930-25932
ORF3a	180	S180S		syn	tcT	tcA	237	61	0.257384	25930-25932
ORF3a	180	S180S		syn	tcT	tcG	237	42	0.177215	25930-25932
ORF3a	180	S180A		nonsyn	Tct	Gct	56	56	1	25930-25932
ORF3a	180	S180del		del	TCT	---	35	35	1	25930-25932
ORF3a	180	S180N		nonsyn	TCt	AAt	13	9	0.692308	25930-25932
ORF3a	180	S180N		nonsyn	TCT	AAC	13	4	0.307692	25930-25932
ORF3a	180	S180C		nonsyn	tCt	tGt	4	4	1	25930-25932
ORF3a	180	S180T		nonsyn	Tct	Act	3	3	1	25930-25932
ORF3a	180	S180del1		del	tcT	tc-	3	1	0.333333	25930-25932
ORF3a	180	S180del1		del	tCt	t-t	3	1	0.333333	25930-25932
ORF3a	180	S180del1		del	Tct	-ct	3	1	0.333333	25930-25932
ORF3a	180	S180E		nonsyn	TCT	GAA	1	1	1	25930-25932

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	180	S180P	Tct	Cct	5609	5612	All	0.001073
ORF3a	180	S180P	TcT	CcC	3	5612	All	0.000001
ORF3a	180	S180P	Tct	Cct	5369	5372	B.1.2	0.047276
ORF3a	180	S180P	TcT	CcC	3	5372	B.1.2	0.000026
ORF3a	180	S180F	tCt	tTt	1875	1877	All	0.000359
ORF3a	180	S180F	tCT	tTC	2	1877	All	0
ORF3a	180	S180F	tCt	tTt	1281	1281	AY.90	0.876797
ORF3a	180	S180Y	tCt	tAt	421	430	All	0.000081
ORF3a	180	S180Y	tCT	tAC	9	430	All	0.000002
ORF3a	180	S180S	tcT	tcC	134	237	All	0.000026
ORF3a	180	S180S	tcT	tcA	61	237	All	0.000012
ORF3a	180	S180S	tcT	tcG	42	237	All	0.000008
ORF3a	180	S180Y	tCt	tAt	175	175	B.1.1.7	0.000157
ORF3a	180	S180F	tCt	tTt	108	108	B.1.636	0.724832
ORF3a	180	S180F	tCt	tTt	80	80	B.1.1.7	0.000072
ORF3a	180	S180P	Tct	Cct	57	57	B.1.1.7	0.000051
ORF3a	180	S180A	Tct	Gct	56	56	All	0.000011
ORF3a	180	S180S	tcT	tcA	41	56	B.1.1.7	0.000037
ORF3a	180	S180S	tcT	tcC	10	56	B.1.1.7	0.000009
ORF3a	180	S180S	tcT	tcG	5	56	B.1.1.7	0.000004
ORF3a	180	S180Y	tCt	tAt	54	55	AY.43	0.000239
ORF3a	180	S180Y	tCT	tAC	1	55	AY.43	0.000004
ORF3a	180	S180Y	tCt	tAt	45	45	AY.44	0.000274
ORF3a	180	S180P	Tct	Cct	40	40	B.1.596	0.003486
ORF3a	180	S180F	tCt	tTt	39	39	B.1.617.2	0.000147
ORF3a	180	S180del	TCT	---	35	35	All	0.000007
ORF3a	180	S180F	tCt	tTt	35	35	AY.4	0.000054
ORF3a	180	S180A	Tct	Gct	34	34	B.1.177.58	0.045273
ORF3a	180	S180F	tCt	tTt	31	31	B.1.1.28	0.009648
ORF3a	180	S180Y	tCt	tAt	29	29	AY.26	0.000821
ORF3a	180	S180P	Tct	Cct	27	27	B.1	0.000247
ORF3a	180	S180S	tcT	tcG	21	24	B.1.429	0.000494
ORF3a	180	S180S	tcT	tcA	3	24	B.1.429	0.000071
ORF3a	180	S180P	Tct	Cct	19	19	AY.4	0.00003
ORF3a	180	S180F	tCt	tTt	18	18	P.1.2	0.020809
ORF3a	180	S180P	Tct	Cct	17	17	B.1.36.22	0.020531
ORF3a	180	S180F	tCt	tTt	15	15	AY.34.1	0.007649
ORF3a	180	S180F	tCt	tTt	14	14	AY.37	0.004425
ORF3a	180	S180F	tCt	tTt	14	14	B.1	0.000128
ORF3a	180	S180Y	tCt	tAt	14	14	B.1.2	0.000123
ORF3a	180	S180N	TCt	AAt	9	13	All	0.000002
ORF3a	180	S180N	TCT	AAC	4	13	All	0.000001
ORF3a	180	S180F	tCt	tTt	13	13	AY.25	0.000078
ORF3a	180	S180S	tcT	tcC	9	13	AY.4	0.000014
ORF3a	180	S180S	tcT	tcG	3	13	AY.4	0.000005
ORF3a	180	S180S	tcT	tcA	1	13	AY.4	0.000002
ORF3a	180	S180S	tcT	tcC	9	13	B.1.617.2	0.000034
ORF3a	180	S180S	tcT	tcA	3	13	B.1.617.2	0.000011
ORF3a	180	S180S	tcT	tcG	1	13	B.1.617.2	0.000004
ORF3a	180	S180F	tCt	tTt	12	12	AY.119	0.000424
ORF3a	180	S180S	tcT	tcC	12	12	AY.3	0.000119
ORF3a	180	S180F	tCt	tTt	12	12	B.1.1.306	0.005261
ORF3a	180	S180F	tCt	tTt	12	12	B.1.526	0.000282
ORF3a	180	S180F	tCt	tTt	10	11	AY.3	0.000099
ORF3a	180	S180F	tCT	tTC	1	11	AY.3	0.00001
ORF3a	180	S180S	tcT	tcC	11	11	AY.6	0.000452
ORF3a	180	S180P	Tct	Cct	11	11	B.1.617.2	0.000041
ORF3a	180	S180F	tCt	tTt	10	10	AY.103	0.000062
ORF3a	180	S180Y	tCt	tAt	8	10	B.1.617.2	0.00003
ORF3a	180	S180Y	tCT	tAC	2	10	B.1.617.2	0.000008
ORF3a	180	S180F	tCt	tTt	9	9	AY.20	0.00035
ORF3a	180	S180Y	tCt	tAt	9	9	AY.74	0.001041
ORF3a	180	S180F	tCt	tTt	9	9	B.1.1	0.000163
ORF3a	180	S180F	tCt	tTt	9	9	B.1.1.214	0.000499
ORF3a	180	S180F	tCt	tTt	9	9	B.1.2	0.000079
ORF3a	180	S180Y	tCt	tAt	8	8	AY.20	0.000311
ORF3a	180	S180Y	tCt	tAt	8	8	AY.4	0.000012
ORF3a	180	S180F	tCt	tTt	8	8	AY.43	0.000035
ORF3a	180	S180S	tcT	tcC	7	8	AY.44	0.000043
ORF3a	180	S180F	tCt	tTt	7	8	AY.44	0.000043
ORF3a	180	S180S	tcT	tcG	1	8	AY.44	0.000006
ORF3a	180	S180F	tCT	tTC	1	8	AY.44	0.000006
ORF3a	180	S180Y	tCt	tAt	8	8	B.1.1.519	0.000318
ORF3a	180	S180P	Tct	Cct	7	7	AY.98.1	0.000339
ORF3a	180	S180F	tCt	tTt	7	7	B.1.177	0.000092
ORF3a	180	S180Y	tCt	tAt	7	7	B.1.311	0.001922
ORF3a	180	S180F	tCt	tTt	7	7	B.1.429	0.000165
ORF3a	180	S180del	TCT	---	6	6	B.1.1.7	0.000005
ORF3a	180	S180S	tcT	tcC	6	6	B.1.36.18	0.002521
ORF3a	180	S180F	tCt	tTt	6	6	B.1.549	0.043165
ORF3a	180	S180P	Tct	Cct	6	6	B.1.575.1	0.014634
ORF3a	180	S180S	tcT	tcC	6	6	C.36.2	0.206897
ORF3a	180	S180Y	tCT	tAC	6	6	P.1	0.000095
ORF3a	180	S180F	tCt	tTt	6	6	P.2	0.00112
ORF3a	180	S180S	tcT	tcC	5	5	AY.39	0.000124
ORF3a	180	S180S	tcT	tcC	5	5	AY.43	0.000022
ORF3a	180	S180P	Tct	Cct	5	5	AY.47	0.000156
ORF3a	180	S180P	Tct	Cct	5	5	AY.9.2	0.000184
ORF3a	180	S180P	Tct	Cct	5	5	B.1.1	0.000091
ORF3a	180	S180S	tcT	tcC	5	5	B.1.1.157	0.004566
ORF3a	180	S180S	tcT	tcG	5	5	B.1.36	0.00073
ORF3a	180	S180P	Tct	Cct	5	5	D.2	0.000375
ORF3a	180	S180F	tCt	tTt	4	4	AD.2	0.000876
ORF3a	180	S180C	tCt	tGt	4	4	All	0.000001
ORF3a	180	S180S	tcT	tcC	4	4	AY.100	0.000184
ORF3a	180	S180Y	tCt	tAt	4	4	AY.100	0.000184
ORF3a	180	S180S	tcT	tcA	2	4	AY.25	0.000012
ORF3a	180	S180S	tcT	tcC	2	4	AY.25	0.000012
ORF3a	180	S180F	tCt	tTt	4	4	AY.26	0.000113
ORF3a	180	S180P	Tct	Cct	4	4	AY.33	0.000267
ORF3a	180	S180del	TCT	---	4	4	AY.43	0.000018
ORF3a	180	S180Y	tCt	tAt	4	4	AY.5	0.000083
ORF3a	180	S180Y	tCt	tAt	4	4	B.1	0.000037
ORF3a	180	S180F	tCt	tTt	4	4	B.1.1.50	0.002716
ORF3a	180	S180A	Tct	Gct	4	4	B.1.240	0.000862
ORF3a	180	S180S	tcT	tcC	3	4	D.2	0.000225
ORF3a	180	S180S	tcT	tcG	1	4	D.2	0.000075
ORF3a	180	S180F	tCt	tTt	4	4	P.1	0.000063
ORF3a	180	S180T	Tct	Act	3	3	All	0.000001
ORF3a	180	S180del1	Tct	-ct	1	3	All	0
ORF3a	180	S180del1	tCt	t-t	1	3	All	0
ORF3a	180	S180del1	tcT	tc-	1	3	All	0
ORF3a	180	S180S	tcT	tcC	2	3	AY.102	0.000053
ORF3a	180	S180S	tcT	tcA	1	3	AY.102	0.000027
ORF3a	180	S180Y	tCt	tAt	3	3	AY.103	0.000019
ORF3a	180	S180S	tcT	tcC	3	3	AY.103	0.000019
ORF3a	180	S180Y	tCt	tAt	3	3	AY.110	0.000338
ORF3a	180	S180Y	tCt	tAt	3	3	AY.23	0.000209
ORF3a	180	S180F	tCt	tTt	3	3	AY.54	0.000286
ORF3a	180	S180S	tcT	tcC	3	3	AY.61	0.000314
ORF3a	180	S180F	tCt	tTt	3	3	AY.75	0.000168
ORF3a	180	S180S	tcT	tcC	3	3	B.1	0.000027
ORF3a	180	S180F	tCt	tTt	3	3	B.1.1.525	0.016393
ORF3a	180	S180del	TCT	---	3	3	B.1.177	0.00004
ORF3a	180	S180S	tcT	tcC	2	3	B.1.2	0.000018
ORF3a	180	S180S	tcT	tcA	1	3	B.1.2	0.000009
ORF3a	180	S180S	tcT	tcA	3	3	B.1.218	0.015464
ORF3a	180	S180S	tcT	tcC	2	3	B.1.243	0.000139
ORF3a	180	S180S	tcT	tcA	1	3	B.1.243	0.00007
ORF3a	180	S180del	TCT	---	3	3	B.1.617.2	0.000011
ORF3a	180	S180S	tcT	tcC	3	3	C.36.3	0.001702
ORF3a	180	S180S	tcT	tcC	3	3	P.1.14	0.000143
ORF3a	180	S180del	TCT	---	2	2		0.111111
ORF3a	180	S180F	tCt	tTt	2	2	AU.3	0.004219
ORF3a	180	S180P	Tct	Cct	2	2	AY.103	0.000012
ORF3a	180	S180F	tCt	tTt	2	2	AY.118	0.000125
ORF3a	180	S180F	tCt	tTt	2	2	AY.121	0.000271
ORF3a	180	S180P	Tct	Cct	2	2	AY.14	0.000176
ORF3a	180	S180S	tcT	tcA	1	2	AY.20	0.000039
ORF3a	180	S180S	tcT	tcC	1	2	AY.20	0.000039
ORF3a	180	S180N	TCt	AAt	2	2	AY.26	0.000057
ORF3a	180	S180P	Tct	Cct	2	2	AY.3.1	0.000171
ORF3a	180	S180Y	tCt	tAt	2	2	AY.33	0.000134
ORF3a	180	S180Y	tCt	tAt	2	2	AY.37	0.000632
ORF3a	180	S180F	tCt	tTt	2	2	AY.4.2	0.000043
ORF3a	180	S180P	Tct	Cct	2	2	AY.44	0.000012
ORF3a	180	S180A	Tct	Gct	2	2	AY.47	0.000062
ORF3a	180	S180F	tCt	tTt	2	2	AY.5	0.000041
ORF3a	180	S180Y	tCt	tAt	2	2	AY.54	0.000191
ORF3a	180	S180F	tCt	tTt	2	2	AY.7	0.000392
ORF3a	180	S180S	tcT	tcC	2	2	AY.75.1	0.000361
ORF3a	180	S180del	TCT	---	2	2	B.1	0.000018
ORF3a	180	S180S	tcT	tcG	1	2	B.1.1.306	0.000438
ORF3a	180	S180S	tcT	tcC	1	2	B.1.1.306	0.000438
ORF3a	180	S180S	tcT	tcC	2	2	B.1.1.369	0.000892
ORF3a	180	S180F	tCt	tTt	2	2	B.1.1.434	0.000697
ORF3a	180	S180Y	tCt	tAt	2	2	B.1.1.70	0.000682
ORF3a	180	S180F	tCt	tTt	2	2	B.1.160	0.000062
ORF3a	180	S180F	tCt	tTt	2	2	B.1.177.81	0.000379
ORF3a	180	S180N	TCT	AAC	1	2	B.1.221	0.000071
ORF3a	180	S180N	TCt	AAt	1	2	B.1.221	0.000071
ORF3a	180	S180F	tCt	tTt	2	2	B.1.234	0.000264
ORF3a	180	S180F	tCt	tTt	2	2	B.1.258	0.000133
ORF3a	180	S180P	Tct	Cct	2	2	B.1.36.1	0.002281
ORF3a	180	S180S	tcT	tcG	2	2	B.1.36.10	0.009569
ORF3a	180	S180F	tCt	tTt	2	2	B.1.367	0.001585
ORF3a	180	S180P	Tct	Cct	2	2	B.1.406	0.012121
ORF3a	180	S180A	Tct	Gct	2	2	B.1.427	0.000101
ORF3a	180	S180N	TCt	AAt	2	2	B.1.429	0.000047
ORF3a	180	S180P	Tct	Cct	2	2	B.1.429	0.000047
ORF3a	180	S180F	tCt	tTt	2	2	B.1.538	0.016129
ORF3a	180	S180F	tCt	tTt	2	2	B.1.595	0.000522
ORF3a	180	S180F	tCt	tTt	2	2	B.1.621	0.000177
ORF3a	180	S180Y	tCt	tAt	2	2	B.3	0.001661
ORF3a	180	S180S	tcT	tcC	2	2	P.1.17.1	0.00175
ORF3a	180	S180F	tCt	tTt	2	2	P.4	0.007605
ORF3a	180	S180F	tCt	tTt	2	2	P.7	0.008734
ORF3a	180	S180Y	tCt	tAt	1	1	A.1	0.000282
ORF3a	180	S180S	tcT	tcC	1	1	A.5	0.001923
ORF3a	180	S180E	TCT	GAA	1	1	All	0
ORF3a	180	S180P	Tct	Cct	1	1	AY.100	0.000046
ORF3a	180	S180F	tCt	tTt	1	1	AY.100	0.000046
ORF3a	180	S180A	Tct	Gct	1	1	AY.102	0.000027
ORF3a	180	S180A	Tct	Gct	1	1	AY.103	0.000006
ORF3a	180	S180N	TCT	AAC	1	1	AY.103	0.000006
ORF3a	180	S180F	tCt	tTt	1	1	AY.116.1	0.000311
ORF3a	180	S180P	Tct	Cct	1	1	AY.117	0.000085
ORF3a	180	S180Y	tCt	tAt	1	1	AY.117	0.000085
ORF3a	180	S180Y	tCt	tAt	1	1	AY.12	0.000316
ORF3a	180	S180del	TCT	---	1	1	AY.120	0.000037
ORF3a	180	S180F	tCt	tTt	1	1	AY.120	0.000037
ORF3a	180	S180A	Tct	Gct	1	1	AY.120	0.000037
ORF3a	180	S180Y	tCt	tAt	1	1	AY.120	0.000037
ORF3a	180	S180A	Tct	Gct	1	1	AY.16	0.00038
ORF3a	180	S180P	Tct	Cct	1	1	AY.23	0.00007
ORF3a	180	S180Y	tCt	tAt	1	1	AY.25	0.000006
ORF3a	180	S180P	Tct	Cct	1	1	AY.25	0.000006
ORF3a	180	S180P	Tct	Cct	1	1	AY.27	0.000065
ORF3a	180	S180F	tCt	tTt	1	1	AY.28	0.00189
ORF3a	180	S180F	tCt	tTt	1	1	AY.29	0.000016
ORF3a	180	S180Y	tCt	tAt	1	1	AY.29	0.000016
ORF3a	180	S180S	tcT	tcG	1	1	AY.29	0.000016
ORF3a	180	S180Y	tCt	tAt	1	1	AY.3	0.00001
ORF3a	180	S180S	tcT	tcC	1	1	AY.33	0.000067
ORF3a	180	S180F	tCt	tTt	1	1	AY.39	0.000025
ORF3a	180	S180T	Tct	Act	1	1	AY.39	0.000025
ORF3a	180	S180P	Tct	Cct	1	1	AY.39	0.000025
ORF3a	180	S180A	Tct	Gct	1	1	AY.4	0.000002
ORF3a	180	S180C	tCt	tGt	1	1	AY.4.2.1	0.000149
ORF3a	180	S180del	TCT	---	1	1	AY.4.5	0.000107
ORF3a	180	S180N	TCt	AAt	1	1	AY.42	0.00004
ORF3a	180	S180S	tcT	tcA	1	1	AY.42	0.00004
ORF3a	180	S180C	tCt	tGt	1	1	AY.43	0.000004
ORF3a	180	S180P	Tct	Cct	1	1	AY.43	0.000004
ORF3a	180	S180A	Tct	Gct	1	1	AY.43	0.000004
ORF3a	180	S180C	tCt	tGt	1	1	AY.44	0.000006
ORF3a	180	S180A	Tct	Gct	1	1	AY.44	0.000006
ORF3a	180	S180P	Tct	Cct	1	1	AY.46	0.000104
ORF3a	180	S180F	tCt	tTt	1	1	AY.58	0.000907
ORF3a	180	S180F	tCt	tTt	1	1	AY.61	0.000105
ORF3a	180	S180F	tCt	tTt	1	1	AY.65	0.000533
ORF3a	180	S180F	tCt	tTt	1	1	AY.67	0.000464
ORF3a	180	S180del	TCT	---	1	1	AY.68	0.000274
ORF3a	180	S180del	TCT	---	1	1	AY.69	0.000187
ORF3a	180	S180F	tCt	tTt	1	1	AY.7.1	0.000113
ORF3a	180	S180del	TCT	---	1	1	AY.7.2	0.000559
ORF3a	180	S180S	tcT	tcC	1	1	AY.85	0.000427
ORF3a	180	S180del	TCT	---	1	1	AY.9	0.000068
ORF3a	180	S180F	tCt	tTt	1	1	AY.9.2	0.000037
ORF3a	180	S180Y	tCt	tAt	1	1	AY.9.2	0.000037
ORF3a	180	S180del	TCT	---	1	1	AY.98.1	0.000048
ORF3a	180	S180Y	tCt	tAt	1	1	B	0.000128
ORF3a	180	S180del	TCT	---	1	1	B	0.000128
ORF3a	180	S180N	TCT	AAC	1	1	B.1	0.000009
ORF3a	180	S180S	tcT	tcC	1	1	B.1.1	0.000018
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.1	0.000018
ORF3a	180	S180F	tCt	tTt	1	1	B.1.1.176	0.000439
ORF3a	180	S180P	Tct	Cct	1	1	B.1.1.286	0.002899
ORF3a	180	S180F	tCt	tTt	1	1	B.1.1.304	0.002809
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.1.311	0.000358
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.1.37	0.000193
ORF3a	180	S180N	TCt	AAt	1	1	B.1.1.397	0.002252
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.1.432	0.001266
ORF3a	180	S180S	tcT	tcC	1	1	B.1.1.519	0.00004
ORF3a	180	S180T	Tct	Act	1	1	B.1.1.7	0.000001
ORF3a	180	S180A	Tct	Gct	1	1	B.1.1.7	0.000001
ORF3a	180	S180del1	Tct	-ct	1	1	B.1.1.7	0.000001
ORF3a	180	S180N	TCt	AAt	1	1	B.1.1.7	0.000001
ORF3a	180	S180F	tCt	tTt	1	1	B.1.126	0.001276
ORF3a	180	S180P	Tct	Cct	1	1	B.1.157	0.002985
ORF3a	180	S180E	TCT	GAA	1	1	B.1.157	0.002985
ORF3a	180	S180del	TCT	---	1	1	B.1.160	0.000031
ORF3a	180	S180S	tcT	tcC	1	1	B.1.160	0.000031
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.177	0.000013
ORF3a	180	S180S	tcT	tcA	1	1	B.1.177	0.000013
ORF3a	180	S180F	tCt	tTt	1	1	B.1.177.15	0.000631
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.177.4	0.000211
ORF3a	180	S180del	TCT	---	1	1	B.1.177.51	0.004566
ORF3a	180	S180P	Tct	Cct	1	1	B.1.177.73	0.000566
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.177.8	0.000752
ORF3a	180	S180del	TCT	---	1	1	B.1.177.9	0.001332
ORF3a	180	S180F	tCt	tTt	1	1	B.1.189	0.004292
ORF3a	180	S180del1	tCt	t-t	1	1	B.1.2	0.000009
ORF3a	180	S180A	Tct	Gct	1	1	B.1.2	0.000009
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.218	0.005155
ORF3a	180	S180F	tCt	tTt	1	1	B.1.223	0.002778
ORF3a	180	S180F	tCt	tTt	1	1	B.1.240	0.000216
ORF3a	180	S180S	tcT	tcC	1	1	B.1.241	0.000812
ORF3a	180	S180P	Tct	Cct	1	1	B.1.243	0.00007
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.243	0.00007
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.301	0.005917
ORF3a	180	S180S	tcT	tcC	1	1	B.1.351	0.00003
ORF3a	180	S180F	tCt	tTt	1	1	B.1.351.3	0.000876
ORF3a	180	S180F	tCt	tTt	1	1	B.1.36	0.000146
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.36	0.000146
ORF3a	180	S180del	TCT	---	1	1	B.1.36.1	0.00114
ORF3a	180	S180P	Tct	Cct	1	1	B.1.367	0.000792
ORF3a	180	S180F	tCt	tTt	1	1	B.1.375	0.00082
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.396	0.000706
ORF3a	180	S180S	tcT	tcC	1	1	B.1.40	0.019608
ORF3a	180	S180F	tCt	tTt	1	1	B.1.400	0.000429
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.427	0.00005
ORF3a	180	S180del	TCT	---	1	1	B.1.427	0.00005
ORF3a	180	S180P	Tct	Cct	1	1	B.1.427	0.00005
ORF3a	180	S180F	tCt	tTt	1	1	B.1.427	0.00005
ORF3a	180	S180A	Tct	Gct	1	1	B.1.429	0.000024
ORF3a	180	S180F	tCt	tTt	1	1	B.1.459	0.004082
ORF3a	180	S180F	tCt	tTt	1	1	B.1.470	0.001404
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.497	0.000315
ORF3a	180	S180F	tCt	tTt	1	1	B.1.517	0.000427
ORF3a	180	S180Y	tCt	tAt	1	1	B.1.525	0.000113
ORF3a	180	S180F	tCt	tTt	1	1	B.1.525	0.000113
ORF3a	180	S180P	Tct	Cct	1	1	B.1.526	0.000024
ORF3a	180	S180F	tCt	tTt	1	1	B.1.540	0.009709
ORF3a	180	S180F	tCt	tTt	1	1	B.1.596	0.000087
ORF3a	180	S180del1	tcT	tc-	1	1	B.1.596	0.000087
ORF3a	180	S180F	tCt	tTt	1	1	B.1.609	0.000479
ORF3a	180	S180N	TCt	AAt	1	1	B.1.617.2	0.000004
ORF3a	180	S180T	Tct	Act	1	1	B.1.617.2	0.000004
ORF3a	180	S180A	Tct	Gct	1	1	B.1.637	0.000073
ORF3a	180	S180S	tcT	tcA	1	1	B.33	0.021277
ORF3a	180	S180S	tcT	tcC	1	1	B.39	0.002331
ORF3a	180	S180del	TCT	---	1	1	B.55	0.00295
ORF3a	180	S180F	tCt	tTt	1	1	B.6.6	0.000889
ORF3a	180	S180Y	tCt	tAt	1	1	C.37	0.000116
ORF3a	180	S180F	tCt	tTt	1	1	D.2	0.000075
ORF3a	180	S180C	tCt	tGt	1	1	D.2	0.000075
ORF3a	180	S180S	tcT	tcG	1	1	N.3	0.005814
ORF3a	180	S180N	TCT	AAC	1	1	P.1	0.000016
ORF3a	180	S180A	Tct	Gct	1	1	P.1	0.000016
ORF3a	180	S180P	Tct	Cct	1	1	P.1	0.000016
ORF3a	180	S180P	Tct	Cct	1	1	P.1.10	0.000269
ORF3a	180	S180F	tCt	tTt	1	1	P.1.12	0.000484
ORF3a	180	S180F	tCt	tTt	1	1	P.1.15	0.000232
ORF3a	180	S180S	tcT	tcA	1	1	P.1.15	0.000232
ORF3a	180	S180del	TCT	---	1	1	Q.1	0.000126
ORF3a	180	S180A	Tct	Gct	1	1	Q.4	0.000455
ORF3a	180	S180P	Tct	Cct	1	1	Q.8	0.000165
ORF3a	180	S180A	Tct	Gct	1	1	Q.8	0.000165
ORF3a	180	S180S	tcT	tcC	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.