CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 64

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	64	T64T		syn	acC	acT	7369	7104	0.964039	25582-25584
ORF3a	64	T64T		syn	acC	acA	7369	147	0.0199484	25582-25584
ORF3a	64	T64T		syn	acC	acG	7369	118	0.016013	25582-25584
ORF3a	64	T64I		nonsyn	aCc	aTc	4580	4579	0.999782	25582-25584
ORF3a	64	T64I		nonsyn	aCC	aTT	4580	1	0.000218341	25582-25584
ORF3a	64	T64N		nonsyn	aCc	aAc	192	192	1	25582-25584
ORF3a	64	T64A		nonsyn	Acc	Gcc	115	113	0.982609	25582-25584
ORF3a	64	T64A		nonsyn	AcC	GcT	115	2	0.0173913	25582-25584
ORF3a	64	T64S		nonsyn	Acc	Tcc	110	102	0.927273	25582-25584
ORF3a	64	T64S		nonsyn	aCc	aGc	110	5	0.0454545	25582-25584
ORF3a	64	T64S		nonsyn	AcC	TcA	110	2	0.0181818	25582-25584
ORF3a	64	T64S		nonsyn	AcC	TcT	110	1	0.00909091	25582-25584
ORF3a	64	T64del		del	ACC	---	53	53	1	25582-25584
ORF3a	64	T64P		nonsyn	Acc	Ccc	7	7	1	25582-25584
ORF3a	64	T64del1		del	aCc	a-c	5	3	0.6	25582-25584
ORF3a	64	T64del1		del	acC	ac-	5	2	0.4	25582-25584
ORF3a	64	T64F		nonsyn	ACc	TTc	3	2	0.666667	25582-25584
ORF3a	64	T64F		nonsyn	ACC	TTT	3	1	0.333333	25582-25584
ORF3a	64	T64M		nonsyn	aCC	aTG	2	2	1	25582-25584
ORF3a	64	T64C		nonsyn	ACc	TGc	2	2	1	25582-25584
ORF3a	64	T64R		nonsyn	aCC	aGA	2	2	1	25582-25584
ORF3a	64	T64X		nonsyn	ACC	TGA	2	2	1	25582-25584
ORF3a	64	T64D		nonsyn	ACC	GAT	2	2	1	25582-25584
ORF3a	64	T64H		nonsyn	ACc	CAc	1	1	1	25582-25584
ORF3a	64	T64del2		del	ACC	--G	1	1	1	25582-25584

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	64	T64T	acC	acT	7104	7369	All	0.001359
ORF3a	64	T64T	acC	acA	147	7369	All	0.000028
ORF3a	64	T64T	acC	acG	118	7369	All	0.000023
ORF3a	64	T64I	aCc	aTc	4579	4580	All	0.000876
ORF3a	64	T64I	aCC	aTT	1	4580	All	0
ORF3a	64	T64T	acC	acT	2711	2711	AY.33	0.181035
ORF3a	64	T64T	acC	acT	1108	1152	B.1.1.7	0.000992
ORF3a	64	T64T	acC	acG	32	1152	B.1.1.7	0.000029
ORF3a	64	T64T	acC	acA	12	1152	B.1.1.7	0.000011
ORF3a	64	T64I	aCc	aTc	833	833	AY.4	0.001297
ORF3a	64	T64I	aCc	aTc	750	750	B.1.177.58	0.998668
ORF3a	64	T64T	acC	acT	668	676	B.1.1.519	0.026527
ORF3a	64	T64T	acC	acG	8	676	B.1.1.519	0.000318
ORF3a	64	T64I	aCc	aTc	634	634	B.1.1.7	0.000568
ORF3a	64	T64T	acC	acT	451	451	AY.26	0.012768
ORF3a	64	T64I	aCc	aTc	405	405	B.1.617.2	0.001525
ORF3a	64	T64T	acC	acT	403	403	B.1.258.17	0.041901
ORF3a	64	T64I	aCc	aTc	378	378	AY.43	0.001675
ORF3a	64	T64I	aCc	aTc	234	234	AY.102	0.006204
ORF3a	64	T64I	aCc	aTc	216	216	AY.3	0.002148
ORF3a	64	T64N	aCc	aAc	192	192	All	0.000037
ORF3a	64	T64T	acC	acT	181	185	B.1.617.2	0.000682
ORF3a	64	T64T	acC	acA	4	185	B.1.617.2	0.000015
ORF3a	64	T64I	aCc	aTc	172	172	B.1.626	0.982857
ORF3a	64	T64T	acC	acT	141	158	AY.4	0.000219
ORF3a	64	T64T	acC	acG	10	158	AY.4	0.000016
ORF3a	64	T64T	acC	acA	7	158	AY.4	0.000011
ORF3a	64	T64T	acC	acT	144	148	AY.25	0.000866
ORF3a	64	T64T	acC	acG	2	148	AY.25	0.000012
ORF3a	64	T64T	acC	acA	2	148	AY.25	0.000012
ORF3a	64	T64N	aCc	aAc	131	131	B.1.429	0.003082
ORF3a	64	T64A	Acc	Gcc	113	115	All	0.000022
ORF3a	64	T64A	AcC	GcT	2	115	All	0
ORF3a	64	T64T	acC	acT	112	112	B.1.595	0.029228
ORF3a	64	T64S	Acc	Tcc	102	110	All	0.00002
ORF3a	64	T64S	aCc	aGc	5	110	All	0.000001
ORF3a	64	T64S	AcC	TcA	2	110	All	0
ORF3a	64	T64S	AcC	TcT	1	110	All	0
ORF3a	64	T64T	acC	acT	53	108	AY.3	0.000527
ORF3a	64	T64T	acC	acA	53	108	AY.3	0.000527
ORF3a	64	T64T	acC	acG	2	108	AY.3	0.00002
ORF3a	64	T64T	acC	acT	98	98	AY.100	0.004509
ORF3a	64	T64T	acC	acT	88	90	B.1.2	0.000775
ORF3a	64	T64T	acC	acG	1	90	B.1.2	0.000009
ORF3a	64	T64T	acC	acA	1	90	B.1.2	0.000009
ORF3a	64	T64S	Acc	Tcc	88	89	AY.3	0.000875
ORF3a	64	T64S	aCc	aGc	1	89	AY.3	0.00001
ORF3a	64	T64T	acC	acT	68	86	AY.103	0.000422
ORF3a	64	T64T	acC	acA	17	86	AY.103	0.000106
ORF3a	64	T64T	acC	acG	1	86	AY.103	0.000006
ORF3a	64	T64T	acC	acT	78	81	AY.43	0.000346
ORF3a	64	T64T	acC	acG	3	81	AY.43	0.000013
ORF3a	64	T64T	acC	acT	53	76	AY.44	0.000323
ORF3a	64	T64T	acC	acA	23	76	AY.44	0.00014
ORF3a	64	T64I	aCc	aTc	74	74	B.1	0.000678
ORF3a	64	T64I	aCc	aTc	66	66	B.1.36.35	0.171875
ORF3a	64	T64I	aCc	aTc	64	64	AY.47	0.001991
ORF3a	64	T64I	aCc	aTc	61	61	AY.39	0.001507
ORF3a	64	T64T	acC	acG	54	61	P.2	0.010078
ORF3a	64	T64T	acC	acT	7	61	P.2	0.001306
ORF3a	64	T64T	acC	acT	56	56	B.1.526	0.001316
ORF3a	64	T64del	ACC	---	53	53	All	0.00001
ORF3a	64	T64I	aCc	aTc	50	50	AY.103	0.00031
ORF3a	64	T64T	acC	acT	45	45	B.1.305	0.096774
ORF3a	64	T64I	aCc	aTc	44	44	B.1.2	0.000387
ORF3a	64	T64A	Acc	Gcc	42	42	B.1.617.2	0.000158
ORF3a	64	T64I	aCc	aTc	40	40	AY.44	0.000243
ORF3a	64	T64I	aCc	aTc	35	35	AY.5	0.000723
ORF3a	64	T64T	acC	acT	33	34	B.1	0.000302
ORF3a	64	T64T	acC	acA	1	34	B.1	0.000009
ORF3a	64	T64T	acC	acT	33	34	B.1.1	0.000599
ORF3a	64	T64T	acC	acA	1	34	B.1.1	0.000018
ORF3a	64	T64I	aCc	aTc	30	30	AY.20	0.001166
ORF3a	64	T64I	aCc	aTc	27	27	B.1.177	0.000356
ORF3a	64	T64I	aCc	aTc	26	26	AY.25	0.000156
ORF3a	64	T64A	Acc	Gcc	24	24	P.1	0.000378
ORF3a	64	T64T	acC	acT	22	23	P.1	0.000347
ORF3a	64	T64T	acC	acG	1	23	P.1	0.000016
ORF3a	64	T64I	aCc	aTc	19	19	AY.34.1	0.009689
ORF3a	64	T64I	aCc	aTc	19	19	B.1.177.21	0.001453
ORF3a	64	T64I	aCc	aTc	17	17	AY.26	0.000481
ORF3a	64	T64N	aCc	aAc	17	17	AY.3	0.000169
ORF3a	64	T64T	acC	acT	17	17	AY.37	0.005373
ORF3a	64	T64T	acC	acT	17	17	B.1.221	0.001208
ORF3a	64	T64I	aCc	aTc	17	17	B.1.509	0.014719
ORF3a	64	T64I	aCc	aTc	15	15	AY.33	0.001002
ORF3a	64	T64T	acC	acT	14	14	AY.102	0.000371
ORF3a	64	T64T	acC	acT	14	14	AY.39	0.000346
ORF3a	64	T64I	aCc	aTc	14	14	B.1.234	0.001847
ORF3a	64	T64T	acC	acT	14	14	Q.4	0.006367
ORF3a	64	T64T	acC	acT	13	13	AE.8	0.006357
ORF3a	64	T64T	acC	acA	13	13	B.1.470	0.018258
ORF3a	64	T64T	acC	acT	12	12	AY.45	0.00146
ORF3a	64	T64T	acC	acT	12	12	B.1.351	0.000357
ORF3a	64	T64T	acC	acT	11	11	AW.1	0.033537
ORF3a	64	T64I	aCc	aTc	11	11	AY.100	0.000506
ORF3a	64	T64I	aCc	aTc	11	11	AY.120	0.000409
ORF3a	64	T64T	acC	acT	11	11	AY.36	0.00163
ORF3a	64	T64T	acC	acT	10	11	AY.85	0.004272
ORF3a	64	T64T	acC	acG	1	11	AY.85	0.000427
ORF3a	64	T64del	ACC	---	11	11	B.1.1.7	0.00001
ORF3a	64	T64T	acC	acT	11	11	B.1.160	0.000343
ORF3a	64	T64I	aCc	aTc	11	11	P.1	0.000173
ORF3a	64	T64I	aCc	aTc	10	10	AY.29	0.000158
ORF3a	64	T64T	acC	acT	10	10	AY.98	0.00079
ORF3a	64	T64A	Acc	Gcc	10	10	B.1.1.7	0.000009
ORF3a	64	T64T	acC	acT	10	10	P.1.14	0.000478
ORF3a	64	T64I	aCc	aTc	9	9	AY.117	0.000761
ORF3a	64	T64I	aCc	aTc	9	9	AY.23	0.000628
ORF3a	64	T64I	aCc	aTc	9	9	AY.36	0.001334
ORF3a	64	T64I	aCc	aTc	9	9	AY.46	0.000937
ORF3a	64	T64I	aCc	aTc	9	9	AY.98.1	0.000436
ORF3a	64	T64T	acC	acT	8	9	B.1.243	0.000557
ORF3a	64	T64T	acC	acA	1	9	B.1.243	0.00007
ORF3a	64	T64T	acC	acT	9	9	B.1.400	0.003861
ORF3a	64	T64T	acC	acT	9	9	B.1.617.1	0.001161
ORF3a	64	T64T	acC	acT	4	8		0.222222
ORF3a	64	T64S	Acc	Tcc	3	8		0.166667
ORF3a	64	T64S	aCc	aGc	2	8		0.111111
ORF3a	64	T64T	acC	acG	2	8		0.111111
ORF3a	64	T64S	AcC	TcA	2	8		0.111111
ORF3a	64	T64T	acC	acA	2	8		0.111111
ORF3a	64	T64S	AcC	TcT	1	8		0.055556
ORF3a	64	T64T	acC	acT	7	8	AY.4.2	0.000152
ORF3a	64	T64T	acC	acA	1	8	AY.4.2	0.000022
ORF3a	64	T64I	aCc	aTc	8	8	AY.42	0.000322
ORF3a	64	T64T	acC	acT	6	8	AY.9.2	0.00022
ORF3a	64	T64T	acC	acA	2	8	AY.9.2	0.000073
ORF3a	64	T64T	acC	acT	8	8	AY.9.2.1	0.01581
ORF3a	64	T64I	aCc	aTc	8	8	AY.91	0.005844
ORF3a	64	T64I	aCc	aTc	8	8	B.1.1	0.000145
ORF3a	64	T64P	Acc	Ccc	7	7	All	0.000001
ORF3a	64	T64T	acC	acT	7	7	AY.9.1	0.000586
ORF3a	64	T64T	acC	acT	7	7	AZ.2.1	0.056911
ORF3a	64	T64T	acC	acT	7	7	B.1.177	0.000092
ORF3a	64	T64T	acC	acT	7	7	B.1.258	0.000466
ORF3a	64	T64I	aCc	aTc	7	7	B.1.351	0.000208
ORF3a	64	T64I	aCc	aTc	7	7	B.1.526	0.000165
ORF3a	64	T64T	acC	acT	7	7	B.1.621	0.00062
ORF3a	64	T64I	aCc	aTc	6	6	AY.45	0.00073
ORF3a	64	T64T	acC	acT	6	6	AY.47	0.000187
ORF3a	64	T64T	acC	acT	6	6	AY.61	0.000629
ORF3a	64	T64I	aCc	aTc	6	6	AY.93	0.001638
ORF3a	64	T64A	Acc	Gcc	6	6	AY.98	0.000474
ORF3a	64	T64I	aCc	aTc	6	6	B.1.1.318	0.001811
ORF3a	64	T64T	acC	acT	6	6	B.1.1.318	0.001811
ORF3a	64	T64N	aCc	aAc	6	6	B.1.177	0.000079
ORF3a	64	T64I	aCc	aTc	6	6	B.1.639	0.130435
ORF3a	64	T64del1	aCc	a-c	3	5	All	0.000001
ORF3a	64	T64del1	acC	ac-	2	5	All	0
ORF3a	64	T64I	aCc	aTc	5	5	AY.118	0.000313
ORF3a	64	T64I	aCc	aTc	5	5	AY.119	0.000177
ORF3a	64	T64T	acC	acT	5	5	AY.29	0.000079
ORF3a	64	T64T	acC	acT	5	5	AY.3.1	0.000426
ORF3a	64	T64T	acC	acT	5	5	AY.4.5	0.000537
ORF3a	64	T64T	acC	acT	5	5	AY.6	0.000206
ORF3a	64	T64I	aCc	aTc	5	5	AY.92	0.001436
ORF3a	64	T64T	acC	acT	5	5	AY.95	0.003805
ORF3a	64	T64I	aCc	aTc	5	5	AY.98	0.000395
ORF3a	64	T64T	acC	acT	5	5	B.1.1.135	0.023474
ORF3a	64	T64T	acC	acT	4	5	B.1.1.28	0.001245
ORF3a	64	T64T	acC	acG	1	5	B.1.1.28	0.000311
ORF3a	64	T64T	acC	acT	5	5	B.1.1.434	0.001743
ORF3a	64	T64T	acC	acT	5	5	B.1.1.63	0.001929
ORF3a	64	T64del	ACC	---	5	5	B.1.177	0.000066
ORF3a	64	T64I	aCc	aTc	5	5	B.1.427	0.000252
ORF3a	64	T64T	acC	acT	5	5	B.1.429	0.000118
ORF3a	64	T64I	aCc	aTc	5	5	B.1.575	0.001517
ORF3a	64	T64I	aCc	aTc	5	5	B.1.634	0.017123
ORF3a	64	T64T	acC	acT	5	5	P.5	0.068493
ORF3a	64	T64I	aCc	aTc	3	4		0.166667
ORF3a	64	T64A	Acc	Gcc	2	4		0.111111
ORF3a	64	T64A	AcC	GcT	2	4		0.111111
ORF3a	64	T64I	aCC	aTT	1	4		0.055556
ORF3a	64	T64T	acC	acT	4	4	AY.121	0.000541
ORF3a	64	T64T	acC	acT	4	4	AY.16.1	0.00188
ORF3a	64	T64T	acC	acT	3	4	AY.20	0.000117
ORF3a	64	T64T	acC	acA	1	4	AY.20	0.000039
ORF3a	64	T64T	acC	acT	4	4	AY.35	0.000932
ORF3a	64	T64T	acC	acT	4	4	AY.39.1.1	0.002899
ORF3a	64	T64del	ACC	---	4	4	AY.4	0.000006
ORF3a	64	T64I	aCc	aTc	4	4	AY.61	0.000419
ORF3a	64	T64T	acC	acT	4	4	AY.75.1	0.000721
ORF3a	64	T64I	aCc	aTc	4	4	AY.84	0.00175
ORF3a	64	T64T	acC	acA	2	4	AY.99.2	0.000184
ORF3a	64	T64T	acC	acT	2	4	AY.99.2	0.000184
ORF3a	64	T64T	acC	acT	4	4	B	0.000511
ORF3a	64	T64N	aCc	aAc	4	4	B.1	0.000037
ORF3a	64	T64T	acC	acT	4	4	B.1.1.214	0.000222
ORF3a	64	T64I	aCc	aTc	4	4	B.1.177.81	0.000757
ORF3a	64	T64A	Acc	Gcc	4	4	B.1.2	0.000035
ORF3a	64	T64I	aCc	aTc	4	4	B.1.596	0.000349
ORF3a	64	T64I	aCc	aTc	4	4	P.1.10	0.001078
ORF3a	64	T64I	aCc	aTc	4	4	P.1.14	0.000191
ORF3a	64	T64T	acC	acT	3	3	A.23.1	0.002113
ORF3a	64	T64F	ACc	TTc	2	3	All	0
ORF3a	64	T64F	ACC	TTT	1	3	All	0
ORF3a	64	T64T	acC	acT	3	3	AU.1	0.003797
ORF3a	64	T64I	aCc	aTc	3	3	AY.1	0.001187
ORF3a	64	T64I	aCc	aTc	3	3	AY.10	0.00159
ORF3a	64	T64T	acC	acT	3	3	AY.106	0.001005
ORF3a	64	T64I	aCc	aTc	3	3	AY.110	0.000338
ORF3a	64	T64N	aCc	aAc	3	3	AY.117	0.000254
ORF3a	64	T64T	acC	acT	3	3	AY.23	0.000209
ORF3a	64	T64del	ACC	---	3	3	AY.25	0.000018
ORF3a	64	T64A	Acc	Gcc	3	3	AY.3	0.00003
ORF3a	64	T64I	aCc	aTc	3	3	AY.34	0.000291
ORF3a	64	T64I	aCc	aTc	3	3	AY.35	0.000699
ORF3a	64	T64S	Acc	Tcc	3	3	AY.4	0.000005
ORF3a	64	T64T	acC	acT	3	3	AY.4.2.1	0.000447
ORF3a	64	T64T	acC	acT	3	3	AY.46.4	0.000494
ORF3a	64	T64T	acC	acT	3	3	AY.46.5	0.000595
ORF3a	64	T64I	aCc	aTc	3	3	AY.5.4	0.00083
ORF3a	64	T64I	aCc	aTc	3	3	AY.7.1	0.000338
ORF3a	64	T64I	aCc	aTc	3	3	AY.75	0.000168
ORF3a	64	T64I	aCc	aTc	3	3	AY.9.2	0.00011
ORF3a	64	T64T	acC	acT	3	3	B.1.1.1	0.00098
ORF3a	64	T64T	acC	acT	3	3	B.1.1.128	0.021277
ORF3a	64	T64T	acC	acT	3	3	B.1.1.397	0.006757
ORF3a	64	T64T	acC	acT	3	3	B.1.1.398	0.009677
ORF3a	64	T64I	aCc	aTc	3	3	B.1.1.519	0.000119
ORF3a	64	T64N	aCc	aAc	3	3	B.1.1.7	0.000003
ORF3a	64	T64I	aCc	aTc	3	3	B.1.146	0.012712
ORF3a	64	T64N	aCc	aAc	3	3	B.1.160	0.000094
ORF3a	64	T64I	aCc	aTc	3	3	B.1.221	0.000213
ORF3a	64	T64T	acC	acT	3	3	B.1.239	0.003663
ORF3a	64	T64N	aCc	aAc	3	3	B.1.243	0.000209
ORF3a	64	T64I	aCc	aTc	3	3	B.1.429	0.000071
ORF3a	64	T64I	aCc	aTc	3	3	B.1.466.2	0.001174
ORF3a	64	T64I	aCc	aTc	3	3	B.1.595	0.000783
ORF3a	64	T64del	ACC	---	3	3	B.1.617.2	0.000011
ORF3a	64	T64T	acC	acT	3	3	C.16	0.003181
ORF3a	64	T64T	acC	acT	3	3	C.37	0.000348
ORF3a	64	T64I	aCc	aTc	3	3	C.37	0.000348
ORF3a	64	T64T	acC	acT	3	3	Q.8	0.000495
ORF3a	64	T64del	ACC	---	3	3	U.3	0.011583
ORF3a	64	T64C	ACc	TGc	2	2		0.111111
ORF3a	64	T64X	ACC	TGA	2	2		0.111111
ORF3a	64	T64R	aCC	aGA	2	2		0.111111
ORF3a	64	T64M	aCC	aTG	2	2		0.111111
ORF3a	64	T64F	ACC	TTT	1	2		0.055556
ORF3a	64	T64F	ACc	TTc	1	2		0.055556
ORF3a	64	T64C	ACc	TGc	2	2	All	0
ORF3a	64	T64M	aCC	aTG	2	2	All	0
ORF3a	64	T64D	ACC	GAT	2	2	All	0
ORF3a	64	T64R	aCC	aGA	2	2	All	0
ORF3a	64	T64X	ACC	TGA	2	2	All	0
ORF3a	64	T64T	acC	acT	2	2	AY.1	0.000791
ORF3a	64	T64A	Acc	Gcc	2	2	AY.103	0.000012
ORF3a	64	T64I	aCc	aTc	2	2	AY.113	0.000285
ORF3a	64	T64I	aCc	aTc	2	2	AY.116	0.000574
ORF3a	64	T64N	aCc	aAc	2	2	AY.120	0.000074
ORF3a	64	T64I	aCc	aTc	2	2	AY.24	0.000862
ORF3a	64	T64del1	acC	ac-	2	2	AY.25	0.000012
ORF3a	64	T64I	aCc	aTc	2	2	AY.28	0.003781
ORF3a	64	T64A	Acc	Gcc	2	2	AY.37	0.000632
ORF3a	64	T64I	aCc	aTc	2	2	AY.4.5	0.000215
ORF3a	64	T64del	ACC	---	2	2	AY.4.5	0.000215
ORF3a	64	T64del	ACC	---	2	2	AY.43	0.000009
ORF3a	64	T64A	Acc	Gcc	2	2	AY.43	0.000009
ORF3a	64	T64T	acC	acT	2	2	AY.46	0.000208
ORF3a	64	T64I	aCc	aTc	2	2	AY.46.1	0.002053
ORF3a	64	T64T	acC	acT	2	2	AY.46.2	0.001271
ORF3a	64	T64T	acC	acT	2	2	AY.46.6	0.000144
ORF3a	64	T64T	acC	acT	2	2	AY.5	0.000041
ORF3a	64	T64T	acC	acT	2	2	AY.5.3	0.000675
ORF3a	64	T64T	acC	acT	2	2	AY.54	0.000191
ORF3a	64	T64T	acC	acT	2	2	AY.65	0.001066
ORF3a	64	T64T	acC	acT	2	2	AY.69	0.000373
ORF3a	64	T64T	acC	acT	2	2	AY.70	0.000417
ORF3a	64	T64T	acC	acT	2	2	AY.71	0.00095
ORF3a	64	T64I	aCc	aTc	2	2	AY.75.1	0.000361
ORF3a	64	T64I	aCc	aTc	2	2	AY.9.1	0.000167
ORF3a	64	T64T	acC	acT	2	2	AY.93	0.000546
ORF3a	64	T64N	aCc	aAc	2	2	AY.98	0.000158
ORF3a	64	T64del	ACC	---	2	2	B.1	0.000018
ORF3a	64	T64S	aCc	aGc	1	2	B.1	0.000009
ORF3a	64	T64S	Acc	Tcc	1	2	B.1	0.000009
ORF3a	64	T64A	Acc	Gcc	2	2	B.1.1	0.000036
ORF3a	64	T64N	aCc	aAc	2	2	B.1.1	0.000036
ORF3a	64	T64T	acC	acT	2	2	B.1.1.216	0.001781
ORF3a	64	T64T	acC	acT	2	2	B.1.1.294	0.002532
ORF3a	64	T64I	aCc	aTc	2	2	B.1.160	0.000062
ORF3a	64	T64T	acC	acT	2	2	B.1.160.16	0.001859
ORF3a	64	T64A	Acc	Gcc	2	2	B.1.177	0.000026
ORF3a	64	T64T	acC	acT	2	2	B.1.177.4	0.000422
ORF3a	64	T64A	Acc	Gcc	2	2	B.1.177.5	0.002484
ORF3a	64	T64T	acC	acT	2	2	B.1.177.81	0.000379
ORF3a	64	T64S	Acc	Tcc	2	2	B.1.2	0.000018
ORF3a	64	T64N	aCc	aAc	2	2	B.1.2	0.000018
ORF3a	64	T64A	Acc	Gcc	2	2	B.1.351	0.000059
ORF3a	64	T64T	acC	acT	2	2	B.1.36	0.000292
ORF3a	64	T64T	acC	acT	2	2	B.1.399	0.003868
ORF3a	64	T64T	acC	acT	2	2	B.1.509	0.001732
ORF3a	64	T64T	acC	acT	2	2	B.1.549	0.014388
ORF3a	64	T64T	acC	acT	2	2	B.1.560	0.009259
ORF3a	64	T64N	aCc	aAc	2	2	B.1.567	0.006667
ORF3a	64	T64T	acC	acT	2	2	B.1.596	0.000174
ORF3a	64	T64I	aCc	aTc	2	2	B.1.617.1	0.000258
ORF3a	64	T64I	aCc	aTc	2	2	B.1.621	0.000177
ORF3a	64	T64T	acC	acT	2	2	B.1.637	0.000146
ORF3a	64	T64T	acC	acT	2	2	C.9	0.060606
ORF3a	64	T64I	aCc	aTc	2	2	D.2	0.00015
ORF3a	64	T64T	acC	acT	2	2	D.2	0.00015
ORF3a	64	T64T	acC	acT	2	2	P.1.17	0.000324
ORF3a	64	T64I	aCc	aTc	2	2	P.1.17.1	0.00175
ORF3a	64	T64T	acC	acT	2	2	Q.3	0.00029
ORF3a	64	T64I	aCc	aTc	2	2	Q.8	0.00033
ORF3a	64	T64N	aCc	aAc	1	1		0.055556
ORF3a	64	T64H	ACc	CAc	1	1		0.055556
ORF3a	64	T64P	Acc	Ccc	1	1		0.055556
ORF3a	64	T64I	aCc	aTc	1	1	A.1	0.000282
ORF3a	64	T64T	acC	acT	1	1	A.2	0.000662
ORF3a	64	T64T	acC	acT	1	1	A.28	0.002646
ORF3a	64	T64del	ACC	---	1	1	AH.3	0.003802
ORF3a	64	T64H	ACc	CAc	1	1	All	0
ORF3a	64	T64del2	ACC	--G	1	1	All	0
ORF3a	64	T64T	acC	acT	1	1	AY.101	0.00049
ORF3a	64	T64I	aCc	aTc	1	1	AY.101	0.00049
ORF3a	64	T64I	aCc	aTc	1	1	AY.106	0.000335
ORF3a	64	T64I	aCc	aTc	1	1	AY.107	0.000466
ORF3a	64	T64T	acC	acT	1	1	AY.108	0.001103
ORF3a	64	T64I	aCc	aTc	1	1	AY.111	0.000183
ORF3a	64	T64del	ACC	---	1	1	AY.111	0.000183
ORF3a	64	T64T	acC	acT	1	1	AY.114	0.000231
ORF3a	64	T64T	acC	acT	1	1	AY.117	0.000085
ORF3a	64	T64S	Acc	Tcc	1	1	AY.117	0.000085
ORF3a	64	T64T	acC	acT	1	1	AY.118	0.000063
ORF3a	64	T64A	Acc	Gcc	1	1	AY.119	0.000035
ORF3a	64	T64T	acC	acT	1	1	AY.119	0.000035
ORF3a	64	T64S	Acc	Tcc	1	1	AY.119	0.000035
ORF3a	64	T64del	ACC	---	1	1	AY.120	0.000037
ORF3a	64	T64T	acC	acT	1	1	AY.120	0.000037
ORF3a	64	T64I	aCc	aTc	1	1	AY.13	0.000161
ORF3a	64	T64T	acC	acT	1	1	AY.13	0.000161
ORF3a	64	T64T	acC	acT	1	1	AY.14	0.000088
ORF3a	64	T64T	acC	acT	1	1	AY.16	0.00038
ORF3a	64	T64I	aCc	aTc	1	1	AY.16.1	0.00047
ORF3a	64	T64del	ACC	---	1	1	AY.23	0.00007
ORF3a	64	T64I	aCc	aTc	1	1	AY.23.1	0.000417
ORF3a	64	T64T	acC	acT	1	1	AY.24	0.000431
ORF3a	64	T64S	Acc	Tcc	1	1	AY.25	0.000006
ORF3a	64	T64A	Acc	Gcc	1	1	AY.26	0.000028
ORF3a	64	T64T	acC	acT	1	1	AY.27	0.000065
ORF3a	64	T64A	Acc	Gcc	1	1	AY.29	0.000016
ORF3a	64	T64N	aCc	aAc	1	1	AY.29	0.000016
ORF3a	64	T64T	acC	acT	1	1	AY.29.1	0.000221
ORF3a	64	T64I	aCc	aTc	1	1	AY.3.1	0.000085
ORF3a	64	T64T	acC	acT	1	1	AY.34	0.000097
ORF3a	64	T64T	acC	acT	1	1	AY.34.1	0.00051
ORF3a	64	T64N	aCc	aAc	1	1	AY.39	0.000025
ORF3a	64	T64del	ACC	---	1	1	AY.39	0.000025
ORF3a	64	T64N	aCc	aAc	1	1	AY.4	0.000002
ORF3a	64	T64I	aCc	aTc	1	1	AY.4.2	0.000022
ORF3a	64	T64T	acC	acT	1	1	AY.42	0.00004
ORF3a	64	T64N	aCc	aAc	1	1	AY.43	0.000004
ORF3a	64	T64S	Acc	Tcc	1	1	AY.44	0.000006
ORF3a	64	T64del	ACC	---	1	1	AY.44	0.000006
ORF3a	64	T64A	Acc	Gcc	1	1	AY.46.2	0.000635
ORF3a	64	T64I	aCc	aTc	1	1	AY.46.4	0.000165
ORF3a	64	T64N	aCc	aAc	1	1	AY.47	0.000031
ORF3a	64	T64T	acC	acT	1	1	AY.48	0.000465
ORF3a	64	T64T	acC	acT	1	1	AY.49	0.003195
ORF3a	64	T64I	aCc	aTc	1	1	AY.5.3	0.000337
ORF3a	64	T64T	acC	acT	1	1	AY.55	0.000917
ORF3a	64	T64I	aCc	aTc	1	1	AY.55	0.000917
ORF3a	64	T64T	acC	acT	1	1	AY.58	0.000907
ORF3a	64	T64I	aCc	aTc	1	1	AY.6	0.000041
ORF3a	64	T64D	ACC	GAT	1	1	AY.67	0.000464
ORF3a	64	T64P	Acc	Ccc	1	1	AY.72	0.001361
ORF3a	64	T64I	aCc	aTc	1	1	AY.73	0.000665
ORF3a	64	T64I	aCc	aTc	1	1	AY.74	0.000116
ORF3a	64	T64T	acC	acT	1	1	AY.75	0.000056
ORF3a	64	T64T	acC	acT	1	1	AY.77	0.001127
ORF3a	64	T64I	aCc	aTc	1	1	AY.82	0.001357
ORF3a	64	T64I	aCc	aTc	1	1	AY.85	0.000427
ORF3a	64	T64T	acC	acT	1	1	AY.9	0.000068
ORF3a	64	T64del	ACC	---	1	1	AY.9	0.000068
ORF3a	64	T64I	aCc	aTc	1	1	AY.9	0.000068
ORF3a	64	T64A	Acc	Gcc	1	1	AY.9	0.000068
ORF3a	64	T64P	Acc	Ccc	1	1	AY.9.2	0.000037
ORF3a	64	T64del	ACC	---	1	1	AY.9.2	0.000037
ORF3a	64	T64T	acC	acT	1	1	AY.91	0.00073
ORF3a	64	T64T	acC	acT	1	1	AY.92	0.000287
ORF3a	64	T64P	Acc	Ccc	1	1	AY.98	0.000079
ORF3a	64	T64T	acC	acT	1	1	AY.98.1	0.000048
ORF3a	64	T64D	ACC	GAT	1	1	AY.99	0.001049
ORF3a	64	T64T	acC	acT	1	1	AZ.1	0.000867
ORF3a	64	T64F	ACc	TTc	1	1	B.1	0.000009
ORF3a	64	T64del1	aCc	a-c	1	1	B.1	0.000009
ORF3a	64	T64A	Acc	Gcc	1	1	B.1	0.000009
ORF3a	64	T64del	ACC	---	1	1	B.1.1	0.000018
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.1	0.000327
ORF3a	64	T64T	acC	acT	1	1	B.1.1.10	0.001115
ORF3a	64	T64del2	ACC	--G	1	1	B.1.1.139	0.022727
ORF3a	64	T64T	acC	acT	1	1	B.1.1.153	0.001095
ORF3a	64	T64T	acC	acT	1	1	B.1.1.170	0.001247
ORF3a	64	T64T	acC	acT	1	1	B.1.1.209	0.008929
ORF3a	64	T64T	acC	acT	1	1	B.1.1.220	0.001859
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.222	0.000204
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.244	0.015385
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.25	0.000569
ORF3a	64	T64T	acC	acT	1	1	B.1.1.25	0.000569
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.266	0.012195
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.274	0.005051
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.277	0.000759
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.28	0.000311
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.3	0.008696
ORF3a	64	T64T	acC	acT	1	1	B.1.1.306	0.000438
ORF3a	64	T64T	acC	acT	1	1	B.1.1.329	0.003846
ORF3a	64	T64T	acC	acT	1	1	B.1.1.344	0.010753
ORF3a	64	T64T	acC	acT	1	1	B.1.1.355	0.015385
ORF3a	64	T64T	acC	acT	1	1	B.1.1.37	0.000193
ORF3a	64	T64T	acC	acT	1	1	B.1.1.372	0.000689
ORF3a	64	T64T	acC	acT	1	1	B.1.1.39	0.00051
ORF3a	64	T64del	ACC	---	1	1	B.1.1.409	0.002833
ORF3a	64	T64T	acC	acT	1	1	B.1.1.418	0.022727
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.420	0.001006
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.464	0.001473
ORF3a	64	T64I	aCc	aTc	1	1	B.1.1.507	0.008696
ORF3a	64	T64S	Acc	Tcc	1	1	B.1.1.519	0.00004
ORF3a	64	T64N	aCc	aAc	1	1	B.1.1.519	0.00004
ORF3a	64	T64T	acC	acA	1	1	B.1.1.71	0.006061
ORF3a	64	T64T	acC	acT	1	1	B.1.111	0.001175
ORF3a	64	T64T	acC	acT	1	1	B.1.143	0.021277
ORF3a	64	T64P	Acc	Ccc	1	1	B.1.160.12	0.00641
ORF3a	64	T64A	Acc	Gcc	1	1	B.1.160.16	0.000929
ORF3a	64	T64T	acC	acT	1	1	B.1.160.22	0.006757
ORF3a	64	T64T	acC	acT	1	1	B.1.160.29	0.004219
ORF3a	64	T64del	ACC	---	1	1	B.1.160.7	0.002079
ORF3a	64	T64del	ACC	---	1	1	B.1.161	0.017241
ORF3a	64	T64T	acC	acT	1	1	B.1.177.20	0.001517
ORF3a	64	T64T	acC	acT	1	1	B.1.177.42	0.000894
ORF3a	64	T64T	acC	acT	1	1	B.1.177.44	0.000519
ORF3a	64	T64T	acC	acA	1	1	B.1.177.57	0.000281
ORF3a	64	T64N	aCc	aAc	1	1	B.1.177.60	0.000218
ORF3a	64	T64T	acC	acT	1	1	B.1.177.73	0.000566
ORF3a	64	T64I	aCc	aTc	1	1	B.1.177.73	0.000566
ORF3a	64	T64T	acC	acT	1	1	B.1.177.77	0.000726
ORF3a	64	T64T	acC	acT	1	1	B.1.198	0.071429
ORF3a	64	T64P	Acc	Ccc	1	1	B.1.2	0.000009
ORF3a	64	T64T	acC	acT	1	1	B.1.210	0.002132
ORF3a	64	T64T	acC	acT	1	1	B.1.221.1	0.002907
ORF3a	64	T64T	acC	acT	1	1	B.1.222	0.001692
ORF3a	64	T64T	acC	acT	1	1	B.1.234	0.000132
ORF3a	64	T64T	acC	acT	1	1	B.1.240	0.000216
ORF3a	64	T64T	acC	acT	1	1	B.1.241	0.000812
ORF3a	64	T64I	aCc	aTc	1	1	B.1.243	0.00007
ORF3a	64	T64T	acC	acT	1	1	B.1.258.11	0.000396
ORF3a	64	T64I	aCc	aTc	1	1	B.1.279	0.000514
ORF3a	64	T64I	aCc	aTc	1	1	B.1.291	0.019231
ORF3a	64	T64T	acC	acT	1	1	B.1.319	0.003049
ORF3a	64	T64T	acC	acT	1	1	B.1.351.2	0.000303
ORF3a	64	T64T	acC	acT	1	1	B.1.351.3	0.000876
ORF3a	64	T64I	aCc	aTc	1	1	B.1.36	0.000146
ORF3a	64	T64T	acC	acT	1	1	B.1.36.17	0.000494
ORF3a	64	T64T	acC	acT	1	1	B.1.36.29	0.000517
ORF3a	64	T64T	acC	acT	1	1	B.1.36.38	0.001642
ORF3a	64	T64I	aCc	aTc	1	1	B.1.362	0.001541
ORF3a	64	T64T	acC	acT	1	1	B.1.367	0.000792
ORF3a	64	T64I	aCc	aTc	1	1	B.1.396	0.000706
ORF3a	64	T64I	aCc	aTc	1	1	B.1.400	0.000429
ORF3a	64	T64del	ACC	---	1	1	B.1.415	0.014286
ORF3a	64	T64N	aCc	aAc	1	1	B.1.428	0.00102
ORF3a	64	T64del	ACC	---	1	1	B.1.429	0.000024
ORF3a	64	T64T	acC	acT	1	1	B.1.438.1	0.000107
ORF3a	64	T64T	acC	acT	1	1	B.1.466.1	0.007194
ORF3a	64	T64T	acC	acT	1	1	B.1.474	0.001901
ORF3a	64	T64del1	aCc	a-c	1	1	B.1.501	0.007353
ORF3a	64	T64I	aCc	aTc	1	1	B.1.510	0.026316
ORF3a	64	T64del1	aCc	a-c	1	1	B.1.511	0.034483
ORF3a	64	T64T	acC	acT	1	1	B.1.517	0.000427
ORF3a	64	T64N	aCc	aAc	1	1	B.1.525	0.000113
ORF3a	64	T64T	acC	acT	1	1	B.1.525	0.000113
ORF3a	64	T64del	ACC	---	1	1	B.1.561	0.000397
ORF3a	64	T64S	aCc	aGc	1	1	B.1.561	0.000397
ORF3a	64	T64I	aCc	aTc	1	1	B.1.565	0.00081
ORF3a	64	T64T	acC	acA	1	1	B.1.567	0.003333
ORF3a	64	T64T	acC	acT	1	1	B.1.576	0.000907
ORF3a	64	T64T	acC	acT	1	1	B.1.577	0.000687
ORF3a	64	T64T	acC	acT	1	1	B.1.590	0.004545
ORF3a	64	T64I	aCc	aTc	1	1	B.1.599	0.00365
ORF3a	64	T64T	acC	acT	1	1	B.1.609	0.000479
ORF3a	64	T64N	aCc	aAc	1	1	B.1.617.2	0.000004
ORF3a	64	T64T	acC	acT	1	1	B.1.625	0.002353
ORF3a	64	T64I	aCc	aTc	1	1	B.1.625	0.002353
ORF3a	64	T64I	aCc	aTc	1	1	B.1.627	0.00202
ORF3a	64	T64T	acC	acT	1	1	B.1.633	0.041667
ORF3a	64	T64T	acC	acT	1	1	B.1.636	0.006711
ORF3a	64	T64del	ACC	---	1	1	B.1.638	0.052632
ORF3a	64	T64del	ACC	---	1	1	B.40	0.000364
ORF3a	64	T64I	aCc	aTc	1	1	B.40	0.000364
ORF3a	64	T64I	aCc	aTc	1	1	B.6	0.00091
ORF3a	64	T64N	aCc	aAc	1	1	C.14	0.004329
ORF3a	64	T64I	aCc	aTc	1	1	C.16	0.00106
ORF3a	64	T64I	aCc	aTc	1	1	C.36.1	0.004149
ORF3a	64	T64P	Acc	Ccc	1	1	D.2	0.000075
ORF3a	64	T64A	Acc	Gcc	1	1	P.1.1	0.000318
ORF3a	64	T64T	acC	acT	1	1	P.1.13	0.000898
ORF3a	64	T64del	ACC	---	1	1	P.1.15	0.000232
ORF3a	64	T64T	acC	acT	1	1	P.1.16	0.000374
ORF3a	64	T64I	aCc	aTc	1	1	P.1.6	0.001946
ORF3a	64	T64T	acC	acT	1	1	P.1.7	0.000319
ORF3a	64	T64I	aCc	aTc	1	1	P.2	0.000187
ORF3a	64	T64T	acC	acA	1	1	Q.1	0.000126
ORF3a	64	T64T	acC	acT	1	1	R.1	0.00009
ORF3a	64	T64I	aCc	aTc	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.