CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 859

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
S	859	T859N		nonsyn	aCt	aAt	24827	24818	0.999637	24137-24139
S	859	T859N		nonsyn	aCT	aAC	24827	9	0.000362509	24137-24139
S	859	T859I		nonsyn	aCt	aTt	9064	9044	0.997793	24137-24139
S	859	T859I		nonsyn	aCT	aTC	9064	20	0.00220653	24137-24139
S	859	T859T		syn	acT	acC	364	224	0.615385	24137-24139
S	859	T859T		syn	acT	acG	364	86	0.236264	24137-24139
S	859	T859T		syn	acT	acA	364	54	0.148352	24137-24139
S	859	T859del		del	ACT	---	148	148	1	24137-24139
S	859	T859A		nonsyn	Act	Gct	67	66	0.985075	24137-24139
S	859	T859A		nonsyn	AcT	GcG	67	1	0.0149254	24137-24139
S	859	T859S		nonsyn	aCt	aGt	44	35	0.795455	24137-24139
S	859	T859S		nonsyn	Act	Tct	44	9	0.204545	24137-24139
S	859	T859del1		del	Act	-ct	10	5	0.5	24137-24139
S	859	T859del1		del	acT	ac-	10	2	0.2	24137-24139
S	859	T859del1		del	ACT	-NG	10	1	0.1	24137-24139
S	859	T859del1		del	aCt	a-t	10	1	0.1	24137-24139
S	859	T859del1		del	ACt	G-t	10	1	0.1	24137-24139
S	859	T859del2		del	aCT	a--	4	2	0.5	24137-24139
S	859	T859del2		del	ACt	--t	4	2	0.5	24137-24139
S	859	T859P		nonsyn	Act	Cct	1	1	1	24137-24139
S	859	T859M		nonsyn	aCT	aTG	1	1	1	24137-24139

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
S	859	T859N	aCt	aAt	24818	24827	All	0.004747
S	859	T859N	aCT	aAC	9	24827	All	0.000002
S	859	T859N	aCt	aAt	13341	13348	B.1.637	0.974863
S	859	T859N	aCT	aAC	7	13348	B.1.637	0.000512
S	859	T859I	aCt	aTt	9044	9064	All	0.00173
S	859	T859I	aCT	aTC	20	9064	All	0.000004
S	859	T859N	aCt	aAt	8533	8535	C.37	0.990367
S	859	T859N	aCT	aAC	2	8535	C.37	0.000232
S	859	T859I	aCt	aTt	2886	2886	AY.4	0.004492
S	859	T859I	aCt	aTt	782	782	AY.34	0.075827
S	859	T859N	aCt	aAt	548	548	B.1	0.005019
S	859	T859I	aCt	aTt	545	545	AY.25	0.003278
S	859	T859I	aCt	aTt	379	379	B.1.2	0.003337
S	859	T859I	aCt	aTt	376	376	B.1.617.2	0.001416
S	859	T859N	aCt	aAt	368	368	C.37.1	0.963351
S	859	T859T	acT	acC	224	364	All	0.000043
S	859	T859T	acT	acG	86	364	All	0.000016
S	859	T859T	acT	acA	54	364	All	0.00001
S	859	T859I	aCt	aTt	309	309	B.1.1.7	0.000277
S	859	T859N	aCt	aAt	307	307	B.1.36.9	0.987138
S	859	T859I	aCt	aTt	298	298	B.1.243	0.020736
S	859	T859N	aCt	aAt	251	251	B.1.617.2	0.000945
S	859	T859N	aCt	aAt	212	212	C.1.2	0.902128
S	859	T859I	aCt	aTt	198	198	AY.44	0.001205
S	859	T859I	aCt	aTt	188	188	AY.43	0.000833
S	859	T859N	aCt	aAt	173	173	B.1.626	0.988571
S	859	T859del	ACT	---	148	148	All	0.000028
S	859	T859N	aCt	aAt	140	140	B.1.1	0.00254
S	859	T859N	aCt	aAt	127	127	B.1.415.1	0.962121
S	859	T859I	aCt	aTt	126	126	B.1	0.001154
S	859	T859I	aCt	aTt	120	120	B.1.160	0.003743
S	859	T859I	aCt	aTt	102	102	B.1.564	0.043441
S	859	T859T	acT	acG	81	100	AY.103	0.000503
S	859	T859T	acT	acC	16	100	AY.103	0.000099
S	859	T859T	acT	acA	3	100	AY.103	0.000019
S	859	T859I	aCt	aTt	96	96	AY.103	0.000596
S	859	T859I	aCt	aTt	85	85	B.1.1	0.001542
S	859	T859I	aCt	aTt	83	83	AH.2	1
S	859	T859I	aCt	aTt	80	80	B.1.534	1
S	859	T859I	aCt	aTt	77	77	AY.98.1	0.003729
S	859	T859I	aCt	aTt	76	76	AY.3	0.000756
S	859	T859I	aCt	aTt	75	75	AY.102	0.001989
S	859	T859A	Act	Gct	66	67	All	0.000013
S	859	T859A	AcT	GcG	1	67	All	0
S	859	T859N	aCt	aAt	65	65	AY.102	0.001723
S	859	T859I	aCt	aTt	65	65	B.1.552	0.984848
S	859	T859I	aCt	aTt	64	64	AY.24	0.027586
S	859	T859I	aCt	aTt	61	61	AY.100	0.002806
S	859	T859I	aCt	aTt	60	60	A.2.5	0.02994
S	859	T859T	acT	acC	60	60	AY.113	0.008543
S	859	T859I	aCt	aTt	58	58	AY.5	0.001198
S	859	T859I	aCt	aTt	58	58	B.1.177	0.000764
S	859	T859I	aCt	aTt	53	53	B.1.351	0.001576
S	859	T859I	aCt	aTt	50	50	P.2	0.009332
S	859	T859I	aCt	aTt	49	49	AY.39	0.001211
S	859	T859N	aCt	aAt	49	49	AY.46.6	0.003538
S	859	T859del	ACT	---	48	48	B.1.1.7	0.000043
S	859	T859I	aCt	aTt	46	46	AY.23	0.003208
S	859	T859I	aCt	aTt	46	46	P.1	0.000725
S	859	T859S	aCt	aGt	35	44	All	0.000007
S	859	T859S	Act	Tct	9	44	All	0.000002
S	859	T859N	aCt	aAt	44	44	B.1.639	0.956522
S	859	T859I	aCt	aTt	43	43	AZ.5	0.150877
S	859	T859I	aCt	aTt	42	42	AY.29	0.000662
S	859	T859N	aCt	aAt	41	41	B.1.1.524	0.854167
S	859	T859I	aCt	aTt	41	41	B.1.177.15	0.025868
S	859	T859I	aCt	aTt	39	39	B.1.1.159	0.182243
S	859	T859I	aCt	aTt	39	39	B.1.36	0.00569
S	859	T859I	aCt	aTt	39	39	B.1.596	0.003398
S	859	T859N	aCt	aAt	38	38	AY.43	0.000168
S	859	T859I	aCt	aTt	38	38	B.1.429	0.000894
S	859	T859I	aCt	aTt	36	36	AY.47	0.00112
S	859	T859N	aCt	aAt	36	36	C.40	1
S	859	T859N	aCt	aAt	32	32	C.36.3.1	0.086957
S	859	T859I	aCt	aTt	30	30	B.1.1.317	0.012351
S	859	T859I	aCt	aTt	29	29	AY.119	0.001024
S	859	T859T	acT	acC	24	29	AY.4	0.000037
S	859	T859T	acT	acA	5	29	AY.4	0.000008
S	859	T859T	acT	acC	28	28	B.1.177	0.000369
S	859	T859N	aCt	aAt	28	28	B.1.214.2	0.016787
S	859	T859N	aCt	aAt	27	27	AY.92	0.007756
S	859	T859A	Act	Gct	26	26	B.1.1.7	0.000023
S	859	T859I	aCt	aTt	26	26	B.1.258.17	0.002703
S	859	T859N	aCt	aAt	26	26	B.1.526	0.000611
S	859	T859T	acT	acA	25	25	AY.42	0.001006
S	859	T859I	aCt	aTt	25	25	B.1.1.483	0.961538
S	859	T859I	aCt	aTt	25	25	B.1.438.1	0.002682
S	859	T859I	aCt	aTt	24	24	AY.4.2	0.000521
S	859	T859I	aCt	aTt	22	22	AY.120	0.000818
S	859	T859I	aCt	aTt	22	22	AY.9.2	0.000808
S	859	T859T	acT	acC	18	22	B.1.1.7	0.000016
S	859	T859T	acT	acA	4	22	B.1.1.7	0.000004
S	859	T859N	aCt	aAt	22	22	B.1.2	0.000194
S	859	T859I	aCt	aTt	21	21	B.1.1.318	0.006337
S	859	T859I	aCt	aTt	21	21	B.1.1.369	0.009371
S	859	T859N	aCt	aAt	21	21	B.1.576	0.019039
S	859	T859I	aCt	aTt	20	20	AY.99.2	0.001843
S	859	T859I	aCT	aTC	19	20	B.1.177.54	0.011522
S	859	T859I	aCt	aTt	1	20	B.1.177.54	0.000606
S	859	T859I	aCt	aTt	20	20	B.1.177.7	0.003297
S	859	T859N	aCt	aAt	19	19	AY.39	0.00047
S	859	T859I	aCt	aTt	19	19	AY.98	0.001501
S	859	T859I	aCt	aTt	19	19	B.1.1.216	0.016919
S	859	T859I	aCt	aTt	19	19	B.1.258	0.001264
S	859	T859T	acT	acC	17	17	AY.43	0.000075
S	859	T859I	aCt	aTt	17	17	AY.73	0.011311
S	859	T859I	aCt	aTt	17	17	B.1.36.31	0.029772
S	859	T859I	aCt	aTt	17	17	B.1.525	0.001924
S	859	T859N	aCt	aAt	17	17	B.1.633	0.708333
S	859	T859I	aCt	aTt	16	16	AY.26	0.000453
S	859	T859N	aCt	aAt	16	16	B.1.1.7	0.000014
S	859	T859I	aCt	aTt	16	16	B.1.526	0.000376
S	859	T859I	aCt	aTt	14	14	AY.61	0.001467
S	859	T859I	aCt	aTt	14	14	B.1.1.305	0.054054
S	859	T859I	aCt	aTt	14	14	B.1.1.521	0.074866
S	859	T859I	aCt	aTt	14	14	B.1.221	0.000994
S	859	T859N	aCt	aAt	14	14	P.1.15	0.003253
S	859	T859I	aCt	aTt	13	13	B.1.1.241	0.026915
S	859	T859I	aCt	aTt	13	13	B.1.177.10	0.011414
S	859	T859I	aCt	aTt	13	13	B.1.466.2	0.005086
S	859	T859I	aCt	aTt	12	12	AY.19	0.013683
S	859	T859N	aCt	aAt	12	12	B	0.001534
S	859	T859I	aCt	aTt	12	12	B.1.1.214	0.000665
S	859	T859I	aCt	aTt	12	12	B.1.177.83	0.017778
S	859	T859N	aCt	aAt	12	12	B.1.638	0.631579
S	859	T859N	aCt	aAt	11	11	AY.36	0.00163
S	859	T859I	aCt	aTt	11	11	AY.5.4	0.003044
S	859	T859I	aCt	aTt	11	11	B.1.1.189	0.016641
S	859	T859N	aCt	aAt	11	11	B.1.1.372	0.007576
S	859	T859del	ACT	---	11	11	B.1.177	0.000145
S	859	T859I	aCt	aTt	11	11	B.1.427	0.000555
S	859	T859I	aCt	aTt	11	11	B.1.501	0.080882
S	859	T859I	aCt	aTt	11	11	B.1.621	0.000974
S	859	T859del1	Act	-ct	5	10	All	0.000001
S	859	T859del1	acT	ac-	2	10	All	0
S	859	T859del1	ACt	G-t	1	10	All	0
S	859	T859del1	ACT	-NG	1	10	All	0
S	859	T859del1	aCt	a-t	1	10	All	0
S	859	T859I	aCt	aTt	10	10	AY.113	0.001424
S	859	T859T	acT	acC	9	10	AY.25	0.000054
S	859	T859T	acT	acA	1	10	AY.25	0.000006
S	859	T859I	aCt	aTt	10	10	AY.41	0.002939
S	859	T859I	aCt	aTt	10	10	AY.42	0.000402
S	859	T859I	aCt	aTt	10	10	AY.75	0.00056
S	859	T859I	aCt	aTt	10	10	B.1.1.363	0.05988
S	859	T859I	aCt	aTt	10	10	B.1.118	0.067114
S	859	T859I	aCt	aTt	10	10	B.1.177.53	0.023923
S	859	T859I	aCt	aTt	10	10	B.1.258.11	0.003964
S	859	T859N	aCt	aAt	10	10	P.1	0.000158
S	859	T859N	aCt	aAt	9	9	AY.103	0.000056
S	859	T859I	aCt	aTt	9	9	AY.114	0.00208
S	859	T859I	aCt	aTt	9	9	AY.36	0.001334
S	859	T859S	aCt	aGt	9	9	AY.99.2	0.000829
S	859	T859I	aCt	aTt	9	9	B.1.1.1	0.00294
S	859	T859I	aCt	aTt	9	9	B.1.1.33	0.003788
S	859	T859I	aCt	aTt	8	8	AY.39.1	0.000317
S	859	T859N	aCt	aAt	8	8	AY.44	0.000049
S	859	T859I	aCt	aTt	8	8	AY.46	0.000833
S	859	T859I	aCt	aTt	8	8	AY.84	0.0035
S	859	T859T	acT	acC	7	8	B.1	0.000064
S	859	T859T	acT	acA	1	8	B.1	0.000009
S	859	T859I	aCt	aTt	8	8	B.1.234	0.001056
S	859	T859I	aCt	aTt	8	8	B.1.236	0.016427
S	859	T859I	aCt	aTt	8	8	D.2	0.0006
S	859	T859I	aCt	aTt	7	7	AH.1	1
S	859	T859A	Act	Gct	7	7	AY.103	0.000043
S	859	T859N	aCt	aAt	7	7	AY.25	0.000042
S	859	T859del	ACT	---	7	7	AY.4.5	0.000752
S	859	T859N	aCt	aAt	7	7	B.1.1.1	0.002287
S	859	T859N	aCt	aAt	7	7	B.1.1.28	0.002179
S	859	T859I	aCt	aTt	7	7	B.1.1.519	0.000278
S	859	T859I	aCt	aTt	7	7	B.1.160.16	0.006506
S	859	T859I	aCt	aTt	7	7	B.1.160.28	0.020468
S	859	T859N	aCt	aAt	7	7	B.1.177.73	0.003964
S	859	T859I	aCt	aTt	7	7	B.1.36.29	0.003621
S	859	T859N	aCt	aAt	7	7	B.1.632	0.04698
S	859	T859N	aCt	aAt	7	7	B.1.636	0.04698
S	859	T859I	aCt	aTt	6	6	AA.1	0.043478
S	859	T859I	aCt	aTt	6	6	AU.2	0.014528
S	859	T859I	aCt	aTt	6	6	AY.111	0.001099
S	859	T859I	aCt	aTt	6	6	AY.13	0.000966
S	859	T859A	Act	Gct	6	6	AY.4	0.000009
S	859	T859del	ACT	---	6	6	AY.43	0.000027
S	859	T859A	Act	Gct	6	6	AY.44	0.000037
S	859	T859I	aCt	aTt	6	6	AY.53	0.001725
S	859	T859I	aCt	aTt	6	6	B.1.177.60	0.001311
S	859	T859N	aCt	aAt	6	6	B.1.177.7	0.000989
S	859	T859T	acT	acC	6	6	B.1.351	0.000178
S	859	T859I	aCt	aTt	6	6	B.1.362	0.009245
S	859	T859N	aCt	aAt	6	6	B.1.596	0.000523
S	859	T859I	aCt	aTt	6	6	B.1.617.1	0.000774
S	859	T859T	acT	acC	3	6	B.1.617.2	0.000011
S	859	T859T	acT	acA	3	6	B.1.617.2	0.000011
S	859	T859N	aCt	aAt	6	6	B.1.623	0.003219
S	859	T859T	acT	acC	6	6	P.1	0.000095
S	859	T859I	aCt	aTt	5	5	A	0.001935
S	859	T859I	aCt	aTt	5	5	AY.117	0.000423
S	859	T859I	aCt	aTt	5	5	AY.20	0.000194
S	859	T859I	aCt	aTt	5	5	AY.45	0.000608
S	859	T859I	aCt	aTt	5	5	AY.46.4	0.000823
S	859	T859I	aCt	aTt	5	5	AY.62	0.002179
S	859	T859N	aCt	aAt	5	5	AY.84	0.002187
S	859	T859I	aCt	aTt	5	5	B.1.1.222	0.00102
S	859	T859I	aCt	aTt	5	5	B.1.177.12	0.000758
S	859	T859I	aCt	aTt	5	5	B.1.177.57	0.001405
S	859	T859I	aCt	aTt	5	5	B.1.218	0.025773
S	859	T859I	aCt	aTt	5	5	B.1.241	0.004058
S	859	T859N	aCt	aAt	5	5	B.1.36	0.00073
S	859	T859I	aCt	aTt	5	5	B.1.521	0.024876
S	859	T859I	aCt	aTt	5	5	B.1.561	0.001985
S	859	T859N	aCt	aAt	5	5	P.1.12	0.00242
S	859	T859N	aCt	aAt	5	5	P.5	0.068493
S	859	T859del2	aCT	a--	2	4	All	0
S	859	T859del2	ACt	--t	2	4	All	0
S	859	T859T	acT	acC	2	4	AY.102	0.000053
S	859	T859T	acT	acA	2	4	AY.102	0.000053
S	859	T859S	aCt	aGt	4	4	AY.103	0.000025
S	859	T859I	aCt	aTt	4	4	AY.118	0.000251
S	859	T859I	aCt	aTt	4	4	AY.120.2.1	0.001993
S	859	T859N	aCt	aAt	4	4	AY.23	0.000279
S	859	T859N	aCt	aAt	4	4	AY.3	0.00004
S	859	T859T	acT	acC	4	4	AY.3	0.00004
S	859	T859I	aCt	aTt	4	4	AY.3.1	0.000341
S	859	T859I	aCt	aTt	4	4	AY.33	0.000267
S	859	T859del	ACT	---	4	4	AY.4	0.000006
S	859	T859S	aCt	aGt	4	4	AY.4	0.000006
S	859	T859N	aCt	aAt	4	4	AY.4	0.000006
S	859	T859N	aCt	aAt	4	4	AY.42	0.000161
S	859	T859I	aCt	aTt	4	4	AY.65	0.002132
S	859	T859I	aCt	aTt	4	4	AY.75.1	0.000721
S	859	T859I	aCt	aTt	4	4	AY.9	0.00027
S	859	T859N	aCt	aAt	4	4	AY.9.2	0.000147
S	859	T859N	aCt	aAt	4	4	AY.98	0.000316
S	859	T859T	acT	acC	4	4	AZ.2	0.003284
S	859	T859I	aCt	aTt	4	4	B	0.000511
S	859	T859I	aCt	aTt	4	4	B.1.1.28	0.001245
S	859	T859I	aCt	aTt	4	4	B.1.1.311	0.001433
S	859	T859I	aCt	aTt	4	4	B.1.1.50	0.002716
S	859	T859I	aCt	aTt	4	4	B.1.170	0.017241
S	859	T859I	aCt	aTt	4	4	B.1.177.21	0.000306
S	859	T859I	aCt	aTt	4	4	B.1.177.86	0.000734
S	859	T859del	ACT	---	4	4	B.1.2	0.000035
S	859	T859T	acT	acC	3	4	B.1.2	0.000026
S	859	T859T	acT	acA	1	4	B.1.2	0.000009
S	859	T859I	aCt	aTt	4	4	B.1.239	0.004884
S	859	T859I	aCt	aTt	4	4	B.1.36.8	0.004
S	859	T859I	aCt	aTt	4	4	B.1.361	0.005155
S	859	T859I	aCt	aTt	4	4	B.1.409	0.003125
S	859	T859N	aCt	aAt	4	4	B.1.427	0.000202
S	859	T859I	aCt	aTt	4	4	B.1.428	0.004082
S	859	T859N	aCt	aAt	4	4	B.1.618	0.016129
S	859	T859I	aCt	aTt	4	4	B.1.625	0.009412
S	859	T859I	aCt	aTt	4	4	C.38	0.032258
S	859	T859N	aCt	aAt	4	4	P.1.1	0.001271
S	859	T859I	aCt	aTt	4	4	P.1.14	0.000191
S	859	T859I	aCt	aTt	4	4	P.5	0.054795
S	859	T859I	aCt	aTt	4	4	W.4	0.005405
S	859	T859I	aCt	aTt	3	3	AY.121	0.000406
S	859	T859N	aCt	aAt	3	3	AY.13	0.000483
S	859	T859I	aCt	aTt	3	3	AY.16	0.001139
S	859	T859N	aCt	aAt	3	3	AY.26	0.000085
S	859	T859I	aCt	aTt	3	3	AY.32	0.001597
S	859	T859I	aCt	aTt	3	3	AY.4.2.1	0.000447
S	859	T859A	Act	Gct	3	3	AY.43	0.000013
S	859	T859N	aCt	aAt	3	3	AY.45	0.000365
S	859	T859N	aCt	aAt	3	3	AY.46	0.000312
S	859	T859I	aCt	aTt	3	3	AY.46.6	0.000217
S	859	T859del	ACT	---	3	3	AY.5	0.000062
S	859	T859N	aCt	aAt	3	3	AY.5	0.000062
S	859	T859I	aCt	aTt	3	3	AY.9.1	0.000251
S	859	T859del	ACT	---	3	3	B.1	0.000027
S	859	T859I	aCt	aTt	3	3	B.1.1.170	0.003741
S	859	T859I	aCt	aTt	3	3	B.1.1.192	0.006928
S	859	T859I	aCt	aTt	3	3	B.1.1.277	0.002276
S	859	T859T	acT	acG	3	3	B.1.1.306	0.001315
S	859	T859N	aCt	aAt	3	3	B.1.1.412	0.022901
S	859	T859I	aCt	aTt	3	3	B.1.1.434	0.001046
S	859	T859N	aCt	aAt	3	3	B.1.1.507	0.026087
S	859	T859N	aCt	aAt	3	3	B.1.1.528	0.014423
S	859	T859del1	Act	-ct	2	3	B.1.1.7	0.000002
S	859	T859del1	acT	ac-	1	3	B.1.1.7	0.000001
S	859	T859del	ACT	---	3	3	B.1.177.4	0.000633
S	859	T859I	aCt	aTt	3	3	B.1.177.56	0.002003
S	859	T859N	aCt	aAt	3	3	B.1.351	0.000089
S	859	T859I	aCt	aTt	3	3	B.1.369	0.000856
S	859	T859I	aCt	aTt	3	3	B.1.381	0.023438
S	859	T859I	aCt	aTt	3	3	B.1.471	0.008197
S	859	T859I	aCt	aTt	3	3	B.1.527	0.011111
S	859	T859I	aCt	aTt	3	3	B.1.595	0.000783
S	859	T859I	aCt	aTt	3	3	B.1.604	0.051724
S	859	T859I	aCt	aTt	3	3	B.1.609	0.001438
S	859	T859N	aCt	aAt	3	3	B.1.609	0.001438
S	859	T859I	aCt	aTt	3	3	C.30	0.005181
S	859	T859N	aCt	aAt	3	3	C.39	0.056604
S	859	T859I	aCt	aTt	2	3	P.1.15	0.000465
S	859	T859I	aCT	aTC	1	3	P.1.15	0.000232
S	859	T859N	aCt	aAt	3	3	P.1.17	0.000485
S	859	T859N	aCt	aAt	3	3	Q.8	0.000495
S	859	T859del	ACT	---	2	2		0.111111
S	859	T859T	acT	acA	2	2	A.1	0.000564
S	859	T859I	aCt	aTt	2	2	AD.2	0.000438
S	859	T859I	aCt	aTt	2	2	AY.105	0.001286
S	859	T859I	aCt	aTt	2	2	AY.107	0.000932
S	859	T859I	aCt	aTt	2	2	AY.108	0.002205
S	859	T859N	aCt	aAt	2	2	AY.108	0.002205
S	859	T859I	aCt	aTt	2	2	AY.116	0.000574
S	859	T859T	acT	acC	2	2	AY.117	0.000169
S	859	T859T	acT	acC	2	2	AY.120	0.000074
S	859	T859I	aCt	aTt	2	2	AY.16.1	0.00094
S	859	T859A	Act	Gct	2	2	AY.33	0.000134
S	859	T859del	ACT	---	2	2	AY.36	0.000296
S	859	T859I	aCt	aTt	2	2	AY.38	0.000999
S	859	T859T	acT	acC	2	2	AY.39	0.000049
S	859	T859del	ACT	---	2	2	AY.39	0.000049
S	859	T859I	aCt	aTt	2	2	AY.4.5	0.000215
S	859	T859S	Act	Tct	2	2	AY.42	0.00008
S	859	T859del1	ACT	-NG	1	2	AY.43	0.000004
S	859	T859del1	acT	ac-	1	2	AY.43	0.000004
S	859	T859N	aCt	aAt	2	2	AY.5.3	0.000675
S	859	T859N	aCt	aAt	2	2	AY.52	0.001629
S	859	T859I	aCt	aTt	2	2	AY.6	0.000082
S	859	T859N	aCt	aAt	2	2	AY.61	0.00021
S	859	T859I	aCt	aTt	2	2	AY.69	0.000373
S	859	T859I	aCt	aTt	2	2	AY.71	0.00095
S	859	T859S	aCt	aGt	2	2	AY.9.2	0.000073
S	859	T859T	acT	acC	2	2	AY.9.2	0.000073
S	859	T859del	ACT	---	2	2	B.1.1	0.000036
S	859	T859N	aCt	aAt	2	2	B.1.1.265	0.006309
S	859	T859N	aCt	aAt	2	2	B.1.1.291	0.001485
S	859	T859N	aCt	aAt	2	2	B.1.1.294	0.002532
S	859	T859N	aCt	aAt	2	2	B.1.1.318	0.000604
S	859	T859I	aCt	aTt	2	2	B.1.1.370	0.025316
S	859	T859N	aCt	aAt	2	2	B.1.1.519	0.000079
S	859	T859I	aCt	aTt	2	2	B.1.1.63	0.000772
S	859	T859S	aCt	aGt	1	2	B.1.1.7	0.000001
S	859	T859S	Act	Tct	1	2	B.1.1.7	0.000001
S	859	T859I	aCt	aTt	2	2	B.1.110.3	0.001437
S	859	T859I	aCt	aTt	2	2	B.1.111	0.00235
S	859	T859N	aCt	aAt	2	2	B.1.160	0.000062
S	859	T859I	aCt	aTt	2	2	B.1.160.14	0.004237
S	859	T859N	aCt	aAt	2	2	B.1.177	0.000026
S	859	T859del	ACT	---	2	2	B.1.177.16	0.001329
S	859	T859del	ACT	---	2	2	B.1.177.63	0.005405
S	859	T859I	aCt	aTt	2	2	B.1.177.73	0.001133
S	859	T859I	aCt	aTt	2	2	B.1.206	0.001631
S	859	T859I	aCt	aTt	2	2	B.1.311	0.000549
S	859	T859N	aCt	aAt	2	2	B.1.311	0.000549
S	859	T859N	aCt	aAt	2	2	B.1.336	0.004878
S	859	T859A	Act	Gct	2	2	B.1.351	0.000059
S	859	T859I	aCt	aTt	2	2	B.1.36.1	0.002281
S	859	T859I	aCt	aTt	2	2	B.1.36.16	0.002849
S	859	T859I	aCt	aTt	2	2	B.1.36.18	0.00084
S	859	T859I	aCt	aTt	2	2	B.1.36.27	0.001527
S	859	T859N	aCt	aAt	2	2	B.1.36.31	0.003503
S	859	T859N	aCt	aAt	2	2	B.1.36.8	0.002
S	859	T859I	aCt	aTt	2	2	B.1.396	0.001411
S	859	T859N	aCt	aAt	2	2	B.1.404	0.002604
S	859	T859I	aCt	aTt	2	2	B.1.404	0.002604
S	859	T859N	aCt	aAt	2	2	B.1.413	0.008511
S	859	T859T	acT	acA	1	2	B.1.466.2	0.000391
S	859	T859T	acT	acC	1	2	B.1.466.2	0.000391
S	859	T859I	aCt	aTt	2	2	B.1.470	0.002809
S	859	T859I	aCt	aTt	2	2	B.1.582	0.000981
S	859	T859A	Act	Gct	2	2	B.1.617.2	0.000008
S	859	T859N	aCt	aAt	2	2	B.1.621	0.000177
S	859	T859N	aCt	aAt	2	2	B.1.9.5	0.011364
S	859	T859N	aCt	aAt	2	2	C.1	0.004785
S	859	T859I	aCt	aTt	2	2	C.36	0.001821
S	859	T859I	aCt	aTt	2	2	N.6	0.014184
S	859	T859A	Act	Gct	2	2	P.1	0.000032
S	859	T859S	aCt	aGt	2	2	P.1	0.000032
S	859	T859I	aCt	aTt	2	2	P.1.17	0.000324
S	859	T859S	aCt	aGt	1	1	A	0.000387
S	859	T859del	ACT	---	1	1	A	0.000387
S	859	T859N	aCt	aAt	1	1	A.2	0.000662
S	859	T859N	aCt	aAt	1	1	A.2.5	0.000499
S	859	T859I	aCt	aTt	1	1	AA.5	0.016129
S	859	T859I	aCt	aTt	1	1	AE.8	0.000489
S	859	T859del	ACT	---	1	1	AH.3	0.003802
S	859	T859P	Act	Cct	1	1	All	0
S	859	T859M	aCT	aTG	1	1	All	0
S	859	T859I	aCt	aTt	1	1	AP.1	0.001502
S	859	T859N	aCt	aAt	1	1	AY.100	0.000046
S	859	T859S	aCt	aGt	1	1	AY.102	0.000027
S	859	T859M	aCT	aTG	1	1	AY.103	0.000006
S	859	T859N	aCt	aAt	1	1	AY.107	0.000466
S	859	T859I	aCt	aTt	1	1	AY.110	0.000113
S	859	T859del2	ACt	--t	1	1	AY.117	0.000085
S	859	T859A	AcT	GcG	1	1	AY.117	0.000085
S	859	T859A	Act	Gct	1	1	AY.119	0.000035
S	859	T859N	aCt	aAt	1	1	AY.119	0.000035
S	859	T859S	Act	Tct	1	1	AY.119	0.000035
S	859	T859T	acT	acC	1	1	AY.119	0.000035
S	859	T859del	ACT	---	1	1	AY.120	0.000037
S	859	T859N	aCt	aAt	1	1	AY.120	0.000037
S	859	T859S	aCt	aGt	1	1	AY.14	0.000088
S	859	T859I	aCt	aTt	1	1	AY.14	0.000088
S	859	T859N	aCt	aAt	1	1	AY.15	0.002222
S	859	T859del1	aCt	a-t	1	1	AY.16	0.00038
S	859	T859I	aCt	aTt	1	1	AY.2	0.000356
S	859	T859S	aCt	aGt	1	1	AY.25	0.000006
S	859	T859del	ACT	---	1	1	AY.25	0.000006
S	859	T859S	aCt	aGt	1	1	AY.26	0.000028
S	859	T859T	acT	acA	1	1	AY.29	0.000016
S	859	T859I	aCt	aTt	1	1	AY.29.1	0.000221
S	859	T859del	ACT	---	1	1	AY.3	0.00001
S	859	T859S	aCt	aGt	1	1	AY.3	0.00001
S	859	T859N	aCt	aAt	1	1	AY.3.1	0.000085
S	859	T859A	Act	Gct	1	1	AY.30	0.000396
S	859	T859N	aCt	aAt	1	1	AY.30	0.000396
S	859	T859I	aCt	aTt	1	1	AY.30	0.000396
S	859	T859A	Act	Gct	1	1	AY.32	0.000532
S	859	T859N	aCt	aAt	1	1	AY.35	0.000233
S	859	T859I	aCt	aTt	1	1	AY.35	0.000233
S	859	T859del	ACT	---	1	1	AY.37	0.000316
S	859	T859N	aCt	aAt	1	1	AY.39.1	0.00004
S	859	T859del2	ACt	--t	1	1	AY.4	0.000002
S	859	T859del1	Act	-ct	1	1	AY.4	0.000002
S	859	T859N	aCt	aAt	1	1	AY.4.2	0.000022
S	859	T859S	aCt	aGt	1	1	AY.4.2.1	0.000149
S	859	T859S	aCt	aGt	1	1	AY.43	0.000004
S	859	T859del	ACT	---	1	1	AY.44	0.000006
S	859	T859S	Act	Tct	1	1	AY.44	0.000006
S	859	T859T	acT	acA	1	1	AY.44	0.000006
S	859	T859I	aCt	aTt	1	1	AY.46.1	0.001027
S	859	T859del	ACT	---	1	1	AY.46.2	0.000635
S	859	T859S	Act	Tct	1	1	AY.5	0.000021
S	859	T859I	aCt	aTt	1	1	AY.52	0.000814
S	859	T859T	acT	acC	1	1	AY.55	0.000917
S	859	T859S	Act	Tct	1	1	AY.55	0.000917
S	859	T859N	aCt	aAt	1	1	AY.55	0.000917
S	859	T859del1	ACt	G-t	1	1	AY.55	0.000917
S	859	T859I	aCt	aTt	1	1	AY.57	0.000656
S	859	T859N	aCt	aAt	1	1	AY.58	0.000907
S	859	T859N	aCt	aAt	1	1	AY.60	0.000938
S	859	T859I	aCt	aTt	1	1	AY.60	0.000938
S	859	T859del	ACT	---	1	1	AY.65	0.000533
S	859	T859A	Act	Gct	1	1	AY.65	0.000533
S	859	T859del	ACT	---	1	1	AY.68	0.000274
S	859	T859T	acT	acG	1	1	AY.7.2	0.000559
S	859	T859I	aCt	aTt	1	1	AY.70	0.000209
S	859	T859del	ACT	---	1	1	AY.72	0.001361
S	859	T859I	aCt	aTt	1	1	AY.74	0.000116
S	859	T859del	ACT	---	1	1	AY.75	0.000056
S	859	T859I	aCt	aTt	1	1	AY.80	0.001129
S	859	T859del	ACT	---	1	1	AY.81	0.001992
S	859	T859I	aCt	aTt	1	1	AY.88	0.000884
S	859	T859I	aCt	aTt	1	1	AY.89	0.004902
S	859	T859A	Act	Gct	1	1	AY.9.2	0.000037
S	859	T859I	aCt	aTt	1	1	AY.92	0.000287
S	859	T859I	aCt	aTt	1	1	AY.93	0.000273
S	859	T859N	aCt	aAt	1	1	AY.99	0.001049
S	859	T859del	ACT	---	1	1	AY.99.1	0.001553
S	859	T859I	aCt	aTt	1	1	AY.99.1	0.001553
S	859	T859N	aCt	aAt	1	1	AY.99.2	0.000092
S	859	T859P	Act	Cct	1	1	B.1	0.000009
S	859	T859S	aCt	aGt	1	1	B.1.1	0.000018
S	859	T859I	aCt	aTt	1	1	B.1.1.121	0.002427
S	859	T859I	aCt	aTt	1	1	B.1.1.176	0.000439
S	859	T859A	Act	Gct	1	1	B.1.1.176	0.000439
S	859	T859T	acT	acA	1	1	B.1.1.186	0.003436
S	859	T859I	aCt	aTt	1	1	B.1.1.190	0.05
S	859	T859I	aCt	aTt	1	1	B.1.1.198	0.001468
S	859	T859I	aCt	aTt	1	1	B.1.1.213	0.021739
S	859	T859del	ACT	---	1	1	B.1.1.218	0.007692
S	859	T859T	acT	acA	1	1	B.1.1.218	0.007692
S	859	T859I	aCt	aTt	1	1	B.1.1.220	0.001859
S	859	T859N	aCt	aAt	1	1	B.1.1.220	0.001859
S	859	T859N	aCt	aAt	1	1	B.1.1.222	0.000204
S	859	T859I	aCt	aTt	1	1	B.1.1.231	0.003096
S	859	T859del	ACT	---	1	1	B.1.1.236	0.006897
S	859	T859I	aCt	aTt	1	1	B.1.1.265	0.003155
S	859	T859I	aCt	aTt	1	1	B.1.1.27	0.00565
S	859	T859del	ACT	---	1	1	B.1.1.28	0.000311
S	859	T859I	aCt	aTt	1	1	B.1.1.306	0.000438
S	859	T859del	ACT	---	1	1	B.1.1.312	0.001912
S	859	T859del	ACT	---	1	1	B.1.1.335	0.012987
S	859	T859I	aCt	aTt	1	1	B.1.1.348	0.000796
S	859	T859N	aCt	aAt	1	1	B.1.1.348	0.000796
S	859	T859I	aCt	aTt	1	1	B.1.1.358	0.034483
S	859	T859T	acT	acG	1	1	B.1.1.369	0.000446
S	859	T859del	ACT	---	1	1	B.1.1.39	0.00051
S	859	T859I	aCt	aTt	1	1	B.1.1.39	0.00051
S	859	T859I	aCt	aTt	1	1	B.1.1.397	0.002252
S	859	T859I	aCt	aTt	1	1	B.1.1.409	0.002833
S	859	T859N	aCt	aAt	1	1	B.1.1.409	0.002833
S	859	T859I	aCt	aTt	1	1	B.1.1.41	0.006329
S	859	T859I	aCt	aTt	1	1	B.1.1.413	0.006897
S	859	T859N	aCt	aAt	1	1	B.1.1.413	0.006897
S	859	T859I	aCt	aTt	1	1	B.1.1.435	0.034483
S	859	T859N	aCt	aAt	1	1	B.1.1.448	0.002033
S	859	T859I	aCt	aTt	1	1	B.1.1.47	0.005348
S	859	T859I	aCt	aTt	1	1	B.1.1.48	0.002874
S	859	T859S	Act	Tct	1	1	B.1.1.519	0.00004
S	859	T859I	aCt	aTt	1	1	B.1.1.70	0.000341
S	859	T859I	aCt	aTt	1	1	B.1.127	0.002198
S	859	T859I	aCt	aTt	1	1	B.1.146	0.004237
S	859	T859I	aCt	aTt	1	1	B.1.149	0.003425
S	859	T859del	ACT	---	1	1	B.1.160	0.000031
S	859	T859del2	aCT	a--	1	1	B.1.160	0.000031
S	859	T859I	aCt	aTt	1	1	B.1.160.7	0.002079
S	859	T859A	Act	Gct	1	1	B.1.177.16	0.000664
S	859	T859del	ACT	---	1	1	B.1.177.17	0.000821
S	859	T859del	ACT	---	1	1	B.1.177.18	0.00116
S	859	T859I	aCt	aTt	1	1	B.1.177.18	0.00116
S	859	T859del	ACT	---	1	1	B.1.177.21	0.000076
S	859	T859I	aCt	aTt	1	1	B.1.177.28	0.007407
S	859	T859I	aCt	aTt	1	1	B.1.177.44	0.000519
S	859	T859N	aCt	aAt	1	1	B.1.177.44	0.000519
S	859	T859del	ACT	---	1	1	B.1.177.48	0.003125
S	859	T859I	aCt	aTt	1	1	B.1.177.52	0.001757
S	859	T859del	ACT	---	1	1	B.1.177.54	0.000606
S	859	T859del	ACT	---	1	1	B.1.177.56	0.000668
S	859	T859del	ACT	---	1	1	B.1.177.58	0.001332
S	859	T859del	ACT	---	1	1	B.1.177.60	0.000218
S	859	T859I	aCt	aTt	1	1	B.1.177.65	0.000665
S	859	T859I	aCt	aTt	1	1	B.1.177.69	0.001484
S	859	T859T	acT	acC	1	1	B.1.177.7	0.000165
S	859	T859I	aCt	aTt	1	1	B.1.177.76	0.002494
S	859	T859N	aCt	aAt	1	1	B.1.177.79	0.002342
S	859	T859N	aCt	aAt	1	1	B.1.177.81	0.000189
S	859	T859I	aCt	aTt	1	1	B.1.177.82	0.000477
S	859	T859del	ACT	---	1	1	B.1.177.83	0.001481
S	859	T859del	ACT	---	1	1	B.1.179	0.003759
S	859	T859S	aCt	aGt	1	1	B.1.206	0.000816
S	859	T859N	aCt	aAt	1	1	B.1.208	0.04
S	859	T859N	aCt	aAt	1	1	B.1.214	0.003663
S	859	T859I	aCt	aTt	1	1	B.1.214.2	0.0006
S	859	T859I	aCt	aTt	1	1	B.1.22	0.001318
S	859	T859N	aCt	aAt	1	1	B.1.221	0.000071
S	859	T859I	aCt	aTt	1	1	B.1.222	0.001692
S	859	T859A	Act	Gct	1	1	B.1.234	0.000132
S	859	T859I	aCt	aTt	1	1	B.1.240	0.000216
S	859	T859N	aCt	aAt	1	1	B.1.241	0.000812
S	859	T859del	ACT	---	1	1	B.1.243	0.00007
S	859	T859N	aCt	aAt	1	1	B.1.243.1	0.022222
S	859	T859del	ACT	---	1	1	B.1.258	0.000067
S	859	T859N	aCt	aAt	1	1	B.1.258	0.000067
S	859	T859I	aCt	aTt	1	1	B.1.258.14	0.00098
S	859	T859I	aCt	aTt	1	1	B.1.265	0.001271
S	859	T859N	aCt	aAt	1	1	B.1.280	0.007143
S	859	T859I	aCt	aTt	1	1	B.1.3	0.002618
S	859	T859I	aCt	aTt	1	1	B.1.320	0.001245
S	859	T859N	aCt	aAt	1	1	B.1.324	0.001605
S	859	T859del	ACT	---	1	1	B.1.329	0.000608
S	859	T859I	aCt	aTt	1	1	B.1.338	0.008621
S	859	T859N	aCt	aAt	1	1	B.1.338	0.008621
S	859	T859I	aCt	aTt	1	1	B.1.346	0.001311
S	859	T859I	aCt	aTt	1	1	B.1.349	0.000715
S	859	T859I	aCt	aTt	1	1	B.1.35	0.008475
S	859	T859N	aCt	aAt	1	1	B.1.350	0.002933
S	859	T859I	aCt	aTt	1	1	B.1.351.2	0.000303
S	859	T859N	aCt	aAt	1	1	B.1.356	0.001727
S	859	T859N	aCt	aAt	1	1	B.1.36.10	0.004785
S	859	T859del	ACT	---	1	1	B.1.36.18	0.00042
S	859	T859I	aCt	aTt	1	1	B.1.36.22	0.001208
S	859	T859I	aCt	aTt	1	1	B.1.36.28	0.005747
S	859	T859del	ACT	---	1	1	B.1.36.39	0.002217
S	859	T859T	acT	acA	1	1	B.1.362.1	0.066667
S	859	T859I	aCt	aTt	1	1	B.1.366	0.004878
S	859	T859N	aCt	aAt	1	1	B.1.367	0.000792
S	859	T859T	acT	acC	1	1	B.1.369	0.000285
S	859	T859N	aCt	aAt	1	1	B.1.375	0.00082
S	859	T859I	aCt	aTt	1	1	B.1.375	0.00082
S	859	T859I	aCt	aTt	1	1	B.1.389	0.001002
S	859	T859S	aCt	aGt	1	1	B.1.396	0.000706
S	859	T859I	aCt	aTt	1	1	B.1.398	0.002976
S	859	T859N	aCt	aAt	1	1	B.1.399	0.001934
S	859	T859N	aCt	aAt	1	1	B.1.411	0.003704
S	859	T859I	aCt	aTt	1	1	B.1.411	0.003704
S	859	T859T	acT	acC	1	1	B.1.422	0.000812
S	859	T859I	aCt	aTt	1	1	B.1.426	0.001009
S	859	T859N	aCt	aAt	1	1	B.1.429	0.000024
S	859	T859A	Act	Gct	1	1	B.1.429	0.000024
S	859	T859I	aCt	aTt	1	1	B.1.439	0.005917
S	859	T859I	aCt	aTt	1	1	B.1.444	0.015873
S	859	T859N	aCt	aAt	1	1	B.1.451	0.008197
S	859	T859I	aCt	aTt	1	1	B.1.456	0.003268
S	859	T859N	aCt	aAt	1	1	B.1.462	0.007246
S	859	T859I	aCt	aTt	1	1	B.1.497	0.000315
S	859	T859I	aCt	aTt	1	1	B.1.503	0.002488
S	859	T859I	aCt	aTt	1	1	B.1.515	0.014493
S	859	T859del2	aCT	a--	1	1	B.1.526	0.000024
S	859	T859N	aCt	aAt	1	1	B.1.533	0.009615
S	859	T859I	aCt	aTt	1	1	B.1.565	0.00081
S	859	T859I	aCt	aTt	1	1	B.1.570	0.002941
S	859	T859I	aCt	aTt	1	1	B.1.575	0.000303
S	859	T859N	aCt	aAt	1	1	B.1.575	0.000303
S	859	T859del	ACT	---	1	1	B.1.580	0.004065
S	859	T859N	aCt	aAt	1	1	B.1.582	0.000491
S	859	T859I	aCt	aTt	1	1	B.1.589	0.007576
S	859	T859T	acT	acC	1	1	B.1.596	0.000087
S	859	T859del	ACT	---	1	1	B.1.596	0.000087
S	859	T859I	aCt	aTt	1	1	B.1.605	0.005952
S	859	T859N	aCt	aAt	1	1	B.1.617.1	0.000129
S	859	T859S	aCt	aGt	1	1	B.1.617.2	0.000004
S	859	T859del	ACT	---	1	1	B.1.617.2	0.000004
S	859	T859I	aCt	aTt	1	1	B.1.617.3	0.002985
S	859	T859I	aCt	aTt	1	1	B.1.619.1	0.000641
S	859	T859A	Act	Gct	1	1	B.1.621	0.000089
S	859	T859I	aCt	aTt	1	1	B.1.621.1	0.000506
S	859	T859I	aCt	aTt	1	1	B.1.623	0.000536
S	859	T859N	aCt	aAt	1	1	B.1.628	0.000352
S	859	T859S	aCt	aGt	1	1	B.1.637	0.000073
S	859	T859del	ACT	---	1	1	B.1.637	0.000073
S	859	T859del1	Act	-ct	1	1	B.1.78	0.008547
S	859	T859del	ACT	---	1	1	B.3	0.000831
S	859	T859I	aCt	aTt	1	1	B.4.1	0.018868
S	859	T859N	aCt	aAt	1	1	C.14	0.004329
S	859	T859N	aCt	aAt	1	1	C.35	0.000774
S	859	T859I	aCt	aTt	1	1	C.36.3	0.000567
S	859	T859N	aCt	aAt	1	1	C.4	0.01
S	859	T859T	acT	acA	1	1	D.2	0.000075
S	859	T859S	Act	Tct	1	1	D.2	0.000075
S	859	T859del	ACT	---	1	1	D.2	0.000075
S	859	T859del1	Act	-ct	1	1	D.2	0.000075
S	859	T859I	aCt	aTt	1	1	P.1.1	0.000318
S	859	T859del	ACT	---	1	1	P.1.1	0.000318
S	859	T859del	ACT	---	1	1	P.1.12	0.000484
S	859	T859del	ACT	---	1	1	P.1.13	0.000898
S	859	T859I	aCt	aTt	1	1	P.1.13	0.000898
S	859	T859del	ACT	---	1	1	P.1.15	0.000232
S	859	T859T	acT	acC	1	1	P.1.15	0.000232
S	859	T859N	aCt	aAt	1	1	P.1.16	0.000374
S	859	T859I	aCt	aTt	1	1	P.1.7	0.000319
S	859	T859T	acT	acC	1	1	P.2	0.000187
S	859	T859I	aCt	aTt	1	1	Q.1	0.000126
S	859	T859I	aCt	aTt	1	1	Q.2	0.000613
S	859	T859N	aCt	aAt	1	1	Q.4	0.000455
S	859	T859del	ACT	---	1	1	U.3	0.003861

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.