CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 679

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	679	N679K		nonsyn	aaT	aaA	4948	2949	0.595998	23597-23599
S	679	N679K		nonsyn	aaT	aaG	4948	1999	0.404002	23597-23599
S	679	N679S		nonsyn	aAt	aGt	483	479	0.991718	23597-23599
S	679	N679S		nonsyn	AAT	TCA	483	2	0.00414079	23597-23599
S	679	N679S		nonsyn	aAT	aGC	483	2	0.00414079	23597-23599
S	679	N679T		nonsyn	aAt	aCt	444	440	0.990991	23597-23599
S	679	N679T		nonsyn	aAT	aCA	444	4	0.00900901	23597-23599
S	679	N679N		syn	aaT	aaC	409	409	1	23597-23599
S	679	N679Y		nonsyn	Aat	Tat	212	209	0.985849	23597-23599
S	679	N679Y		nonsyn	AaT	TaC	212	3	0.0141509	23597-23599
S	679	N679I		nonsyn	aAt	aTt	198	198	1	23597-23599
S	679	N679del		del	AAT	---	161	161	1	23597-23599
S	679	N679D		nonsyn	Aat	Gat	85	85	1	23597-23599
S	679	N679H		nonsyn	Aat	Cat	42	42	1	23597-23599
S	679	N679G		nonsyn	AAt	GGt	9	9	1	23597-23599
S	679	N679del2		del	aAT	a--	5	5	1	23597-23599
S	679	N679R		nonsyn	aAT	aGG	3	3	1	23597-23599
S	679	N679X		nonsyn	AaT	TaA	3	3	1	23597-23599
S	679	N679del1		del	Aat	-at	2	2	1	23597-23599
S	679	N679L		nonsyn	AAT	CTC	1	1	1	23597-23599
S	679	N679E		nonsyn	AaT	GaA	1	1	1	23597-23599

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	679	N679K	aaT	aaA	2949	4948	All	0.000564
S	679	N679K	aaT	aaG	1999	4948	All	0.000382
S	679	N679K	aaT	aaG	1021	1021	P.1.4	0.99707
S	679	N679K	aaT	aaG	665	717	B.1.2	0.005856
S	679	N679K	aaT	aaA	52	717	B.1.2	0.000458
S	679	N679K	aaT	aaA	684	684	P.1.12	0.331075
S	679	N679K	aaT	aaA	609	609	B.1.1.433	0.867521
S	679	N679S	aAt	aGt	479	483	All	0.000092
S	679	N679S	AAT	TCA	2	483	All	0
S	679	N679S	aAT	aGC	2	483	All	0
S	679	N679T	aAt	aCt	440	444	All	0.000084
S	679	N679T	aAT	aCA	4	444	All	0.000001
S	679	N679N	aaT	aaC	409	409	All	0.000078
S	679	N679K	aaT	aaA	253	281	B.1.1	0.00459
S	679	N679K	aaT	aaG	28	281	B.1.1	0.000508
S	679	N679K	aaT	aaA	254	254	B.1.111	0.298472
S	679	N679K	aaT	aaA	249	249	B.1.234	0.032854
S	679	N679Y	Aat	Tat	209	212	All	0.00004
S	679	N679Y	AaT	TaC	3	212	All	0.000001
S	679	N679K	aaT	aaA	210	210	C.1.2	0.893617
S	679	N679I	aAt	aTt	198	198	All	0.000038
S	679	N679del	AAT	---	161	161	All	0.000031
S	679	N679S	aAt	aGt	100	100	AY.27	0.006472
S	679	N679K	aaT	aaA	84	86	B.1.258	0.00559
S	679	N679K	aaT	aaG	2	86	B.1.258	0.000133
S	679	N679D	Aat	Gat	85	85	All	0.000016
S	679	N679K	aaT	aaA	58	85	B.1	0.000531
S	679	N679K	aaT	aaG	27	85	B.1	0.000247
S	679	N679Y	Aat	Tat	79	79	AY.4	0.000123
S	679	N679I	aAt	aTt	78	78	AY.4.2	0.001692
S	679	N679N	aaT	aaC	72	72	AY.4	0.000112
S	679	N679K	aaT	aaG	68	68	B.1.243.2	0.985507
S	679	N679K	aaT	aaA	56	64	P.1	0.000882
S	679	N679K	aaT	aaG	8	64	P.1	0.000126
S	679	N679K	aaT	aaA	63	63	B.1.1.28	0.019608
S	679	N679S	aAt	aGt	61	61	B.1.617.2	0.00023
S	679	N679T	aAt	aCt	59	59	B.1.2	0.00052
S	679	N679Y	Aat	Tat	51	51	B.1.1.7	0.000046
S	679	N679D	Aat	Gat	48	48	B.1.1.7	0.000043
S	679	N679S	aAt	aGt	47	47	AY.4	0.000073
S	679	N679T	aAt	aCt	45	45	B.1.617.2	0.000169
S	679	N679S	aAt	aGt	43	43	B.1.1.7	0.000038
S	679	N679H	Aat	Cat	42	42	All	0.000008
S	679	N679T	aAt	aCt	42	42	AY.3	0.000418
S	679	N679K	aaT	aaA	42	42	B.1.9.5	0.238636
S	679	N679N	aaT	aaC	41	41	AY.25	0.000247
S	679	N679S	aAt	aGt	41	41	AY.29	0.000647
S	679	N679K	aaT	aaA	26	41	B.1.1.7	0.000023
S	679	N679K	aaT	aaG	15	41	B.1.1.7	0.000013
S	679	N679K	aaT	aaG	40	40	B.1.36.1	0.04561
S	679	N679T	aAt	aCt	38	38	AY.4	0.000059
S	679	N679N	aaT	aaC	37	37	AY.44	0.000225
S	679	N679I	aAt	aTt	35	35	AY.43	0.000155
S	679	N679del	AAT	---	35	35	B.1	0.000321
S	679	N679S	aAt	aGt	34	34	AY.121	0.004601
S	679	N679N	aaT	aaC	32	32	B.1.1.7	0.000029
S	679	N679T	aAt	aCt	29	29	AY.26	0.000821
S	679	N679K	aaT	aaA	29	29	C.36.3.1	0.078804
S	679	N679S	aAt	aGt	28	28	AY.39	0.000692
S	679	N679T	aAt	aCt	28	28	B.1.1.7	0.000025
S	679	N679T	aAt	aCt	27	27	AY.25	0.000162
S	679	N679S	aAt	aGt	27	27	B.1.177	0.000356
S	679	N679K	aaT	aaG	26	26	B.1.637	0.0019
S	679	N679N	aaT	aaC	25	25	B.1.2	0.00022
S	679	N679I	aAt	aTt	24	24	AY.103	0.000149
S	679	N679N	aaT	aaC	22	22	AY.43	0.000097
S	679	N679N	aaT	aaC	22	22	B.1.177	0.00029
S	679	N679K	aaT	aaA	22	22	B.1.214.2	0.013189
S	679	N679S	aAt	aGt	21	21	B.1.609	0.010067
S	679	N679T	aAt	aCt	20	20	AY.43	0.000089
S	679	N679K	aaT	aaA	20	20	B.1.1.203	0.338983
S	679	N679K	aaT	aaA	20	20	B.1.560	0.092593
S	679	N679N	aaT	aaC	19	19	B.1.617.2	0.000072
S	679	N679Y	Aat	Tat	18	18	AY.103	0.000112
S	679	N679K	aaT	aaA	18	18	B.1.1.1	0.00588
S	679	N679K	aaT	aaG	18	18	B.1.529	1
S	679	N679T	aAt	aCt	17	17	AY.103	0.000106
S	679	N679K	aaT	aaA	16	16	B.1.177	0.000211
S	679	N679I	aAt	aTt	16	16	B.1.617.2	0.00006
S	679	N679K	aaT	aaA	12	16	C.37	0.001393
S	679	N679K	aaT	aaG	4	16	C.37	0.000464
S	679	N679H	Aat	Cat	15	15	B.1.1	0.000272
S	679	N679del	AAT	---	15	15	B.1.1	0.000272
S	679	N679K	aaT	aaA	15	15	K.2	0.6
S	679	N679K	aaT	aaG	14	14	AY.25	0.000084
S	679	N679K	aaT	aaA	14	14	B.1.470	0.019663
S	679	N679K	aaT	aaG	13	13	B.1.596	0.001133
S	679	N679K	aaT	aaA	13	13	P.1.5	1
S	679	N679N	aaT	aaC	11	11	B.1.1.274	0.055556
S	679	N679del	AAT	---	11	11	B.1.160	0.000343
S	679	N679T	aAt	aCt	10	10	AY.120.1	0.00321
S	679	N679N	aaT	aaC	10	10	AY.3	0.000099
S	679	N679del	AAT	---	10	10	B	0.001278
S	679	N679I	aAt	aTt	10	10	B.1.1.7	0.000009
S	679	N679K	aaT	aaG	5	10	B.1.36	0.00073
S	679	N679K	aaT	aaA	5	10	B.1.36	0.00073
S	679	N679G	AAt	GGt	9	9	All	0.000002
S	679	N679T	aAt	aCt	9	9	AY.9.2	0.000331
S	679	N679H	Aat	Cat	9	9	B.1.1.419	0.066667
S	679	N679D	Aat	Gat	8	8	AY.4	0.000012
S	679	N679N	aaT	aaC	8	8	AY.45	0.000973
S	679	N679T	aAt	aCt	8	8	AY.47	0.000249
S	679	N679K	aaT	aaA	8	8	B.1.1.291	0.005939
S	679	N679H	Aat	Cat	8	8	B.1.1.306	0.003507
S	679	N679del	AAT	---	8	8	B.1.1.7	0.000007
S	679	N679N	aaT	aaC	8	8	B.1.177.7	0.001319
S	679	N679Y	Aat	Tat	8	8	B.1.2	0.00007
S	679	N679del	AAT	---	8	8	B.1.617.2	0.00003
S	679	N679S	aAt	aGt	7	7	AY.103	0.000043
S	679	N679N	aaT	aaC	7	7	AY.103	0.000043
S	679	N679del	AAT	---	7	7	AY.43	0.000031
S	679	N679Y	Aat	Tat	7	7	B.1.177.10	0.006146
S	679	N679Y	Aat	Tat	7	7	B.1.617.2	0.000026
S	679	N679Y	Aat	Tat	7	7	P.1	0.00011
S	679	N679T	aAt	aCt	6	6	AY.102	0.000159
S	679	N679N	aaT	aaC	6	6	AY.20	0.000233
S	679	N679I	aAt	aTt	6	6	AY.3	0.00006
S	679	N679K	aaT	aaA	6	6	B.1.1.317	0.00247
S	679	N679K	aaT	aaA	6	6	B.1.1.382	0.214286
S	679	N679del2	aAT	a--	5	5	All	0.000001
S	679	N679del	AAT	---	5	5	AY.107	0.00233
S	679	N679T	aAt	aCt	5	5	AY.119	0.000177
S	679	N679D	Aat	Gat	5	5	AY.120	0.000186
S	679	N679N	aaT	aaC	5	5	AY.23	0.000349
S	679	N679S	aAt	aGt	5	5	AY.25	0.00003
S	679	N679T	aAt	aCt	4	5	AY.39	0.000099
S	679	N679T	aAT	aCA	1	5	AY.39	0.000025
S	679	N679T	aAt	aCt	5	5	AY.5	0.000103
S	679	N679D	Aat	Gat	5	5	AY.9.2	0.000184
S	679	N679T	aAt	aCt	5	5	AY.99.2	0.000461
S	679	N679N	aaT	aaC	5	5	B.1.1	0.000091
S	679	N679K	aaT	aaG	4	5	B.1.1.25	0.002274
S	679	N679K	aaT	aaA	1	5	B.1.1.25	0.000569
S	679	N679K	aaT	aaA	5	5	B.1.1.372	0.003444
S	679	N679T	aAt	aCt	5	5	B.1.429	0.000118
S	679	N679K	aaT	aaG	5	5	P.1.10	0.001347
S	679	N679N	aaT	aaC	5	5	P.2	0.000933
S	679	N679del	AAT	---	4	4	A	0.001548
S	679	N679N	aaT	aaC	4	4	AY.102	0.000106
S	679	N679del	AAT	---	4	4	AY.4	0.000006
S	679	N679T	aAt	aCt	4	4	AY.4.2	0.000087
S	679	N679T	aAt	aCt	3	4	AY.46	0.000312
S	679	N679T	aAT	aCA	1	4	AY.46	0.000104
S	679	N679S	aAt	aGt	4	4	AY.6	0.000165
S	679	N679T	aAt	aCt	4	4	AY.87	0.003331
S	679	N679D	Aat	Gat	4	4	B.1	0.000037
S	679	N679S	aAt	aGt	4	4	B.1.1.431	0.064516
S	679	N679H	Aat	Cat	4	4	B.1.351	0.000119
S	679	N679K	aaT	aaG	4	4	B.1.411	0.014815
S	679	N679K	aaT	aaA	4	4	B.1.540	0.038835
S	679	N679del	AAT	---	4	4	P.1.15	0.000929
S	679	N679K	aaT	aaA	2	3		0.111111
S	679	N679K	aaT	aaG	1	3		0.055556
S	679	N679X	AaT	TaA	3	3	All	0.000001
S	679	N679R	aAT	aGG	3	3	All	0.000001
S	679	N679N	aaT	aaC	3	3	AY.100	0.000138
S	679	N679del	AAT	---	3	3	AY.103	0.000019
S	679	N679N	aaT	aaC	3	3	AY.118	0.000188
S	679	N679T	aAt	aCt	3	3	AY.12	0.000948
S	679	N679I	aAt	aTt	3	3	AY.14	0.000264
S	679	N679del	AAT	---	3	3	AY.25	0.000018
S	679	N679del	AAT	---	3	3	AY.3	0.00003
S	679	N679N	aaT	aaC	3	3	AY.3.1	0.000256
S	679	N679I	aAt	aTt	3	3	AY.4	0.000005
S	679	N679S	aAt	aGt	3	3	AY.5	0.000062
S	679	N679T	aAt	aCt	3	3	AY.7.1	0.000338
S	679	N679N	aaT	aaC	3	3	AY.92	0.000862
S	679	N679I	aAt	aTt	3	3	B.1	0.000027
S	679	N679K	aaT	aaA	3	3	B.1.1.153	0.003286
S	679	N679K	aaT	aaA	3	3	B.1.1.216	0.002671
S	679	N679K	aaT	aaA	3	3	B.1.1.54	0.009063
S	679	N679G	AAt	GGt	3	3	B.1.1.7	0.000003
S	679	N679K	aaT	aaA	3	3	B.1.177.60	0.000655
S	679	N679R	aAT	aGG	3	3	B.1.2	0.000026
S	679	N679S	aAt	aGt	2	3	B.1.2	0.000018
S	679	N679S	aAT	aGC	1	3	B.1.2	0.000009
S	679	N679K	aaT	aaA	3	3	B.1.221	0.000213
S	679	N679N	aaT	aaC	3	3	B.1.236	0.00616
S	679	N679K	aaT	aaA	3	3	B.1.258.3	0.005025
S	679	N679K	aaT	aaG	3	3	B.1.36.8	0.003
S	679	N679K	aaT	aaG	3	3	B.1.396	0.002117
S	679	N679K	aaT	aaA	3	3	B.1.429	0.000071
S	679	N679N	aaT	aaC	3	3	B.1.509	0.002597
S	679	N679K	aaT	aaA	2	3	B.1.525	0.000226
S	679	N679K	aaT	aaG	1	3	B.1.525	0.000113
S	679	N679K	aaT	aaG	3	3	B.1.526	0.000071
S	679	N679N	aaT	aaC	3	3	B.1.526	0.000071
S	679	N679S	aAt	aGt	3	3	B.1.561	0.001191
S	679	N679Y	AaT	TaC	3	3	B.1.575	0.00091
S	679	N679K	aaT	aaG	3	3	B.1.617.2	0.000011
S	679	N679del	AAT	---	3	3	P.1	0.000047
S	679	N679N	aaT	aaC	3	3	P.1.14	0.000143
S	679	N679X	AaT	TaA	2	2		0.111111
S	679	N679del	AAT	---	2	2		0.111111
S	679	N679T	aAT	aCA	2	2		0.111111
S	679	N679S	AAT	TCA	2	2		0.111111
S	679	N679K	aaT	aaA	1	2	A	0.000387
S	679	N679K	aaT	aaG	1	2	A	0.000387
S	679	N679K	aaT	aaG	2	2	A.2.4	0.006734
S	679	N679H	Aat	Cat	2	2	A.2.5	0.000998
S	679	N679del1	Aat	-at	2	2	All	0
S	679	N679N	aaT	aaC	2	2	AY.101	0.000981
S	679	N679T	aAt	aCt	2	2	AY.113	0.000285
S	679	N679T	aAt	aCt	2	2	AY.118	0.000125
S	679	N679T	aAt	aCt	2	2	AY.121	0.000271
S	679	N679K	aaT	aaA	2	2	AY.20	0.000078
S	679	N679Y	Aat	Tat	2	2	AY.20	0.000078
S	679	N679S	aAt	aGt	2	2	AY.23.1	0.000835
S	679	N679D	Aat	Gat	2	2	AY.29	0.000032
S	679	N679S	aAt	aGt	2	2	AY.3	0.00002
S	679	N679N	aaT	aaC	2	2	AY.34	0.000194
S	679	N679I	aAt	aTt	2	2	AY.39	0.000049
S	679	N679S	aAt	aGt	2	2	AY.4.2	0.000043
S	679	N679T	aAt	aCt	2	2	AY.4.5	0.000215
S	679	N679T	aAt	aCt	2	2	AY.42	0.00008
S	679	N679Y	Aat	Tat	2	2	AY.43	0.000009
S	679	N679del	AAT	---	2	2	AY.44	0.000012
S	679	N679Y	Aat	Tat	2	2	AY.44	0.000012
S	679	N679T	aAt	aCt	2	2	AY.44	0.000012
S	679	N679S	aAt	aGt	2	2	AY.44	0.000012
S	679	N679T	aAt	aCt	2	2	AY.45	0.000243
S	679	N679T	aAt	aCt	2	2	AY.54	0.000191
S	679	N679T	aAt	aCt	2	2	AY.6	0.000082
S	679	N679T	aAt	aCt	2	2	AY.61	0.00021
S	679	N679T	aAt	aCt	2	2	AY.84	0.000875
S	679	N679N	aaT	aaC	2	2	AY.9.2.1	0.003953
S	679	N679T	aAt	aCt	2	2	AY.91	0.001461
S	679	N679T	aAt	aCt	2	2	AY.98.1	0.000097
S	679	N679N	aaT	aaC	2	2	B	0.000256
S	679	N679N	aaT	aaC	2	2	B.1	0.000018
S	679	N679S	aAt	aGt	2	2	B.1	0.000018
S	679	N679S	aAt	aGt	2	2	B.1.1	0.000036
S	679	N679K	aaT	aaA	2	2	B.1.1.148	0.017544
S	679	N679K	aaT	aaA	2	2	B.1.1.161	0.007067
S	679	N679K	aaT	aaA	2	2	B.1.1.198	0.002937
S	679	N679K	aaT	aaA	2	2	B.1.1.306	0.000877
S	679	N679Y	Aat	Tat	2	2	B.1.1.326	0.003521
S	679	N679Y	Aat	Tat	2	2	B.1.1.329	0.007692
S	679	N679K	aaT	aaA	2	2	B.1.1.453	0.016949
S	679	N679K	aaT	aaA	2	2	B.1.1.464	0.002946
S	679	N679K	aaT	aaG	2	2	B.1.110.3	0.001437
S	679	N679G	AAt	GGt	2	2	B.1.177	0.000026
S	679	N679D	Aat	Gat	2	2	B.1.177	0.000026
S	679	N679del	AAT	---	2	2	B.1.177	0.000026
S	679	N679K	aaT	aaA	2	2	B.1.177.23	0.006472
S	679	N679N	aaT	aaC	2	2	B.1.206	0.001631
S	679	N679Y	Aat	Tat	2	2	B.1.232	0.001075
S	679	N679K	aaT	aaA	1	2	B.1.243	0.00007
S	679	N679K	aaT	aaG	1	2	B.1.243	0.00007
S	679	N679N	aaT	aaC	2	2	B.1.258	0.000133
S	679	N679S	aAt	aGt	2	2	B.1.258	0.000133
S	679	N679S	aAt	aGt	2	2	B.1.351	0.000059
S	679	N679T	aAt	aCt	2	2	B.1.351	0.000059
S	679	N679K	aaT	aaG	1	2	B.1.351	0.00003
S	679	N679K	aaT	aaA	1	2	B.1.351	0.00003
S	679	N679Y	Aat	Tat	2	2	B.1.36	0.000292
S	679	N679del	AAT	---	2	2	B.1.416	0.002538
S	679	N679K	aaT	aaG	1	2	B.1.427	0.00005
S	679	N679K	aaT	aaA	1	2	B.1.427	0.00005
S	679	N679K	aaT	aaA	1	2	B.1.456	0.003268
S	679	N679K	aaT	aaG	1	2	B.1.456	0.003268
S	679	N679del	AAT	---	2	2	B.1.462	0.014493
S	679	N679del2	aAT	a--	2	2	B.1.462	0.014493
S	679	N679K	aaT	aaA	2	2	B.1.466.2	0.000782
S	679	N679del	AAT	---	2	2	B.1.621	0.000177
S	679	N679K	aaT	aaA	2	2	C.1	0.004785
S	679	N679S	aAt	aGt	2	2	C.37	0.000232
S	679	N679I	aAt	aTt	2	2	P.1.14	0.000096
S	679	N679K	aaT	aaA	2	2	P.1.15	0.000465
S	679	N679T	aAt	aCt	2	2	P.1.7	0.000639
S	679	N679Y	Aat	Tat	2	2	Q.1	0.000253
S	679	N679N	aaT	aaC	1	1	A	0.000387
S	679	N679T	aAt	aCt	1	1	A	0.000387
S	679	N679del	AAT	---	1	1	A.1	0.000282
S	679	N679K	aaT	aaA	1	1	AB.1	0.008197
S	679	N679E	AaT	GaA	1	1	All	0
S	679	N679L	AAT	CTC	1	1	All	0
S	679	N679T	aAt	aCt	1	1	AY.100	0.000046
S	679	N679K	aaT	aaA	1	1	AY.102	0.000027
S	679	N679D	Aat	Gat	1	1	AY.103	0.000006
S	679	N679N	aaT	aaC	1	1	AY.104	0.001984
S	679	N679I	aAt	aTt	1	1	AY.106	0.000335
S	679	N679S	aAt	aGt	1	1	AY.108	0.001103
S	679	N679T	aAt	aCt	1	1	AY.110	0.000113
S	679	N679N	aaT	aaC	1	1	AY.111	0.000183
S	679	N679S	aAt	aGt	1	1	AY.116	0.000287
S	679	N679S	aAt	aGt	1	1	AY.119	0.000035
S	679	N679I	aAt	aTt	1	1	AY.120	0.000037
S	679	N679D	Aat	Gat	1	1	AY.121	0.000135
S	679	N679T	aAt	aCt	1	1	AY.14	0.000088
S	679	N679T	aAt	aCt	1	1	AY.16	0.00038
S	679	N679T	aAt	aCt	1	1	AY.19	0.00114
S	679	N679T	aAt	aCt	1	1	AY.20	0.000039
S	679	N679T	aAt	aCt	1	1	AY.23	0.00007
S	679	N679T	aAt	aCt	1	1	AY.24	0.000431
S	679	N679I	aAt	aTt	1	1	AY.25	0.000006
S	679	N679Y	Aat	Tat	1	1	AY.25	0.000006
S	679	N679S	aAt	aGt	1	1	AY.26	0.000028
S	679	N679K	aaT	aaG	1	1	AY.26	0.000028
S	679	N679N	aaT	aaC	1	1	AY.29	0.000016
S	679	N679T	aAt	aCt	1	1	AY.29	0.000016
S	679	N679S	aAt	aGt	1	1	AY.29.1	0.000221
S	679	N679H	Aat	Cat	1	1	AY.3	0.00001
S	679	N679T	aAt	aCt	1	1	AY.3.1	0.000085
S	679	N679S	aAt	aGt	1	1	AY.3.1	0.000085
S	679	N679T	aAt	aCt	1	1	AY.30	0.000396
S	679	N679S	aAt	aGt	1	1	AY.32	0.000532
S	679	N679S	aAt	aGt	1	1	AY.33	0.000067
S	679	N679Y	Aat	Tat	1	1	AY.35	0.000233
S	679	N679T	aAt	aCt	1	1	AY.35	0.000233
S	679	N679N	aaT	aaC	1	1	AY.39	0.000025
S	679	N679K	aaT	aaA	1	1	AY.39	0.000025
S	679	N679S	aAt	aGt	1	1	AY.39.1	0.00004
S	679	N679N	aaT	aaC	1	1	AY.39.1	0.00004
S	679	N679K	aaT	aaA	1	1	AY.4	0.000002
S	679	N679H	Aat	Cat	1	1	AY.4	0.000002
S	679	N679N	aaT	aaC	1	1	AY.4.2	0.000022
S	679	N679Y	Aat	Tat	1	1	AY.4.5	0.000107
S	679	N679N	aaT	aaC	1	1	AY.4.5	0.000107
S	679	N679I	aAt	aTt	1	1	AY.41	0.000294
S	679	N679N	aaT	aaC	1	1	AY.42	0.00004
S	679	N679S	aAt	aGt	1	1	AY.43	0.000004
S	679	N679K	aaT	aaA	1	1	AY.44	0.000006
S	679	N679del1	Aat	-at	1	1	AY.44	0.000006
S	679	N679H	Aat	Cat	1	1	AY.44	0.000006
S	679	N679S	aAt	aGt	1	1	AY.45	0.000122
S	679	N679K	aaT	aaA	1	1	AY.46	0.000104
S	679	N679N	aaT	aaC	1	1	AY.46	0.000104
S	679	N679del	AAT	---	1	1	AY.46.2	0.000635
S	679	N679I	aAt	aTt	1	1	AY.46.6	0.000072
S	679	N679K	aaT	aaA	1	1	AY.47	0.000031
S	679	N679N	aaT	aaC	1	1	AY.5	0.000021
S	679	N679Y	Aat	Tat	1	1	AY.5	0.000021
S	679	N679del	AAT	---	1	1	AY.5	0.000021
S	679	N679T	aAt	aCt	1	1	AY.5.4	0.000277
S	679	N679Y	Aat	Tat	1	1	AY.5.4	0.000277
S	679	N679N	aaT	aaC	1	1	AY.54	0.000095
S	679	N679T	aAt	aCt	1	1	AY.55	0.000917
S	679	N679T	aAt	aCt	1	1	AY.57	0.000656
S	679	N679T	aAt	aCt	1	1	AY.58	0.000907
S	679	N679S	aAt	aGt	1	1	AY.59	0.00053
S	679	N679S	aAt	aGt	1	1	AY.61	0.000105
S	679	N679K	aaT	aaA	1	1	AY.61	0.000105
S	679	N679I	aAt	aTt	1	1	AY.61	0.000105
S	679	N679T	aAt	aCt	1	1	AY.65	0.000533
S	679	N679K	aaT	aaA	1	1	AY.67	0.000464
S	679	N679N	aaT	aaC	1	1	AY.68	0.000274
S	679	N679T	aAt	aCt	1	1	AY.69	0.000187
S	679	N679I	aAt	aTt	1	1	AY.70	0.000209
S	679	N679T	aAt	aCt	1	1	AY.70	0.000209
S	679	N679T	aAt	aCt	1	1	AY.75	0.000056
S	679	N679N	aaT	aaC	1	1	AY.75	0.000056
S	679	N679T	aAt	aCt	1	1	AY.75.1	0.00018
S	679	N679T	aAt	aCt	1	1	AY.77	0.001127
S	679	N679del	AAT	---	1	1	AY.84	0.000437
S	679	N679T	aAt	aCt	1	1	AY.9	0.000068
S	679	N679D	Aat	Gat	1	1	AY.9	0.000068
S	679	N679N	aaT	aaC	1	1	AY.9.1	0.000084
S	679	N679del	AAT	---	1	1	AY.9.2	0.000037
S	679	N679S	aAt	aGt	1	1	AY.92	0.000287
S	679	N679S	aAt	aGt	1	1	AY.94	0.000443
S	679	N679I	aAt	aTt	1	1	AY.98	0.000079
S	679	N679S	aAt	aGt	1	1	AY.98	0.000079
S	679	N679del	AAT	---	1	1	AY.99	0.001049
S	679	N679Y	Aat	Tat	1	1	AY.99.2	0.000092
S	679	N679del2	aAT	a--	1	1	B	0.000128
S	679	N679S	aAt	aGt	1	1	B	0.000128
S	679	N679G	AAt	GGt	1	1	B.1	0.000009
S	679	N679T	aAt	aCt	1	1	B.1	0.000009
S	679	N679X	AaT	TaA	1	1	B.1.1	0.000018
S	679	N679D	Aat	Gat	1	1	B.1.1	0.000018
S	679	N679E	AaT	GaA	1	1	B.1.1	0.000018
S	679	N679G	AAt	GGt	1	1	B.1.1	0.000018
S	679	N679Y	Aat	Tat	1	1	B.1.1	0.000018
S	679	N679T	aAt	aCt	1	1	B.1.1.1	0.000327
S	679	N679K	aaT	aaA	1	1	B.1.1.117	0.009709
S	679	N679K	aaT	aaA	1	1	B.1.1.220	0.001859
S	679	N679N	aaT	aaC	1	1	B.1.1.231	0.003096
S	679	N679del	AAT	---	1	1	B.1.1.241	0.00207
S	679	N679K	aaT	aaA	1	1	B.1.1.243	0.004082
S	679	N679S	aAt	aGt	1	1	B.1.1.269	0.001353
S	679	N679K	aaT	aaA	1	1	B.1.1.277	0.000759
S	679	N679S	aAt	aGt	1	1	B.1.1.284	0.000107
S	679	N679K	aaT	aaA	1	1	B.1.1.31	0.066667
S	679	N679K	aaT	aaG	1	1	B.1.1.316	0.000925
S	679	N679K	aaT	aaG	1	1	B.1.1.322	0.008772
S	679	N679S	aAt	aGt	1	1	B.1.1.33	0.000421
S	679	N679del	AAT	---	1	1	B.1.1.354	0.004386
S	679	N679K	aaT	aaA	1	1	B.1.1.37	0.000193
S	679	N679D	Aat	Gat	1	1	B.1.1.37	0.000193
S	679	N679del	AAT	---	1	1	B.1.1.372	0.000689
S	679	N679K	aaT	aaA	1	1	B.1.1.39	0.00051
S	679	N679del	AAT	---	1	1	B.1.1.39	0.00051
S	679	N679K	aaT	aaA	1	1	B.1.1.402	0.011111
S	679	N679K	aaT	aaA	1	1	B.1.1.419	0.007407
S	679	N679K	aaT	aaA	1	1	B.1.1.432	0.001266
S	679	N679del	AAT	---	1	1	B.1.1.482	0.023256
S	679	N679K	aaT	aaG	1	1	B.1.1.486	0.001577
S	679	N679S	aAt	aGt	1	1	B.1.1.519	0.00004
S	679	N679N	aaT	aaC	1	1	B.1.1.519	0.00004
S	679	N679T	aAt	aCt	1	1	B.1.1.519	0.00004
S	679	N679H	Aat	Cat	1	1	B.1.1.519	0.00004
S	679	N679K	aaT	aaA	1	1	B.1.1.523	0.001563
S	679	N679L	AAT	CTC	1	1	B.1.1.7	0.000001
S	679	N679K	aaT	aaA	1	1	B.1.1.99	0.02381
S	679	N679S	aAt	aGt	1	1	B.1.108	0.005814
S	679	N679N	aaT	aaC	1	1	B.1.139	0.000733
S	679	N679K	aaT	aaA	1	1	B.1.158	0.02381
S	679	N679K	aaT	aaA	1	1	B.1.160	0.000031
S	679	N679I	aAt	aTt	1	1	B.1.160	0.000031
S	679	N679del	AAT	---	1	1	B.1.160.20	0.008929
S	679	N679K	aaT	aaA	1	1	B.1.160.32	0.004292
S	679	N679del	AAT	---	1	1	B.1.160.33	0.004425
S	679	N679K	aaT	aaG	1	1	B.1.160.9	0.007194
S	679	N679I	aAt	aTt	1	1	B.1.177	0.000013
S	679	N679I	aAt	aTt	1	1	B.1.177.12	0.000152
S	679	N679del	AAT	---	1	1	B.1.177.16	0.000664
S	679	N679N	aaT	aaC	1	1	B.1.177.21	0.000076
S	679	N679K	aaT	aaA	1	1	B.1.177.21	0.000076
S	679	N679S	aAt	aGt	1	1	B.1.177.44	0.000519
S	679	N679D	Aat	Gat	1	1	B.1.177.7	0.000165
S	679	N679I	aAt	aTt	1	1	B.1.177.75	0.001041
S	679	N679del	AAT	---	1	1	B.1.177.75	0.001041
S	679	N679D	Aat	Gat	1	1	B.1.177.8	0.000752
S	679	N679S	aAt	aGt	1	1	B.1.177.80	0.001912
S	679	N679del	AAT	---	1	1	B.1.177.81	0.000189
S	679	N679K	aaT	aaA	1	1	B.1.177.86	0.000183
S	679	N679D	Aat	Gat	1	1	B.1.177.86	0.000183
S	679	N679D	Aat	Gat	1	1	B.1.2	0.000009
S	679	N679I	aAt	aTt	1	1	B.1.2	0.000009
S	679	N679G	AAt	GGt	1	1	B.1.2	0.000009
S	679	N679D	Aat	Gat	1	1	B.1.221	0.000071
S	679	N679N	aaT	aaC	1	1	B.1.221	0.000071
S	679	N679G	AAt	GGt	1	1	B.1.221	0.000071
S	679	N679S	aAt	aGt	1	1	B.1.221	0.000071
S	679	N679S	aAt	aGt	1	1	B.1.243	0.00007
S	679	N679del2	aAT	a--	1	1	B.1.243	0.00007
S	679	N679N	aaT	aaC	1	1	B.1.243	0.00007
S	679	N679Y	Aat	Tat	1	1	B.1.243	0.00007
S	679	N679del	AAT	---	1	1	B.1.258	0.000067
S	679	N679T	aAt	aCt	1	1	B.1.258	0.000067
S	679	N679K	aaT	aaA	1	1	B.1.258.14	0.00098
S	679	N679N	aaT	aaC	1	1	B.1.258.17	0.000104
S	679	N679K	aaT	aaA	1	1	B.1.284	0.013158
S	679	N679S	aAt	aGt	1	1	B.1.311	0.000275
S	679	N679K	aaT	aaA	1	1	B.1.349	0.000715
S	679	N679N	aaT	aaC	1	1	B.1.351	0.00003
S	679	N679del	AAT	---	1	1	B.1.351	0.00003
S	679	N679Y	Aat	Tat	1	1	B.1.351.3	0.000876
S	679	N679N	aaT	aaC	1	1	B.1.36	0.000146
S	679	N679del1	Aat	-at	1	1	B.1.36	0.000146
S	679	N679K	aaT	aaA	1	1	B.1.36.29	0.000517
S	679	N679N	aaT	aaC	1	1	B.1.36.29	0.000517
S	679	N679K	aaT	aaA	1	1	B.1.36.34	0.021277
S	679	N679N	aaT	aaC	1	1	B.1.36.35	0.002604
S	679	N679I	aAt	aTt	1	1	B.1.377	0.004566
S	679	N679K	aaT	aaA	1	1	B.1.408	0.00369
S	679	N679Y	Aat	Tat	1	1	B.1.422	0.000812
S	679	N679del	AAT	---	1	1	B.1.429	0.000024
S	679	N679I	aAt	aTt	1	1	B.1.429	0.000024
S	679	N679Y	Aat	Tat	1	1	B.1.456	0.003268
S	679	N679I	aAt	aTt	1	1	B.1.466.2	0.000391
S	679	N679N	aaT	aaC	1	1	B.1.466.2	0.000391
S	679	N679K	aaT	aaA	1	1	B.1.468	0.005714
S	679	N679K	aaT	aaA	1	1	B.1.497	0.000315
S	679	N679N	aaT	aaC	1	1	B.1.501	0.007353
S	679	N679K	aaT	aaA	1	1	B.1.509	0.000866
S	679	N679del	AAT	---	1	1	B.1.525	0.000113
S	679	N679K	aaT	aaA	1	1	B.1.561	0.000397
S	679	N679N	aaT	aaC	1	1	B.1.575	0.000303
S	679	N679K	aaT	aaA	1	1	B.1.595	0.000261
S	679	N679N	aaT	aaC	1	1	B.1.596	0.000087
S	679	N679S	aAT	aGC	1	1	B.1.596	0.000087
S	679	N679del	AAT	---	1	1	B.1.596	0.000087
S	679	N679K	aaT	aaG	1	1	B.1.609	0.000479
S	679	N679del2	aAT	a--	1	1	B.1.617.1	0.000129
S	679	N679T	aAt	aCt	1	1	B.1.617.1	0.000129
S	679	N679K	aaT	aaA	1	1	B.1.617.1	0.000129
S	679	N679K	aaT	aaA	1	1	B.1.618	0.004032
S	679	N679S	aAt	aGt	1	1	B.1.619	0.000871
S	679	N679K	aaT	aaA	1	1	B.1.619	0.000871
S	679	N679del	AAT	---	1	1	B.1.620	0.000946
S	679	N679del	AAT	---	1	1	B.1.627	0.00202
S	679	N679K	aaT	aaG	1	1	B.1.633	0.041667
S	679	N679del	AAT	---	1	1	B.1.638	0.052632
S	679	N679K	aaT	aaG	1	1	B.1.93	0.000934
S	679	N679K	aaT	aaA	1	1	B.52	0.010101
S	679	N679Y	Aat	Tat	1	1	B.6.8	0.008264
S	679	N679D	Aat	Gat	1	1	C.16	0.00106
S	679	N679Y	Aat	Tat	1	1	C.18	0.002591
S	679	N679S	aAt	aGt	1	1	C.2	0.016129
S	679	N679T	aAt	aCt	1	1	C.23	0.005814
S	679	N679K	aaT	aaG	1	1	C.33	0.058824
S	679	N679K	aaT	aaA	1	1	C.35	0.000774
S	679	N679N	aaT	aaC	1	1	C.36.3	0.000567
S	679	N679Y	Aat	Tat	1	1	C.37	0.000116
S	679	N679del	AAT	---	1	1	C.37	0.000116
S	679	N679Y	Aat	Tat	1	1	N.3	0.005814
S	679	N679K	aaT	aaA	1	1	N.5	0.001767
S	679	N679S	aAt	aGt	1	1	P.1	0.000016
S	679	N679T	aAt	aCt	1	1	P.1	0.000016
S	679	N679N	aaT	aaC	1	1	P.1	0.000016
S	679	N679del	AAT	---	1	1	P.1.13	0.000898
S	679	N679S	aAt	aGt	1	1	P.1.15	0.000232
S	679	N679Y	Aat	Tat	1	1	P.3	0.001595

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.