CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 375

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	375	S375S		syn	tcC	tcT	3366	3065	0.910576	22685-22687
S	375	S375S		syn	tcC	tcA	3366	212	0.0629828	22685-22687
S	375	S375S		syn	tcC	tcG	3366	87	0.0258467	22685-22687
S	375	S375S		syn	TCc	AGc	3366	2	0.000594177	22685-22687
S	375	S375F		nonsyn	tCc	tTc	225	225	1	22685-22687
S	375	S375del		del	TCC	---	70	70	1	22685-22687
S	375	S375P		nonsyn	Tcc	Ccc	63	61	0.968254	22685-22687
S	375	S375P		nonsyn	TcC	CcA	63	2	0.031746	22685-22687
S	375	S375T		nonsyn	Tcc	Acc	42	42	1	22685-22687
S	375	S375Y		nonsyn	tCc	tAc	38	38	1	22685-22687
S	375	S375A		nonsyn	Tcc	Gcc	28	27	0.964286	22685-22687
S	375	S375A		nonsyn	TcC	GcT	28	1	0.0357143	22685-22687
S	375	S375C		nonsyn	tCc	tGc	7	7	1	22685-22687
S	375	S375del1		del	tcC	tc-	3	2	0.666667	22685-22687
S	375	S375del1		del	Tcc	-cc	3	1	0.333333	22685-22687
S	375	S375del2		del	TCc	--c	2	1	0.5	22685-22687
S	375	S375del2		del	TCC	--N	2	1	0.5	22685-22687
S	375	S375N		nonsyn	TCc	AAc	1	1	1	22685-22687

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	375	S375S	tcC	tcT	3065	3366	All	0.000586
S	375	S375S	tcC	tcA	212	3366	All	0.000041
S	375	S375S	tcC	tcG	87	3366	All	0.000017
S	375	S375S	TCc	AGc	2	3366	All	0
S	375	S375S	tcC	tcT	635	781	AY.4	0.000988
S	375	S375S	tcC	tcA	145	781	AY.4	0.000226
S	375	S375S	tcC	tcG	1	781	AY.4	0.000002
S	375	S375S	tcC	tcT	548	573	B.1.1.7	0.000491
S	375	S375S	tcC	tcG	20	573	B.1.1.7	0.000018
S	375	S375S	tcC	tcA	5	573	B.1.1.7	0.000004
S	375	S375F	tCc	tTc	225	225	All	0.000043
S	375	S375S	tcC	tcT	220	220	B.1.1.333	0.236814
S	375	S375S	tcC	tcT	182	182	AV.1	0.919192
S	375	S375S	tcC	tcT	113	134	B.1.617.2	0.000425
S	375	S375S	tcC	tcA	11	134	B.1.617.2	0.000041
S	375	S375S	tcC	tcG	10	134	B.1.617.2	0.000038
S	375	S375S	tcC	tcT	126	129	B.1	0.001154
S	375	S375S	tcC	tcA	2	129	B.1	0.000018
S	375	S375S	tcC	tcG	1	129	B.1	0.000009
S	375	S375S	tcC	tcT	88	95	B.1.177	0.001159
S	375	S375S	tcC	tcG	6	95	B.1.177	0.000079
S	375	S375S	tcC	tcA	1	95	B.1.177	0.000013
S	375	S375S	tcC	tcT	90	90	B.1.1.312	0.172084
S	375	S375S	tcC	tcT	74	81	AY.44	0.00045
S	375	S375S	tcC	tcA	7	81	AY.44	0.000043
S	375	S375S	tcC	tcT	75	76	AY.25	0.000451
S	375	S375S	tcC	tcA	1	76	AY.25	0.000006
S	375	S375del	TCC	---	70	70	All	0.000013
S	375	S375S	tcC	tcT	67	67	AY.43	0.000297
S	375	S375S	tcC	tcT	66	66	AY.3	0.000656
S	375	S375F	tCc	tTc	66	66	AY.4	0.000103
S	375	S375P	Tcc	Ccc	61	63	All	0.000012
S	375	S375P	TcC	CcA	2	63	All	0
S	375	S375S	tcC	tcT	46	46	B.1.346	0.060288
S	375	S375S	tcC	tcT	41	43	AY.103	0.000255
S	375	S375S	tcC	tcA	2	43	AY.103	0.000012
S	375	S375T	Tcc	Acc	42	42	All	0.000008
S	375	S375S	tcC	tcT	40	40	AY.100	0.00184
S	375	S375Y	tCc	tAc	38	38	All	0.000007
S	375	S375F	tCc	tTc	38	38	B.1.617.2	0.000143
S	375	S375S	tcC	tcT	36	36	AY.99	0.037775
S	375	S375S	tcC	tcT	32	33	B.1.2	0.000282
S	375	S375S	tcC	tcG	1	33	B.1.2	0.000009
S	375	S375S	tcC	tcT	32	33	B.1.526	0.000752
S	375	S375S	tcC	tcA	1	33	B.1.526	0.000024
S	375	S375S	tcC	tcT	32	32	B.1.596	0.002788
S	375	S375S	tcC	tcT	24	32	P.1	0.000378
S	375	S375S	tcC	tcG	5	32	P.1	0.000079
S	375	S375S	tcC	tcA	3	32	P.1	0.000047
S	375	S375S	tcC	tcT	30	31	B.1.1	0.000544
S	375	S375S	tcC	tcA	1	31	B.1.1	0.000018
S	375	S375A	Tcc	Gcc	27	28	All	0.000005
S	375	S375A	TcC	GcT	1	28	All	0
S	375	S375T	Tcc	Acc	25	25	B.1.1.7	0.000022
S	375	S375del	TCC	---	25	25	B.1.1.7	0.000022
S	375	S375S	tcC	tcT	24	24	AY.119	0.000847
S	375	S375S	tcC	tcG	13	23	AY.102	0.000345
S	375	S375S	tcC	tcT	10	23	AY.102	0.000265
S	375	S375P	Tcc	Ccc	21	21	AY.9.2	0.000771
S	375	S375S	tcC	tcT	20	20	B.1.1.519	0.000794
S	375	S375S	tcC	tcT	17	18	AY.26	0.000481
S	375	S375S	tcC	tcG	1	18	AY.26	0.000028
S	375	S375S	tcC	tcT	15	15	AY.114	0.003467
S	375	S375S	tcC	tcT	14	15	AY.75	0.000784
S	375	S375S	tcC	tcA	1	15	AY.75	0.000056
S	375	S375S	tcC	tcT	15	15	B.1.599	0.054745
S	375	S375S	tcC	tcT	14	14	AD.2	0.003065
S	375	S375S	tcC	tcT	12	14	AY.39	0.000297
S	375	S375S	tcC	tcG	1	14	AY.39	0.000025
S	375	S375S	tcC	tcA	1	14	AY.39	0.000025
S	375	S375Y	tCc	tAc	13	13	AY.119	0.000459
S	375	S375S	tcC	tcT	13	13	AY.29	0.000205
S	375	S375S	tcC	tcA	7	12	AY.4.2	0.000152
S	375	S375S	tcC	tcT	4	12	AY.4.2	0.000087
S	375	S375S	tcC	tcG	1	12	AY.4.2	0.000022
S	375	S375F	tCc	tTc	11	11	AY.103	0.000068
S	375	S375F	tCc	tTc	11	11	AY.43	0.000049
S	375	S375S	tcC	tcT	7	10	AY.121	0.000947
S	375	S375S	tcC	tcA	3	10	AY.121	0.000406
S	375	S375S	tcC	tcG	9	10	AY.47	0.00028
S	375	S375S	tcC	tcT	1	10	AY.47	0.000031
S	375	S375S	tcC	tcT	10	10	C.37	0.001161
S	375	S375Y	tCc	tAc	9	9	AY.4	0.000014
S	375	S375F	tCc	tTc	9	9	B.1.1.7	0.000008
S	375	S375S	tcC	tcT	8	8	AY.5	0.000165
S	375	S375S	tcC	tcT	8	8	AY.7	0.001568
S	375	S375S	tcC	tcT	8	8	B.1.110.3	0.005747
S	375	S375C	tCc	tGc	7	7	All	0.000001
S	375	S375S	tcC	tcT	7	7	AY.110	0.000789
S	375	S375P	Tcc	Ccc	7	7	AY.4	0.000011
S	375	S375F	tCc	tTc	7	7	AY.44	0.000043
S	375	S375S	tcC	tcT	7	7	AY.92	0.002011
S	375	S375S	tcC	tcT	7	7	B.1.1.525	0.038251
S	375	S375S	tcC	tcT	6	7	B.1.1.70	0.002046
S	375	S375S	tcC	tcG	1	7	B.1.1.70	0.000341
S	375	S375S	tcC	tcT	7	7	B.1.351	0.000208
S	375	S375S	tcC	tcT	7	7	B.1.36	0.001021
S	375	S375F	tCc	tTc	6	6	AY.120	0.000223
S	375	S375S	tcC	tcT	6	6	B.1.160	0.000187
S	375	S375S	tcC	tcT	6	6	B.1.575	0.00182
S	375	S375S	tcC	tcT	5	5	AY.20	0.000194
S	375	S375F	tCc	tTc	5	5	AY.29	0.000079
S	375	S375S	tcC	tcT	5	5	AY.34	0.000485
S	375	S375S	tcC	tcT	3	5	AY.39.1	0.000119
S	375	S375S	tcC	tcA	2	5	AY.39.1	0.000079
S	375	S375S	tcC	tcT	4	5	AY.42	0.000161
S	375	S375S	tcC	tcA	1	5	AY.42	0.00004
S	375	S375S	tcC	tcT	5	5	AY.65	0.002665
S	375	S375S	tcC	tcT	5	5	AY.9.2	0.000184
S	375	S375S	tcC	tcT	5	5	B.1.466.2	0.001956
S	375	S375S	tcC	tcT	4	4	A.2.5	0.001996
S	375	S375F	tCc	tTc	4	4	AY.3	0.00004
S	375	S375S	tcC	tcT	4	4	AY.45	0.000487
S	375	S375S	tcC	tcT	4	4	AY.46.4	0.000658
S	375	S375del	TCC	---	4	4	B.1	0.000037
S	375	S375F	tCc	tTc	4	4	B.1	0.000037
S	375	S375S	tcC	tcT	4	4	B.1.177.63	0.010811
S	375	S375S	tcC	tcT	4	4	B.1.177.77	0.002905
S	375	S375S	tcC	tcT	4	4	B.1.221	0.000284
S	375	S375del	TCC	---	4	4	B.1.258	0.000266
S	375	S375S	tcC	tcT	4	4	B.1.36.18	0.001681
S	375	S375S	tcC	tcT	4	4	B.1.408	0.01476
S	375	S375S	tcC	tcT	3	4	B.1.429	0.000071
S	375	S375S	tcC	tcG	1	4	B.1.429	0.000024
S	375	S375del	TCC	---	4	4	B.1.617.2	0.000015
S	375	S375S	tcC	tcT	3	4	P.1.14	0.000143
S	375	S375S	tcC	tcA	1	4	P.1.14	0.000048
S	375	S375S	tcC	tcT	3	4	P.1.15	0.000697
S	375	S375S	tcC	tcA	1	4	P.1.15	0.000232
S	375	S375S	tcC	tcT	4	4	Q.1	0.000505
S	375	S375S	tcC	tcA	4	4	Q.2	0.002454
S	375	S375del1	tcC	tc-	2	3	All	0
S	375	S375del1	Tcc	-cc	1	3	All	0
S	375	S375A	Tcc	Gcc	3	3	AY.102	0.00008
S	375	S375S	tcC	tcT	3	3	AY.118	0.000188
S	375	S375S	tcC	tcG	3	3	AY.13	0.000483
S	375	S375S	tcC	tcT	3	3	AY.16	0.001139
S	375	S375A	Tcc	Gcc	3	3	AY.4	0.000005
S	375	S375F	tCc	tTc	3	3	AY.42	0.000121
S	375	S375T	Tcc	Acc	3	3	AY.43	0.000013
S	375	S375S	tcC	tcT	3	3	AY.61	0.000314
S	375	S375S	tcC	tcT	3	3	AY.75.1	0.000541
S	375	S375F	tCc	tTc	3	3	AY.9.2	0.00011
S	375	S375P	Tcc	Ccc	3	3	B.1.1.7	0.000003
S	375	S375S	tcC	tcT	3	3	B.1.177.4	0.000633
S	375	S375S	tcC	tcT	3	3	B.1.177.45	0.001144
S	375	S375F	tCc	tTc	3	3	B.1.2	0.000026
S	375	S375S	tcC	tcT	3	3	B.1.311	0.000824
S	375	S375S	tcC	tcT	3	3	B.1.362	0.004622
S	375	S375S	tcC	tcT	3	3	B.1.427	0.000151
S	375	S375S	tcC	tcT	2	3	B.1.560	0.009259
S	375	S375S	tcC	tcA	1	3	B.1.560	0.00463
S	375	S375P	Tcc	Ccc	3	3	B.1.617.2	0.000011
S	375	S375F	tCc	tTc	3	3	B.1.637	0.000219
S	375	S375S	tcC	tcT	3	3	Q.8	0.000495
S	375	S375S	tcC	tcT	2	3	R.1	0.00018
S	375	S375S	tcC	tcA	1	3	R.1	0.00009
S	375	S375P	Tcc	Ccc	2	2		0.111111
S	375	S375S	TCc	AGc	2	2		0.111111
S	375	S375T	Tcc	Acc	2	2		0.111111
S	375	S375F	tCc	tTc	2	2		0.111111
S	375	S375C	tCc	tGc	2	2		0.111111
S	375	S375del2	TCc	--c	1	2	All	0
S	375	S375del2	TCC	--N	1	2	All	0
S	375	S375S	tcC	tcA	2	2	AY.104	0.003968
S	375	S375S	tcC	tcT	2	2	AY.113	0.000285
S	375	S375F	tCc	tTc	2	2	AY.119	0.000071
S	375	S375S	tcC	tcT	1	2	AY.120	0.000037
S	375	S375S	tcC	tcG	1	2	AY.120	0.000037
S	375	S375A	Tcc	Gcc	2	2	AY.20	0.000078
S	375	S375S	tcC	tcA	1	2	AY.23	0.00007
S	375	S375S	tcC	tcT	1	2	AY.23	0.00007
S	375	S375Y	tCc	tAc	2	2	AY.25	0.000012
S	375	S375P	Tcc	Ccc	2	2	AY.3	0.00002
S	375	S375S	tcC	tcT	2	2	AY.32	0.001065
S	375	S375S	tcC	tcT	2	2	AY.36	0.000296
S	375	S375F	tCc	tTc	2	2	AY.39	0.000049
S	375	S375A	Tcc	Gcc	2	2	AY.39	0.000049
S	375	S375F	tCc	tTc	2	2	AY.39.1	0.000079
S	375	S375del	TCC	---	2	2	AY.4.5	0.000215
S	375	S375P	Tcc	Ccc	2	2	AY.43	0.000009
S	375	S375del	TCC	---	2	2	AY.43	0.000009
S	375	S375S	tcC	tcT	2	2	AY.46.2	0.001271
S	375	S375S	tcC	tcT	2	2	AY.54	0.000191
S	375	S375S	tcC	tcT	2	2	AY.6	0.000082
S	375	S375F	tCc	tTc	2	2	AY.61	0.00021
S	375	S375F	tCc	tTc	2	2	AY.65	0.001066
S	375	S375S	tcC	tcT	2	2	AY.74	0.000231
S	375	S375F	tCc	tTc	2	2	AY.75	0.000112
S	375	S375S	tcC	tcT	2	2	AY.79	0.002421
S	375	S375F	tCc	tTc	2	2	AY.85	0.000854
S	375	S375F	tCc	tTc	2	2	AY.9	0.000135
S	375	S375F	tCc	tTc	2	2	AY.9.1	0.000167
S	375	S375S	tcC	tcT	2	2	AY.9.1	0.000167
S	375	S375A	Tcc	Gcc	2	2	B.1	0.000018
S	375	S375del	TCC	---	2	2	B.1.1.1	0.000653
S	375	S375S	tcC	tcT	2	2	B.1.1.141	0.004024
S	375	S375S	tcC	tcT	2	2	B.1.1.28	0.000622
S	375	S375S	tcC	tcT	2	2	B.1.1.434	0.000697
S	375	S375S	tcC	tcT	2	2	B.1.1.47	0.010695
S	375	S375A	Tcc	Gcc	2	2	B.1.1.7	0.000002
S	375	S375Y	tCc	tAc	2	2	B.1.177	0.000026
S	375	S375del	TCC	---	2	2	B.1.2	0.000018
S	375	S375S	tcC	tcT	2	2	B.1.243	0.000139
S	375	S375S	tcC	tcA	1	2	B.1.258	0.000067
S	375	S375S	tcC	tcT	1	2	B.1.258	0.000067
S	375	S375S	tcC	tcT	2	2	B.1.367	0.001585
S	375	S375Y	tCc	tAc	2	2	B.1.429	0.000047
S	375	S375S	tcC	tcT	2	2	B.1.438.1	0.000215
S	375	S375S	tcC	tcT	2	2	B.1.564	0.000852
S	375	S375F	tCc	tTc	2	2	B.1.595	0.000522
S	375	S375del	TCC	---	2	2	B.1.596	0.000174
S	375	S375S	tcC	tcT	2	2	B.1.628	0.000705
S	375	S375A	TcC	GcT	1	2	B.1.91	0.002075
S	375	S375A	Tcc	Gcc	1	2	B.1.91	0.002075
S	375	S375S	tcC	tcT	2	2	N.5	0.003534
S	375	S375S	tcC	tcT	1	2	P.1.12	0.000484
S	375	S375S	tcC	tcG	1	2	P.1.12	0.000484
S	375	S375S	tcC	tcT	2	2	P.1.9	0.009615
S	375	S375S	tcC	tcT	2	2	P.2	0.000373
S	375	S375S	tcC	tcA	2	2	Q.3	0.00029
S	375	S375S	tcC	tcT	2	2	Q.7	0.002222
S	375	S375T	Tcc	Acc	1	1	A	0.000387
S	375	S375S	tcC	tcT	1	1	A.1	0.000282
S	375	S375S	tcC	tcT	1	1	A.23.1	0.000704
S	375	S375S	tcC	tcT	1	1	A.27	0.001656
S	375	S375N	TCc	AAc	1	1	All	0
S	375	S375S	tcC	tcT	1	1	AT.1	0.005128
S	375	S375F	tCc	tTc	1	1	AU.2	0.002421
S	375	S375P	Tcc	Ccc	1	1	AY.100	0.000046
S	375	S375F	tCc	tTc	1	1	AY.100	0.000046
S	375	S375P	Tcc	Ccc	1	1	AY.102	0.000027
S	375	S375del2	TCc	--c	1	1	AY.102	0.000027
S	375	S375Y	tCc	tAc	1	1	AY.102	0.000027
S	375	S375F	tCc	tTc	1	1	AY.102	0.000027
S	375	S375A	Tcc	Gcc	1	1	AY.103	0.000006
S	375	S375Y	tCc	tAc	1	1	AY.103	0.000006
S	375	S375S	tcC	tcG	1	1	AY.105	0.000643
S	375	S375del	TCC	---	1	1	AY.107	0.000466
S	375	S375S	tcC	tcT	1	1	AY.108	0.001103
S	375	S375F	tCc	tTc	1	1	AY.110	0.000113
S	375	S375S	tcC	tcG	1	1	AY.116	0.000287
S	375	S375S	tcC	tcG	1	1	AY.117	0.000085
S	375	S375A	Tcc	Gcc	1	1	AY.119	0.000035
S	375	S375P	Tcc	Ccc	1	1	AY.120	0.000037
S	375	S375F	tCc	tTc	1	1	AY.120.1	0.000321
S	375	S375S	tcC	tcG	1	1	AY.120.2.1	0.000498
S	375	S375T	Tcc	Acc	1	1	AY.121	0.000135
S	375	S375F	tCc	tTc	1	1	AY.121	0.000135
S	375	S375P	Tcc	Ccc	1	1	AY.16.1	0.00047
S	375	S375F	tCc	tTc	1	1	AY.20	0.000039
S	375	S375T	Tcc	Acc	1	1	AY.23	0.00007
S	375	S375del	TCC	---	1	1	AY.23	0.00007
S	375	S375S	tcC	tcA	1	1	AY.23.1	0.000417
S	375	S375C	tCc	tGc	1	1	AY.25	0.000006
S	375	S375F	tCc	tTc	1	1	AY.25	0.000006
S	375	S375F	tCc	tTc	1	1	AY.26	0.000028
S	375	S375F	tCc	tTc	1	1	AY.27	0.000065
S	375	S375del	TCC	---	1	1	AY.3	0.00001
S	375	S375Y	tCc	tAc	1	1	AY.3	0.00001
S	375	S375A	Tcc	Gcc	1	1	AY.32	0.000532
S	375	S375Y	tCc	tAc	1	1	AY.33	0.000067
S	375	S375S	tcC	tcT	1	1	AY.33	0.000067
S	375	S375A	Tcc	Gcc	1	1	AY.33	0.000067
S	375	S375S	tcC	tcG	1	1	AY.34.1	0.00051
S	375	S375del	TCC	---	1	1	AY.35	0.000233
S	375	S375S	tcC	tcT	1	1	AY.35	0.000233
S	375	S375P	Tcc	Ccc	1	1	AY.39	0.000025
S	375	S375P	Tcc	Ccc	1	1	AY.39.1	0.00004
S	375	S375T	Tcc	Acc	1	1	AY.4	0.000002
S	375	S375F	tCc	tTc	1	1	AY.4.2	0.000022
S	375	S375P	Tcc	Ccc	1	1	AY.4.2.1	0.000149
S	375	S375Y	tCc	tAc	1	1	AY.42	0.00004
S	375	S375P	Tcc	Ccc	1	1	AY.44	0.000006
S	375	S375T	Tcc	Acc	1	1	AY.44	0.000006
S	375	S375F	tCc	tTc	1	1	AY.45	0.000122
S	375	S375del	TCC	---	1	1	AY.46	0.000104
S	375	S375A	Tcc	Gcc	1	1	AY.46.2	0.000635
S	375	S375del	TCC	---	1	1	AY.46.2	0.000635
S	375	S375S	tcC	tcT	1	1	AY.46.6	0.000072
S	375	S375P	Tcc	Ccc	1	1	AY.47	0.000031
S	375	S375A	Tcc	Gcc	1	1	AY.47	0.000031
S	375	S375S	tcC	tcT	1	1	AY.5.3	0.000337
S	375	S375F	tCc	tTc	1	1	AY.54	0.000095
S	375	S375S	tcC	tcT	1	1	AY.59	0.00053
S	375	S375A	Tcc	Gcc	1	1	AY.61	0.000105
S	375	S375S	tcC	tcT	1	1	AY.64	0.000595
S	375	S375del	TCC	---	1	1	AY.67	0.000464
S	375	S375S	tcC	tcT	1	1	AY.7.1	0.000113
S	375	S375S	tcC	tcT	1	1	AY.70	0.000209
S	375	S375del	TCC	---	1	1	AY.72	0.001361
S	375	S375del	TCC	---	1	1	AY.75.1	0.00018
S	375	S375S	tcC	tcG	1	1	AY.77	0.001127
S	375	S375S	tcC	tcT	1	1	AY.8	0.000606
S	375	S375S	tcC	tcT	1	1	AY.9	0.000068
S	375	S375del	TCC	---	1	1	AY.9	0.000068
S	375	S375A	Tcc	Gcc	1	1	AY.96	0.002075
S	375	S375S	tcC	tcT	1	1	AY.98	0.000079
S	375	S375S	tcC	tcT	1	1	AY.98.1	0.000048
S	375	S375del1	Tcc	-cc	1	1	B	0.000128
S	375	S375P	Tcc	Ccc	1	1	B.1	0.000009
S	375	S375T	Tcc	Acc	1	1	B.1	0.000009
S	375	S375Y	tCc	tAc	1	1	B.1	0.000009
S	375	S375del	TCC	---	1	1	B.1.1	0.000018
S	375	S375T	Tcc	Acc	1	1	B.1.1	0.000018
S	375	S375A	Tcc	Gcc	1	1	B.1.1	0.000018
S	375	S375P	TcC	CcA	1	1	B.1.1	0.000018
S	375	S375S	tcC	tcG	1	1	B.1.1.10	0.001115
S	375	S375del	TCC	---	1	1	B.1.1.137	0.0125
S	375	S375S	tcC	tcT	1	1	B.1.1.161	0.003534
S	375	S375P	Tcc	Ccc	1	1	B.1.1.176	0.000439
S	375	S375F	tCc	tTc	1	1	B.1.1.214	0.000055
S	375	S375F	tCc	tTc	1	1	B.1.1.257	0.009709
S	375	S375S	tcC	tcT	1	1	B.1.1.263	0.001558
S	375	S375S	tcC	tcG	1	1	B.1.1.273	0.006757
S	375	S375P	Tcc	Ccc	1	1	B.1.1.274	0.005051
S	375	S375S	tcC	tcT	1	1	B.1.1.306	0.000438
S	375	S375S	tcC	tcG	1	1	B.1.1.315	0.008475
S	375	S375del	TCC	---	1	1	B.1.1.315	0.008475
S	375	S375S	tcC	tcG	1	1	B.1.1.317	0.000412
S	375	S375C	tCc	tGc	1	1	B.1.1.318	0.000302
S	375	S375F	tCc	tTc	1	1	B.1.1.326	0.001761
S	375	S375T	Tcc	Acc	1	1	B.1.1.37	0.000193
S	375	S375S	tcC	tcT	1	1	B.1.1.39	0.00051
S	375	S375F	tCc	tTc	1	1	B.1.1.39	0.00051
S	375	S375S	tcC	tcT	1	1	B.1.1.448	0.002033
S	375	S375del	TCC	---	1	1	B.1.1.519	0.00004
S	375	S375del	TCC	---	1	1	B.1.1.521	0.005348
S	375	S375S	tcC	tcT	1	1	B.1.1.523	0.001563
S	375	S375Y	tCc	tAc	1	1	B.1.1.7	0.000001
S	375	S375N	TCc	AAc	1	1	B.1.1.7	0.000001
S	375	S375F	tCc	tTc	1	1	B.1.1.70	0.000341
S	375	S375P	Tcc	Ccc	1	1	B.1.1.8	0.003584
S	375	S375P	Tcc	Ccc	1	1	B.1.111	0.001175
S	375	S375del2	TCC	--N	1	1	B.1.140	0.018868
S	375	S375S	tcC	tcT	1	1	B.1.140	0.018868
S	375	S375F	tCc	tTc	1	1	B.1.160	0.000031
S	375	S375C	tCc	tGc	1	1	B.1.160	0.000031
S	375	S375T	Tcc	Acc	1	1	B.1.177	0.000013
S	375	S375del	TCC	---	1	1	B.1.177	0.000013
S	375	S375C	tCc	tGc	1	1	B.1.177	0.000013
S	375	S375F	tCc	tTc	1	1	B.1.177	0.000013
S	375	S375del	TCC	---	1	1	B.1.177.18	0.00116
S	375	S375S	tcC	tcT	1	1	B.1.177.19	0.001431
S	375	S375S	tcC	tcT	1	1	B.1.177.21	0.000076
S	375	S375S	tcC	tcT	1	1	B.1.177.29	0.066667
S	375	S375P	Tcc	Ccc	1	1	B.1.177.32	0.00135
S	375	S375del	TCC	---	1	1	B.1.177.57	0.000281
S	375	S375S	tcC	tcA	1	1	B.1.177.60	0.000218
S	375	S375S	tcC	tcT	1	1	B.1.177.73	0.000566
S	375	S375del	TCC	---	1	1	B.1.177.87	0.000728
S	375	S375P	Tcc	Ccc	1	1	B.1.2	0.000009
S	375	S375T	Tcc	Acc	1	1	B.1.2	0.000009
S	375	S375S	tcC	tcT	1	1	B.1.218	0.005155
S	375	S375Y	tCc	tAc	1	1	B.1.221	0.000071
S	375	S375S	tcC	tcT	1	1	B.1.221.4	0.004167
S	375	S375S	tcC	tcT	1	1	B.1.222	0.001692
S	375	S375S	tcC	tcT	1	1	B.1.234	0.000132
S	375	S375P	Tcc	Ccc	1	1	B.1.236	0.002053
S	375	S375del	TCC	---	1	1	B.1.242	0.018868
S	375	S375F	tCc	tTc	1	1	B.1.243	0.00007
S	375	S375A	Tcc	Gcc	1	1	B.1.258	0.000067
S	375	S375P	TcC	CcA	1	1	B.1.258.17	0.000104
S	375	S375S	tcC	tcT	1	1	B.1.258.17	0.000104
S	375	S375S	tcC	tcT	1	1	B.1.289	0.00266
S	375	S375F	tCc	tTc	1	1	B.1.311	0.000275
S	375	S375S	tcC	tcT	1	1	B.1.349	0.000715
S	375	S375F	tCc	tTc	1	1	B.1.351	0.00003
S	375	S375S	tcC	tcT	1	1	B.1.36.17	0.000494
S	375	S375S	tcC	tcT	1	1	B.1.36.22	0.001208
S	375	S375S	tcC	tcT	1	1	B.1.36.29	0.000517
S	375	S375del1	tcC	tc-	1	1	B.1.36.29	0.000517
S	375	S375S	tcC	tcT	1	1	B.1.36.8	0.001
S	375	S375del1	tcC	tc-	1	1	B.1.361	0.001289
S	375	S375S	tcC	tcT	1	1	B.1.369	0.000285
S	375	S375S	tcC	tcT	1	1	B.1.400	0.000429
S	375	S375del	TCC	---	1	1	B.1.409	0.000781
S	375	S375P	Tcc	Ccc	1	1	B.1.427	0.00005
S	375	S375T	Tcc	Acc	1	1	B.1.427	0.00005
S	375	S375F	tCc	tTc	1	1	B.1.427	0.00005
S	375	S375A	Tcc	Gcc	1	1	B.1.429	0.000024
S	375	S375F	tCc	tTc	1	1	B.1.438.1	0.000107
S	375	S375del	TCC	---	1	1	B.1.446	0.02
S	375	S375F	tCc	tTc	1	1	B.1.452	0.013699
S	375	S375S	tcC	tcT	1	1	B.1.453	0.003236
S	375	S375Y	tCc	tAc	1	1	B.1.466.2	0.000391
S	375	S375S	tcC	tcT	1	1	B.1.468	0.005714
S	375	S375S	tcC	tcT	1	1	B.1.495	0.009091
S	375	S375S	tcC	tcT	1	1	B.1.497	0.000315
S	375	S375P	Tcc	Ccc	1	1	B.1.503	0.002488
S	375	S375C	tCc	tGc	1	1	B.1.525	0.000113
S	375	S375T	Tcc	Acc	1	1	B.1.526	0.000024
S	375	S375F	tCc	tTc	1	1	B.1.564	0.000426
S	375	S375S	tcC	tcT	1	1	B.1.581	0.009434
S	375	S375S	tcC	tcT	1	1	B.1.588	0.00091
S	375	S375S	tcC	tcT	1	1	B.1.595.3	0.026316
S	375	S375S	tcC	tcT	1	1	B.1.595.4	0.007299
S	375	S375S	tcC	tcT	1	1	B.1.602	0.006536
S	375	S375F	tCc	tTc	1	1	B.1.617.1	0.000129
S	375	S375Y	tCc	tAc	1	1	B.1.617.2	0.000004
S	375	S375S	tcC	tcT	1	1	B.1.619	0.000871
S	375	S375S	tcC	tcT	1	1	B.1.619.1	0.000641
S	375	S375del	TCC	---	1	1	B.1.620	0.000946
S	375	S375P	Tcc	Ccc	1	1	B.1.627	0.00202
S	375	S375S	tcC	tcT	1	1	B.1.9.5	0.005682
S	375	S375S	tcC	tcT	1	1	B.1.91	0.002075
S	375	S375P	Tcc	Ccc	1	1	B.39	0.002331
S	375	S375S	tcC	tcA	1	1	B.6	0.00091
S	375	S375S	tcC	tcT	1	1	C.26	0.007353
S	375	S375S	tcC	tcG	1	1	C.27	0.018519
S	375	S375F	tCc	tTc	1	1	C.37	0.000116
S	375	S375S	tcC	tcT	1	1	C.37.1	0.002618
S	375	S375F	tCc	tTc	1	1	D.2	0.000075
S	375	S375A	Tcc	Gcc	1	1	P.1.17	0.000162
S	375	S375S	tcC	tcA	1	1	P.1.8	0.004785

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.