CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 2

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
N	2	S2Y		nonsyn	tCt	tAt	10993	10976	0.998454	28277-28279
N	2	S2Y		nonsyn	tCT	tAC	10993	17	0.00154644	28277-28279
N	2	S2P		nonsyn	Tct	Cct	2374	2356	0.992418	28277-28279
N	2	S2P		nonsyn	TcT	CcC	2374	12	0.00505476	28277-28279
N	2	S2P		nonsyn	TcT	CcA	2374	5	0.00210615	28277-28279
N	2	S2P		nonsyn	TcT	CcG	2374	1	0.00042123	28277-28279
N	2	S2F		nonsyn	tCt	tTt	807	795	0.98513	28277-28279
N	2	S2F		nonsyn	tCT	tTC	807	12	0.0148699	28277-28279
N	2	S2S		syn	tcT	tcC	135	102	0.755556	28277-28279
N	2	S2S		syn	tcT	tcA	135	31	0.22963	28277-28279
N	2	S2S		syn	tcT	tcG	135	2	0.0148148	28277-28279
N	2	S2T		nonsyn	Tct	Act	110	89	0.809091	28277-28279
N	2	S2T		nonsyn	TcT	AcA	110	21	0.190909	28277-28279
N	2	S2A		nonsyn	Tct	Gct	106	105	0.990566	28277-28279
N	2	S2A		nonsyn	TcT	GcC	106	1	0.00943396	28277-28279
N	2	S2N		nonsyn	TCt	AAt	95	90	0.947368	28277-28279
N	2	S2N		nonsyn	TCT	AAC	95	5	0.0526316	28277-28279
N	2	S2L		nonsyn	TCT	CTA	91	42	0.461538	28277-28279
N	2	S2L		nonsyn	TCt	CTt	91	31	0.340659	28277-28279
N	2	S2L		nonsyn	TCT	CTC	91	13	0.142857	28277-28279
N	2	S2L		nonsyn	TCT	CTG	91	4	0.043956	28277-28279
N	2	S2L		nonsyn	tCT	tTG	91	1	0.010989	28277-28279
N	2	S2I		nonsyn	TCt	ATt	57	39	0.684211	28277-28279
N	2	S2I		nonsyn	TCT	ATA	57	18	0.315789	28277-28279
N	2	S2X		nonsyn	tCT	tAA	23	23	1	28277-28279
N	2	S2del1		del	Tct	-ct	15	7	0.466667	28277-28279
N	2	S2del1		del	tcT	tc-	15	3	0.2	28277-28279
N	2	S2del1		del	TCT	-TG	15	3	0.2	28277-28279
N	2	S2del1		del	tCt	t-t	15	2	0.133333	28277-28279
N	2	S2del		del	TCT	---	11	11	1	28277-28279
N	2	S2Q		nonsyn	TCT	CAA	6	4	0.666667	28277-28279
N	2	S2Q		nonsyn	TCT	CAG	6	2	0.333333	28277-28279
N	2	S2K		nonsyn	TCT	AAA	3	2	0.666667	28277-28279
N	2	S2K		nonsyn	TCT	AAG	3	1	0.333333	28277-28279
N	2	S2V		nonsyn	TCt	GTt	3	1	0.333333	28277-28279
N	2	S2V		nonsyn	TCT	GTC	3	1	0.333333	28277-28279
N	2	S2V		nonsyn	TCT	GTA	3	1	0.333333	28277-28279
N	2	S2C		nonsyn	tCt	tGt	2	2	1	28277-28279
N	2	S2E		nonsyn	TCT	GAA	2	2	1	28277-28279
N	2	S2del2		del	TCt	--t	2	2	1	28277-28279
N	2	S2H		nonsyn	TCT	CAC	2	2	1	28277-28279

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
N	2	S2Y	tCt	tAt	10976	10993	All	0.002099
N	2	S2Y	tCT	tAC	17	10993	All	0.000003
N	2	S2Y	tCt	tAt	8491	8493	B.1.525	0.960846
N	2	S2Y	tCT	tAC	2	8493	B.1.525	0.000226
N	2	S2P	Tct	Cct	2356	2374	All	0.000451
N	2	S2P	TcT	CcC	12	2374	All	0.000002
N	2	S2P	TcT	CcA	5	2374	All	0.000001
N	2	S2P	TcT	CcG	1	2374	All	0
N	2	S2P	Tct	Cct	1827	1827	B.1.36.29	0.945163
N	2	S2Y	tCt	tAt	1191	1191	B.1.1.348	0.948248
N	2	S2F	tCt	tTt	795	807	All	0.000152
N	2	S2F	tCT	tTC	12	807	All	0.000002
N	2	S2Y	tCt	tAt	617	617	B.1.177.81	0.116812
N	2	S2F	tCt	tTt	314	324	B.1.1.7	0.000281
N	2	S2F	tCT	tTC	10	324	B.1.1.7	0.000009
N	2	S2P	Tct	Cct	214	214	B.1	0.00196
N	2	S2Y	tCt	tAt	191	191	A.23.1	0.134507
N	2	S2Y	tCt	tAt	155	155	B.1.1	0.002812
N	2	S2S	tcT	tcC	102	135	All	0.00002
N	2	S2S	tcT	tcA	31	135	All	0.000006
N	2	S2S	tcT	tcG	2	135	All	0
N	2	S2F	tCt	tTt	134	134	B.1.1.70	0.045703
N	2	S2T	Tct	Act	89	110	All	0.000017
N	2	S2T	TcT	AcA	21	110	All	0.000004
N	2	S2A	Tct	Gct	105	106	All	0.00002
N	2	S2A	TcT	GcC	1	106	All	0
N	2	S2N	TCt	AAt	90	95	All	0.000017
N	2	S2N	TCT	AAC	5	95	All	0.000001
N	2	S2L	TCT	CTA	42	91	All	0.000008
N	2	S2L	TCt	CTt	31	91	All	0.000006
N	2	S2L	TCT	CTC	13	91	All	0.000002
N	2	S2L	TCT	CTG	4	91	All	0.000001
N	2	S2L	tCT	tTG	1	91	All	0
N	2	S2T	Tct	Act	75	86	P.1	0.001182
N	2	S2T	TcT	AcA	11	86	P.1	0.000173
N	2	S2F	tCt	tTt	81	81	C.11	0.861702
N	2	S2Y	tCt	tAt	67	77	P.1	0.001056
N	2	S2Y	tCT	tAC	10	77	P.1	0.000158
N	2	S2N	TCt	AAt	74	76	P.1	0.001166
N	2	S2N	TCT	AAC	2	76	P.1	0.000032
N	2	S2Y	tCt	tAt	70	70	B.1	0.000641
N	2	S2I	TCt	ATt	39	57	All	0.000007
N	2	S2I	TCT	ATA	18	57	All	0.000003
N	2	S2P	Tct	Cct	43	55	B.1.1.7	0.000038
N	2	S2P	TcT	CcC	12	55	B.1.1.7	0.000011
N	2	S2L	TCt	CTt	27	45	B.1.1.7	0.000024
N	2	S2L	TCT	CTC	13	45	B.1.1.7	0.000012
N	2	S2L	TCT	CTA	4	45	B.1.1.7	0.000004
N	2	S2L	TCT	CTG	1	45	B.1.1.7	0.000001
N	2	S2I	TCt	ATt	28	43	P.1	0.000441
N	2	S2I	TCT	ATA	15	43	P.1	0.000236
N	2	S2A	Tct	Gct	42	42	P.1	0.000662
N	2	S2F	tCt	tTt	41	41	B.1.1.322	0.359649
N	2	S2F	tCt	tTt	40	40	B.1	0.000366
N	2	S2F	tCt	tTt	29	29	B.1.565	0.023501
N	2	S2L	TCT	CTA	28	28	P.1	0.000441
N	2	S2F	tCt	tTt	25	25	B.1.1	0.000454
N	2	S2Y	tCt	tAt	25	25	B.1.177	0.000329
N	2	S2P	Tct	Cct	25	25	B.1.36.17	0.012352
N	2	S2X	tCT	tAA	23	23	All	0.000004
N	2	S2S	tcT	tcC	22	22	B.1.429	0.000518
N	2	S2S	tcT	tcC	18	21	B.1.1.7	0.000016
N	2	S2S	tcT	tcA	3	21	B.1.1.7	0.000003
N	2	S2P	Tct	Cct	20	20	B.1.1	0.000363
N	2	S2F	tCt	tTt	20	20	B.1.2	0.000176
N	2	S2Y	tCt	tAt	20	20	B.1.2	0.000176
N	2	S2P	Tct	Cct	20	20	B.1.466.2	0.007825
N	2	S2F	tCt	tTt	19	19	B.1.243	0.001322
N	2	S2P	Tct	Cct	19	19	B.1.36	0.002772
N	2	S2A	Tct	Gct	18	18	P.1.12	0.008712
N	2	S2A	Tct	Gct	17	17	P.1.17	0.00275
N	2	S2P	Tct	Cct	16	16	B.1.1.317	0.006587
N	2	S2X	tCT	tAA	16	16	P.1	0.000252
N	2	S2del1	Tct	-ct	7	15	All	0.000001
N	2	S2del1	tcT	tc-	3	15	All	0.000001
N	2	S2del1	TCT	-TG	3	15	All	0.000001
N	2	S2del1	tCt	t-t	2	15	All	0
N	2	S2Y	tCt	tAt	14	14	AY.4	0.000022
N	2	S2P	Tct	Cct	12	12	B.1.260	0.040134
N	2	S2del	TCT	---	11	11	All	0.000002
N	2	S2F	tCt	tTt	11	11	AY.4	0.000017
N	2	S2Y	tCt	tAt	11	11	B.1.1.307	0.027848
N	2	S2P	Tct	Cct	10	10	B.1.1.354	0.04386
N	2	S2P	Tct	Cct	10	10	B.1.462	0.072464
N	2	S2S	tcT	tcC	9	9	B.1	0.000082
N	2	S2Y	tCt	tAt	9	9	B.1.1.7	0.000008
N	2	S2S	tcT	tcA	7	8	AY.33	0.000467
N	2	S2S	tcT	tcC	1	8	AY.33	0.000067
N	2	S2F	tCt	tTt	8	8	B.1.1.189	0.012103
N	2	S2T	TcT	AcA	7	8	P.1.12	0.003388
N	2	S2T	Tct	Act	1	8	P.1.12	0.000484
N	2	S2Y	tCt	tAt	7	7	AY.103	0.000043
N	2	S2P	Tct	Cct	7	7	AY.20	0.000272
N	2	S2S	tcT	tcC	7	7	AY.4	0.000011
N	2	S2Y	tCt	tAt	7	7	B.1.1.1	0.002287
N	2	S2P	Tct	Cct	7	7	B.1.247	0.104478
N	2	S2S	tcT	tcC	7	7	B.1.396	0.00494
N	2	S2S	tcT	tcA	7	7	B.1.635	0.122807
N	2	S2F	tCt	tTt	7	7	P.1	0.00011
N	2	S2S	tcT	tcC	6	7	P.1	0.000095
N	2	S2S	tcT	tcA	1	7	P.1	0.000016
N	2	S2Q	TCT	CAA	4	6	All	0.000001
N	2	S2Q	TCT	CAG	2	6	All	0
N	2	S2Y	tCt	tAt	6	6	B	0.000767
N	2	S2P	Tct	Cct	6	6	B.1.1.157	0.005479
N	2	S2P	Tct	Cct	6	6	B.1.177.2	0.027273
N	2	S2P	Tct	Cct	6	6	B.1.234	0.000792
N	2	S2A	Tct	Gct	6	6	B.1.36.29	0.003104
N	2	S2I	TCt	ATt	6	6	P.1.12	0.002904
N	2	S2L	TCT	CTA	6	6	P.1.12	0.002904
N	2	S2N	TCt	AAt	6	6	P.1.4	0.005859
N	2	S2T	Tct	Act	6	6	P.1.4	0.005859
N	2	S2Y	tCt	tAt	6	6	P.1.4	0.005859
N	2	S2P	Tct	Cct	5	5	AY.4	0.000008
N	2	S2P	Tct	Cct	5	5	B	0.000639
N	2	S2Y	tCt	tAt	5	5	B.1.177.50	0.023474
N	2	S2P	Tct	Cct	5	5	B.1.36.10	0.023923
N	2	S2P	Tct	Cct	5	5	B.1.456	0.01634
N	2	S2P	Tct	Cct	5	5	B.1.465	0.019011
N	2	S2P	Tct	Cct	5	5	B.1.617.2	0.000019
N	2	S2Q	TCT	CAA	3	5	P.1	0.000047
N	2	S2Q	TCT	CAG	2	5	P.1	0.000032
N	2	S2I	TCt	ATt	4	5	P.1.17	0.000647
N	2	S2I	TCT	ATA	1	5	P.1.17	0.000162
N	2	S2Y	tCt	tAt	4	4	B.1.351	0.000119
N	2	S2S	tcT	tcC	4	4	B.1.36	0.000584
N	2	S2F	tCt	tTt	4	4	B.1.526	0.000094
N	2	S2P	Tct	Cct	4	4	B.1.617.1	0.000516
N	2	S2P	TcT	CcA	4	4	P.1	0.000063
N	2	S2A	Tct	Gct	4	4	P.1.10	0.001078
N	2	S2N	TCt	AAt	4	4	P.1.12	0.001936
N	2	S2S	tcT	tcC	4	4	Q.1	0.000505
N	2	S2K	TCT	AAA	2	3	All	0
N	2	S2K	TCT	AAG	1	3	All	0
N	2	S2V	TCT	GTA	1	3	All	0
N	2	S2V	TCT	GTC	1	3	All	0
N	2	S2V	TCt	GTt	1	3	All	0
N	2	S2P	Tct	Cct	3	3	AY.3	0.00003
N	2	S2P	Tct	Cct	3	3	AY.43	0.000013
N	2	S2Y	tCt	tAt	3	3	AY.62	0.001307
N	2	S2P	Tct	Cct	3	3	AY.68	0.000821
N	2	S2S	tcT	tcC	3	3	AY.98.1	0.000145
N	2	S2del1	TCT	-TG	1	3	B.1	0.000009
N	2	S2del1	tCt	t-t	1	3	B.1	0.000009
N	2	S2del1	Tct	-ct	1	3	B.1	0.000009
N	2	S2S	tcT	tcA	2	3	B.1.1	0.000036
N	2	S2S	tcT	tcC	1	3	B.1.1	0.000018
N	2	S2Y	tCt	tAt	3	3	B.1.1.180	0.032258
N	2	S2F	tCt	tTt	3	3	B.1.1.216	0.002671
N	2	S2Y	tCt	tAt	3	3	B.1.1.269	0.00406
N	2	S2F	tCt	tTt	3	3	B.1.1.306	0.001315
N	2	S2F	tCt	tTt	3	3	B.1.1.354	0.013158
N	2	S2Y	tCt	tAt	3	3	B.1.1.369	0.001339
N	2	S2Y	tCt	tAt	3	3	B.1.1.372	0.002066
N	2	S2del	TCT	---	3	3	B.1.1.7	0.000003
N	2	S2P	Tct	Cct	3	3	B.1.157	0.008955
N	2	S2F	tCt	tTt	3	3	B.1.258	0.0002
N	2	S2Y	tCt	tAt	3	3	B.1.36	0.000438
N	2	S2F	tCt	tTt	3	3	B.1.429	0.000071
N	2	S2P	Tct	Cct	3	3	B.1.460	0.053571
N	2	S2L	TCT	CTG	1	3	B.1.526	0.000024
N	2	S2L	TCt	CTt	1	3	B.1.526	0.000024
N	2	S2L	tCT	tTG	1	3	B.1.526	0.000024
N	2	S2P	Tct	Cct	3	3	B.1.9.5	0.017045
N	2	S2Y	tCt	tAt	3	3	C.37	0.000348
N	2	S2K	TCT	AAA	2	3	P.1	0.000032
N	2	S2K	TCT	AAG	1	3	P.1	0.000016
N	2	S2I	TCT	ATA	2	3	P.1.10	0.000539
N	2	S2I	TCt	ATt	1	3	P.1.10	0.000269
N	2	S2T	Tct	Act	2	3	P.1.15	0.000465
N	2	S2N	TCt	AAt	2	3	P.1.15	0.000465
N	2	S2Y	tCt	tAt	2	3	P.1.15	0.000465
N	2	S2N	TCT	AAC	1	3	P.1.15	0.000232
N	2	S2T	TcT	AcA	1	3	P.1.15	0.000232
N	2	S2Y	tCT	tAC	1	3	P.1.15	0.000232
N	2	S2X	tCT	tAA	3	3	P.1.17	0.000485
N	2	S2T	Tct	Act	3	3	P.1.2	0.003468
N	2	S2N	TCt	AAt	3	3	P.1.2	0.003468
N	2	S2Y	tCt	tAt	3	3	P.1.2	0.003468
N	2	S2A	TcT	GcC	1	2		0.055556
N	2	S2F	tCT	tTC	1	2		0.055556
N	2	S2A	Tct	Gct	1	2		0.055556
N	2	S2F	tCt	tTt	1	2		0.055556
N	2	S2V	TCT	GTC	1	2		0.055556
N	2	S2V	TCt	GTt	1	2		0.055556
N	2	S2P	Tct	Cct	2	2	A	0.000774
N	2	S2del2	TCt	--t	2	2	All	0
N	2	S2H	TCT	CAC	2	2	All	0
N	2	S2E	TCT	GAA	2	2	All	0
N	2	S2C	tCt	tGt	2	2	All	0
N	2	S2F	tCt	tTt	2	2	AY.102	0.000053
N	2	S2F	tCt	tTt	2	2	AY.4.2	0.000043
N	2	S2F	tCt	tTt	2	2	AY.44	0.000012
N	2	S2S	tcT	tcC	1	2	AY.44	0.000006
N	2	S2S	tcT	tcA	1	2	AY.44	0.000006
N	2	S2S	tcT	tcC	2	2	AY.46.6	0.000144
N	2	S2S	tcT	tcC	1	2	AY.59	0.00053
N	2	S2S	tcT	tcA	1	2	AY.59	0.00053
N	2	S2P	Tct	Cct	2	2	AY.67	0.000929
N	2	S2P	Tct	Cct	2	2	AY.75.1	0.000361
N	2	S2L	TCT	CTA	2	2	B	0.000256
N	2	S2A	Tct	Gct	2	2	B.1	0.000018
N	2	S2Y	tCt	tAt	2	2	B.1.1.174	0.006757
N	2	S2F	tCt	tTt	2	2	B.1.157	0.00597
N	2	S2P	Tct	Cct	2	2	B.1.177	0.000026
N	2	S2del1	tcT	tc-	2	2	B.1.214.2	0.001199
N	2	S2P	Tct	Cct	2	2	B.1.258	0.000133
N	2	S2A	Tct	Gct	2	2	B.1.351	0.000059
N	2	S2L	TCt	CTt	2	2	B.1.36.29	0.001035
N	2	S2P	Tct	Cct	2	2	B.1.36.31	0.003503
N	2	S2F	tCt	tTt	2	2	B.1.378	0.013699
N	2	S2S	tcT	tcA	2	2	B.1.408	0.00738
N	2	S2del2	TCt	--t	2	2	B.1.525	0.000226
N	2	S2del1	tcT	tc-	1	2	B.1.525	0.000113
N	2	S2del1	TCT	-TG	1	2	B.1.525	0.000113
N	2	S2P	Tct	Cct	1	2	B.1.526	0.000024
N	2	S2P	TcT	CcG	1	2	B.1.526	0.000024
N	2	S2Y	tCt	tAt	2	2	B.1.533	0.019231
N	2	S2P	Tct	Cct	2	2	B.1.533	0.019231
N	2	S2P	Tct	Cct	2	2	B.1.588	0.00182
N	2	S2Y	tCt	tAt	2	2	B.1.596	0.000174
N	2	S2Y	tCt	tAt	2	2	B.1.609	0.000959
N	2	S2del	TCT	---	2	2	B.1.617.2	0.000008
N	2	S2S	tcT	tcC	2	2	B.1.617.2	0.000008
N	2	S2Y	tCt	tAt	2	2	C.16	0.002121
N	2	S2del	TCT	---	2	2	P.1	0.000032
N	2	S2S	tcT	tcA	2	2	P.1.13	0.001797
N	2	S2S	tcT	tcA	2	2	P.1.14	0.000096
N	2	S2T	TcT	AcA	2	2	P.1.17	0.000324
N	2	S2N	TCt	AAt	1	2	P.1.17	0.000162
N	2	S2N	TCT	AAC	1	2	P.1.17	0.000162
N	2	S2F	tCt	tTt	2	2	Q.2	0.001227
N	2	S2F	tCt	tTt	2	2	Q.3	0.00029
N	2	S2S	tcT	tcC	1	1		0.055556
N	2	S2C	tCt	tGt	1	1		0.055556
N	2	S2A	Tct	Gct	1	1	A	0.000387
N	2	S2S	tcT	tcC	1	1	A.2	0.000662
N	2	S2P	Tct	Cct	1	1	A.2.2	0.001689
N	2	S2S	tcT	tcC	1	1	A.2.5	0.000499
N	2	S2F	tCt	tTt	1	1	A.24	0.071429
N	2	S2Y	tCt	tAt	1	1	AY.100	0.000046
N	2	S2S	tcT	tcG	1	1	AY.103	0.000006
N	2	S2F	tCt	tTt	1	1	AY.103	0.000006
N	2	S2P	Tct	Cct	1	1	AY.117	0.000085
N	2	S2Y	tCt	tAt	1	1	AY.119	0.000035
N	2	S2A	Tct	Gct	1	1	AY.16	0.00038
N	2	S2S	tcT	tcC	1	1	AY.20	0.000039
N	2	S2P	Tct	Cct	1	1	AY.23	0.00007
N	2	S2F	tCt	tTt	1	1	AY.23	0.00007
N	2	S2S	tcT	tcA	1	1	AY.3	0.00001
N	2	S2F	tCt	tTt	1	1	AY.3	0.00001
N	2	S2Y	tCt	tAt	1	1	AY.3	0.00001
N	2	S2L	TCT	CTG	1	1	AY.32	0.000532
N	2	S2P	Tct	Cct	1	1	AY.34	0.000097
N	2	S2Y	tCt	tAt	1	1	AY.36	0.000148
N	2	S2Y	tCt	tAt	1	1	AY.37	0.000316
N	2	S2P	Tct	Cct	1	1	AY.39	0.000025
N	2	S2S	tcT	tcC	1	1	AY.4.2	0.000022
N	2	S2P	Tct	Cct	1	1	AY.4.2	0.000022
N	2	S2F	tCt	tTt	1	1	AY.43	0.000004
N	2	S2P	Tct	Cct	1	1	AY.44	0.000006
N	2	S2del	TCT	---	1	1	AY.44	0.000006
N	2	S2S	tcT	tcC	1	1	AY.46.2	0.000635
N	2	S2del	TCT	---	1	1	AY.5	0.000021
N	2	S2F	tCt	tTt	1	1	AY.5	0.000021
N	2	S2L	TCT	CTG	1	1	AY.6	0.000041
N	2	S2C	tCt	tGt	1	1	AY.62	0.000436
N	2	S2F	tCt	tTt	1	1	AY.9.1	0.000084
N	2	S2del1	Tct	-ct	1	1	B.1.1	0.000018
N	2	S2del	TCT	---	1	1	B.1.1	0.000018
N	2	S2F	tCt	tTt	1	1	B.1.1.1	0.000327
N	2	S2Y	tCt	tAt	1	1	B.1.1.10	0.001115
N	2	S2Y	tCt	tAt	1	1	B.1.1.171	0.003676
N	2	S2P	Tct	Cct	1	1	B.1.1.189	0.001513
N	2	S2Y	tCt	tAt	1	1	B.1.1.198	0.001468
N	2	S2F	tCt	tTt	1	1	B.1.1.214	0.000055
N	2	S2A	Tct	Gct	1	1	B.1.1.216	0.00089
N	2	S2Y	tCt	tAt	1	1	B.1.1.220	0.001859
N	2	S2Y	tCt	tAt	1	1	B.1.1.222	0.000204
N	2	S2P	Tct	Cct	1	1	B.1.1.222	0.000204
N	2	S2F	tCt	tTt	1	1	B.1.1.254	0.011236
N	2	S2F	tCt	tTt	1	1	B.1.1.28	0.000311
N	2	S2Y	tCt	tAt	1	1	B.1.1.28	0.000311
N	2	S2P	Tct	Cct	1	1	B.1.1.28	0.000311
N	2	S2T	Tct	Act	1	1	B.1.1.298	0.000862
N	2	S2Y	tCt	tAt	1	1	B.1.1.318	0.000302
N	2	S2Y	tCt	tAt	1	1	B.1.1.326	0.001761
N	2	S2Y	tCt	tAt	1	1	B.1.1.398	0.003226
N	2	S2P	Tct	Cct	1	1	B.1.1.409	0.002833
N	2	S2S	tcT	tcC	1	1	B.1.1.413	0.006897
N	2	S2F	tCt	tTt	1	1	B.1.1.413	0.006897
N	2	S2Y	tCt	tAt	1	1	B.1.1.416	0.000905
N	2	S2F	tCt	tTt	1	1	B.1.1.420	0.001006
N	2	S2Y	tCt	tAt	1	1	B.1.1.442	0.018519
N	2	S2P	Tct	Cct	1	1	B.1.1.448	0.002033
N	2	S2Y	tCt	tAt	1	1	B.1.1.462	0.008621
N	2	S2F	tCt	tTt	1	1	B.1.1.487	0.005587
N	2	S2Y	tCt	tAt	1	1	B.1.1.50	0.000679
N	2	S2P	Tct	Cct	1	1	B.1.1.50	0.000679
N	2	S2Y	tCt	tAt	1	1	B.1.1.519	0.00004
N	2	S2P	Tct	Cct	1	1	B.1.1.58	0.005376
N	2	S2Y	tCt	tAt	1	1	B.1.1.63	0.000386
N	2	S2del1	TCT	-TG	1	1	B.1.1.7	0.000001
N	2	S2Y	tCt	tAt	1	1	B.1.1.89	0.006061
N	2	S2F	tCt	tTt	1	1	B.1.1.95	0.019608
N	2	S2Y	tCt	tAt	1	1	B.1.1.99	0.02381
N	2	S2F	tCt	tTt	1	1	B.1.160	0.000031
N	2	S2S	tcT	tcC	1	1	B.1.160.16	0.000929
N	2	S2Y	tCt	tAt	1	1	B.1.160.32	0.004292
N	2	S2Y	tCt	tAt	1	1	B.1.162	0.005025
N	2	S2A	Tct	Gct	1	1	B.1.177	0.000013
N	2	S2F	tCt	tTt	1	1	B.1.177.4	0.000211
N	2	S2S	tcT	tcC	1	1	B.1.177.43	0.001477
N	2	S2L	TCt	CTt	1	1	B.1.177.63	0.002703
N	2	S2Y	tCt	tAt	1	1	B.1.177.7	0.000165
N	2	S2P	Tct	Cct	1	1	B.1.177.73	0.000566
N	2	S2S	tcT	tcA	1	1	B.1.177.86	0.000183
N	2	S2P	Tct	Cct	1	1	B.1.177.87	0.000728
N	2	S2S	tcT	tcC	1	1	B.1.2	0.000009
N	2	S2P	Tct	Cct	1	1	B.1.2	0.000009
N	2	S2del1	tCt	t-t	1	1	B.1.2	0.000009
N	2	S2S	tcT	tcC	1	1	B.1.206	0.000816
N	2	S2P	Tct	Cct	1	1	B.1.214	0.003663
N	2	S2F	tCt	tTt	1	1	B.1.214.2	0.0006
N	2	S2P	Tct	Cct	1	1	B.1.221	0.000071
N	2	S2Y	tCt	tAt	1	1	B.1.221	0.000071
N	2	S2S	tcT	tcC	1	1	B.1.221	0.000071
N	2	S2Y	tCt	tAt	1	1	B.1.23	0.006061
N	2	S2A	Tct	Gct	1	1	B.1.243	0.00007
N	2	S2P	Tct	Cct	1	1	B.1.243	0.00007
N	2	S2A	Tct	Gct	1	1	B.1.247	0.014925
N	2	S2del1	Tct	-ct	1	1	B.1.247	0.014925
N	2	S2Y	tCt	tAt	1	1	B.1.311	0.000275
N	2	S2F	tCt	tTt	1	1	B.1.351	0.00003
N	2	S2A	Tct	Gct	1	1	B.1.351.3	0.000876
N	2	S2Y	tCt	tAt	1	1	B.1.351.3	0.000876
N	2	S2del1	Tct	-ct	1	1	B.1.36	0.000146
N	2	S2A	Tct	Gct	1	1	B.1.36	0.000146
N	2	S2F	tCt	tTt	1	1	B.1.36	0.000146
N	2	S2P	Tct	Cct	1	1	B.1.36.16	0.001425
N	2	S2A	Tct	Gct	1	1	B.1.36.16	0.001425
N	2	S2F	tCt	tTt	1	1	B.1.36.17	0.000494
N	2	S2P	Tct	Cct	1	1	B.1.36.19	0.009259
N	2	S2P	Tct	Cct	1	1	B.1.36.2	0.010753
N	2	S2P	Tct	Cct	1	1	B.1.36.22	0.001208
N	2	S2P	Tct	Cct	1	1	B.1.36.24	0.006173
N	2	S2del1	Tct	-ct	1	1	B.1.36.29	0.000517
N	2	S2P	Tct	Cct	1	1	B.1.36.8	0.001
N	2	S2T	Tct	Act	1	1	B.1.369	0.000285
N	2	S2Y	tCt	tAt	1	1	B.1.375	0.00082
N	2	S2P	Tct	Cct	1	1	B.1.396	0.000706
N	2	S2Y	tCt	tAt	1	1	B.1.396	0.000706
N	2	S2P	Tct	Cct	1	1	B.1.399	0.001934
N	2	S2S	tcT	tcC	1	1	B.1.424	0.008065
N	2	S2F	tCt	tTt	1	1	B.1.427	0.00005
N	2	S2P	Tct	Cct	1	1	B.1.432	0.011236
N	2	S2Y	tCt	tAt	1	1	B.1.439	0.005917
N	2	S2F	tCt	tTt	1	1	B.1.443	0.004673
N	2	S2A	Tct	Gct	1	1	B.1.462	0.007246
N	2	S2P	Tct	Cct	1	1	B.1.466	0.023256
N	2	S2Y	tCt	tAt	1	1	B.1.466.2	0.000391
N	2	S2F	tCt	tTt	1	1	B.1.466.2	0.000391
N	2	S2del1	Tct	-ct	1	1	B.1.468	0.005714
N	2	S2Y	tCt	tAt	1	1	B.1.470	0.001404
N	2	S2P	Tct	Cct	1	1	B.1.491	0.052632
N	2	S2S	tcT	tcC	1	1	B.1.507	0.011236
N	2	S2Y	tCT	tAC	1	1	B.1.524	0.001406
N	2	S2F	tCT	tTC	1	1	B.1.525	0.000113
N	2	S2del	TCT	---	1	1	B.1.525	0.000113
N	2	S2S	tcT	tcG	1	1	B.1.526	0.000024
N	2	S2Y	tCt	tAt	1	1	B.1.526	0.000024
N	2	S2Y	tCt	tAt	1	1	B.1.535	0.028571
N	2	S2P	Tct	Cct	1	1	B.1.537	0.02
N	2	S2P	Tct	Cct	1	1	B.1.548	0.035714
N	2	S2P	Tct	Cct	1	1	B.1.560	0.00463
N	2	S2P	Tct	Cct	1	1	B.1.561	0.000397
N	2	S2F	tCt	tTt	1	1	B.1.596	0.000087
N	2	S2S	tcT	tcA	1	1	B.1.596	0.000087
N	2	S2Y	tCt	tAt	1	1	B.1.597	0.00463
N	2	S2Y	tCt	tAt	1	1	B.1.617.2	0.000004
N	2	S2del1	Tct	-ct	1	1	B.1.617.2	0.000004
N	2	S2P	Tct	Cct	1	1	B.1.621	0.000089
N	2	S2P	Tct	Cct	1	1	B.4.1	0.018868
N	2	S2F	tCt	tTt	1	1	B.40	0.000364
N	2	S2Y	tCt	tAt	1	1	B.55	0.00295
N	2	S2P	Tct	Cct	1	1	C.23	0.005814
N	2	S2F	tCt	tTt	1	1	C.35	0.000774
N	2	S2Y	tCt	tAt	1	1	C.35	0.000774
N	2	S2A	Tct	Gct	1	1	C.37	0.000116
N	2	S2Y	tCt	tAt	1	1	C.40	0.027778
N	2	S2F	tCt	tTt	1	1	D.2	0.000075
N	2	S2P	Tct	Cct	1	1	D.2	0.000075
N	2	S2V	TCT	GTA	1	1	P.1	0.000016
N	2	S2E	TCT	GAA	1	1	P.1	0.000016
N	2	S2X	tCT	tAA	1	1	P.1.10	0.000269
N	2	S2X	tCT	tAA	1	1	P.1.12	0.000484
N	2	S2Y	tCt	tAt	1	1	P.1.12	0.000484
N	2	S2H	TCT	CAC	1	1	P.1.12	0.000484
N	2	S2A	Tct	Gct	1	1	P.1.13	0.000898
N	2	S2Y	tCT	tAC	1	1	P.1.13	0.000898
N	2	S2X	tCT	tAA	1	1	P.1.13	0.000898
N	2	S2N	TCT	AAC	1	1	P.1.14	0.000048
N	2	S2A	Tct	Gct	1	1	P.1.14	0.000048
N	2	S2L	TCT	CTA	1	1	P.1.14	0.000048
N	2	S2H	TCT	CAC	1	1	P.1.15	0.000232
N	2	S2X	tCT	tAA	1	1	P.1.15	0.000232
N	2	S2Q	TCT	CAA	1	1	P.1.15	0.000232
N	2	S2Y	tCt	tAt	1	1	P.1.16	0.000374
N	2	S2Y	tCT	tAC	1	1	P.1.17	0.000162
N	2	S2E	TCT	GAA	1	1	P.1.17	0.000162
N	2	S2P	TcT	CcA	1	1	P.1.17	0.000162
N	2	S2L	TCT	CTA	1	1	P.1.17	0.000162
N	2	S2Y	tCT	tAC	1	1	P.1.7	0.000319
N	2	S2Y	tCt	tAt	1	1	P.2	0.000187
N	2	S2F	tCt	tTt	1	1	P.2	0.000187
N	2	S2F	tCt	tTt	1	1	Q.1	0.000126
N	2	S2F	tCt	tTt	1	1	Q.4	0.000455
N	2	S2F	tCt	tTt	1	1	Q.8	0.000165

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.