CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 7

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	7	Q7K		nonsyn	Caa	Aaa	4548	4548	1	28292-28294
N	7	Q7H		nonsyn	caA	caT	412	217	0.526699	28292-28294
N	7	Q7H		nonsyn	caA	caC	412	195	0.473301	28292-28294
N	7	Q7R		nonsyn	cAa	cGa	405	404	0.997531	28292-28294
N	7	Q7R		nonsyn	cAA	cGT	405	1	0.00246914	28292-28294
N	7	Q7L		nonsyn	cAa	cTa	116	111	0.956897	28292-28294
N	7	Q7L		nonsyn	cAA	cTT	116	5	0.0431034	28292-28294
N	7	Q7P		nonsyn	cAa	cCa	113	113	1	28292-28294
N	7	Q7Q		syn	caA	caG	109	109	1	28292-28294
N	7	Q7del		del	CAA	---	36	36	1	28292-28294
N	7	Q7X		nonsyn	Caa	Taa	12	9	0.75	28292-28294
N	7	Q7X		nonsyn	CaA	TaG	12	3	0.25	28292-28294
N	7	Q7del1		del	cAa	c-a	6	6	1	28292-28294
N	7	Q7D		nonsyn	CaA	GaC	6	6	1	28292-28294
N	7	Q7E		nonsyn	Caa	Gaa	5	5	1	28292-28294
N	7	Q7del2		del	cAA	c--	5	4	0.8	28292-28294
N	7	Q7del2		del	CAa	--a	5	1	0.2	28292-28294
N	7	Q7V		nonsyn	CAa	GTa	2	2	1	28292-28294
N	7	Q7W		nonsyn	CAA	TGG	1	1	1	28292-28294
N	7	Q7N		nonsyn	CaA	AaT	1	1	1	28292-28294
N	7	Q7C		nonsyn	CAA	TGT	1	1	1	28292-28294

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	7	Q7K	Caa	Aaa	4548	4548	All	0.00087
N	7	Q7K	Caa	Aaa	1642	1642	B.1.36.36	0.988561
N	7	Q7K	Caa	Aaa	463	463	AY.4	0.000721
N	7	Q7H	caA	caT	217	412	All	0.000042
N	7	Q7H	caA	caC	195	412	All	0.000037
N	7	Q7R	cAa	cGa	404	405	All	0.000077
N	7	Q7R	cAA	cGT	1	405	All	0
N	7	Q7K	Caa	Aaa	396	396	AY.6	0.016287
N	7	Q7R	cAa	cGa	170	170	B.1.258	0.011313
N	7	Q7K	Caa	Aaa	159	159	B.1.160	0.004959
N	7	Q7K	Caa	Aaa	137	137	A	0.053019
N	7	Q7K	Caa	Aaa	125	125	B.1.1.7	0.000112
N	7	Q7L	cAa	cTa	111	116	All	0.000021
N	7	Q7L	cAA	cTT	5	116	All	0.000001
N	7	Q7P	cAa	cCa	113	113	All	0.000022
N	7	Q7K	Caa	Aaa	111	111	AY.103	0.000689
N	7	Q7Q	caA	caG	109	109	All	0.000021
N	7	Q7K	Caa	Aaa	108	108	AY.3	0.001074
N	7	Q7K	Caa	Aaa	108	108	B.1.617.2	0.000407
N	7	Q7K	Caa	Aaa	97	97	B.1.596	0.008452
N	7	Q7P	cAa	cCa	88	88	R.1	0.007921
N	7	Q7K	Caa	Aaa	83	83	AY.26	0.00235
N	7	Q7R	cAa	cGa	74	74	B.1.324	0.11878
N	7	Q7K	Caa	Aaa	70	70	B.1.2	0.000616
N	7	Q7H	caA	caC	43	57	B.1.2	0.000379
N	7	Q7H	caA	caT	14	57	B.1.2	0.000123
N	7	Q7K	Caa	Aaa	52	52	B.1	0.000476
N	7	Q7K	Caa	Aaa	48	48	B.1.177	0.000632
N	7	Q7H	caA	caC	34	44	B.1.617.2	0.000128
N	7	Q7H	caA	caT	10	44	B.1.617.2	0.000038
N	7	Q7H	caA	caT	41	43	AY.103	0.000255
N	7	Q7H	caA	caC	2	43	AY.103	0.000012
N	7	Q7H	caA	caC	40	40	B.1.142	0.115942
N	7	Q7K	Caa	Aaa	39	39	B.1.177.16	0.025914
N	7	Q7K	Caa	Aaa	37	37	C.19	1
N	7	Q7del	CAA	---	36	36	All	0.000007
N	7	Q7K	Caa	Aaa	36	36	B.1.637	0.002631
N	7	Q7K	Caa	Aaa	35	35	B.1.351	0.00104
N	7	Q7K	Caa	Aaa	34	34	B.1.1	0.000617
N	7	Q7L	cAa	cTa	31	31	B.1.1.7	0.000028
N	7	Q7H	caA	caT	18	28	AY.4	0.000028
N	7	Q7H	caA	caC	10	28	AY.4	0.000016
N	7	Q7H	caA	caT	28	28	B.1.1.50	0.019009
N	7	Q7K	Caa	Aaa	28	28	B.1.526	0.000658
N	7	Q7K	Caa	Aaa	27	27	AY.25	0.000162
N	7	Q7H	caA	caT	27	27	B.1.1.7	0.000024
N	7	Q7K	Caa	Aaa	26	26	B.1.1.222	0.005304
N	7	Q7K	Caa	Aaa	26	26	B.1.1.311	0.009312
N	7	Q7K	Caa	Aaa	23	23	AY.44	0.00014
N	7	Q7K	Caa	Aaa	23	23	B.1.221	0.001634
N	7	Q7H	caA	caT	23	23	B.1.324	0.036918
N	7	Q7K	Caa	Aaa	22	22	AY.33	0.001469
N	7	Q7R	cAa	cGa	22	22	P.2	0.004106
N	7	Q7K	Caa	Aaa	21	21	AY.5	0.000434
N	7	Q7K	Caa	Aaa	18	18	B.1.429	0.000424
N	7	Q7H	caA	caC	15	15	AY.102	0.000398
N	7	Q7H	caA	caC	15	15	AY.42	0.000603
N	7	Q7K	Caa	Aaa	15	15	B.1.36	0.002189
N	7	Q7K	Caa	Aaa	14	14	AY.4.2	0.000304
N	7	Q7K	Caa	Aaa	14	14	B.1.177.81	0.002651
N	7	Q7K	Caa	Aaa	14	14	B.1.282	0.208955
N	7	Q7K	Caa	Aaa	13	13	AY.39	0.000321
N	7	Q7H	caA	caT	7	13	B.1.1	0.000127
N	7	Q7H	caA	caC	6	13	B.1.1	0.000109
N	7	Q7L	cAa	cTa	13	13	B.1.177.60	0.00284
N	7	Q7X	Caa	Taa	9	12	All	0.000002
N	7	Q7X	CaA	TaG	3	12	All	0.000001
N	7	Q7L	cAa	cTa	12	12	B.1.1.298	0.010345
N	7	Q7Q	caA	caG	12	12	B.1.627	0.024242
N	7	Q7K	Caa	Aaa	11	11	AD.2	0.002409
N	7	Q7K	Caa	Aaa	11	11	AY.43	0.000049
N	7	Q7Q	caA	caG	11	11	AY.44	0.000067
N	7	Q7H	caA	caC	9	11	B.1	0.000082
N	7	Q7H	caA	caT	2	11	B.1	0.000018
N	7	Q7K	Caa	Aaa	11	11	B.1.1.519	0.000437
N	7	Q7K	Caa	Aaa	11	11	B.1.243	0.000765
N	7	Q7K	Caa	Aaa	10	10	B.1.621	0.000885
N	7	Q7K	Caa	Aaa	10	10	P.1.14	0.000478
N	7	Q7K	Caa	Aaa	9	9	AY.20	0.00035
N	7	Q7del	CAA	---	9	9	AY.99.2	0.000829
N	7	Q7K	Caa	Aaa	9	9	B.1.1.1	0.00294
N	7	Q7R	cAa	cGa	9	9	B.1.1.263	0.014019
N	7	Q7K	Caa	Aaa	9	9	B.1.1.28	0.002801
N	7	Q7R	cAa	cGa	9	9	B.1.617.2	0.000034
N	7	Q7K	Caa	Aaa	9	9	B.1.9.4	0.055215
N	7	Q7K	Caa	Aaa	8	8	AY.23	0.000558
N	7	Q7K	Caa	Aaa	8	8	AY.47	0.000249
N	7	Q7R	cAa	cGa	8	8	B.1.1	0.000145
N	7	Q7Q	caA	caG	8	8	B.1.1.7	0.000007
N	7	Q7Q	caA	caG	8	8	B.1.2	0.00007
N	7	Q7Q	caA	caG	8	8	B.1.351	0.000238
N	7	Q7R	cAa	cGa	7	7	AY.26	0.000198
N	7	Q7P	cAa	cCa	7	7	AY.3	0.00007
N	7	Q7K	Caa	Aaa	7	7	AY.35	0.001631
N	7	Q7Q	caA	caG	7	7	AY.4	0.000011
N	7	Q7L	cAa	cTa	7	7	AY.4	0.000011
N	7	Q7Q	caA	caG	7	7	AY.43	0.000031
N	7	Q7K	Caa	Aaa	7	7	B.1.234	0.000924
N	7	Q7K	Caa	Aaa	6	6	A.2	0.003971
N	7	Q7D	CaA	GaC	6	6	All	0.000001
N	7	Q7del1	cAa	c-a	6	6	All	0.000001
N	7	Q7K	Caa	Aaa	6	6	AY.100	0.000276
N	7	Q7P	cAa	cCa	6	6	AY.103	0.000037
N	7	Q7K	Caa	Aaa	6	6	AY.116	0.001721
N	7	Q7Q	caA	caG	6	6	AY.26	0.00017
N	7	Q7K	Caa	Aaa	6	6	AY.5.3	0.002024
N	7	Q7K	Caa	Aaa	6	6	AY.53	0.001725
N	7	Q7Q	caA	caG	6	6	B.1	0.000055
N	7	Q7K	Caa	Aaa	6	6	B.1.1.216	0.005343
N	7	Q7K	Caa	Aaa	6	6	B.1.36.8	0.006
N	7	Q7R	cAa	cGa	6	6	B.1.441	0.057692
N	7	Q7R	cAa	cGa	6	6	B.1.621	0.000531
N	7	Q7K	Caa	Aaa	5	5	A.1	0.001409
N	7	Q7K	Caa	Aaa	5	5	A.23.1	0.003521
N	7	Q7E	Caa	Gaa	5	5	All	0.000001
N	7	Q7del2	cAA	c--	4	5	All	0.000001
N	7	Q7del2	CAa	--a	1	5	All	0
N	7	Q7R	cAa	cGa	5	5	AY.3	0.00005
N	7	Q7R	cAa	cGa	5	5	AY.4	0.000008
N	7	Q7K	Caa	Aaa	5	5	AY.40	0.004822
N	7	Q7del	CAA	---	5	5	AY.43	0.000022
N	7	Q7R	cAa	cGa	5	5	AY.67	0.002321
N	7	Q7R	cAa	cGa	5	5	B.1	0.000046
N	7	Q7K	Caa	Aaa	5	5	B.1.1.317	0.002058
N	7	Q7K	Caa	Aaa	5	5	B.1.1.39	0.002548
N	7	Q7R	cAa	cGa	5	5	B.1.2	0.000044
N	7	Q7L	cAa	cTa	4	5	B.1.2	0.000035
N	7	Q7L	cAA	cTT	1	5	B.1.2	0.000009
N	7	Q7K	Caa	Aaa	5	5	B.1.311	0.001373
N	7	Q7R	cAa	cGa	5	5	B.1.351.5	0.002998
N	7	Q7K	Caa	Aaa	5	5	B.1.427	0.000252
N	7	Q7H	caA	caT	3	5	B.1.596	0.000261
N	7	Q7H	caA	caC	2	5	B.1.596	0.000174
N	7	Q7D	CaA	GaC	5	5	P.1	0.000079
N	7	Q7K	Caa	Aaa	4	4	AY.102	0.000106
N	7	Q7H	caA	caT	4	4	AY.116.1	0.001246
N	7	Q7K	Caa	Aaa	4	4	AY.118	0.000251
N	7	Q7R	cAa	cGa	4	4	AY.119	0.000141
N	7	Q7K	Caa	Aaa	4	4	AY.120	0.000149
N	7	Q7H	caA	caT	3	4	AY.120	0.000112
N	7	Q7H	caA	caC	1	4	AY.120	0.000037
N	7	Q7H	caA	caT	4	4	AY.29	0.000063
N	7	Q7K	Caa	Aaa	4	4	AY.29	0.000063
N	7	Q7L	cAA	cTT	4	4	AY.3	0.00004
N	7	Q7K	Caa	Aaa	4	4	AY.34	0.000388
N	7	Q7R	cAa	cGa	4	4	AY.38	0.001997
N	7	Q7K	Caa	Aaa	4	4	AY.45	0.000487
N	7	Q7K	Caa	Aaa	4	4	AY.75	0.000224
N	7	Q7K	Caa	Aaa	4	4	AY.9.2	0.000147
N	7	Q7K	Caa	Aaa	4	4	AY.98.1	0.000194
N	7	Q7K	Caa	Aaa	4	4	B.1.1.207	0.004728
N	7	Q7L	cAa	cTa	4	4	B.1.1.214	0.000222
N	7	Q7K	Caa	Aaa	4	4	B.1.1.370	0.050633
N	7	Q7R	cAa	cGa	4	4	B.1.177	0.000053
N	7	Q7K	Caa	Aaa	4	4	B.1.177.51	0.018265
N	7	Q7Q	caA	caG	4	4	B.1.595	0.001044
N	7	Q7K	Caa	Aaa	4	4	B.1.597	0.018519
N	7	Q7K	Caa	Aaa	4	4	B.1.628	0.001409
N	7	Q7R	cAa	cGa	4	4	B.26	0.058824
N	7	Q7K	Caa	Aaa	4	4	P.1	0.000063
N	7	Q7del	CAA	---	4	4	P.1	0.000063
N	7	Q7P	cAa	cCa	4	4	P.1	0.000063
N	7	Q7K	Caa	Aaa	3	3	AY.1	0.001187
N	7	Q7K	Caa	Aaa	3	3	AY.111	0.000549
N	7	Q7K	Caa	Aaa	3	3	AY.119	0.000106
N	7	Q7K	Caa	Aaa	3	3	AY.16.1	0.00141
N	7	Q7K	Caa	Aaa	3	3	AY.2	0.001068
N	7	Q7Q	caA	caG	3	3	AY.20	0.000117
N	7	Q7H	caA	caT	3	3	AY.20	0.000117
N	7	Q7L	cAa	cTa	3	3	AY.25	0.000018
N	7	Q7K	Caa	Aaa	3	3	AY.29.1	0.000662
N	7	Q7K	Caa	Aaa	3	3	AY.36	0.000445
N	7	Q7K	Caa	Aaa	3	3	AY.39.1	0.000119
N	7	Q7Q	caA	caG	3	3	AY.4.2	0.000065
N	7	Q7L	cAa	cTa	3	3	AY.43	0.000013
N	7	Q7L	cAa	cTa	3	3	AY.44	0.000018
N	7	Q7R	cAa	cGa	3	3	AY.44	0.000018
N	7	Q7K	Caa	Aaa	3	3	AY.46	0.000312
N	7	Q7K	Caa	Aaa	3	3	AY.46.4	0.000494
N	7	Q7K	Caa	Aaa	3	3	AY.54	0.000286
N	7	Q7K	Caa	Aaa	3	3	AY.74	0.000347
N	7	Q7Q	caA	caG	3	3	AY.9.2	0.00011
N	7	Q7K	Caa	Aaa	3	3	B.1.1.284	0.000322
N	7	Q7R	cAa	cGa	3	3	B.1.1.519	0.000119
N	7	Q7del	CAA	---	3	3	B.1.1.7	0.000003
N	7	Q7K	Caa	Aaa	3	3	B.1.177.72	0.010169
N	7	Q7K	Caa	Aaa	3	3	B.1.351.3	0.002629
N	7	Q7H	caA	caT	2	3	B.1.429	0.000047
N	7	Q7H	caA	caC	1	3	B.1.429	0.000024
N	7	Q7K	Caa	Aaa	3	3	B.1.438.1	0.000322
N	7	Q7K	Caa	Aaa	3	3	B.1.466.2	0.001174
N	7	Q7K	Caa	Aaa	3	3	B.1.490	0.3
N	7	Q7R	cAa	cGa	3	3	B.3.1	0.004975
N	7	Q7Q	caA	caG	3	3	C.18	0.007772
N	7	Q7K	Caa	Aaa	3	3	C.36.3	0.001702
N	7	Q7K	Caa	Aaa	3	3	C.37	0.000348
N	7	Q7K	Caa	Aaa	3	3	D.2	0.000225
N	7	Q7H	caA	caT	3	3	P.1	0.000047
N	7	Q7K	Caa	Aaa	3	3	R.1	0.00027
N	7	Q7V	CAa	GTa	2	2	All	0
N	7	Q7R	cAa	cGa	2	2	AU.2	0.004843
N	7	Q7K	Caa	Aaa	2	2	AY.106	0.00067
N	7	Q7K	Caa	Aaa	2	2	AY.117	0.000169
N	7	Q7K	Caa	Aaa	2	2	AY.12	0.000632
N	7	Q7H	caA	caT	2	2	AY.121	0.000271
N	7	Q7K	Caa	Aaa	2	2	AY.13	0.000322
N	7	Q7K	Caa	Aaa	2	2	AY.19	0.002281
N	7	Q7L	cAa	cTa	2	2	AY.23	0.000139
N	7	Q7H	caA	caT	1	2	AY.25	0.000006
N	7	Q7H	caA	caC	1	2	AY.25	0.000006
N	7	Q7H	caA	caC	2	2	AY.26	0.000057
N	7	Q7K	Caa	Aaa	2	2	AY.30	0.000791
N	7	Q7H	caA	caT	2	2	AY.33	0.000134
N	7	Q7K	Caa	Aaa	2	2	AY.38	0.000999
N	7	Q7K	Caa	Aaa	2	2	AY.42	0.00008
N	7	Q7R	cAa	cGa	2	2	AY.43	0.000009
N	7	Q7H	caA	caC	2	2	AY.44	0.000012
N	7	Q7del	CAA	---	2	2	AY.46	0.000208
N	7	Q7K	Caa	Aaa	2	2	AY.61	0.00021
N	7	Q7Q	caA	caG	2	2	AY.61	0.00021
N	7	Q7K	Caa	Aaa	2	2	AY.63	0.000774
N	7	Q7K	Caa	Aaa	2	2	AY.94	0.000885
N	7	Q7H	caA	caT	1	2	AY.98.1	0.000048
N	7	Q7H	caA	caC	1	2	AY.98.1	0.000048
N	7	Q7K	Caa	Aaa	2	2	AY.99.2	0.000184
N	7	Q7K	Caa	Aaa	2	2	AZ.1	0.001735
N	7	Q7K	Caa	Aaa	2	2	AZ.2	0.001642
N	7	Q7K	Caa	Aaa	2	2	B	0.000256
N	7	Q7K	Caa	Aaa	2	2	B.1.1.214	0.000111
N	7	Q7K	Caa	Aaa	2	2	B.1.1.25	0.001137
N	7	Q7K	Caa	Aaa	2	2	B.1.1.33	0.000842
N	7	Q7H	caA	caT	2	2	B.1.1.348	0.001592
N	7	Q7K	Caa	Aaa	2	2	B.1.1.37	0.000386
N	7	Q7H	caA	caT	2	2	B.1.1.39	0.001019
N	7	Q7del1	cAa	c-a	2	2	B.1.1.7	0.000002
N	7	Q7P	cAa	cCa	2	2	B.1.1.7	0.000002
N	7	Q7K	Caa	Aaa	2	2	B.1.1.70	0.000682
N	7	Q7H	caA	caT	2	2	B.1.177	0.000026
N	7	Q7K	Caa	Aaa	2	2	B.1.177.21	0.000153
N	7	Q7K	Caa	Aaa	2	2	B.1.177.65	0.001331
N	7	Q7K	Caa	Aaa	2	2	B.1.177.80	0.003824
N	7	Q7K	Caa	Aaa	2	2	B.1.221.1	0.005814
N	7	Q7L	cAa	cTa	2	2	B.1.258	0.000133
N	7	Q7K	Caa	Aaa	2	2	B.1.258	0.000133
N	7	Q7K	Caa	Aaa	2	2	B.1.258.17	0.000208
N	7	Q7K	Caa	Aaa	2	2	B.1.400	0.000858
N	7	Q7K	Caa	Aaa	2	2	B.1.405	0.024691
N	7	Q7R	cAa	cGa	2	2	B.1.422	0.001625
N	7	Q7Q	caA	caG	2	2	B.1.429	0.000047
N	7	Q7K	Caa	Aaa	2	2	B.1.453	0.006472
N	7	Q7L	cAa	cTa	2	2	B.1.526	0.000047
N	7	Q7K	Caa	Aaa	2	2	B.1.561	0.000794
N	7	Q7K	Caa	Aaa	2	2	B.1.617.1	0.000258
N	7	Q7H	caA	caC	2	2	B.1.617.1	0.000258
N	7	Q7Q	caA	caG	2	2	B.1.617.2	0.000008
N	7	Q7K	Caa	Aaa	2	2	C.16	0.002121
N	7	Q7R	cAa	cGa	2	2	C.26	0.014706
N	7	Q7R	cAa	cGa	2	2	C.37	0.000232
N	7	Q7H	caA	caC	2	2	N.4	0.008511
N	7	Q7K	Caa	Aaa	2	2	N.6	0.014184
N	7	Q7V	CAa	GTa	2	2	P.1	0.000032
N	7	Q7del2	cAA	c--	2	2	P.1	0.000032
N	7	Q7K	Caa	Aaa	2	2	P.2	0.000373
N	7	Q7Q	caA	caG	2	2	P.3	0.00319
N	7	Q7R	cAa	cGa	2	2	Q.1	0.000253
N	7	Q7L	cAa	cTa	2	2	Q.8	0.00033
N	7	Q7H	caA	caT	1	1	A.18	0.05
N	7	Q7H	caA	caT	1	1	A.2.4	0.003367
N	7	Q7K	Caa	Aaa	1	1	A.2.5	0.000499
N	7	Q7N	CaA	AaT	1	1	All	0
N	7	Q7W	CAA	TGG	1	1	All	0
N	7	Q7C	CAA	TGT	1	1	All	0
N	7	Q7K	Caa	Aaa	1	1	AU.1	0.001266
N	7	Q7del	CAA	---	1	1	AY.100	0.000046
N	7	Q7R	cAa	cGa	1	1	AY.101	0.00049
N	7	Q7del	CAA	---	1	1	AY.101	0.00049
N	7	Q7L	cAa	cTa	1	1	AY.103	0.000006
N	7	Q7R	cAa	cGa	1	1	AY.103	0.000006
N	7	Q7H	caA	caC	1	1	AY.105	0.000643
N	7	Q7K	Caa	Aaa	1	1	AY.107	0.000466
N	7	Q7K	Caa	Aaa	1	1	AY.109	0.00074
N	7	Q7K	Caa	Aaa	1	1	AY.110	0.000113
N	7	Q7K	Caa	Aaa	1	1	AY.116.1	0.000311
N	7	Q7E	Caa	Gaa	1	1	AY.118	0.000063
N	7	Q7H	caA	caC	1	1	AY.119	0.000035
N	7	Q7R	cAa	cGa	1	1	AY.120	0.000037
N	7	Q7E	Caa	Gaa	1	1	AY.120	0.000037
N	7	Q7del2	CAa	--a	1	1	AY.120.1	0.000321
N	7	Q7K	Caa	Aaa	1	1	AY.120.2	0.001285
N	7	Q7K	Caa	Aaa	1	1	AY.121	0.000135
N	7	Q7K	Caa	Aaa	1	1	AY.16	0.00038
N	7	Q7L	cAa	cTa	1	1	AY.20	0.000039
N	7	Q7del	CAA	---	1	1	AY.23	0.00007
N	7	Q7R	cAa	cGa	1	1	AY.25	0.000006
N	7	Q7K	Caa	Aaa	1	1	AY.27	0.000065
N	7	Q7P	cAa	cCa	1	1	AY.29	0.000016
N	7	Q7L	cAa	cTa	1	1	AY.29	0.000016
N	7	Q7Q	caA	caG	1	1	AY.29	0.000016
N	7	Q7K	Caa	Aaa	1	1	AY.3.1	0.000085
N	7	Q7del	CAA	---	1	1	AY.33	0.000067
N	7	Q7K	Caa	Aaa	1	1	AY.37	0.000316
N	7	Q7R	cAa	cGa	1	1	AY.39	0.000025
N	7	Q7Q	caA	caG	1	1	AY.39.1	0.00004
N	7	Q7R	cAa	cGa	1	1	AY.4.2	0.000022
N	7	Q7K	Caa	Aaa	1	1	AY.4.2.1	0.000149
N	7	Q7Q	caA	caG	1	1	AY.4.4	0.000409
N	7	Q7del	CAA	---	1	1	AY.4.4	0.000409
N	7	Q7K	Caa	Aaa	1	1	AY.41	0.000294
N	7	Q7H	caA	caT	1	1	AY.43	0.000004
N	7	Q7del	CAA	---	1	1	AY.44	0.000006
N	7	Q7R	cAa	cGa	1	1	AY.45	0.000122
N	7	Q7del	CAA	---	1	1	AY.46.3	0.000934
N	7	Q7R	cAa	cGa	1	1	AY.46.4	0.000165
N	7	Q7K	Caa	Aaa	1	1	AY.46.5	0.000198
N	7	Q7del	CAA	---	1	1	AY.46.6	0.000072
N	7	Q7R	cAa	cGa	1	1	AY.5	0.000021
N	7	Q7del	CAA	---	1	1	AY.5.3	0.000337
N	7	Q7Q	caA	caG	1	1	AY.56	0.001605
N	7	Q7H	caA	caT	1	1	AY.58	0.000907
N	7	Q7K	Caa	Aaa	1	1	AY.58	0.000907
N	7	Q7K	Caa	Aaa	1	1	AY.59	0.00053
N	7	Q7R	cAa	cGa	1	1	AY.6	0.000041
N	7	Q7L	cAa	cTa	1	1	AY.61	0.000105
N	7	Q7X	Caa	Taa	1	1	AY.62	0.000436
N	7	Q7K	Caa	Aaa	1	1	AY.68	0.000274
N	7	Q7H	caA	caT	1	1	AY.69	0.000187
N	7	Q7K	Caa	Aaa	1	1	AY.7	0.000196
N	7	Q7K	Caa	Aaa	1	1	AY.70	0.000209
N	7	Q7K	Caa	Aaa	1	1	AY.75.1	0.00018
N	7	Q7H	caA	caT	1	1	AY.75.1	0.00018
N	7	Q7K	Caa	Aaa	1	1	AY.76	0.004831
N	7	Q7K	Caa	Aaa	1	1	AY.80	0.001129
N	7	Q7K	Caa	Aaa	1	1	AY.85	0.000427
N	7	Q7K	Caa	Aaa	1	1	AY.87	0.000833
N	7	Q7K	Caa	Aaa	1	1	AY.88	0.000884
N	7	Q7K	Caa	Aaa	1	1	AY.9	0.000068
N	7	Q7K	Caa	Aaa	1	1	AY.9.1	0.000084
N	7	Q7R	cAa	cGa	1	1	AY.9.2	0.000037
N	7	Q7K	Caa	Aaa	1	1	AY.91	0.00073
N	7	Q7P	cAa	cCa	1	1	AY.92	0.000287
N	7	Q7H	caA	caC	1	1	AY.92	0.000287
N	7	Q7K	Caa	Aaa	1	1	AY.92	0.000287
N	7	Q7H	caA	caC	1	1	B	0.000128
N	7	Q7E	Caa	Gaa	1	1	B.1	0.000009
N	7	Q7X	Caa	Taa	1	1	B.1	0.000009
N	7	Q7L	cAa	cTa	1	1	B.1.1	0.000018
N	7	Q7del	CAA	---	1	1	B.1.1	0.000018
N	7	Q7K	Caa	Aaa	1	1	B.1.1.10	0.001115
N	7	Q7K	Caa	Aaa	1	1	B.1.1.121	0.002427
N	7	Q7K	Caa	Aaa	1	1	B.1.1.13	0.035714
N	7	Q7K	Caa	Aaa	1	1	B.1.1.153	0.001095
N	7	Q7R	cAa	cGa	1	1	B.1.1.157	0.000913
N	7	Q7L	cAa	cTa	1	1	B.1.1.186	0.003436
N	7	Q7E	Caa	Gaa	1	1	B.1.1.210	0.005714
N	7	Q7R	cAa	cGa	1	1	B.1.1.214	0.000055
N	7	Q7R	cAa	cGa	1	1	B.1.1.216	0.00089
N	7	Q7H	caA	caC	1	1	B.1.1.216	0.00089
N	7	Q7K	Caa	Aaa	1	1	B.1.1.277	0.000759
N	7	Q7R	cAa	cGa	1	1	B.1.1.291	0.000742
N	7	Q7R	cAa	cGa	1	1	B.1.1.294	0.001266
N	7	Q7K	Caa	Aaa	1	1	B.1.1.297	0.002237
N	7	Q7K	Caa	Aaa	1	1	B.1.1.304	0.002809
N	7	Q7K	Caa	Aaa	1	1	B.1.1.306	0.000438
N	7	Q7K	Caa	Aaa	1	1	B.1.1.310	0.015152
N	7	Q7K	Caa	Aaa	1	1	B.1.1.312	0.001912
N	7	Q7K	Caa	Aaa	1	1	B.1.1.318	0.000302
N	7	Q7K	Caa	Aaa	1	1	B.1.1.348	0.000796
N	7	Q7K	Caa	Aaa	1	1	B.1.1.351	0.002793
N	7	Q7L	cAa	cTa	1	1	B.1.1.354	0.004386
N	7	Q7R	cAa	cGa	1	1	B.1.1.368	0.003086
N	7	Q7K	Caa	Aaa	1	1	B.1.1.389	0.006061
N	7	Q7R	cAa	cGa	1	1	B.1.1.409	0.002833
N	7	Q7K	Caa	Aaa	1	1	B.1.1.434	0.000349
N	7	Q7R	cAa	cGa	1	1	B.1.1.485	0.016667
N	7	Q7L	cAa	cTa	1	1	B.1.1.487	0.005587
N	7	Q7L	cAa	cTa	1	1	B.1.1.519	0.00004
N	7	Q7K	Caa	Aaa	1	1	B.1.1.525	0.005464
N	7	Q7K	Caa	Aaa	1	1	B.1.1.63	0.000386
N	7	Q7del2	cAA	c--	1	1	B.1.1.7	0.000001
N	7	Q7X	Caa	Taa	1	1	B.1.1.7	0.000001
N	7	Q7K	Caa	Aaa	1	1	B.1.110	0.004525
N	7	Q7K	Caa	Aaa	1	1	B.1.111	0.001175
N	7	Q7K	Caa	Aaa	1	1	B.1.157	0.002985
N	7	Q7X	Caa	Taa	1	1	B.1.157	0.002985
N	7	Q7X	Caa	Taa	1	1	B.1.160.16	0.000929
N	7	Q7K	Caa	Aaa	1	1	B.1.160.30	0.002976
N	7	Q7L	cAa	cTa	1	1	B.1.160.8	0.001289
N	7	Q7L	cAa	cTa	1	1	B.1.177	0.000013
N	7	Q7K	Caa	Aaa	1	1	B.1.177.12	0.000152
N	7	Q7K	Caa	Aaa	1	1	B.1.177.4	0.000211
N	7	Q7K	Caa	Aaa	1	1	B.1.177.44	0.000519
N	7	Q7C	CAA	TGT	1	1	B.1.177.63	0.002703
N	7	Q7X	Caa	Taa	1	1	B.1.177.83	0.001481
N	7	Q7R	cAa	cGa	1	1	B.1.177.86	0.000183
N	7	Q7K	Caa	Aaa	1	1	B.1.177.86	0.000183
N	7	Q7K	Caa	Aaa	1	1	B.1.195	0.005025
N	7	Q7del1	cAa	c-a	1	1	B.1.2	0.000009
N	7	Q7X	Caa	Taa	1	1	B.1.2	0.000009
N	7	Q7K	Caa	Aaa	1	1	B.1.206	0.000816
N	7	Q7L	cAa	cTa	1	1	B.1.214.2	0.0006
N	7	Q7H	caA	caT	1	1	B.1.223	0.002778
N	7	Q7P	cAa	cCa	1	1	B.1.234	0.000132
N	7	Q7L	cAa	cTa	1	1	B.1.234	0.000132
N	7	Q7Q	caA	caG	1	1	B.1.234	0.000132
N	7	Q7L	cAa	cTa	1	1	B.1.235	0.002519
N	7	Q7H	caA	caC	1	1	B.1.237	0.004975
N	7	Q7K	Caa	Aaa	1	1	B.1.241	0.000812
N	7	Q7Q	caA	caG	1	1	B.1.243	0.00007
N	7	Q7H	caA	caT	1	1	B.1.243	0.00007
N	7	Q7R	cAa	cGa	1	1	B.1.243	0.00007
N	7	Q7K	Caa	Aaa	1	1	B.1.258.14	0.00098
N	7	Q7R	cAa	cGa	1	1	B.1.258.17	0.000104
N	7	Q7K	Caa	Aaa	1	1	B.1.279	0.000514
N	7	Q7H	caA	caT	1	1	B.1.298	0.002114
N	7	Q7Q	caA	caG	1	1	B.1.311	0.000275
N	7	Q7K	Caa	Aaa	1	1	B.1.320	0.001245
N	7	Q7K	Caa	Aaa	1	1	B.1.346	0.001311
N	7	Q7H	caA	caT	1	1	B.1.351	0.00003
N	7	Q7L	cAa	cTa	1	1	B.1.351	0.00003
N	7	Q7L	cAa	cTa	1	1	B.1.36	0.000146
N	7	Q7K	Caa	Aaa	1	1	B.1.36.1	0.00114
N	7	Q7Q	caA	caG	1	1	B.1.36.17	0.000494
N	7	Q7K	Caa	Aaa	1	1	B.1.36.22	0.001208
N	7	Q7K	Caa	Aaa	1	1	B.1.36.23	0.016393
N	7	Q7K	Caa	Aaa	1	1	B.1.36.25	0.002208
N	7	Q7K	Caa	Aaa	1	1	B.1.36.29	0.000517
N	7	Q7K	Caa	Aaa	1	1	B.1.36.33	0.007576
N	7	Q7L	cAa	cTa	1	1	B.1.367	0.000792
N	7	Q7K	Caa	Aaa	1	1	B.1.384	0.1
N	7	Q7L	cAa	cTa	1	1	B.1.396	0.000706
N	7	Q7del1	cAa	c-a	1	1	B.1.400	0.000429
N	7	Q7Q	caA	caG	1	1	B.1.416.1	0.001563
N	7	Q7K	Caa	Aaa	1	1	B.1.422	0.000812
N	7	Q7R	cAa	cGa	1	1	B.1.427	0.00005
N	7	Q7L	cAa	cTa	1	1	B.1.429	0.000024
N	7	Q7R	cAa	cGa	1	1	B.1.432	0.011236
N	7	Q7K	Caa	Aaa	1	1	B.1.469	0.00361
N	7	Q7K	Caa	Aaa	1	1	B.1.471	0.002732
N	7	Q7K	Caa	Aaa	1	1	B.1.474	0.001901
N	7	Q7K	Caa	Aaa	1	1	B.1.480	0.002488
N	7	Q7K	Caa	Aaa	1	1	B.1.509	0.000866
N	7	Q7K	Caa	Aaa	1	1	B.1.560	0.00463
N	7	Q7H	caA	caT	1	1	B.1.561	0.000397
N	7	Q7del1	cAa	c-a	1	1	B.1.564	0.000426
N	7	Q7K	Caa	Aaa	1	1	B.1.575	0.000303
N	7	Q7del1	cAa	c-a	1	1	B.1.580	0.004065
N	7	Q7P	cAa	cCa	1	1	B.1.595	0.000261
N	7	Q7L	cAa	cTa	1	1	B.1.595	0.000261
N	7	Q7K	Caa	Aaa	1	1	B.1.595	0.000261
N	7	Q7W	CAA	TGG	1	1	B.1.617.2	0.000004
N	7	Q7del	CAA	---	1	1	B.1.617.2	0.000004
N	7	Q7E	Caa	Gaa	1	1	B.1.617.2	0.000004
N	7	Q7L	cAa	cTa	1	1	B.1.617.2	0.000004
N	7	Q7Q	caA	caG	1	1	B.1.620	0.000946
N	7	Q7H	caA	caC	1	1	B.1.621	0.000089
N	7	Q7L	cAa	cTa	1	1	B.1.621.1	0.000506
N	7	Q7K	Caa	Aaa	1	1	B.40	0.000364
N	7	Q7H	caA	caT	1	1	C.35	0.000774
N	7	Q7R	cAa	cGa	1	1	C.36	0.000911
N	7	Q7K	Caa	Aaa	1	1	C.36.1	0.004149
N	7	Q7H	caA	caT	1	1	D.2	0.000075
N	7	Q7X	Caa	Taa	1	1	D.2	0.000075
N	7	Q7Q	caA	caG	1	1	D.2	0.000075
N	7	Q7K	Caa	Aaa	1	1	L.3	0.003546
N	7	Q7R	cAA	cGT	1	1	P.1	0.000016
N	7	Q7X	CaA	TaG	1	1	P.1	0.000016
N	7	Q7N	CaA	AaT	1	1	P.1	0.000016
N	7	Q7R	cAa	cGa	1	1	P.1.12	0.000484
N	7	Q7D	CaA	GaC	1	1	P.1.12	0.000484
N	7	Q7del	CAA	---	1	1	P.1.12	0.000484
N	7	Q7P	cAa	cCa	1	1	P.1.12	0.000484
N	7	Q7del2	cAA	c--	1	1	P.1.13	0.000898
N	7	Q7X	CaA	TaG	1	1	P.1.14	0.000048
N	7	Q7X	CaA	TaG	1	1	P.1.15	0.000232
N	7	Q7K	Caa	Aaa	1	1	P.1.15	0.000232
N	7	Q7P	cAa	cCa	1	1	P.1.17	0.000162
N	7	Q7K	Caa	Aaa	1	1	P.1.7	0.000319
N	7	Q7del	CAA	---	1	1	P.1.7	0.000319
N	7	Q7X	Caa	Taa	1	1	Q.3	0.000145
N	7	Q7L	cAa	cTa	1	1	V.2	0.032258
N	7	Q7Q	caA	caG	1	1	Z.1	0.00289

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.