CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 289

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	289	Q289H		nonsyn	caG	caT	4796	4125	0.860092	29138-29140
N	289	Q289H		nonsyn	caG	caC	4796	671	0.139908	29138-29140
N	289	Q289Q		syn	caG	caA	1609	1609	1	29138-29140
N	289	Q289L		nonsyn	cAg	cTg	530	530	1	29138-29140
N	289	Q289R		nonsyn	cAg	cGg	117	117	1	29138-29140
N	289	Q289K		nonsyn	Cag	Aag	67	67	1	29138-29140
N	289	Q289P		nonsyn	cAg	cCg	34	34	1	29138-29140
N	289	Q289del		del	CAG	---	12	12	1	29138-29140
N	289	Q289E		nonsyn	Cag	Gag	12	12	1	29138-29140
N	289	Q289X		nonsyn	Cag	Tag	8	8	1	29138-29140
N	289	Q289W		nonsyn	CAg	TGg	3	3	1	29138-29140
N	289	Q289Y		nonsyn	CaG	TaT	2	2	1	29138-29140
N	289	Q289S		nonsyn	CAG	TCA	2	1	0.5	29138-29140
N	289	Q289S		nonsyn	CAG	AGT	2	1	0.5	29138-29140
N	289	Q289del1		del	caG	ca-	1	1	1	29138-29140
N	289	Q289N		nonsyn	CaG	AaC	1	1	1	29138-29140
N	289	Q289del2		del	cAG	c--	1	1	1	29138-29140

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	289	Q289H	caG	caT	4125	4796	All	0.000789
N	289	Q289H	caG	caC	671	4796	All	0.000128
N	289	Q289Q	caG	caA	1609	1609	All	0.000308
N	289	Q289Q	caG	caA	698	698	B.1.517	0.298036
N	289	Q289H	caG	caT	575	690	AY.4	0.000895
N	289	Q289H	caG	caC	115	690	AY.4	0.000179
N	289	Q289H	caG	caT	552	596	B.1.1.7	0.000494
N	289	Q289H	caG	caC	44	596	B.1.1.7	0.000039
N	289	Q289L	cAg	cTg	530	530	All	0.000101
N	289	Q289H	caG	caT	516	516	AY.33	0.034457
N	289	Q289L	cAg	cTg	259	259	AY.4	0.000403
N	289	Q289Q	caG	caA	252	252	B.1.1.7	0.000226
N	289	Q289H	caG	caT	117	221	AY.25	0.000704
N	289	Q289H	caG	caC	104	221	AY.25	0.000626
N	289	Q289H	caG	caT	193	199	B.1.351	0.005737
N	289	Q289H	caG	caC	6	199	B.1.351	0.000178
N	289	Q289H	caG	caT	187	188	AY.111	0.034249
N	289	Q289H	caG	caC	1	188	AY.111	0.000183
N	289	Q289Q	caG	caA	188	188	B.1.517.1	0.989474
N	289	Q289Q	caG	caA	172	172	AY.4	0.000268
N	289	Q289H	caG	caT	132	170	B.1.617.2	0.000497
N	289	Q289H	caG	caC	38	170	B.1.617.2	0.000143
N	289	Q289L	cAg	cTg	142	142	AY.43	0.000629
N	289	Q289H	caG	caT	116	136	B.1.2	0.001021
N	289	Q289H	caG	caC	20	136	B.1.2	0.000176
N	289	Q289R	cAg	cGg	117	117	All	0.000022
N	289	Q289H	caG	caT	104	115	AY.44	0.000633
N	289	Q289H	caG	caC	11	115	AY.44	0.000067
N	289	Q289H	caG	caT	84	104	B.1	0.000769
N	289	Q289H	caG	caC	20	104	B.1	0.000183
N	289	Q289H	caG	caT	103	103	B.1.243	0.007167
N	289	Q289H	caG	caT	94	102	AY.43	0.000416
N	289	Q289H	caG	caC	8	102	AY.43	0.000035
N	289	Q289R	cAg	cGg	92	92	B.1.1.7	0.000082
N	289	Q289Q	caG	caA	88	88	AY.43	0.00039
N	289	Q289H	caG	caT	81	87	B.1.177	0.001067
N	289	Q289H	caG	caC	6	87	B.1.177	0.000079
N	289	Q289H	caG	caT	68	77	AY.103	0.000422
N	289	Q289H	caG	caC	9	77	AY.103	0.000056
N	289	Q289K	Cag	Aag	67	67	All	0.000013
N	289	Q289H	caG	caT	56	65	P.1	0.000882
N	289	Q289H	caG	caC	9	65	P.1	0.000142
N	289	Q289H	caG	caT	64	64	AY.46.6	0.004621
N	289	Q289H	caG	caT	45	58	B.1.160	0.001403
N	289	Q289H	caG	caC	13	58	B.1.160	0.000405
N	289	Q289H	caG	caT	56	56	B.1.525	0.006337
N	289	Q289H	caG	caT	47	51	AY.3	0.000467
N	289	Q289H	caG	caC	4	51	AY.3	0.00004
N	289	Q289H	caG	caT	41	41	B.1.177.75	0.042664
N	289	Q289H	caG	caC	23	40	B.1.1.519	0.000913
N	289	Q289H	caG	caT	17	40	B.1.1.519	0.000675
N	289	Q289H	caG	caT	26	39	B.1.429	0.000612
N	289	Q289H	caG	caC	13	39	B.1.429	0.000306
N	289	Q289H	caG	caT	30	37	B.1.1	0.000544
N	289	Q289H	caG	caC	7	37	B.1.1	0.000127
N	289	Q289Q	caG	caA	35	35	B.1	0.000321
N	289	Q289P	cAg	cCg	34	34	All	0.000007
N	289	Q289H	caG	caT	31	34	AY.39	0.000766
N	289	Q289H	caG	caC	3	34	AY.39	0.000074
N	289	Q289H	caG	caC	32	34	B.1.637	0.002338
N	289	Q289H	caG	caT	2	34	B.1.637	0.000146
N	289	Q289L	cAg	cTg	31	31	AY.39	0.000766
N	289	Q289H	caG	caC	20	31	B.1.221	0.001421
N	289	Q289H	caG	caT	11	31	B.1.221	0.000781
N	289	Q289H	caG	caC	26	31	B.1.596	0.002266
N	289	Q289H	caG	caT	5	31	B.1.596	0.000436
N	289	Q289H	caG	caT	22	29	AY.102	0.000583
N	289	Q289H	caG	caC	7	29	AY.102	0.000186
N	289	Q289Q	caG	caA	25	25	B.1.617.2	0.000094
N	289	Q289H	caG	caT	22	24	AY.4.2	0.000477
N	289	Q289H	caG	caC	2	24	AY.4.2	0.000043
N	289	Q289H	caG	caT	18	23	AY.29	0.000284
N	289	Q289H	caG	caC	5	23	AY.29	0.000079
N	289	Q289H	caG	caT	21	23	AY.9.2	0.000771
N	289	Q289H	caG	caC	2	23	AY.9.2	0.000073
N	289	Q289H	caG	caT	19	22	A.2.5	0.009481
N	289	Q289H	caG	caC	3	22	A.2.5	0.001497
N	289	Q289H	caG	caT	21	22	AY.20	0.000816
N	289	Q289H	caG	caC	1	22	AY.20	0.000039
N	289	Q289H	caG	caT	17	22	B.1.526	0.0004
N	289	Q289H	caG	caC	5	22	B.1.526	0.000118
N	289	Q289H	caG	caT	21	21	AY.39.1	0.000832
N	289	Q289H	caG	caT	20	20	AY.4.5	0.00215
N	289	Q289H	caG	caT	19	20	AY.5	0.000392
N	289	Q289H	caG	caC	1	20	AY.5	0.000021
N	289	Q289L	cAg	cTg	19	19	B.1.1.7	0.000017
N	289	Q289K	Cag	Aag	19	19	B.1.214.2	0.011391
N	289	Q289H	caG	caT	19	19	P.1.14	0.000908
N	289	Q289H	caG	caT	18	18	B.1.177.10	0.015803
N	289	Q289H	caG	caT	17	18	B.1.351.2	0.005144
N	289	Q289H	caG	caC	1	18	B.1.351.2	0.000303
N	289	Q289H	caG	caT	18	18	B.1.36	0.002626
N	289	Q289H	caG	caT	17	17	B.1.258.17	0.001768
N	289	Q289H	caG	caT	12	16	AY.119	0.000424
N	289	Q289H	caG	caC	4	16	AY.119	0.000141
N	289	Q289H	caG	caC	16	16	P.1.10	0.004312
N	289	Q289H	caG	caT	15	15	AY.6	0.000617
N	289	Q289H	caG	caT	15	15	R.1	0.00135
N	289	Q289H	caG	caT	14	14	AY.42	0.000563
N	289	Q289Q	caG	caA	14	14	B.1.427	0.000707
N	289	Q289L	cAg	cTg	13	13	AY.103	0.000081
N	289	Q289H	caG	caT	13	13	AY.61	0.001362
N	289	Q289Q	caG	caA	13	13	B.1.258	0.000865
N	289	Q289H	caG	caT	11	13	C.37	0.001277
N	289	Q289H	caG	caC	2	13	C.37	0.000232
N	289	Q289del	CAG	---	12	12	All	0.000002
N	289	Q289E	Cag	Gag	12	12	All	0.000002
N	289	Q289H	caG	caT	9	12	AY.47	0.00028
N	289	Q289H	caG	caC	3	12	AY.47	0.000093
N	289	Q289Q	caG	caA	12	12	B.1.466.2	0.004695
N	289	Q289H	caG	caT	10	11	AY.117	0.000845
N	289	Q289H	caG	caC	1	11	AY.117	0.000085
N	289	Q289H	caG	caT	6	11	AY.75	0.000336
N	289	Q289H	caG	caC	5	11	AY.75	0.00028
N	289	Q289H	caG	caT	8	11	AY.98.1	0.000387
N	289	Q289H	caG	caC	3	11	AY.98.1	0.000145
N	289	Q289Q	caG	caA	11	11	B.1.637	0.000804
N	289	Q289H	caG	caT	9	10	AY.26	0.000255
N	289	Q289H	caG	caC	1	10	AY.26	0.000028
N	289	Q289H	caG	caT	10	10	AY.3.1	0.000853
N	289	Q289H	caG	caT	10	10	B.1.234	0.001319
N	289	Q289L	cAg	cTg	10	10	P.1	0.000158
N	289	Q289P	cAg	cCg	9	9	AY.4	0.000014
N	289	Q289K	Cag	Aag	9	9	B.1.1.7	0.000008
N	289	Q289H	caG	caT	9	9	B.1.258	0.000599
N	289	Q289X	Cag	Tag	8	8	All	0.000002
N	289	Q289H	caG	caT	7	8	AY.100	0.000322
N	289	Q289H	caG	caC	1	8	AY.100	0.000046
N	289	Q289H	caG	caT	8	8	AY.120	0.000297
N	289	Q289Q	caG	caA	8	8	B.1.2	0.00007
N	289	Q289L	cAg	cTg	8	8	B.1.617.2	0.00003
N	289	Q289H	caG	caT	8	8	B.1.621	0.000708
N	289	Q289K	Cag	Aag	7	7	AY.16	0.002658
N	289	Q289Q	caG	caA	7	7	AY.3	0.00007
N	289	Q289E	Cag	Gag	7	7	AY.3	0.00007
N	289	Q289H	caG	caT	7	7	AY.74	0.00081
N	289	Q289H	caG	caT	7	7	B.1.438.1	0.000751
N	289	Q289H	caG	caT	7	7	B.1.564	0.002981
N	289	Q289H	caG	caT	7	7	D.2	0.000525
N	289	Q289H	caG	caT	7	7	P.2	0.001306
N	289	Q289Q	caG	caA	6	6	AY.39	0.000148
N	289	Q289H	caG	caC	5	6	AY.69	0.000933
N	289	Q289H	caG	caT	1	6	AY.69	0.000187
N	289	Q289H	caG	caT	6	6	AY.70	0.001251
N	289	Q289H	caG	caT	6	6	B.1.1.33	0.002525
N	289	Q289H	caG	caC	6	6	B.1.258.7	0.011472
N	289	Q289H	caG	caT	6	6	B.1.427	0.000303
N	289	Q289H	caG	caT	6	6	B.1.459	0.02449
N	289	Q289Q	caG	caA	6	6	B.1.507	0.067416
N	289	Q289H	caG	caC	5	5	A.22	0.333333
N	289	Q289L	cAg	cTg	5	5	AY.3	0.00005
N	289	Q289H	caG	caT	4	5	AY.34	0.000388
N	289	Q289H	caG	caC	1	5	AY.34	0.000097
N	289	Q289H	caG	caT	5	5	AY.36	0.000741
N	289	Q289H	caG	caT	5	5	AY.92	0.001436
N	289	Q289H	caG	caT	5	5	B.1.139	0.003666
N	289	Q289H	caG	caT	5	5	B.1.177.44	0.002595
N	289	Q289H	caG	caT	5	5	B.1.258.2	0.022523
N	289	Q289H	caG	caT	5	5	B.1.456	0.01634
N	289	Q289H	caG	caT	5	5	B.40	0.001821
N	289	Q289H	caG	caT	5	5	B.6	0.00455
N	289	Q289H	caG	caT	4	4	A.21	0.01108
N	289	Q289Q	caG	caA	4	4	AY.103	0.000025
N	289	Q289H	caG	caT	3	4	AY.118	0.000188
N	289	Q289H	caG	caC	1	4	AY.118	0.000063
N	289	Q289H	caG	caT	4	4	AY.121	0.000541
N	289	Q289L	cAg	cTg	4	4	AY.25	0.000024
N	289	Q289H	caG	caT	4	4	AY.27	0.000259
N	289	Q289Q	caG	caA	4	4	AY.29	0.000063
N	289	Q289Q	caG	caA	4	4	AY.47	0.000124
N	289	Q289H	caG	caT	2	4	AY.54	0.000191
N	289	Q289H	caG	caC	2	4	AY.54	0.000191
N	289	Q289H	caG	caT	3	4	AY.7.1	0.000338
N	289	Q289H	caG	caC	1	4	AY.7.1	0.000113
N	289	Q289H	caG	caT	4	4	AY.99.2	0.000369
N	289	Q289L	cAg	cTg	4	4	B.1.1	0.000073
N	289	Q289H	caG	caT	4	4	B.1.1.214	0.000222
N	289	Q289H	caG	caT	4	4	B.1.1.216	0.003562
N	289	Q289H	caG	caC	3	4	B.1.1.318	0.000905
N	289	Q289H	caG	caT	1	4	B.1.1.318	0.000302
N	289	Q289Q	caG	caA	4	4	B.1.1.519	0.000159
N	289	Q289P	cAg	cCg	4	4	B.1.1.7	0.000004
N	289	Q289H	caG	caT	4	4	B.1.177.77	0.002905
N	289	Q289H	caG	caC	4	4	B.1.177.80	0.007648
N	289	Q289K	Cag	Aag	4	4	B.1.311	0.001098
N	289	Q289H	caG	caT	4	4	B.1.582	0.001963
N	289	Q289W	CAg	TGg	3	3	All	0.000001
N	289	Q289K	Cag	Aag	3	3	AY.103	0.000019
N	289	Q289H	caG	caT	3	3	AY.23	0.000209
N	289	Q289L	cAg	cTg	3	3	AY.42	0.000121
N	289	Q289del	CAG	---	3	3	AY.43	0.000013
N	289	Q289P	cAg	cCg	3	3	AY.44	0.000018
N	289	Q289L	cAg	cTg	3	3	AY.44	0.000018
N	289	Q289H	caG	caT	2	3	AY.45	0.000243
N	289	Q289H	caG	caC	1	3	AY.45	0.000122
N	289	Q289H	caG	caT	3	3	AY.46	0.000312
N	289	Q289K	Cag	Aag	3	3	AY.47	0.000093
N	289	Q289H	caG	caT	3	3	AY.57	0.001969
N	289	Q289H	caG	caT	3	3	AY.7	0.000588
N	289	Q289H	caG	caT	3	3	AY.73	0.001996
N	289	Q289H	caG	caT	3	3	AY.84	0.001312
N	289	Q289H	caG	caC	3	3	AY.9	0.000203
N	289	Q289K	Cag	Aag	3	3	B.1	0.000027
N	289	Q289L	cAg	cTg	3	3	B.1.1.216	0.002671
N	289	Q289H	caG	caT	2	3	B.1.1.298	0.001724
N	289	Q289H	caG	caC	1	3	B.1.1.298	0.000862
N	289	Q289H	caG	caT	2	3	B.1.1.348	0.001592
N	289	Q289H	caG	caC	1	3	B.1.1.348	0.000796
N	289	Q289H	caG	caC	3	3	B.1.1.434	0.001046
N	289	Q289R	cAg	cGg	3	3	B.1.177	0.00004
N	289	Q289H	caG	caT	2	3	B.1.177.79	0.004684
N	289	Q289H	caG	caC	1	3	B.1.177.79	0.002342
N	289	Q289R	cAg	cGg	3	3	B.1.2	0.000026
N	289	Q289H	caG	caT	3	3	B.1.258.11	0.001189
N	289	Q289H	caG	caT	3	3	B.1.36.29	0.001552
N	289	Q289H	caG	caT	2	3	B.1.466.2	0.000782
N	289	Q289H	caG	caC	1	3	B.1.466.2	0.000391
N	289	Q289Q	caG	caA	3	3	B.1.596	0.000261
N	289	Q289H	caG	caC	2	3	B.1.617.1	0.000258
N	289	Q289H	caG	caT	1	3	B.1.617.1	0.000129
N	289	Q289P	cAg	cCg	3	3	B.1.617.2	0.000011
N	289	Q289H	caG	caT	3	3	C.23	0.017442
N	289	Q289H	caG	caT	3	3	C.36.3	0.001702
N	289	Q289Q	caG	caA	3	3	P.1.12	0.001452
N	289	Q289H	caG	caT	3	3	P.1.2	0.003468
N	289	Q289Q	caG	caA	3	3	Q.8	0.000495
N	289	Q289W	CAg	TGg	2	2		0.111111
N	289	Q289X	Cag	Tag	2	2		0.111111
N	289	Q289H	caG	caT	2	2	A.1	0.000564
N	289	Q289Y	CaG	TaT	2	2	All	0
N	289	Q289S	CAG	TCA	1	2	All	0
N	289	Q289S	CAG	AGT	1	2	All	0
N	289	Q289Q	caG	caA	2	2	AY.100	0.000092
N	289	Q289P	cAg	cCg	2	2	AY.100	0.000092
N	289	Q289P	cAg	cCg	2	2	AY.103	0.000012
N	289	Q289H	caG	caT	2	2	AY.16	0.000759
N	289	Q289H	caG	caT	2	2	AY.19	0.002281
N	289	Q289K	Cag	Aag	2	2	AY.25	0.000012
N	289	Q289H	caG	caC	2	2	AY.29.1	0.000441
N	289	Q289P	cAg	cCg	2	2	AY.3	0.00002
N	289	Q289R	cAg	cGg	2	2	AY.4	0.000003
N	289	Q289K	Cag	Aag	2	2	AY.4	0.000003
N	289	Q289H	caG	caT	2	2	AY.4.4	0.000818
N	289	Q289R	cAg	cGg	2	2	AY.43	0.000009
N	289	Q289K	Cag	Aag	2	2	AY.43	0.000009
N	289	Q289H	caG	caT	1	2	AY.46.4	0.000165
N	289	Q289H	caG	caC	1	2	AY.46.4	0.000165
N	289	Q289Q	caG	caA	2	2	AY.46.6	0.000144
N	289	Q289L	cAg	cTg	2	2	AY.47	0.000062
N	289	Q289H	caG	caT	1	2	AY.5.3	0.000337
N	289	Q289H	caG	caC	1	2	AY.5.3	0.000337
N	289	Q289H	caG	caT	2	2	AY.52	0.001629
N	289	Q289H	caG	caT	2	2	AY.7.2	0.001119
N	289	Q289L	cAg	cTg	2	2	AY.71	0.00095
N	289	Q289H	caG	caT	2	2	AY.9.1	0.000167
N	289	Q289E	Cag	Gag	2	2	AY.94	0.000885
N	289	Q289H	caG	caT	2	2	AY.98	0.000158
N	289	Q289Q	caG	caA	2	2	B.1.1.141	0.004024
N	289	Q289Q	caG	caA	2	2	B.1.1.157	0.001826
N	289	Q289P	cAg	cCg	2	2	B.1.1.222	0.000408
N	289	Q289H	caG	caT	1	2	B.1.1.28	0.000311
N	289	Q289H	caG	caC	1	2	B.1.1.28	0.000311
N	289	Q289H	caG	caT	2	2	B.1.1.306	0.000877
N	289	Q289H	caG	caT	2	2	B.1.1.311	0.000716
N	289	Q289L	cAg	cTg	2	2	B.1.1.354	0.008772
N	289	Q289H	caG	caT	2	2	B.1.1.416	0.00181
N	289	Q289H	caG	caC	2	2	B.1.1.57	0.022989
N	289	Q289Y	CaG	TaT	2	2	B.1.1.7	0.000002
N	289	Q289H	caG	caC	2	2	B.1.12	0.016
N	289	Q289H	caG	caT	2	2	B.1.157	0.00597
N	289	Q289Q	caG	caA	2	2	B.1.160	0.000062
N	289	Q289H	caG	caT	2	2	B.1.177.86	0.000367
N	289	Q289L	cAg	cTg	2	2	B.1.2	0.000018
N	289	Q289H	caG	caT	2	2	B.1.311	0.000549
N	289	Q289Q	caG	caA	2	2	B.1.36	0.000292
N	289	Q289H	caG	caT	2	2	B.1.36.39	0.004435
N	289	Q289H	caG	caT	2	2	B.1.426	0.002018
N	289	Q289Q	caG	caA	2	2	B.1.429	0.000047
N	289	Q289H	caG	caT	2	2	B.1.433	0.00639
N	289	Q289H	caG	caT	2	2	B.1.561	0.000794
N	289	Q289H	caG	caT	2	2	B.1.575	0.000607
N	289	Q289H	caG	caT	2	2	B.1.595	0.000522
N	289	Q289H	caG	caT	2	2	B.1.597	0.009259
N	289	Q289P	cAg	cCg	2	2	B.1.609	0.000959
N	289	Q289H	caG	caT	2	2	B.1.621.1	0.001012
N	289	Q289H	caG	caT	2	2	B.12	0.012821
N	289	Q289Q	caG	caA	2	2	C.36.3	0.001134
N	289	Q289H	caG	caT	2	2	P.1.1	0.000635
N	289	Q289H	caG	caT	1	2	P.1.15	0.000232
N	289	Q289H	caG	caC	1	2	P.1.15	0.000232
N	289	Q289H	caG	caT	1	2	P.1.17	0.000162
N	289	Q289H	caG	caC	1	2	P.1.17	0.000162
N	289	Q289H	caG	caT	2	2	P.1.7	0.000639
N	289	Q289Q	caG	caA	2	2	Q.1	0.000253
N	289	Q289K	Cag	Aag	1	1	A.2.2	0.001689
N	289	Q289H	caG	caT	1	1	A.2.5.3	0.010309
N	289	Q289Q	caG	caA	1	1	A.21	0.00277
N	289	Q289R	cAg	cGg	1	1	A.23.1	0.000704
N	289	Q289X	Cag	Tag	1	1	AD.2	0.000219
N	289	Q289H	caG	caT	1	1	AH.3	0.003802
N	289	Q289N	CaG	AaC	1	1	All	0
N	289	Q289del2	cAG	c--	1	1	All	0
N	289	Q289del1	caG	ca-	1	1	All	0
N	289	Q289H	caG	caC	1	1	AU.3	0.00211
N	289	Q289R	cAg	cGg	1	1	AY.100	0.000046
N	289	Q289E	Cag	Gag	1	1	AY.103	0.000006
N	289	Q289R	cAg	cGg	1	1	AY.103	0.000006
N	289	Q289H	caG	caT	1	1	AY.106	0.000335
N	289	Q289H	caG	caC	1	1	AY.109	0.00074
N	289	Q289H	caG	caT	1	1	AY.110	0.000113
N	289	Q289H	caG	caT	1	1	AY.116	0.000287
N	289	Q289L	cAg	cTg	1	1	AY.117	0.000085
N	289	Q289Q	caG	caA	1	1	AY.117	0.000085
N	289	Q289H	caG	caT	1	1	AY.13	0.000161
N	289	Q289H	caG	caT	1	1	AY.14	0.000088
N	289	Q289R	cAg	cGg	1	1	AY.14	0.000088
N	289	Q289K	Cag	Aag	1	1	AY.14	0.000088
N	289	Q289del1	caG	ca-	1	1	AY.16	0.00038
N	289	Q289R	cAg	cGg	1	1	AY.16.1	0.00047
N	289	Q289H	caG	caT	1	1	AY.24	0.000431
N	289	Q289del	CAG	---	1	1	AY.25	0.000006
N	289	Q289R	cAg	cGg	1	1	AY.25	0.000006
N	289	Q289K	Cag	Aag	1	1	AY.26	0.000028
N	289	Q289Q	caG	caA	1	1	AY.29.1	0.000221
N	289	Q289H	caG	caC	1	1	AY.30	0.000396
N	289	Q289Q	caG	caA	1	1	AY.32	0.000532
N	289	Q289H	caG	caT	1	1	AY.37	0.000316
N	289	Q289E	Cag	Gag	1	1	AY.4	0.000002
N	289	Q289Q	caG	caA	1	1	AY.4.2	0.000022
N	289	Q289H	caG	caC	1	1	AY.4.2.1	0.000149
N	289	Q289L	cAg	cTg	1	1	AY.4.5	0.000107
N	289	Q289P	cAg	cCg	1	1	AY.4.5	0.000107
N	289	Q289P	cAg	cCg	1	1	AY.40	0.000964
N	289	Q289H	caG	caC	1	1	AY.41	0.000294
N	289	Q289K	Cag	Aag	1	1	AY.42	0.00004
N	289	Q289Q	caG	caA	1	1	AY.44	0.000006
N	289	Q289H	caG	caC	1	1	AY.46.2	0.000635
N	289	Q289H	caG	caT	1	1	AY.46.3	0.000934
N	289	Q289L	cAg	cTg	1	1	AY.46.6	0.000072
N	289	Q289P	cAg	cCg	1	1	AY.47	0.000031
N	289	Q289L	cAg	cTg	1	1	AY.48	0.000465
N	289	Q289L	cAg	cTg	1	1	AY.5	0.000021
N	289	Q289H	caG	caT	1	1	AY.53	0.000288
N	289	Q289L	cAg	cTg	1	1	AY.54	0.000095
N	289	Q289H	caG	caT	1	1	AY.55	0.000917
N	289	Q289L	cAg	cTg	1	1	AY.57	0.000656
N	289	Q289H	caG	caC	1	1	AY.59	0.00053
N	289	Q289Q	caG	caA	1	1	AY.61	0.000105
N	289	Q289K	Cag	Aag	1	1	AY.65	0.000533
N	289	Q289del	CAG	---	1	1	AY.67	0.000464
N	289	Q289L	cAg	cTg	1	1	AY.69	0.000187
N	289	Q289H	caG	caC	1	1	AY.71	0.000475
N	289	Q289R	cAg	cGg	1	1	AY.71	0.000475
N	289	Q289K	Cag	Aag	1	1	AY.75	0.000056
N	289	Q289P	cAg	cCg	1	1	AY.75	0.000056
N	289	Q289del	CAG	---	1	1	AY.75	0.000056
N	289	Q289R	cAg	cGg	1	1	AY.9.2	0.000037
N	289	Q289H	caG	caT	1	1	AY.91	0.00073
N	289	Q289H	caG	caC	1	1	AY.95	0.000761
N	289	Q289H	caG	caC	1	1	AY.99	0.001049
N	289	Q289Q	caG	caA	1	1	AY.99.1	0.001553
N	289	Q289S	CAG	TCA	1	1	B	0.000128
N	289	Q289del	CAG	---	1	1	B.1	0.000009
N	289	Q289L	cAg	cTg	1	1	B.1	0.000009
N	289	Q289X	Cag	Tag	1	1	B.1.1	0.000018
N	289	Q289del	CAG	---	1	1	B.1.1	0.000018
N	289	Q289Q	caG	caA	1	1	B.1.1	0.000018
N	289	Q289K	Cag	Aag	1	1	B.1.1.1	0.000327
N	289	Q289H	caG	caT	1	1	B.1.1.113	0.006993
N	289	Q289L	cAg	cTg	1	1	B.1.1.161	0.003534
N	289	Q289H	caG	caC	1	1	B.1.1.161	0.003534
N	289	Q289H	caG	caT	1	1	B.1.1.174	0.003378
N	289	Q289Q	caG	caA	1	1	B.1.1.176	0.000439
N	289	Q289H	caG	caT	1	1	B.1.1.189	0.001513
N	289	Q289H	caG	caT	1	1	B.1.1.192	0.002309
N	289	Q289K	Cag	Aag	1	1	B.1.1.201	0.02439
N	289	Q289H	caG	caT	1	1	B.1.1.205	0.003717
N	289	Q289H	caG	caT	1	1	B.1.1.219	0.005
N	289	Q289L	cAg	cTg	1	1	B.1.1.219	0.005
N	289	Q289Q	caG	caA	1	1	B.1.1.222	0.000204
N	289	Q289H	caG	caT	1	1	B.1.1.222	0.000204
N	289	Q289H	caG	caC	1	1	B.1.1.269	0.001353
N	289	Q289S	CAG	AGT	1	1	B.1.1.27	0.00565
N	289	Q289H	caG	caT	1	1	B.1.1.284	0.000107
N	289	Q289Q	caG	caA	1	1	B.1.1.306	0.000438
N	289	Q289H	caG	caT	1	1	B.1.1.307	0.002532
N	289	Q289H	caG	caT	1	1	B.1.1.317	0.000412
N	289	Q289H	caG	caT	1	1	B.1.1.322	0.008772
N	289	Q289L	cAg	cTg	1	1	B.1.1.33	0.000421
N	289	Q289H	caG	caT	1	1	B.1.1.331	0.011628
N	289	Q289Q	caG	caA	1	1	B.1.1.348	0.000796
N	289	Q289H	caG	caT	1	1	B.1.1.37	0.000193
N	289	Q289H	caG	caT	1	1	B.1.1.376	0.005952
N	289	Q289Q	caG	caA	1	1	B.1.1.413	0.006897
N	289	Q289H	caG	caT	1	1	B.1.1.47	0.005348
N	289	Q289H	caG	caC	1	1	B.1.1.521	0.005348
N	289	Q289H	caG	caT	1	1	B.1.1.526	0.003546
N	289	Q289H	caG	caT	1	1	B.1.1.54	0.003021
N	289	Q289E	Cag	Gag	1	1	B.1.1.7	0.000001
N	289	Q289N	CaG	AaC	1	1	B.1.1.7	0.000001
N	289	Q289del	CAG	---	1	1	B.1.1.7	0.000001
N	289	Q289H	caG	caT	1	1	B.1.1.70	0.000341
N	289	Q289H	caG	caT	1	1	B.1.110	0.004525
N	289	Q289X	Cag	Tag	1	1	B.1.146	0.004237
N	289	Q289H	caG	caC	1	1	B.1.147	0.000756
N	289	Q289L	cAg	cTg	1	1	B.1.160	0.000031
N	289	Q289X	Cag	Tag	1	1	B.1.160	0.000031
N	289	Q289L	cAg	cTg	1	1	B.1.160.16	0.000929
N	289	Q289Q	caG	caA	1	1	B.1.177	0.000013
N	289	Q289H	caG	caC	1	1	B.1.177.15	0.000631
N	289	Q289H	caG	caT	1	1	B.1.177.23	0.003236
N	289	Q289H	caG	caT	1	1	B.1.177.24	0.001295
N	289	Q289Q	caG	caA	1	1	B.1.177.42	0.000894
N	289	Q289H	caG	caT	1	1	B.1.177.48	0.003125
N	289	Q289R	cAg	cGg	1	1	B.1.177.54	0.000606
N	289	Q289W	CAg	TGg	1	1	B.1.177.63	0.002703
N	289	Q289del	CAG	---	1	1	B.1.177.83	0.001481
N	289	Q289H	caG	caT	1	1	B.1.177.83	0.001481
N	289	Q289H	caG	caT	1	1	B.1.177.87	0.000728
N	289	Q289H	caG	caC	1	1	B.1.199	0.004132
N	289	Q289X	Cag	Tag	1	1	B.1.2	0.000009
N	289	Q289del2	cAG	c--	1	1	B.1.2	0.000009
N	289	Q289H	caG	caT	1	1	B.1.206	0.000816
N	289	Q289H	caG	caT	1	1	B.1.210	0.002132
N	289	Q289Q	caG	caA	1	1	B.1.221	0.000071
N	289	Q289R	cAg	cGg	1	1	B.1.221	0.000071
N	289	Q289del	CAG	---	1	1	B.1.221	0.000071
N	289	Q289H	caG	caT	1	1	B.1.221.4	0.004167
N	289	Q289H	caG	caT	1	1	B.1.232	0.000537
N	289	Q289P	cAg	cCg	1	1	B.1.234	0.000132
N	289	Q289H	caG	caC	1	1	B.1.237	0.004975
N	289	Q289H	caG	caT	1	1	B.1.240	0.000216
N	289	Q289Q	caG	caA	1	1	B.1.240	0.000216
N	289	Q289L	cAg	cTg	1	1	B.1.243	0.00007
N	289	Q289H	caG	caT	1	1	B.1.249	0.0625
N	289	Q289Q	caG	caA	1	1	B.1.258.17	0.000104
N	289	Q289H	caG	caC	1	1	B.1.258.3	0.001675
N	289	Q289L	cAg	cTg	1	1	B.1.311	0.000275
N	289	Q289R	cAg	cGg	1	1	B.1.311	0.000275
N	289	Q289R	cAg	cGg	1	1	B.1.314	0.007519
N	289	Q289H	caG	caT	1	1	B.1.320	0.001245
N	289	Q289H	caG	caT	1	1	B.1.340	0.004292
N	289	Q289H	caG	caT	1	1	B.1.349	0.000715
N	289	Q289H	caG	caT	1	1	B.1.351.3	0.000876
N	289	Q289R	cAg	cGg	1	1	B.1.351.5	0.0006
N	289	Q289H	caG	caT	1	1	B.1.36.18	0.00042
N	289	Q289R	cAg	cGg	1	1	B.1.36.27	0.000763
N	289	Q289Q	caG	caA	1	1	B.1.378	0.006849
N	289	Q289H	caG	caT	1	1	B.1.400	0.000429
N	289	Q289H	caG	caT	1	1	B.1.434	0.052632
N	289	Q289Q	caG	caA	1	1	B.1.448	0.002625
N	289	Q289H	caG	caT	1	1	B.1.462	0.007246
N	289	Q289H	caG	caT	1	1	B.1.473	0.019231
N	289	Q289H	caG	caT	1	1	B.1.492	0.007042
N	289	Q289H	caG	caT	1	1	B.1.506	0.02381
N	289	Q289Q	caG	caA	1	1	B.1.509	0.000866
N	289	Q289H	caG	caT	1	1	B.1.515	0.014493
N	289	Q289H	caG	caC	1	1	B.1.517	0.000427
N	289	Q289L	cAg	cTg	1	1	B.1.526	0.000024
N	289	Q289Q	caG	caA	1	1	B.1.526	0.000024
N	289	Q289H	caG	caC	1	1	B.1.544	0.006024
N	289	Q289del	CAG	---	1	1	B.1.560	0.00463
N	289	Q289Q	caG	caA	1	1	B.1.564	0.000426
N	289	Q289H	caG	caT	1	1	B.1.565	0.00081
N	289	Q289H	caG	caT	1	1	B.1.588	0.00091
N	289	Q289Q	caG	caA	1	1	B.1.590	0.004545
N	289	Q289L	cAg	cTg	1	1	B.1.595	0.000261
N	289	Q289H	caG	caT	1	1	B.1.595.1	0.005848
N	289	Q289Q	caG	caA	1	1	B.1.609	0.000479
N	289	Q289K	Cag	Aag	1	1	B.1.612	0.002653
N	289	Q289K	Cag	Aag	1	1	B.1.617.2	0.000004
N	289	Q289H	caG	caC	1	1	B.1.628	0.000352
N	289	Q289H	caG	caC	1	1	B.1.78	0.008547
N	289	Q289H	caG	caC	1	1	B.29	0.003509
N	289	Q289H	caG	caT	1	1	B.3	0.000831
N	289	Q289K	Cag	Aag	1	1	B.3	0.000831
N	289	Q289Q	caG	caA	1	1	B.3.1	0.001658
N	289	Q289H	caG	caT	1	1	C.16	0.00106
N	289	Q289K	Cag	Aag	1	1	C.35	0.000774
N	289	Q289H	caG	caT	1	1	C.36	0.000911
N	289	Q289R	cAg	cGg	1	1	C.37	0.000116
N	289	Q289Q	caG	caA	1	1	D.2	0.000075
N	289	Q289X	Cag	Tag	1	1	D.2	0.000075
N	289	Q289Q	caG	caA	1	1	P.1	0.000016
N	289	Q289K	Cag	Aag	1	1	P.1	0.000016
N	289	Q289H	caG	caC	1	1	P.1.12	0.000484
N	289	Q289H	caG	caT	1	1	P.1.13	0.000898
N	289	Q289Q	caG	caA	1	1	P.1.17	0.000162
N	289	Q289Q	caG	caA	1	1	P.1.7	0.000319
N	289	Q289H	caG	caT	1	1	Q.1	0.000126
N	289	Q289H	caG	caT	1	1	Q.3	0.000145
N	289	Q289H	caG	caT	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.