CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = E : CodonNum = 21

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
E	21	L21F		nonsyn	Ctt	Ttt	10606	10605	0.999906	26305-26307
E	21	L21F		nonsyn	CtT	TtC	10606	1	0.0000942863	26305-26307
E	21	L21V		nonsyn	Ctt	Gtt	2316	2316	1	26305-26307
E	21	L21L		syn	ctT	ctA	1288	1156	0.897516	26305-26307
E	21	L21L		syn	ctT	ctC	1288	78	0.060559	26305-26307
E	21	L21L		syn	ctT	ctG	1288	53	0.0411491	26305-26307
E	21	L21L		syn	CtT	TtA	1288	1	0.000776398	26305-26307
E	21	L21del1		del	Ctt	-tt	878	870	0.990888	26305-26307
E	21	L21del1		del	ctT	ct-	878	5	0.00569476	26305-26307
E	21	L21del1		del	CtT	-tC	878	1	0.00113895	26305-26307
E	21	L21del1		del	cTt	c-t	878	1	0.00113895	26305-26307
E	21	L21del1		del	cTT	c-N	878	1	0.00113895	26305-26307
E	21	L21I		nonsyn	Ctt	Att	468	467	0.997863	26305-26307
E	21	L21I		nonsyn	CtT	AtA	468	1	0.00213675	26305-26307
E	21	L21del		del	CTT	---	68	68	1	26305-26307
E	21	L21P		nonsyn	cTt	cCt	27	26	0.962963	26305-26307
E	21	L21P		nonsyn	cTT	cCC	27	1	0.037037	26305-26307
E	21	L21del2		del	cTT	c--	8	8	1	26305-26307
E	21	L21S		nonsyn	CTt	TCt	5	4	0.8	26305-26307
E	21	L21S		nonsyn	CTT	TCC	5	1	0.2	26305-26307
E	21	L21H		nonsyn	cTt	cAt	3	2	0.666667	26305-26307
E	21	L21H		nonsyn	cTT	cAC	3	1	0.333333	26305-26307
E	21	L21Q		nonsyn	cTT	cAG	2	1	0.5	26305-26307
E	21	L21C		nonsyn	CTt	TGt	2	1	0.5	26305-26307
E	21	L21C		nonsyn	CTT	TGC	2	1	0.5	26305-26307
E	21	L21R		nonsyn	cTt	cGt	2	1	0.5	26305-26307
E	21	L21R		nonsyn	cTT	cGC	2	1	0.5	26305-26307
E	21	L21Q		nonsyn	cTT	cAA	2	1	0.5	26305-26307
E	21	L21K		nonsyn	CTT	AAA	1	1	1	26305-26307
E	21	L21N		nonsyn	CTt	AAt	1	1	1	26305-26307
E	21	L21Y		nonsyn	CTt	TAt	1	1	1	26305-26307

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
E	21	L21F	Ctt	Ttt	10605	10606	All	0.002028
E	21	L21F	CtT	TtC	1	10606	All	0
E	21	L21F	Ctt	Ttt	7650	7650	B.1.525	0.865678
E	21	L21V	Ctt	Gtt	2316	2316	All	0.000443
E	21	L21V	Ctt	Gtt	2104	2104	B.1.596	0.183339
E	21	L21L	ctT	ctA	1156	1288	All	0.000221
E	21	L21L	ctT	ctC	78	1288	All	0.000015
E	21	L21L	ctT	ctG	53	1288	All	0.00001
E	21	L21L	CtT	TtA	1	1288	All	0
E	21	L21L	ctT	ctA	981	1016	B.1.1.7	0.000878
E	21	L21L	ctT	ctC	32	1016	B.1.1.7	0.000029
E	21	L21L	ctT	ctG	3	1016	B.1.1.7	0.000003
E	21	L21del1	Ctt	-tt	870	878	All	0.000166
E	21	L21del1	ctT	ct-	5	878	All	0.000001
E	21	L21del1	cTT	c-N	1	878	All	0
E	21	L21del1	CtT	-tC	1	878	All	0
E	21	L21del1	cTt	c-t	1	878	All	0
E	21	L21F	Ctt	Ttt	810	810	B.1.1.7	0.000725
E	21	L21del1	Ctt	-tt	710	710	B.1.525	0.080344
E	21	L21I	Ctt	Att	467	468	All	0.000089
E	21	L21I	CtT	AtA	1	468	All	0
E	21	L21F	Ctt	Ttt	279	279	AY.4	0.000434
E	21	L21F	Ctt	Ttt	212	212	B.1.1.63	0.08179
E	21	L21I	Ctt	Att	199	199	C.1.2	0.846809
E	21	L21F	Ctt	Ttt	149	149	B.1	0.001365
E	21	L21I	Ctt	Att	126	126	AY.39	0.003114
E	21	L21F	Ctt	Ttt	94	94	B.1.2	0.000828
E	21	L21F	Ctt	Ttt	91	91	AY.22	0.190377
E	21	L21F	Ctt	Ttt	86	86	B.1.617.2	0.000324
E	21	L21V	Ctt	Gtt	83	83	B.1.1.7	0.000074
E	21	L21del1	Ctt	-tt	77	77	B.1.523	0.188725
E	21	L21del	CTT	---	68	68	All	0.000013
E	21	L21F	Ctt	Ttt	62	62	B.1.128	0.03939
E	21	L21F	Ctt	Ttt	60	60	B.1.1	0.001088
E	21	L21F	Ctt	Ttt	58	58	B.1.429	0.001365
E	21	L21L	ctT	ctA	53	56	AY.25	0.000319
E	21	L21L	ctT	ctC	3	56	AY.25	0.000018
E	21	L21F	Ctt	Ttt	55	55	B.1.1.101	0.55
E	21	L21F	Ctt	Ttt	53	53	AY.44	0.000323
E	21	L21F	Ctt	Ttt	49	49	B.1.1.311	0.01755
E	21	L21F	Ctt	Ttt	46	46	P.1	0.000725
E	21	L21V	Ctt	Gtt	39	39	B.1.1.222	0.007956
E	21	L21F	Ctt	Ttt	37	37	AY.26	0.001047
E	21	L21L	ctT	ctG	37	37	B.1.1.222	0.007548
E	21	L21L	ctT	ctA	37	37	B.1.617.1	0.004772
E	21	L21F	Ctt	Ttt	36	36	AY.20	0.001399
E	21	L21V	Ctt	Gtt	35	35	B.1.2	0.000308
E	21	L21F	Ctt	Ttt	33	33	AY.3	0.000328
E	21	L21F	Ctt	Ttt	31	31	B.1.177	0.000408
E	21	L21F	Ctt	Ttt	30	30	AY.43	0.000133
E	21	L21F	Ctt	Ttt	30	30	B.1.1.39	0.015291
E	21	L21I	Ctt	Att	30	30	C.36.3.1	0.081522
E	21	L21P	cTt	cCt	26	27	All	0.000005
E	21	L21P	cTT	cCC	1	27	All	0
E	21	L21F	Ctt	Ttt	26	26	AY.103	0.000161
E	21	L21I	Ctt	Att	25	25	AY.47	0.000778
E	21	L21L	ctT	ctA	24	24	AY.23	0.001674
E	21	L21F	Ctt	Ttt	24	24	B.1.1.519	0.000953
E	21	L21del1	Ctt	-tt	23	23	B.1.177.21	0.001759
E	21	L21F	Ctt	Ttt	22	22	AY.25	0.000132
E	21	L21V	Ctt	Gtt	22	22	B.1.258	0.001464
E	21	L21F	Ctt	Ttt	20	20	B.1.1.400	1
E	21	L21del1	Ctt	-tt	20	20	B.1.1.7	0.000018
E	21	L21I	Ctt	Att	20	20	B.1.214.2	0.01199
E	21	L21F	Ctt	Ttt	17	17	P.1.14	0.000813
E	21	L21L	ctT	ctG	10	15	B.1	0.000092
E	21	L21L	ctT	ctC	3	15	B.1	0.000027
E	21	L21L	ctT	ctA	2	15	B.1	0.000018
E	21	L21F	Ctt	Ttt	14	14	B.1.526	0.000329
E	21	L21L	ctT	ctA	10	14	P.1	0.000158
E	21	L21L	ctT	ctC	4	14	P.1	0.000063
E	21	L21F	Ctt	Ttt	13	13	AY.100	0.000598
E	21	L21F	Ctt	Ttt	13	13	AY.61	0.001362
E	21	L21F	Ctt	Ttt	13	13	B.1.470	0.018258
E	21	L21F	Ctt	Ttt	12	12	B.1.523	0.029412
E	21	L21F	Ctt	Ttt	11	11	AY.102	0.000292
E	21	L21F	Ctt	Ttt	11	11	AY.4.2	0.000239
E	21	L21F	Ctt	Ttt	11	11	B.1.160	0.000343
E	21	L21F	Ctt	Ttt	11	11	B.1.351	0.000327
E	21	L21F	Ctt	Ttt	10	10	AY.110	0.001127
E	21	L21L	ctT	ctC	10	10	AY.29	0.000158
E	21	L21P	cTt	cCt	10	10	AY.75	0.00056
E	21	L21V	Ctt	Gtt	10	10	B.1	0.000092
E	21	L21F	Ctt	Ttt	10	10	B.1.234	0.001319
E	21	L21F	Ctt	Ttt	10	10	Q.8	0.001649
E	21	L21F	Ctt	Ttt	9	9	AY.29	0.000142
E	21	L21F	Ctt	Ttt	9	9	AY.5	0.000186
E	21	L21F	Ctt	Ttt	9	9	B.1.1.216	0.008014
E	21	L21L	ctT	ctA	9	9	B.1.1.337	0.032374
E	21	L21del2	cTT	c--	8	8	All	0.000002
E	21	L21F	Ctt	Ttt	8	8	AY.46.4	0.001316
E	21	L21F	Ctt	Ttt	8	8	B.1.1.205	0.02974
E	21	L21del	CTT	---	8	8	P.1	0.000126
E	21	L21del	CTT	---	8	8	P.1.15	0.001859
E	21	L21F	Ctt	Ttt	7	7	AY.34.1	0.00357
E	21	L21L	ctT	ctA	6	7	AY.46	0.000624
E	21	L21L	ctT	ctC	1	7	AY.46	0.000104
E	21	L21F	Ctt	Ttt	7	7	AY.74	0.00081
E	21	L21F	Ctt	Ttt	7	7	AY.90	0.004791
E	21	L21F	Ctt	Ttt	7	7	B.1.243	0.000487
E	21	L21F	Ctt	Ttt	7	7	B.1.497	0.002203
E	21	L21del	CTT	---	7	7	B.1.621	0.00062
E	21	L21I	Ctt	Att	6	6	AY.20	0.000233
E	21	L21F	Ctt	Ttt	6	6	AY.39.1	0.000238
E	21	L21L	ctT	ctA	6	6	AY.44	0.000037
E	21	L21del	CTT	---	6	6	B	0.000767
E	21	L21I	Ctt	Att	6	6	B.1	0.000055
E	21	L21F	Ctt	Ttt	6	6	B.1.1.462	0.051724
E	21	L21F	Ctt	Ttt	6	6	B.1.177.81	0.001136
E	21	L21L	ctT	ctC	5	6	B.1.2	0.000044
E	21	L21L	ctT	ctA	1	6	B.1.2	0.000009
E	21	L21del1	Ctt	-tt	6	6	B.1.221	0.000426
E	21	L21F	Ctt	Ttt	6	6	B.1.36	0.000875
E	21	L21F	Ctt	Ttt	6	6	B.1.575	0.00182
E	21	L21F	Ctt	Ttt	6	6	B.1.621	0.000531
E	21	L21F	Ctt	Ttt	6	6	D.2	0.00045
E	21	L21del1	Ctt	-tt	6	6	Q.4	0.002729
E	21	L21S	CTt	TCt	4	5	All	0.000001
E	21	L21S	CTT	TCC	1	5	All	0
E	21	L21L	ctT	ctC	2	5	AY.4	0.000003
E	21	L21L	ctT	ctA	2	5	AY.4	0.000003
E	21	L21L	ctT	ctG	1	5	AY.4	0.000002
E	21	L21F	Ctt	Ttt	5	5	AY.9	0.000338
E	21	L21F	Ctt	Ttt	5	5	AY.98	0.000395
E	21	L21I	Ctt	Att	5	5	B.1.1	0.000091
E	21	L21F	Ctt	Ttt	5	5	B.1.1.222	0.00102
E	21	L21F	Ctt	Ttt	5	5	B.1.1.398	0.016129
E	21	L21F	Ctt	Ttt	5	5	B.1.258	0.000333
E	21	L21F	Ctt	Ttt	5	5	B.1.258.17	0.00052
E	21	L21I	Ctt	Att	5	5	B.1.258.2	0.022523
E	21	L21del1	Ctt	-tt	5	5	B.1.617.2	0.000019
E	21	L21I	Ctt	Att	5	5	B.1.617.2	0.000019
E	21	L21V	Ctt	Gtt	5	5	B.1.617.2	0.000019
E	21	L21F	Ctt	Ttt	5	5	B.28	0.016393
E	21	L21F	Ctt	Ttt	5	5	C.37	0.00058
E	21	L21F	Ctt	Ttt	5	5	P.1.1	0.001588
E	21	L21F	Ctt	Ttt	4	4	AY.119	0.000141
E	21	L21F	Ctt	Ttt	4	4	AY.120.2.1	0.001993
E	21	L21I	Ctt	Att	4	4	AY.3.1	0.000341
E	21	L21F	Ctt	Ttt	4	4	AY.42	0.000161
E	21	L21L	ctT	ctA	3	4	AY.43	0.000013
E	21	L21L	ctT	ctG	1	4	AY.43	0.000004
E	21	L21F	Ctt	Ttt	4	4	AY.6	0.000165
E	21	L21F	Ctt	Ttt	4	4	AY.98.1	0.000194
E	21	L21F	Ctt	Ttt	4	4	AZ.2	0.003284
E	21	L21del	CTT	---	4	4	B.1	0.000037
E	21	L21L	ctT	ctC	2	4	B.1.1	0.000036
E	21	L21L	ctT	ctA	2	4	B.1.1	0.000036
E	21	L21F	Ctt	Ttt	4	4	B.1.1.33	0.001684
E	21	L21P	cTt	cCt	4	4	B.1.1.7	0.000004
E	21	L21F	Ctt	Ttt	4	4	B.1.427	0.000202
E	21	L21F	Ctt	Ttt	3	3	A.2.5	0.001497
E	21	L21H	cTt	cAt	2	3	All	0
E	21	L21H	cTT	cAC	1	3	All	0
E	21	L21F	Ctt	Ttt	3	3	AY.117	0.000254
E	21	L21F	Ctt	Ttt	3	3	AY.120	0.000112
E	21	L21F	Ctt	Ttt	3	3	AY.14	0.000264
E	21	L21F	Ctt	Ttt	3	3	AY.16	0.001139
E	21	L21del	CTT	---	3	3	AY.25	0.000018
E	21	L21F	Ctt	Ttt	3	3	AY.39	0.000074
E	21	L21I	Ctt	Att	3	3	AY.4	0.000005
E	21	L21del	CTT	---	3	3	AY.43	0.000013
E	21	L21F	Ctt	Ttt	3	3	AY.9.2	0.00011
E	21	L21F	Ctt	Ttt	3	3	B	0.000383
E	21	L21P	cTt	cCt	3	3	B.1	0.000027
E	21	L21del1	Ctt	-tt	1	3	B.1	0.000009
E	21	L21del1	cTT	c-N	1	3	B.1	0.000009
E	21	L21del1	ctT	ct-	1	3	B.1	0.000009
E	21	L21F	Ctt	Ttt	3	3	B.1.1.28	0.000934
E	21	L21F	Ctt	Ttt	3	3	B.1.1.429	0.013825
E	21	L21F	Ctt	Ttt	3	3	B.1.1.434	0.001046
E	21	L21F	Ctt	Ttt	3	3	B.1.1.48	0.008621
E	21	L21del	CTT	---	3	3	B.1.1.7	0.000003
E	21	L21I	Ctt	Att	3	3	B.1.177	0.00004
E	21	L21F	Ctt	Ttt	3	3	B.1.177.21	0.000229
E	21	L21F	Ctt	Ttt	3	3	B.1.177.60	0.000655
E	21	L21F	Ctt	Ttt	3	3	B.1.177.86	0.00055
E	21	L21del1	Ctt	-tt	3	3	B.1.351	0.000089
E	21	L21F	Ctt	Ttt	3	3	B.1.369	0.000856
E	21	L21del1	Ctt	-tt	3	3	B.1.470	0.004213
E	21	L21F	Ctt	Ttt	3	3	B.1.509	0.002597
E	21	L21del	CTT	---	3	3	B.1.525	0.000339
E	21	L21F	Ctt	Ttt	3	3	B.1.616	0.073171
E	21	L21L	ctT	ctC	2	3	B.1.617.2	0.000008
E	21	L21L	ctT	ctA	1	3	B.1.617.2	0.000004
E	21	L21I	Ctt	Att	3	3	C.37	0.000348
E	21	L21del1	Ctt	-tt	2	3	P.1	0.000032
E	21	L21del1	ctT	ct-	1	3	P.1	0.000016
E	21	L21I	Ctt	Att	3	3	Q.3	0.000435
E	21	L21F	Ctt	Ttt	3	3	Q.3	0.000435
E	21	L21del2	cTT	c--	2	2		0.111111
E	21	L21S	CTt	TCt	1	2		0.055556
E	21	L21P	cTT	cCC	1	2		0.055556
E	21	L21F	Ctt	Ttt	1	2		0.055556
E	21	L21R	cTT	cGC	1	2		0.055556
E	21	L21P	cTt	cCt	1	2		0.055556
E	21	L21F	CtT	TtC	1	2		0.055556
E	21	L21C	CTt	TGt	1	2		0.055556
E	21	L21R	cTt	cGt	1	2		0.055556
E	21	L21C	CTT	TGC	1	2		0.055556
E	21	L21S	CTT	TCC	1	2		0.055556
E	21	L21F	Ctt	Ttt	2	2	A.27	0.003311
E	21	L21R	cTT	cGC	1	2	All	0
E	21	L21C	CTt	TGt	1	2	All	0
E	21	L21Q	cTT	cAA	1	2	All	0
E	21	L21Q	cTT	cAG	1	2	All	0
E	21	L21R	cTt	cGt	1	2	All	0
E	21	L21C	CTT	TGC	1	2	All	0
E	21	L21I	Ctt	Att	2	2	AY.103	0.000012
E	21	L21L	ctT	ctA	2	2	AY.103	0.000012
E	21	L21F	Ctt	Ttt	2	2	AY.111	0.000366
E	21	L21F	Ctt	Ttt	2	2	AY.116	0.000574
E	21	L21F	Ctt	Ttt	2	2	AY.118	0.000125
E	21	L21V	Ctt	Gtt	2	2	AY.119	0.000071
E	21	L21F	Ctt	Ttt	2	2	AY.23	0.000139
E	21	L21V	Ctt	Gtt	2	2	AY.25	0.000012
E	21	L21del	CTT	---	2	2	AY.26	0.000057
E	21	L21F	Ctt	Ttt	2	2	AY.38	0.000999
E	21	L21del	CTT	---	2	2	AY.39	0.000049
E	21	L21F	Ctt	Ttt	2	2	AY.4.2.1	0.000298
E	21	L21F	Ctt	Ttt	2	2	AY.4.5	0.000215
E	21	L21I	Ctt	Att	2	2	AY.42	0.00008
E	21	L21F	Ctt	Ttt	2	2	AY.48	0.00093
E	21	L21L	ctT	ctC	2	2	AY.53	0.000575
E	21	L21F	Ctt	Ttt	2	2	AY.60	0.001876
E	21	L21F	Ctt	Ttt	2	2	AY.72	0.002721
E	21	L21V	Ctt	Gtt	2	2	B.1.1	0.000036
E	21	L21F	Ctt	Ttt	2	2	B.1.1.153	0.002191
E	21	L21F	Ctt	Ttt	2	2	B.1.1.218	0.015385
E	21	L21F	Ctt	Ttt	2	2	B.1.1.25	0.001137
E	21	L21L	ctT	ctA	2	2	B.1.1.27	0.011299
E	21	L21F	Ctt	Ttt	2	2	B.1.1.284	0.000215
E	21	L21F	Ctt	Ttt	2	2	B.1.1.306	0.000877
E	21	L21F	Ctt	Ttt	2	2	B.1.1.316	0.00185
E	21	L21F	Ctt	Ttt	2	2	B.1.1.317	0.000823
E	21	L21F	Ctt	Ttt	2	2	B.1.1.318	0.000604
E	21	L21F	Ctt	Ttt	2	2	B.1.1.339	0.021053
E	21	L21F	Ctt	Ttt	2	2	B.1.1.419	0.014815
E	21	L21F	Ctt	Ttt	2	2	B.1.147	0.001512
E	21	L21F	Ctt	Ttt	2	2	B.1.177.17	0.001642
E	21	L21F	Ctt	Ttt	2	2	B.1.177.35	0.001382
E	21	L21F	Ctt	Ttt	2	2	B.1.177.57	0.000562
E	21	L21F	Ctt	Ttt	2	2	B.1.177.72	0.00678
E	21	L21F	Ctt	Ttt	2	2	B.1.190	0.02
E	21	L21F	Ctt	Ttt	2	2	B.1.221	0.000142
E	21	L21F	Ctt	Ttt	2	2	B.1.311	0.000549
E	21	L21F	Ctt	Ttt	2	2	B.1.396	0.001411
E	21	L21F	Ctt	Ttt	2	2	B.1.416	0.002538
E	21	L21F	Ctt	Ttt	2	2	B.1.425	0.005988
E	21	L21V	Ctt	Gtt	2	2	B.1.429	0.000047
E	21	L21F	Ctt	Ttt	2	2	B.1.466.1	0.014388
E	21	L21F	Ctt	Ttt	2	2	B.1.537	0.04
E	21	L21I	Ctt	Att	1	2	B.1.621	0.000089
E	21	L21I	CtT	AtA	1	2	B.1.621	0.000089
E	21	L21I	Ctt	Att	2	2	B.1.637	0.000146
E	21	L21F	Ctt	Ttt	2	2	B.1.638	0.105263
E	21	L21I	Ctt	Att	2	2	B.4.7	0.020202
E	21	L21del	CTT	---	2	2	C.37	0.000232
E	21	L21del2	cTT	c--	2	2	C.37	0.000232
E	21	L21del	CTT	---	2	2	C.37.1	0.005236
E	21	L21I	Ctt	Att	2	2	P.1	0.000032
E	21	L21L	ctT	ctA	2	2	P.1.14	0.000096
E	21	L21F	Ctt	Ttt	2	2	P.2	0.000373
E	21	L21F	Ctt	Ttt	2	2	P.7	0.008734
E	21	L21L	ctT	ctC	1	1		0.055556
E	21	L21F	Ctt	Ttt	1	1	A	0.000387
E	21	L21L	ctT	ctG	1	1	A.2.4	0.003367
E	21	L21F	Ctt	Ttt	1	1	A.23.1	0.000704
E	21	L21F	Ctt	Ttt	1	1	AD.2	0.000219
E	21	L21F	Ctt	Ttt	1	1	AH.2	0.012048
E	21	L21Y	CTt	TAt	1	1	All	0
E	21	L21N	CTt	AAt	1	1	All	0
E	21	L21K	CTT	AAA	1	1	All	0
E	21	L21del	CTT	---	1	1	AY.10	0.00053
E	21	L21L	ctT	ctC	1	1	AY.102	0.000027
E	21	L21del	CTT	---	1	1	AY.118	0.000063
E	21	L21del1	Ctt	-tt	1	1	AY.119	0.000035
E	21	L21F	Ctt	Ttt	1	1	AY.121	0.000135
E	21	L21F	Ctt	Ttt	1	1	AY.16.1	0.00047
E	21	L21L	ctT	ctA	1	1	AY.16.1	0.00047
E	21	L21F	Ctt	Ttt	1	1	AY.19	0.00114
E	21	L21del1	Ctt	-tt	1	1	AY.20	0.000039
E	21	L21del1	Ctt	-tt	1	1	AY.23	0.00007
E	21	L21S	CTt	TCt	1	1	AY.23	0.00007
E	21	L21del1	Ctt	-tt	1	1	AY.24	0.000431
E	21	L21del1	Ctt	-tt	1	1	AY.25	0.000006
E	21	L21del2	cTT	c--	1	1	AY.25	0.000006
E	21	L21I	Ctt	Att	1	1	AY.25	0.000006
E	21	L21V	Ctt	Gtt	1	1	AY.3	0.00001
E	21	L21del1	Ctt	-tt	1	1	AY.3	0.00001
E	21	L21F	Ctt	Ttt	1	1	AY.3.1	0.000085
E	21	L21F	Ctt	Ttt	1	1	AY.33	0.000067
E	21	L21F	Ctt	Ttt	1	1	AY.34	0.000097
E	21	L21del1	ctT	ct-	1	1	AY.34.1	0.00051
E	21	L21F	Ctt	Ttt	1	1	AY.37	0.000316
E	21	L21del1	Ctt	-tt	1	1	AY.39	0.000025
E	21	L21L	ctT	ctA	1	1	AY.39	0.000025
E	21	L21V	Ctt	Gtt	1	1	AY.4	0.000002
E	21	L21S	CTt	TCt	1	1	AY.4	0.000002
E	21	L21P	cTt	cCt	1	1	AY.4	0.000002
E	21	L21I	Ctt	Att	1	1	AY.4.2	0.000022
E	21	L21L	ctT	ctC	1	1	AY.4.5	0.000107
E	21	L21del	CTT	---	1	1	AY.41	0.000294
E	21	L21I	Ctt	Att	1	1	AY.43	0.000004
E	21	L21P	cTt	cCt	1	1	AY.43	0.000004
E	21	L21I	Ctt	Att	1	1	AY.44	0.000006
E	21	L21V	Ctt	Gtt	1	1	AY.44	0.000006
E	21	L21del1	Ctt	-tt	1	1	AY.44	0.000006
E	21	L21F	Ctt	Ttt	1	1	AY.45	0.000122
E	21	L21L	ctT	ctC	1	1	AY.45	0.000122
E	21	L21F	Ctt	Ttt	1	1	AY.46	0.000104
E	21	L21F	Ctt	Ttt	1	1	AY.46.1	0.001027
E	21	L21del1	Ctt	-tt	1	1	AY.46.6	0.000072
E	21	L21F	Ctt	Ttt	1	1	AY.46.6	0.000072
E	21	L21F	Ctt	Ttt	1	1	AY.47	0.000031
E	21	L21F	Ctt	Ttt	1	1	AY.5.3	0.000337
E	21	L21del	CTT	---	1	1	AY.54	0.000095
E	21	L21P	cTt	cCt	1	1	AY.6	0.000041
E	21	L21I	Ctt	Att	1	1	AY.67	0.000464
E	21	L21L	ctT	ctA	1	1	AY.67	0.000464
E	21	L21del	CTT	---	1	1	AY.68	0.000274
E	21	L21P	cTt	cCt	1	1	AY.69	0.000187
E	21	L21F	Ctt	Ttt	1	1	AY.69	0.000187
E	21	L21F	Ctt	Ttt	1	1	AY.70	0.000209
E	21	L21F	Ctt	Ttt	1	1	AY.71	0.000475
E	21	L21V	Ctt	Gtt	1	1	AY.75	0.000056
E	21	L21del	CTT	---	1	1	AY.75	0.000056
E	21	L21F	Ctt	Ttt	1	1	AY.75.1	0.00018
E	21	L21F	Ctt	Ttt	1	1	AY.8	0.000606
E	21	L21F	Ctt	Ttt	1	1	AY.83	0.001724
E	21	L21F	Ctt	Ttt	1	1	AY.85	0.000427
E	21	L21L	ctT	ctA	1	1	AY.92	0.000287
E	21	L21F	Ctt	Ttt	1	1	AY.92	0.000287
E	21	L21I	Ctt	Att	1	1	AY.98	0.000079
E	21	L21del1	CtT	-tC	1	1	B	0.000128
E	21	L21H	cTt	cAt	1	1	B.1	0.000009
E	21	L21del2	cTT	c--	1	1	B.1	0.000009
E	21	L21Y	CTt	TAt	1	1	B.1	0.000009
E	21	L21S	CTt	TCt	1	1	B.1	0.000009
E	21	L21del1	Ctt	-tt	1	1	B.1.1	0.000018
E	21	L21del	CTT	---	1	1	B.1.1	0.000018
E	21	L21L	ctT	ctC	1	1	B.1.1.153	0.001095
E	21	L21F	Ctt	Ttt	1	1	B.1.1.176	0.000439
E	21	L21I	Ctt	Att	1	1	B.1.1.214	0.000055
E	21	L21F	Ctt	Ttt	1	1	B.1.1.220	0.001859
E	21	L21F	Ctt	Ttt	1	1	B.1.1.269	0.001353
E	21	L21F	Ctt	Ttt	1	1	B.1.1.273	0.006757
E	21	L21L	ctT	ctA	1	1	B.1.1.28	0.000311
E	21	L21V	Ctt	Gtt	1	1	B.1.1.337	0.003597
E	21	L21F	Ctt	Ttt	1	1	B.1.1.37	0.000193
E	21	L21F	Ctt	Ttt	1	1	B.1.1.386	0.066667
E	21	L21F	Ctt	Ttt	1	1	B.1.1.402	0.011111
E	21	L21F	Ctt	Ttt	1	1	B.1.1.409	0.002833
E	21	L21del1	ctT	ct-	1	1	B.1.1.409	0.002833
E	21	L21L	ctT	ctC	1	1	B.1.1.423	0.0625
E	21	L21L	ctT	ctA	1	1	B.1.1.434	0.000349
E	21	L21F	Ctt	Ttt	1	1	B.1.1.507	0.008696
E	21	L21del1	Ctt	-tt	1	1	B.1.1.519	0.00004
E	21	L21F	Ctt	Ttt	1	1	B.1.1.526	0.003546
E	21	L21F	Ctt	Ttt	1	1	B.1.1.58	0.005376
E	21	L21I	Ctt	Att	1	1	B.1.1.7	0.000001
E	21	L21del	CTT	---	1	1	B.1.1.8	0.003584
E	21	L21F	Ctt	Ttt	1	1	B.1.1.95	0.019608
E	21	L21F	Ctt	Ttt	1	1	B.1.149	0.003425
E	21	L21L	ctT	ctC	1	1	B.1.160	0.000031
E	21	L21del	CTT	---	1	1	B.1.177	0.000013
E	21	L21P	cTt	cCt	1	1	B.1.177	0.000013
E	21	L21L	ctT	ctA	1	1	B.1.177	0.000013
E	21	L21F	Ctt	Ttt	1	1	B.1.177.33	0.001645
E	21	L21F	Ctt	Ttt	1	1	B.1.177.4	0.000211
E	21	L21F	Ctt	Ttt	1	1	B.1.177.5	0.001242
E	21	L21F	Ctt	Ttt	1	1	B.1.177.52	0.001757
E	21	L21P	cTt	cCt	1	1	B.1.177.63	0.002703
E	21	L21F	Ctt	Ttt	1	1	B.1.177.82	0.000477
E	21	L21del1	Ctt	-tt	1	1	B.1.2	0.000009
E	21	L21F	Ctt	Ttt	1	1	B.1.206	0.000816
E	21	L21H	cTT	cAC	1	1	B.1.210	0.002132
E	21	L21del	CTT	---	1	1	B.1.218	0.005155
E	21	L21I	Ctt	Att	1	1	B.1.221	0.000071
E	21	L21L	ctT	ctA	1	1	B.1.234	0.000132
E	21	L21F	Ctt	Ttt	1	1	B.1.237	0.004975
E	21	L21F	Ctt	Ttt	1	1	B.1.240	0.000216
E	21	L21del	CTT	---	1	1	B.1.258	0.000067
E	21	L21del1	Ctt	-tt	1	1	B.1.258	0.000067
E	21	L21V	Ctt	Gtt	1	1	B.1.264	0.012346
E	21	L21L	ctT	ctC	1	1	B.1.265	0.001271
E	21	L21F	Ctt	Ttt	1	1	B.1.305	0.002151
E	21	L21V	Ctt	Gtt	1	1	B.1.311	0.000275
E	21	L21L	ctT	ctC	1	1	B.1.344	0.008197
E	21	L21F	Ctt	Ttt	1	1	B.1.346	0.001311
E	21	L21P	cTt	cCt	1	1	B.1.36.1	0.00114
E	21	L21F	Ctt	Ttt	1	1	B.1.36.24	0.006173
E	21	L21F	Ctt	Ttt	1	1	B.1.36.29	0.000517
E	21	L21F	Ctt	Ttt	1	1	B.1.36.31	0.001751
E	21	L21F	Ctt	Ttt	1	1	B.1.375	0.00082
E	21	L21F	Ctt	Ttt	1	1	B.1.456	0.003268
E	21	L21F	Ctt	Ttt	1	1	B.1.499	0.00105
E	21	L21L	ctT	ctA	1	1	B.1.515	0.014493
E	21	L21V	Ctt	Gtt	1	1	B.1.525	0.000113
E	21	L21L	CtT	TtA	1	1	B.1.525	0.000113
E	21	L21L	ctT	ctC	1	1	B.1.526	0.000024
E	21	L21V	Ctt	Gtt	1	1	B.1.526	0.000024
E	21	L21F	Ctt	Ttt	1	1	B.1.533	0.009615
E	21	L21F	Ctt	Ttt	1	1	B.1.564	0.000426
E	21	L21F	Ctt	Ttt	1	1	B.1.565	0.00081
E	21	L21I	Ctt	Att	1	1	B.1.576	0.000907
E	21	L21F	Ctt	Ttt	1	1	B.1.577	0.000687
E	21	L21F	Ctt	Ttt	1	1	B.1.582	0.000491
E	21	L21F	Ctt	Ttt	1	1	B.1.597	0.00463
E	21	L21F	Ctt	Ttt	1	1	B.1.609	0.000479
E	21	L21del1	cTt	c-t	1	1	B.1.617.1	0.000129
E	21	L21F	Ctt	Ttt	1	1	B.1.617.1	0.000129
E	21	L21Q	cTT	cAG	1	1	B.1.617.2	0.000004
E	21	L21H	cTt	cAt	1	1	B.1.621	0.000089
E	21	L21L	ctT	ctA	1	1	B.1.621	0.000089
E	21	L21del2	cTT	c--	1	1	B.1.621	0.000089
E	21	L21Q	cTT	cAA	1	1	B.1.621	0.000089
E	21	L21N	CTt	AAt	1	1	B.1.621	0.000089
E	21	L21K	CTT	AAA	1	1	B.1.621	0.000089
E	21	L21F	Ctt	Ttt	1	1	B.1.623	0.000536
E	21	L21I	Ctt	Att	1	1	B.1.623	0.000536
E	21	L21del	CTT	---	1	1	B.1.627	0.00202
E	21	L21F	Ctt	Ttt	1	1	B.1.636	0.006711
E	21	L21F	Ctt	Ttt	1	1	B.1.637	0.000073
E	21	L21P	cTt	cCt	1	1	B.1.637	0.000073
E	21	L21del	CTT	---	1	1	B.1.638	0.052632
E	21	L21I	Ctt	Att	1	1	B.6	0.00091
E	21	L21F	Ctt	Ttt	1	1	B.6	0.00091
E	21	L21I	Ctt	Att	1	1	C.1	0.002392
E	21	L21del1	Ctt	-tt	1	1	C.36	0.000911
E	21	L21F	Ctt	Ttt	1	1	C.36	0.000911
E	21	L21L	ctT	ctC	1	1	C.37	0.000116
E	21	L21V	Ctt	Gtt	1	1	C.37	0.000116
E	21	L21del2	cTT	c--	1	1	P.1	0.000016
E	21	L21L	ctT	ctA	1	1	P.1.1	0.000318
E	21	L21F	Ctt	Ttt	1	1	P.1.10	0.000269
E	21	L21F	Ctt	Ttt	1	1	P.1.12	0.000484
E	21	L21del	CTT	---	1	1	P.1.13	0.000898
E	21	L21del1	ctT	ct-	1	1	P.1.15	0.000232
E	21	L21F	Ctt	Ttt	1	1	P.1.16	0.000374
E	21	L21F	Ctt	Ttt	1	1	P.1.6	0.001946
E	21	L21L	ctT	ctC	1	1	P.1.7	0.000319
E	21	L21del	CTT	---	1	1	P.1.7	0.000319
E	21	L21F	Ctt	Ttt	1	1	P.1.7	0.000319
E	21	L21F	Ctt	Ttt	1	1	P.3	0.001595
E	21	L21F	Ctt	Ttt	1	1	Q.1	0.000126
E	21	L21F	Ctt	Ttt	1	1	Q.4	0.000455
E	21	L21L	ctT	ctA	1	1	Q.8	0.000165
E	21	L21F	Ctt	Ttt	1	1	R.1	0.00009
E	21	L21L	ctT	ctA	1	1	W.1	0.008696
E	21	L21F	Ctt	Ttt	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.