CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 6

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	6	V6F		nonsyn	Gtt	Ttt	4075	4075	1	21578-21580
S	6	V6A		nonsyn	gTt	gCt	1724	1723	0.99942	21578-21580
S	6	V6A		nonsyn	gTT	gCC	1724	1	0.000580046	21578-21580
S	6	V6I		nonsyn	Gtt	Att	504	499	0.990079	21578-21580
S	6	V6I		nonsyn	GtT	AtA	504	5	0.00992064	21578-21580
S	6	V6V		syn	gtT	gtC	286	230	0.804196	21578-21580
S	6	V6V		syn	gtT	gtA	286	43	0.15035	21578-21580
S	6	V6V		syn	gtT	gtG	286	13	0.0454545	21578-21580
S	6	V6L		nonsyn	Gtt	Ctt	85	83	0.976471	21578-21580
S	6	V6L		nonsyn	GtT	CtA	85	2	0.0235294	21578-21580
S	6	V6del		del	GTT	---	74	74	1	21578-21580
S	6	V6G		nonsyn	gTt	gGt	11	11	1	21578-21580
S	6	V6del1		del	Gtt	-tt	10	6	0.6	21578-21580
S	6	V6del1		del	gTt	g-t	10	3	0.3	21578-21580
S	6	V6del1		del	gtT	gt-	10	1	0.1	21578-21580
S	6	V6D		nonsyn	gTt	gAt	5	5	1	21578-21580
S	6	V6C		nonsyn	GTt	TGt	3	3	1	21578-21580
S	6	V6H		nonsyn	GTt	CAt	3	2	0.666667	21578-21580
S	6	V6del2		del	gTT	g--	3	2	0.666667	21578-21580
S	6	V6E		nonsyn	gTT	gAA	3	2	0.666667	21578-21580
S	6	V6E		nonsyn	gTT	gAG	3	1	0.333333	21578-21580
S	6	V6H		nonsyn	GTT	CAC	3	1	0.333333	21578-21580
S	6	V6del2		del	GTt	--t	3	1	0.333333	21578-21580
S	6	V6Q		nonsyn	GTT	CAA	2	2	1	21578-21580
S	6	V6T		nonsyn	GTt	ACt	2	2	1	21578-21580
S	6	V6N		nonsyn	GTt	AAt	1	1	1	21578-21580

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	6	V6F	Gtt	Ttt	4075	4075	All	0.000779
S	6	V6F	Gtt	Ttt	1927	1927	AY.43	0.008538
S	6	V6A	gTt	gCt	1723	1724	All	0.00033
S	6	V6A	gTT	gCC	1	1724	All	0
S	6	V6A	gTt	gCt	1627	1627	B.1.1.7	0.001457
S	6	V6I	Gtt	Att	499	504	All	0.000095
S	6	V6I	GtT	AtA	5	504	All	0.000001
S	6	V6V	gtT	gtC	230	286	All	0.000044
S	6	V6V	gtT	gtA	43	286	All	0.000008
S	6	V6V	gtT	gtG	13	286	All	0.000002
S	6	V6F	Gtt	Ttt	283	283	B.1.1.7	0.000253
S	6	V6F	Gtt	Ttt	279	279	AY.44	0.001698
S	6	V6F	Gtt	Ttt	216	216	AY.4	0.000336
S	6	V6F	Gtt	Ttt	185	185	B.1.617.2	0.000697
S	6	V6F	Gtt	Ttt	180	180	B.1.320	0.224159
S	6	V6F	Gtt	Ttt	139	139	B.1.160.11	0.794286
S	6	V6V	gtT	gtC	102	102	B.1.1.416	0.092308
S	6	V6I	Gtt	Att	102	102	B.1.1.7	0.000091
S	6	V6L	Gtt	Ctt	83	85	All	0.000016
S	6	V6L	GtT	CtA	2	85	All	0
S	6	V6I	Gtt	Att	79	84	AY.4	0.000123
S	6	V6I	GtT	AtA	5	84	AY.4	0.000008
S	6	V6F	Gtt	Ttt	81	81	B.1	0.000742
S	6	V6del	GTT	---	74	74	All	0.000014
S	6	V6F	Gtt	Ttt	67	67	AY.103	0.000416
S	6	V6I	Gtt	Att	63	63	B.1.241	0.051136
S	6	V6A	gTt	gCt	41	41	AY.103	0.000255
S	6	V6I	Gtt	Att	35	35	B.1.36.18	0.014706
S	6	V6F	Gtt	Ttt	34	34	B.1.2	0.000299
S	6	V6F	Gtt	Ttt	33	33	AY.46.6	0.002383
S	6	V6I	Gtt	Att	32	32	B.1.617.2	0.00012
S	6	V6F	Gtt	Ttt	31	31	AY.3	0.000308
S	6	V6F	Gtt	Ttt	30	30	P.1	0.000473
S	6	V6V	gtT	gtA	24	29	AY.43	0.000106
S	6	V6V	gtT	gtC	5	29	AY.43	0.000022
S	6	V6I	Gtt	Att	25	25	AY.44	0.000152
S	6	V6F	Gtt	Ttt	24	24	B.1.1.483	0.923077
S	6	V6F	Gtt	Ttt	21	21	AY.121	0.002842
S	6	V6L	Gtt	Ctt	21	21	AY.4.2	0.000455
S	6	V6V	gtT	gtC	11	20	AY.4	0.000017
S	6	V6V	gtT	gtA	8	20	AY.4	0.000012
S	6	V6V	gtT	gtG	1	20	AY.4	0.000002
S	6	V6F	Gtt	Ttt	20	20	B.1.1	0.000363
S	6	V6F	Gtt	Ttt	20	20	B.1.1.203	0.338983
S	6	V6F	Gtt	Ttt	20	20	B.1.349	0.014296
S	6	V6V	gtT	gtC	19	20	B.1.564	0.008092
S	6	V6V	gtT	gtG	1	20	B.1.564	0.000426
S	6	V6F	Gtt	Ttt	18	18	AY.5.3	0.006073
S	6	V6V	gtT	gtC	17	17	B.1.1.7	0.000015
S	6	V6F	Gtt	Ttt	15	15	AY.102	0.000398
S	6	V6I	Gtt	Att	15	15	AY.9.2	0.000551
S	6	V6I	Gtt	Att	15	15	P.1	0.000236
S	6	V6I	Gtt	Att	14	14	AY.103	0.000087
S	6	V6del	GTT	---	14	14	AY.44	0.000085
S	6	V6F	Gtt	Ttt	14	14	B.1.177	0.000184
S	6	V6L	Gtt	Ctt	13	13	P.1	0.000205
S	6	V6I	Gtt	Att	12	12	B.1	0.00011
S	6	V6I	Gtt	Att	12	12	B.1.1.25	0.006822
S	6	V6F	Gtt	Ttt	12	12	B.1.528	0.571429
S	6	V6G	gTt	gGt	11	11	All	0.000002
S	6	V6L	Gtt	Ctt	11	11	AY.25	0.000066
S	6	V6L	Gtt	Ctt	11	11	AY.43	0.000049
S	6	V6F	Gtt	Ttt	11	11	AY.5	0.000227
S	6	V6del1	Gtt	-tt	6	10	All	0.000001
S	6	V6del1	gTt	g-t	3	10	All	0.000001
S	6	V6del1	gtT	gt-	1	10	All	0
S	6	V6F	Gtt	Ttt	10	10	AY.120	0.000372
S	6	V6F	Gtt	Ttt	10	10	AY.25	0.00006
S	6	V6F	Gtt	Ttt	10	10	AY.47	0.000311
S	6	V6I	Gtt	Att	10	10	AY.98.1	0.000484
S	6	V6F	Gtt	Ttt	10	10	B.1.160	0.000312
S	6	V6F	Gtt	Ttt	10	10	B.1.351	0.000297
S	6	V6F	Gtt	Ttt	9	9	B.1.429	0.000212
S	6	V6F	Gtt	Ttt	9	9	B.1.526	0.000212
S	6	V6F	Gtt	Ttt	9	9	P.5	0.123288
S	6	V6F	Gtt	Ttt	8	8	AY.119	0.000282
S	6	V6V	gtT	gtC	8	8	AY.120	0.000297
S	6	V6F	Gtt	Ttt	8	8	AY.20	0.000311
S	6	V6I	Gtt	Att	8	8	AY.3	0.00008
S	6	V6L	Gtt	Ctt	8	8	AY.4	0.000012
S	6	V6F	Gtt	Ttt	8	8	AY.93	0.002185
S	6	V6V	gtT	gtC	6	8	B.1	0.000055
S	6	V6V	gtT	gtA	1	8	B.1	0.000009
S	6	V6V	gtT	gtG	1	8	B.1	0.000009
S	6	V6F	Gtt	Ttt	8	8	B.1.1.441	0.4
S	6	V6F	Gtt	Ttt	8	8	B.1.1.519	0.000318
S	6	V6F	Gtt	Ttt	8	8	B.1.243	0.000557
S	6	V6I	Gtt	Att	8	8	B.1.243	0.000557
S	6	V6V	gtT	gtC	8	8	B.1.617.2	0.00003
S	6	V6del	GTT	---	8	8	B.1.617.2	0.00003
S	6	V6F	Gtt	Ttt	8	8	B.1.637	0.000585
S	6	V6F	Gtt	Ttt	7	7	AY.26	0.000198
S	6	V6F	Gtt	Ttt	7	7	AY.9	0.000473
S	6	V6F	Gtt	Ttt	7	7	P.1.17	0.001132
S	6	V6F	Gtt	Ttt	6	6	AY.100	0.000276
S	6	V6V	gtT	gtC	5	6	AY.103	0.000031
S	6	V6V	gtT	gtA	1	6	AY.103	0.000006
S	6	V6F	Gtt	Ttt	6	6	AY.113	0.000854
S	6	V6del	GTT	---	6	6	AY.33	0.000401
S	6	V6I	Gtt	Att	6	6	AY.5	0.000124
S	6	V6F	Gtt	Ttt	6	6	AY.64	0.003571
S	6	V6F	Gtt	Ttt	6	6	AY.75	0.000336
S	6	V6F	Gtt	Ttt	6	6	B.1.177.44	0.003114
S	6	V6F	Gtt	Ttt	6	6	B.1.177.57	0.001686
S	6	V6V	gtT	gtC	6	6	P.2	0.00112
S	6	V6D	gTt	gAt	5	5	All	0.000001
S	6	V6I	Gtt	Att	5	5	AY.25	0.00003
S	6	V6A	gTt	gCt	5	5	AY.4	0.000008
S	6	V6F	Gtt	Ttt	5	5	AY.42	0.000201
S	6	V6F	Gtt	Ttt	5	5	AY.78	0.007704
S	6	V6A	gTt	gCt	5	5	B.1.1	0.000091
S	6	V6F	Gtt	Ttt	5	5	B.1.1.214	0.000277
S	6	V6F	Gtt	Ttt	5	5	B.1.1.284	0.000537
S	6	V6del	GTT	---	5	5	B.1.1.7	0.000004
S	6	V6I	Gtt	Att	5	5	B.1.2	0.000044
S	6	V6F	Gtt	Ttt	5	5	B.1.36	0.00073
S	6	V6L	GtT	CtA	2	4		0.111111
S	6	V6L	Gtt	Ctt	2	4		0.111111
S	6	V6F	Gtt	Ttt	4	4	A.28	0.010582
S	6	V6I	Gtt	Att	4	4	AY.100	0.000184
S	6	V6V	gtT	gtC	3	4	AY.100	0.000138
S	6	V6V	gtT	gtA	1	4	AY.100	0.000046
S	6	V6F	Gtt	Ttt	4	4	AY.39	0.000099
S	6	V6F	Gtt	Ttt	4	4	AY.4.2	0.000087
S	6	V6I	Gtt	Att	4	4	AY.43	0.000018
S	6	V6V	gtT	gtC	4	4	AY.75	0.000224
S	6	V6F	Gtt	Ttt	4	4	AY.98.1	0.000194
S	6	V6del	GTT	---	4	4	B.1.1	0.000073
S	6	V6V	gtT	gtC	4	4	B.1.110.3	0.002874
S	6	V6F	Gtt	Ttt	4	4	B.1.177.60	0.000874
S	6	V6A	gTt	gCt	3	4	B.1.221	0.000213
S	6	V6A	gTT	gCC	1	4	B.1.221	0.000071
S	6	V6F	Gtt	Ttt	4	4	B.1.232	0.002149
S	6	V6I	Gtt	Att	4	4	B.1.396	0.002823
S	6	V6F	Gtt	Ttt	4	4	B.1.400	0.001716
S	6	V6F	Gtt	Ttt	4	4	B.1.596	0.000349
S	6	V6I	Gtt	Att	3	3	A.2.5	0.001497
S	6	V6F	Gtt	Ttt	3	3	AE.8	0.001467
S	6	V6C	GTt	TGt	3	3	All	0.000001
S	6	V6H	GTt	CAt	2	3	All	0
S	6	V6E	gTT	gAA	2	3	All	0
S	6	V6del2	gTT	g--	2	3	All	0
S	6	V6E	gTT	gAG	1	3	All	0
S	6	V6del2	GTt	--t	1	3	All	0
S	6	V6H	GTT	CAC	1	3	All	0
S	6	V6I	Gtt	Att	3	3	AY.102	0.00008
S	6	V6F	Gtt	Ttt	3	3	AY.118	0.000188
S	6	V6F	Gtt	Ttt	3	3	AY.19	0.003421
S	6	V6V	gtT	gtC	3	3	AY.25	0.000018
S	6	V6I	Gtt	Att	3	3	AY.26	0.000085
S	6	V6F	Gtt	Ttt	3	3	AY.29	0.000047
S	6	V6A	gTt	gCt	3	3	AY.36	0.000445
S	6	V6F	Gtt	Ttt	3	3	AY.39.1	0.000119
S	6	V6del	GTT	---	3	3	AY.43	0.000013
S	6	V6F	Gtt	Ttt	3	3	AY.46	0.000312
S	6	V6F	Gtt	Ttt	3	3	AY.6	0.000123
S	6	V6L	Gtt	Ctt	3	3	AY.61	0.000314
S	6	V6F	Gtt	Ttt	3	3	AY.70	0.000626
S	6	V6del	GTT	---	3	3	B.1	0.000027
S	6	V6V	gtT	gtC	3	3	B.1.1	0.000054
S	6	V6F	Gtt	Ttt	3	3	B.1.1.317	0.001235
S	6	V6L	Gtt	Ctt	3	3	B.1.1.7	0.000003
S	6	V6G	gTt	gGt	3	3	B.1.1.7	0.000003
S	6	V6A	gTt	gCt	3	3	B.1.160	0.000094
S	6	V6F	Gtt	Ttt	3	3	B.1.234	0.000396
S	6	V6V	gtT	gtC	2	3	B.1.429	0.000047
S	6	V6V	gtT	gtG	1	3	B.1.429	0.000024
S	6	V6F	Gtt	Ttt	3	3	B.1.466.2	0.001174
S	6	V6I	Gtt	Att	3	3	B.1.517	0.001281
S	6	V6V	gtT	gtC	3	3	B.1.526	0.000071
S	6	V6V	gtT	gtA	3	3	B.1.596	0.000261
S	6	V6F	Gtt	Ttt	3	3	B.1.617.1	0.000387
S	6	V6F	Gtt	Ttt	3	3	B.1.617.3	0.008955
S	6	V6del	GTT	---	3	3	P.1	0.000047
S	6	V6F	Gtt	Ttt	3	3	P.1.2	0.003468
S	6	V6F	Gtt	Ttt	3	3	Q.1	0.000379
S	6	V6Q	GTT	CAA	2	2		0.111111
S	6	V6D	gTt	gAt	2	2		0.111111
S	6	V6H	GTt	CAt	2	2		0.111111
S	6	V6E	gTT	gAA	2	2		0.111111
S	6	V6V	gtT	gtA	2	2		0.111111
S	6	V6F	Gtt	Ttt	2	2	A	0.000774
S	6	V6F	Gtt	Ttt	2	2	A.2.5	0.000998
S	6	V6F	Gtt	Ttt	2	2	A.23.1	0.001408
S	6	V6Q	GTT	CAA	2	2	All	0
S	6	V6T	GTt	ACt	2	2	All	0
S	6	V6F	Gtt	Ttt	2	2	AY.106	0.00067
S	6	V6F	Gtt	Ttt	2	2	AY.116.1	0.000623
S	6	V6F	Gtt	Ttt	2	2	AY.23	0.000139
S	6	V6del	GTT	---	2	2	AY.25	0.000012
S	6	V6F	Gtt	Ttt	2	2	AY.29.1	0.000441
S	6	V6A	gTt	gCt	2	2	AY.3	0.00002
S	6	V6F	Gtt	Ttt	2	2	AY.3.1	0.000171
S	6	V6I	Gtt	Att	2	2	AY.33	0.000134
S	6	V6F	Gtt	Ttt	2	2	AY.34.1	0.00102
S	6	V6F	Gtt	Ttt	2	2	AY.4.5	0.000215
S	6	V6A	gTt	gCt	2	2	AY.43	0.000009
S	6	V6L	Gtt	Ctt	2	2	AY.44	0.000012
S	6	V6V	gtT	gtC	2	2	AY.44	0.000012
S	6	V6I	Gtt	Att	2	2	AY.45	0.000243
S	6	V6V	gtT	gtG	2	2	AY.46.5	0.000397
S	6	V6F	Gtt	Ttt	2	2	AY.61	0.00021
S	6	V6I	Gtt	Att	2	2	AY.69	0.000373
S	6	V6F	Gtt	Ttt	2	2	AY.71	0.00095
S	6	V6F	Gtt	Ttt	2	2	AY.9.2	0.000073
S	6	V6F	Gtt	Ttt	2	2	AY.98	0.000158
S	6	V6A	gTt	gCt	2	2	B.1	0.000018
S	6	V6A	gTt	gCt	2	2	B.1.1.153	0.002191
S	6	V6F	Gtt	Ttt	2	2	B.1.1.220	0.003717
S	6	V6F	Gtt	Ttt	2	2	B.1.1.258	0.006515
S	6	V6F	Gtt	Ttt	2	2	B.1.1.306	0.000877
S	6	V6T	GTt	ACt	2	2	B.1.1.416	0.00181
S	6	V6V	gtT	gtC	2	2	B.1.160.7	0.004158
S	6	V6I	Gtt	Att	2	2	B.1.177	0.000026
S	6	V6del	GTT	---	2	2	B.1.2	0.000018
S	6	V6V	gtT	gtC	1	2	B.1.2	0.000009
S	6	V6V	gtT	gtG	1	2	B.1.2	0.000009
S	6	V6F	Gtt	Ttt	2	2	B.1.221	0.000142
S	6	V6F	Gtt	Ttt	2	2	B.1.241	0.001623
S	6	V6F	Gtt	Ttt	2	2	B.1.258	0.000133
S	6	V6V	gtT	gtC	2	2	B.1.258	0.000133
S	6	V6F	Gtt	Ttt	2	2	B.1.265	0.002541
S	6	V6G	gTt	gGt	2	2	B.1.351	0.000059
S	6	V6A	gTt	gCt	2	2	B.1.351	0.000059
S	6	V6I	Gtt	Att	2	2	B.1.36	0.000292
S	6	V6F	Gtt	Ttt	2	2	B.1.36.8	0.002
S	6	V6del	GTT	---	2	2	B.1.525	0.000226
S	6	V6F	Gtt	Ttt	2	2	B.1.595	0.000522
S	6	V6F	Gtt	Ttt	2	2	B.1.595.1	0.011696
S	6	V6F	Gtt	Ttt	2	2	B.1.609	0.000959
S	6	V6A	gTt	gCt	2	2	B.1.617.2	0.000008
S	6	V6I	Gtt	Att	2	2	B.1.618	0.008065
S	6	V6F	Gtt	Ttt	2	2	B.1.619	0.001742
S	6	V6F	Gtt	Ttt	2	2	B.1.621	0.000177
S	6	V6F	Gtt	Ttt	2	2	B.1.628	0.000705
S	6	V6F	Gtt	Ttt	2	2	D.2	0.00015
S	6	V6V	gtT	gtC	2	2	P.1	0.000032
S	6	V6I	Gtt	Att	2	2	P.2	0.000373
S	6	V6V	gtT	gtG	2	2	Q.8	0.00033
S	6	V6L	Gtt	Ctt	1	1	A.1	0.000282
S	6	V6F	Gtt	Ttt	1	1	A.2	0.000662
S	6	V6del	GTT	---	1	1	A.2.4	0.003367
S	6	V6V	gtT	gtG	1	1	A.2.4	0.003367
S	6	V6F	Gtt	Ttt	1	1	AD.2	0.000219
S	6	V6N	GTt	AAt	1	1	All	0
S	6	V6F	Gtt	Ttt	1	1	AY.10	0.00053
S	6	V6del	GTT	---	1	1	AY.100	0.000046
S	6	V6del1	gtT	gt-	1	1	AY.103	0.000006
S	6	V6del	GTT	---	1	1	AY.103	0.000006
S	6	V6F	Gtt	Ttt	1	1	AY.105	0.000643
S	6	V6I	Gtt	Att	1	1	AY.107	0.000466
S	6	V6F	Gtt	Ttt	1	1	AY.108	0.001103
S	6	V6A	gTt	gCt	1	1	AY.113	0.000142
S	6	V6F	Gtt	Ttt	1	1	AY.114	0.000231
S	6	V6del	GTT	---	1	1	AY.14	0.000088
S	6	V6L	Gtt	Ctt	1	1	AY.15	0.002222
S	6	V6F	Gtt	Ttt	1	1	AY.16	0.00038
S	6	V6F	Gtt	Ttt	1	1	AY.16.1	0.00047
S	6	V6I	Gtt	Att	1	1	AY.20	0.000039
S	6	V6A	gTt	gCt	1	1	AY.20	0.000039
S	6	V6V	gtT	gtC	1	1	AY.23	0.00007
S	6	V6F	Gtt	Ttt	1	1	AY.23.1	0.000417
S	6	V6A	gTt	gCt	1	1	AY.23.1	0.000417
S	6	V6A	gTt	gCt	1	1	AY.24	0.000431
S	6	V6G	gTt	gGt	1	1	AY.25	0.000006
S	6	V6A	gTt	gCt	1	1	AY.26	0.000028
S	6	V6L	Gtt	Ctt	1	1	AY.27	0.000065
S	6	V6F	Gtt	Ttt	1	1	AY.27	0.000065
S	6	V6L	Gtt	Ctt	1	1	AY.29	0.000016
S	6	V6A	gTt	gCt	1	1	AY.29	0.000016
S	6	V6V	gtT	gtG	1	1	AY.3	0.00001
S	6	V6del	GTT	---	1	1	AY.3	0.00001
S	6	V6I	Gtt	Att	1	1	AY.3.1	0.000085
S	6	V6F	Gtt	Ttt	1	1	AY.30	0.000396
S	6	V6F	Gtt	Ttt	1	1	AY.33	0.000067
S	6	V6I	Gtt	Att	1	1	AY.35	0.000233
S	6	V6C	GTt	TGt	1	1	AY.36	0.000148
S	6	V6del	GTT	---	1	1	AY.38	0.000499
S	6	V6I	Gtt	Att	1	1	AY.39.1	0.00004
S	6	V6del1	Gtt	-tt	1	1	AY.4	0.000002
S	6	V6F	Gtt	Ttt	1	1	AY.4.2.1	0.000149
S	6	V6del	GTT	---	1	1	AY.4.3	0.000842
S	6	V6F	Gtt	Ttt	1	1	AY.41	0.000294
S	6	V6A	gTt	gCt	1	1	AY.42	0.00004
S	6	V6del	GTT	---	1	1	AY.42	0.00004
S	6	V6del1	Gtt	-tt	1	1	AY.43	0.000004
S	6	V6A	gTt	gCt	1	1	AY.46	0.000104
S	6	V6F	Gtt	Ttt	1	1	AY.46.1	0.001027
S	6	V6del1	Gtt	-tt	1	1	AY.46.6	0.000072
S	6	V6A	gTt	gCt	1	1	AY.46.6	0.000072
S	6	V6I	Gtt	Att	1	1	AY.46.6	0.000072
S	6	V6V	gtT	gtA	1	1	AY.5	0.000021
S	6	V6A	gTt	gCt	1	1	AY.5	0.000021
S	6	V6F	Gtt	Ttt	1	1	AY.53	0.000288
S	6	V6V	gtT	gtA	1	1	AY.53	0.000288
S	6	V6del	GTT	---	1	1	AY.54	0.000095
S	6	V6V	gtT	gtC	1	1	AY.55	0.000917
S	6	V6F	Gtt	Ttt	1	1	AY.55	0.000917
S	6	V6I	Gtt	Att	1	1	AY.59	0.00053
S	6	V6I	Gtt	Att	1	1	AY.6	0.000041
S	6	V6A	gTt	gCt	1	1	AY.61	0.000105
S	6	V6I	Gtt	Att	1	1	AY.67	0.000464
S	6	V6del	GTT	---	1	1	AY.68	0.000274
S	6	V6A	gTt	gCt	1	1	AY.69	0.000187
S	6	V6V	gtT	gtC	1	1	AY.7.1	0.000113
S	6	V6F	Gtt	Ttt	1	1	AY.72	0.001361
S	6	V6F	Gtt	Ttt	1	1	AY.74	0.000116
S	6	V6F	Gtt	Ttt	1	1	AY.88	0.000884
S	6	V6F	Gtt	Ttt	1	1	AY.9.1	0.000084
S	6	V6F	Gtt	Ttt	1	1	AY.90	0.000684
S	6	V6F	Gtt	Ttt	1	1	AY.99.1	0.001553
S	6	V6A	gTt	gCt	1	1	AY.99.2	0.000092
S	6	V6L	Gtt	Ctt	1	1	B.1	0.000009
S	6	V6del1	gTt	g-t	1	1	B.1	0.000009
S	6	V6G	gTt	gGt	1	1	B.1	0.000009
S	6	V6I	Gtt	Att	1	1	B.1.1	0.000018
S	6	V6G	gTt	gGt	1	1	B.1.1	0.000018
S	6	V6L	Gtt	Ctt	1	1	B.1.1	0.000018
S	6	V6I	Gtt	Att	1	1	B.1.1.10	0.001115
S	6	V6G	gTt	gGt	1	1	B.1.1.157	0.000913
S	6	V6F	Gtt	Ttt	1	1	B.1.1.163	0.007634
S	6	V6V	gtT	gtC	1	1	B.1.1.170	0.001247
S	6	V6E	gTT	gAG	1	1	B.1.1.214	0.000055
S	6	V6L	Gtt	Ctt	1	1	B.1.1.240	0.004695
S	6	V6F	Gtt	Ttt	1	1	B.1.1.241	0.00207
S	6	V6F	Gtt	Ttt	1	1	B.1.1.28	0.000311
S	6	V6F	Gtt	Ttt	1	1	B.1.1.283	0.023256
S	6	V6A	gTt	gCt	1	1	B.1.1.306	0.000438
S	6	V6del	GTT	---	1	1	B.1.1.315	0.008475
S	6	V6F	Gtt	Ttt	1	1	B.1.1.37	0.000193
S	6	V6F	Gtt	Ttt	1	1	B.1.1.378	0.007299
S	6	V6F	Gtt	Ttt	1	1	B.1.1.39	0.00051
S	6	V6V	gtT	gtC	1	1	B.1.1.39	0.00051
S	6	V6F	Gtt	Ttt	1	1	B.1.1.432	0.001266
S	6	V6del	GTT	---	1	1	B.1.1.46	0.004367
S	6	V6F	Gtt	Ttt	1	1	B.1.1.50	0.000679
S	6	V6A	gTt	gCt	1	1	B.1.1.50	0.000679
S	6	V6A	gTt	gCt	1	1	B.1.1.519	0.00004
S	6	V6V	gtT	gtG	1	1	B.1.1.519	0.00004
S	6	V6F	Gtt	Ttt	1	1	B.1.1.56	0.017857
S	6	V6V	gtT	gtC	1	1	B.1.1.63	0.000386
S	6	V6del1	Gtt	-tt	1	1	B.1.1.7	0.000001
S	6	V6D	gTt	gAt	1	1	B.1.1.7	0.000001
S	6	V6N	GTt	AAt	1	1	B.1.1.7	0.000001
S	6	V6F	Gtt	Ttt	1	1	B.1.1.70	0.000341
S	6	V6C	GTt	TGt	1	1	B.1.110.3	0.000718
S	6	V6F	Gtt	Ttt	1	1	B.1.111	0.001175
S	6	V6F	Gtt	Ttt	1	1	B.1.143	0.021277
S	6	V6C	GTt	TGt	1	1	B.1.160	0.000031
S	6	V6D	gTt	gAt	1	1	B.1.160	0.000031
S	6	V6F	Gtt	Ttt	1	1	B.1.160.12	0.00641
S	6	V6F	Gtt	Ttt	1	1	B.1.160.32	0.004292
S	6	V6V	gtT	gtG	1	1	B.1.177	0.000013
S	6	V6D	gTt	gAt	1	1	B.1.177	0.000013
S	6	V6del1	Gtt	-tt	1	1	B.1.177.12	0.000152
S	6	V6F	Gtt	Ttt	1	1	B.1.177.16	0.000664
S	6	V6A	gTt	gCt	1	1	B.1.177.17	0.000821
S	6	V6F	Gtt	Ttt	1	1	B.1.177.17	0.000821
S	6	V6F	Gtt	Ttt	1	1	B.1.177.31	0.011494
S	6	V6F	Gtt	Ttt	1	1	B.1.177.4	0.000211
S	6	V6L	Gtt	Ctt	1	1	B.1.177.4	0.000211
S	6	V6del	GTT	---	1	1	B.1.177.68	0.015152
S	6	V6F	Gtt	Ttt	1	1	B.1.177.73	0.000566
S	6	V6del	GTT	---	1	1	B.1.177.83	0.001481
S	6	V6F	Gtt	Ttt	1	1	B.1.177.86	0.000183
S	6	V6F	Gtt	Ttt	1	1	B.1.199	0.004132
S	6	V6del2	gTT	g--	1	1	B.1.2	0.000009
S	6	V6del	GTT	---	1	1	B.1.232	0.000537
S	6	V6A	gTt	gCt	1	1	B.1.243	0.00007
S	6	V6del	GTT	---	1	1	B.1.258.16	0.001637
S	6	V6V	gtT	gtC	1	1	B.1.311	0.000275
S	6	V6V	gtT	gtC	1	1	B.1.351	0.00003
S	6	V6F	Gtt	Ttt	1	1	B.1.356	0.001727
S	6	V6V	gtT	gtC	1	1	B.1.36	0.000146
S	6	V6A	gTt	gCt	1	1	B.1.36	0.000146
S	6	V6F	Gtt	Ttt	1	1	B.1.36.31	0.001751
S	6	V6F	Gtt	Ttt	1	1	B.1.36.39	0.002217
S	6	V6G	gTt	gGt	1	1	B.1.36.8	0.001
S	6	V6A	gTt	gCt	1	1	B.1.369	0.000285
S	6	V6F	Gtt	Ttt	1	1	B.1.369	0.000285
S	6	V6F	Gtt	Ttt	1	1	B.1.389	0.001002
S	6	V6F	Gtt	Ttt	1	1	B.1.396	0.000706
S	6	V6A	gTt	gCt	1	1	B.1.427	0.00005
S	6	V6A	gTt	gCt	1	1	B.1.428	0.00102
S	6	V6I	Gtt	Att	1	1	B.1.429	0.000024
S	6	V6del	GTT	---	1	1	B.1.453	0.003236
S	6	V6del1	gTt	g-t	1	1	B.1.459	0.004082
S	6	V6F	Gtt	Ttt	1	1	B.1.503	0.002488
S	6	V6F	Gtt	Ttt	1	1	B.1.510	0.026316
S	6	V6F	Gtt	Ttt	1	1	B.1.525	0.000113
S	6	V6del	GTT	---	1	1	B.1.526	0.000024
S	6	V6V	gtT	gtC	1	1	B.1.527	0.003704
S	6	V6F	Gtt	Ttt	1	1	B.1.560	0.00463
S	6	V6V	gtT	gtC	1	1	B.1.565	0.00081
S	6	V6I	Gtt	Att	1	1	B.1.575	0.000303
S	6	V6F	Gtt	Ttt	1	1	B.1.580	0.004065
S	6	V6I	Gtt	Att	1	1	B.1.589	0.007576
S	6	V6del2	GTt	--t	1	1	B.1.617.2	0.000004
S	6	V6del2	gTT	g--	1	1	B.1.617.3	0.002985
S	6	V6del	GTT	---	1	1	B.1.620	0.000946
S	6	V6A	gTt	gCt	1	1	B.1.620	0.000946
S	6	V6del1	Gtt	-tt	1	1	B.1.621	0.000089
S	6	V6I	Gtt	Att	1	1	B.1.621	0.000089
S	6	V6del	GTT	---	1	1	B.1.637	0.000073
S	6	V6F	Gtt	Ttt	1	1	B.1.97	0.025641
S	6	V6F	Gtt	Ttt	1	1	B.27	0.015385
S	6	V6F	Gtt	Ttt	1	1	B.6.1	0.026316
S	6	V6V	gtT	gtA	1	1	C.18	0.002591
S	6	V6F	Gtt	Ttt	1	1	C.30	0.001727
S	6	V6F	Gtt	Ttt	1	1	C.36.3.1	0.002717
S	6	V6G	gTt	gGt	1	1	D.2	0.000075
S	6	V6H	GTT	CAC	1	1	P.1	0.000016
S	6	V6del1	gTt	g-t	1	1	P.1	0.000016
S	6	V6del	GTT	---	1	1	P.1.10	0.000269
S	6	V6F	Gtt	Ttt	1	1	P.1.14	0.000048
S	6	V6A	gTt	gCt	1	1	P.1.14	0.000048
S	6	V6V	gtT	gtC	1	1	P.1.14	0.000048
S	6	V6L	Gtt	Ctt	1	1	P.1.4	0.000977
S	6	V6F	Gtt	Ttt	1	1	P.1.7	0.000319
S	6	V6F	Gtt	Ttt	1	1	P.2	0.000187
S	6	V6del	GTT	---	1	1	Q.8	0.000165
S	6	V6F	Gtt	Ttt	1	1	W.1	0.008696

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.