CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 654

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	654	E654Q		nonsyn	Gaa	Caa	1478	1478	1	23522-23524
S	654	E654E		syn	gaA	gaG	875	875	1	23522-23524
S	654	E654K		nonsyn	Gaa	Aaa	639	639	1	23522-23524
S	654	E654V		nonsyn	gAa	gTa	529	528	0.99811	23522-23524
S	654	E654V		nonsyn	gAA	gTT	529	1	0.00189036	23522-23524
S	654	E654A		nonsyn	gAa	gCa	223	223	1	23522-23524
S	654	E654D		nonsyn	gaA	gaC	82	67	0.817073	23522-23524
S	654	E654D		nonsyn	gaA	gaT	82	15	0.182927	23522-23524
S	654	E654G		nonsyn	gAa	gGa	58	56	0.965517	23522-23524
S	654	E654G		nonsyn	gAA	gGG	58	1	0.0172414	23522-23524
S	654	E654G		nonsyn	gAA	gGT	58	1	0.0172414	23522-23524
S	654	E654del		del	GAA	---	50	50	1	23522-23524
S	654	E654X		nonsyn	Gaa	Taa	28	27	0.964286	23522-23524
S	654	E654X		nonsyn	GAa	TGa	28	1	0.0357143	23522-23524
S	654	E654del1		del	gAa	g-a	8	7	0.875	23522-23524
S	654	E654del1		del	gaA	ga-	8	1	0.125	23522-23524
S	654	E654S		nonsyn	GAA	TCT	5	4	0.8	23522-23524
S	654	E654S		nonsyn	GAa	TCa	5	1	0.2	23522-23524
S	654	E654I		nonsyn	GAa	ATa	3	3	1	23522-23524
S	654	E654del2		del	gAA	g--	2	2	1	23522-23524
S	654	E654F		nonsyn	GAA	TTT	2	2	1	23522-23524
S	654	E654R		nonsyn	GAa	AGa	1	1	1	23522-23524
S	654	E654Y		nonsyn	GaA	TaT	1	1	1	23522-23524
S	654	E654L		nonsyn	GAa	TTa	1	1	1	23522-23524

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	654	E654Q	Gaa	Caa	1478	1478	All	0.000283
S	654	E654E	gaA	gaG	875	875	All	0.000167
S	654	E654E	gaA	gaG	659	659	B.1.1.7	0.00059
S	654	E654K	Gaa	Aaa	639	639	All	0.000122
S	654	E654V	gAa	gTa	528	529	All	0.000101
S	654	E654V	gAA	gTT	1	529	All	0
S	654	E654V	gAa	gTa	224	224	AY.25	0.001347
S	654	E654A	gAa	gCa	223	223	All	0.000043
S	654	E654Q	Gaa	Caa	197	197	B.1.1.277	0.149469
S	654	E654Q	Gaa	Caa	170	170	AY.4	0.000265
S	654	E654A	gAa	gCa	142	142	B.1.1.7	0.000127
S	654	E654Q	Gaa	Caa	134	134	B.1.1.7	0.00012
S	654	E654Q	Gaa	Caa	122	122	B.1.499	0.128151
S	654	E654K	Gaa	Aaa	90	90	B.1.2	0.000792
S	654	E654K	Gaa	Aaa	87	87	AY.4	0.000135
S	654	E654Q	Gaa	Caa	85	85	AY.98.1	0.004117
S	654	E654D	gaA	gaC	67	82	All	0.000013
S	654	E654D	gaA	gaT	15	82	All	0.000003
S	654	E654K	Gaa	Aaa	79	79	B.1.405	0.975309
S	654	E654V	gAa	gTa	79	79	B.1.617.2	0.000297
S	654	E654Q	Gaa	Caa	78	78	B.1.2	0.000687
S	654	E654Q	Gaa	Caa	68	68	B.1	0.000623
S	654	E654Q	Gaa	Caa	68	68	B.1.1.189	0.102874
S	654	E654Q	Gaa	Caa	68	68	B.1.36.24	0.419753
S	654	E654G	gAa	gGa	56	58	All	0.000011
S	654	E654G	gAA	gGT	1	58	All	0
S	654	E654G	gAA	gGG	1	58	All	0
S	654	E654E	gaA	gaG	52	52	P.1.1	0.016518
S	654	E654del	GAA	---	50	50	All	0.00001
S	654	E654E	gaA	gaG	48	48	AY.113	0.006835
S	654	E654K	Gaa	Aaa	47	47	B.1	0.00043
S	654	E654Q	Gaa	Caa	45	45	B.1.526	0.001058
S	654	E654Q	Gaa	Caa	45	45	B.1.562	0.833333
S	654	E654Q	Gaa	Caa	42	42	B.1.177	0.000553
S	654	E654K	Gaa	Aaa	41	41	B.1.1.7	0.000037
S	654	E654Q	Gaa	Caa	41	41	P.1.7	0.013091
S	654	E654Q	Gaa	Caa	40	40	AY.29	0.000631
S	654	E654Q	Gaa	Caa	39	39	B.1.1	0.000707
S	654	E654V	gAa	gTa	37	37	AY.43	0.000164
S	654	E654K	Gaa	Aaa	34	34	AY.33	0.00227
S	654	E654K	Gaa	Aaa	33	33	B.1.1.63	0.012731
S	654	E654K	Gaa	Aaa	29	29	B.1.617.2	0.000109
S	654	E654X	Gaa	Taa	27	28	All	0.000005
S	654	E654X	GAa	TGa	1	28	All	0
S	654	E654D	gaA	gaC	28	28	B.1.1.1	0.009147
S	654	E654Q	Gaa	Caa	28	28	B.1.1.222	0.005712
S	654	E654K	Gaa	Aaa	26	26	AY.20	0.00101
S	654	E654D	gaA	gaC	25	25	AY.39	0.000618
S	654	E654G	gAa	gGa	23	23	B.1.1	0.000417
S	654	E654V	gAa	gTa	23	23	B.1.1.7	0.000021
S	654	E654A	gAa	gCa	21	21	AY.25	0.000126
S	654	E654Q	Gaa	Caa	19	19	B.1.627	0.038384
S	654	E654K	Gaa	Aaa	17	17	B.1.1	0.000308
S	654	E654V	gAa	gTa	17	17	B.1.111	0.019976
S	654	E654Q	Gaa	Caa	16	16	AY.25	0.000096
S	654	E654Q	Gaa	Caa	16	16	B.1.1.174	0.054054
S	654	E654V	gAa	gTa	15	15	AY.39	0.000371
S	654	E654K	Gaa	Aaa	15	15	B.1.36	0.002189
S	654	E654E	gaA	gaG	13	13	AY.4	0.00002
S	654	E654Q	Gaa	Caa	13	13	AY.44	0.000079
S	654	E654X	Gaa	Taa	13	13	B.1.1.7	0.000012
S	654	E654A	gAa	gCa	12	12	B.1.177.55	0.027972
S	654	E654V	gAa	gTa	12	12	B.1.564	0.005111
S	654	E654Q	Gaa	Caa	11	11	AY.47	0.000342
S	654	E654V	gAa	gTa	10	10	AY.4	0.000016
S	654	E654K	Gaa	Aaa	10	10	B.1.164	0.149254
S	654	E654E	gaA	gaG	10	10	B.1.2	0.000088
S	654	E654V	gAa	gTa	10	10	B.1.265	0.012706
S	654	E654Q	Gaa	Caa	10	10	B.1.617.2	0.000038
S	654	E654Q	Gaa	Caa	10	10	Q.6	0.066225
S	654	E654K	Gaa	Aaa	9	9	AY.43	0.00004
S	654	E654K	Gaa	Aaa	9	9	AY.44	0.000055
S	654	E654V	gAa	gTa	9	9	B.1.351	0.000268
S	654	E654E	gaA	gaG	9	9	B.1.617.2	0.000034
S	654	E654del1	gAa	g-a	7	8	All	0.000001
S	654	E654del1	gaA	ga-	1	8	All	0
S	654	E654del	GAA	---	8	8	B.1	0.000073
S	654	E654K	Gaa	Aaa	8	8	B.1.258	0.000532
S	654	E654K	Gaa	Aaa	7	7	AY.25	0.000042
S	654	E654Q	Gaa	Caa	7	7	AY.26	0.000198
S	654	E654K	Gaa	Aaa	7	7	AY.3	0.00007
S	654	E654V	gAa	gTa	6	7	B.1	0.000055
S	654	E654V	gAA	gTT	1	7	B.1	0.000009
S	654	E654D	gaA	gaT	6	7	B.1.1.7	0.000005
S	654	E654D	gaA	gaC	1	7	B.1.1.7	0.000001
S	654	E654E	gaA	gaG	7	7	B.1.177.44	0.003633
S	654	E654K	Gaa	Aaa	7	7	B.1.351	0.000208
S	654	E654E	gaA	gaG	7	7	B.1.429	0.000165
S	654	E654E	gaA	gaG	6	6		0.333333
S	654	E654Q	Gaa	Caa	6	6	AY.23.1	0.002504
S	654	E654K	Gaa	Aaa	6	6	B.1.443	0.028037
S	654	E654A	gAa	gCa	6	6	B.1.524	0.008439
S	654	E654G	gAa	gGa	6	6	P.1	0.000095
S	654	E654V	gAa	gTa	6	6	P.1	0.000095
S	654	E654Q	Gaa	Caa	6	6	P.1	0.000095
S	654	E654S	GAA	TCT	4	5	All	0.000001
S	654	E654S	GAa	TCa	1	5	All	0
S	654	E654V	gAa	gTa	5	5	AY.103	0.000031
S	654	E654Q	Gaa	Caa	5	5	AY.39.1	0.000198
S	654	E654X	Gaa	Taa	5	5	B.1	0.000046
S	654	E654G	gAa	gGa	3	5	B.1	0.000027
S	654	E654G	gAA	gGG	1	5	B.1	0.000009
S	654	E654G	gAA	gGT	1	5	B.1	0.000009
S	654	E654E	gaA	gaG	5	5	B.1.1	0.000091
S	654	E654del	GAA	---	5	5	B.1.1.7	0.000004
S	654	E654Q	Gaa	Caa	5	5	B.1.351	0.000149
S	654	E654E	gaA	gaG	5	5	B.1.351	0.000149
S	654	E654E	gaA	gaG	5	5	B.1.575	0.001517
S	654	E654V	gAa	gTa	5	5	B.1.628	0.001762
S	654	E654K	Gaa	Aaa	4	4	AY.102	0.000106
S	654	E654Q	Gaa	Caa	4	4	AY.103	0.000025
S	654	E654A	gAa	gCa	4	4	AY.106	0.00134
S	654	E654E	gaA	gaG	4	4	AY.111	0.000733
S	654	E654del	GAA	---	4	4	AY.43	0.000018
S	654	E654A	gAa	gCa	4	4	AY.44	0.000024
S	654	E654E	gaA	gaG	4	4	B.1	0.000037
S	654	E654E	gaA	gaG	4	4	B.1.160	0.000125
S	654	E654E	gaA	gaG	4	4	B.1.177	0.000053
S	654	E654Q	Gaa	Caa	4	4	B.1.456	0.013072
S	654	E654V	gAa	gTa	4	4	B.1.551	0.005161
S	654	E654Q	Gaa	Caa	4	4	B.1.596	0.000349
S	654	E654G	gAa	gGa	4	4	B.1.617.2	0.000015
S	654	E654Q	Gaa	Caa	4	4	B.1.621	0.000354
S	654	E654del	GAA	---	4	4	P.1	0.000063
S	654	E654A	gAa	gCa	4	4	P.1	0.000063
S	654	E654I	GAa	ATa	3	3	All	0.000001
S	654	E654Q	Gaa	Caa	3	3	AY.102	0.00008
S	654	E654A	gAa	gCa	3	3	AY.103	0.000019
S	654	E654A	gAa	gCa	3	3	AY.119	0.000106
S	654	E654V	gAa	gTa	3	3	AY.119	0.000106
S	654	E654del	GAA	---	3	3	AY.25	0.000018
S	654	E654V	gAa	gTa	3	3	AY.33	0.0002
S	654	E654E	gaA	gaG	3	3	AY.43	0.000013
S	654	E654V	gAa	gTa	3	3	AY.45	0.000365
S	654	E654V	gAa	gTa	3	3	AY.5	0.000062
S	654	E654K	Gaa	Aaa	3	3	AY.6	0.000123
S	654	E654Q	Gaa	Caa	3	3	AY.61	0.000314
S	654	E654A	gAa	gCa	3	3	AY.85	0.001282
S	654	E654V	gAa	gTa	3	3	AY.98.1	0.000145
S	654	E654K	Gaa	Aaa	3	3	AZ.5	0.010526
S	654	E654del1	gAa	g-a	2	3	B.1	0.000018
S	654	E654D	gaA	gaC	2	3	B.1	0.000018
S	654	E654del1	gaA	ga-	1	3	B.1	0.000009
S	654	E654D	gaA	gaT	1	3	B.1	0.000009
S	654	E654V	gAa	gTa	3	3	B.1.1.326	0.005282
S	654	E654Q	Gaa	Caa	3	3	B.1.1.519	0.000119
S	654	E654A	gAa	gCa	3	3	B.1.1.519	0.000119
S	654	E654Q	Gaa	Caa	3	3	B.1.1.526	0.010638
S	654	E654G	gAa	gGa	3	3	B.1.177	0.00004
S	654	E654K	Gaa	Aaa	3	3	B.1.221	0.000213
S	654	E654E	gaA	gaG	3	3	B.1.427	0.000151
S	654	E654K	Gaa	Aaa	3	3	B.1.499	0.003151
S	654	E654del	GAA	---	3	3	B.1.617.2	0.000011
S	654	E654del	GAA	---	3	3	B.1.621	0.000266
S	654	E654K	Gaa	Aaa	3	3	P.1	0.000047
S	654	E654del	GAA	---	3	3	P.1.15	0.000697
S	654	E654K	Gaa	Aaa	2	2		0.111111
S	654	E654del2	gAA	g--	2	2	All	0
S	654	E654F	GAA	TTT	2	2	All	0
S	654	E654V	gAa	gTa	2	2	AY.102	0.000053
S	654	E654E	gaA	gaG	2	2	AY.103	0.000012
S	654	E654K	Gaa	Aaa	2	2	AY.12	0.000632
S	654	E654A	gAa	gCa	2	2	AY.20	0.000078
S	654	E654V	gAa	gTa	2	2	AY.23	0.000139
S	654	E654Q	Gaa	Caa	2	2	AY.29.1	0.000441
S	654	E654E	gaA	gaG	2	2	AY.39	0.000049
S	654	E654K	Gaa	Aaa	2	2	AY.39.1	0.000079
S	654	E654X	Gaa	Taa	2	2	AY.4	0.000003
S	654	E654V	gAa	gTa	2	2	AY.44	0.000012
S	654	E654K	Gaa	Aaa	2	2	AY.58	0.001815
S	654	E654D	gaA	gaC	2	2	AY.6	0.000082
S	654	E654K	Gaa	Aaa	2	2	AY.64	0.00119
S	654	E654V	gAa	gTa	2	2	AY.7.1	0.000225
S	654	E654K	Gaa	Aaa	2	2	AY.74	0.000231
S	654	E654V	gAa	gTa	2	2	AY.98	0.000158
S	654	E654V	gAa	gTa	2	2	AY.99.2	0.000184
S	654	E654X	GAa	TGa	1	2	B.1.1	0.000018
S	654	E654X	Gaa	Taa	1	2	B.1.1	0.000018
S	654	E654K	Gaa	Aaa	2	2	B.1.1.216	0.001781
S	654	E654K	Gaa	Aaa	2	2	B.1.1.291	0.001485
S	654	E654G	gAa	gGa	2	2	B.1.1.294	0.002532
S	654	E654A	gAa	gCa	2	2	B.1.1.63	0.000772
S	654	E654G	gAa	gGa	2	2	B.1.1.7	0.000002
S	654	E654V	gAa	gTa	2	2	B.1.146	0.008475
S	654	E654D	gaA	gaT	2	2	B.1.177	0.000026
S	654	E654D	gaA	gaT	2	2	B.1.177.86	0.000367
S	654	E654V	gAa	gTa	2	2	B.1.2	0.000018
S	654	E654G	gAa	gGa	2	2	B.1.236	0.004107
S	654	E654Q	Gaa	Caa	2	2	B.1.351.2	0.000605
S	654	E654Q	Gaa	Caa	2	2	B.1.36	0.000292
S	654	E654V	gAa	gTa	2	2	B.1.36	0.000292
S	654	E654K	Gaa	Aaa	2	2	B.1.400	0.000858
S	654	E654K	Gaa	Aaa	2	2	B.1.429	0.000047
S	654	E654Q	Gaa	Caa	2	2	B.1.495	0.018182
S	654	E654K	Gaa	Aaa	2	2	B.1.526	0.000047
S	654	E654K	Gaa	Aaa	2	2	B.1.617.1	0.000258
S	654	E654Q	Gaa	Caa	2	2	B.1.617.1	0.000258
S	654	E654E	gaA	gaG	2	2	B.31	0.007463
S	654	E654A	gAa	gCa	2	2	B.6	0.00182
S	654	E654K	Gaa	Aaa	2	2	C.36	0.001821
S	654	E654K	Gaa	Aaa	2	2	C.37	0.000232
S	654	E654K	Gaa	Aaa	2	2	P.1.12	0.000968
S	654	E654A	gAa	gCa	2	2	P.1.14	0.000096
S	654	E654Q	Gaa	Caa	2	2	Q.3	0.00029
S	654	E654V	gAa	gTa	1	1	A.19	0.009434
S	654	E654Q	Gaa	Caa	1	1	A.2	0.000662
S	654	E654L	GAa	TTa	1	1	All	0
S	654	E654Y	GaA	TaT	1	1	All	0
S	654	E654R	GAa	AGa	1	1	All	0
S	654	E654V	gAa	gTa	1	1	AU.2	0.002421
S	654	E654V	gAa	gTa	1	1	AY.10	0.00053
S	654	E654I	GAa	ATa	1	1	AY.100	0.000046
S	654	E654Q	Gaa	Caa	1	1	AY.100	0.000046
S	654	E654E	gaA	gaG	1	1	AY.102	0.000027
S	654	E654S	GAa	TCa	1	1	AY.102	0.000027
S	654	E654del	GAA	---	1	1	AY.103	0.000006
S	654	E654K	Gaa	Aaa	1	1	AY.103	0.000006
S	654	E654V	gAa	gTa	1	1	AY.107	0.000466
S	654	E654Q	Gaa	Caa	1	1	AY.110	0.000113
S	654	E654S	GAA	TCT	1	1	AY.113	0.000142
S	654	E654Q	Gaa	Caa	1	1	AY.113	0.000142
S	654	E654D	gaA	gaC	1	1	AY.113	0.000142
S	654	E654V	gAa	gTa	1	1	AY.117	0.000085
S	654	E654K	Gaa	Aaa	1	1	AY.117	0.000085
S	654	E654Q	Gaa	Caa	1	1	AY.119	0.000035
S	654	E654Q	Gaa	Caa	1	1	AY.120	0.000037
S	654	E654K	Gaa	Aaa	1	1	AY.120	0.000037
S	654	E654E	gaA	gaG	1	1	AY.16	0.00038
S	654	E654Q	Gaa	Caa	1	1	AY.16	0.00038
S	654	E654del1	gAa	g-a	1	1	AY.16	0.00038
S	654	E654E	gaA	gaG	1	1	AY.20	0.000039
S	654	E654X	Gaa	Taa	1	1	AY.25	0.000006
S	654	E654E	gaA	gaG	1	1	AY.25	0.000006
S	654	E654V	gAa	gTa	1	1	AY.26	0.000028
S	654	E654D	gaA	gaT	1	1	AY.29	0.000016
S	654	E654K	Gaa	Aaa	1	1	AY.29	0.000016
S	654	E654Q	Gaa	Caa	1	1	AY.3	0.00001
S	654	E654S	GAA	TCT	1	1	AY.3	0.00001
S	654	E654del	GAA	---	1	1	AY.3	0.00001
S	654	E654D	gaA	gaT	1	1	AY.3	0.00001
S	654	E654K	Gaa	Aaa	1	1	AY.3.1	0.000085
S	654	E654Q	Gaa	Caa	1	1	AY.3.1	0.000085
S	654	E654K	Gaa	Aaa	1	1	AY.34	0.000097
S	654	E654Q	Gaa	Caa	1	1	AY.34.1	0.00051
S	654	E654V	gAa	gTa	1	1	AY.36	0.000148
S	654	E654del	GAA	---	1	1	AY.37	0.000316
S	654	E654E	gaA	gaG	1	1	AY.38	0.000499
S	654	E654R	GAa	AGa	1	1	AY.4	0.000002
S	654	E654A	gAa	gCa	1	1	AY.4	0.000002
S	654	E654D	gaA	gaC	1	1	AY.4	0.000002
S	654	E654V	gAa	gTa	1	1	AY.4.2	0.000022
S	654	E654K	Gaa	Aaa	1	1	AY.4.2	0.000022
S	654	E654Q	Gaa	Caa	1	1	AY.4.2	0.000022
S	654	E654D	gaA	gaC	1	1	AY.4.5	0.000107
S	654	E654Q	Gaa	Caa	1	1	AY.42	0.00004
S	654	E654Q	Gaa	Caa	1	1	AY.43	0.000004
S	654	E654X	Gaa	Taa	1	1	AY.43	0.000004
S	654	E654I	GAa	ATa	1	1	AY.43	0.000004
S	654	E654del1	gAa	g-a	1	1	AY.44	0.000006
S	654	E654del	GAA	---	1	1	AY.44	0.000006
S	654	E654G	gAa	gGa	1	1	AY.44	0.000006
S	654	E654del	GAA	---	1	1	AY.46	0.000104
S	654	E654V	gAa	gTa	1	1	AY.46	0.000104
S	654	E654Q	Gaa	Caa	1	1	AY.46	0.000104
S	654	E654V	gAa	gTa	1	1	AY.46.1	0.001027
S	654	E654S	GAA	TCT	1	1	AY.46.6	0.000072
S	654	E654V	gAa	gTa	1	1	AY.46.6	0.000072
S	654	E654D	gaA	gaC	1	1	AY.46.6	0.000072
S	654	E654K	Gaa	Aaa	1	1	AY.47	0.000031
S	654	E654V	gAa	gTa	1	1	AY.47	0.000031
S	654	E654E	gaA	gaG	1	1	AY.5	0.000021
S	654	E654Q	Gaa	Caa	1	1	AY.54	0.000095
S	654	E654K	Gaa	Aaa	1	1	AY.59	0.00053
S	654	E654G	gAa	gGa	1	1	AY.6	0.000041
S	654	E654K	Gaa	Aaa	1	1	AY.66	0.00107
S	654	E654I	GAa	ATa	1	1	AY.67	0.000464
S	654	E654E	gaA	gaG	1	1	AY.67	0.000464
S	654	E654Q	Gaa	Caa	1	1	AY.67	0.000464
S	654	E654Q	Gaa	Caa	1	1	AY.68	0.000274
S	654	E654V	gAa	gTa	1	1	AY.68	0.000274
S	654	E654Q	Gaa	Caa	1	1	AY.7	0.000196
S	654	E654Q	Gaa	Caa	1	1	AY.74	0.000116
S	654	E654Q	Gaa	Caa	1	1	AY.75	0.000056
S	654	E654Q	Gaa	Caa	1	1	AY.75.1	0.00018
S	654	E654del	GAA	---	1	1	AY.84	0.000437
S	654	E654del	GAA	---	1	1	AY.85	0.000427
S	654	E654A	gAa	gCa	1	1	AY.9	0.000068
S	654	E654D	gaA	gaT	1	1	AY.9	0.000068
S	654	E654V	gAa	gTa	1	1	AY.9.1	0.000084
S	654	E654del	GAA	---	1	1	AY.9.2	0.000037
S	654	E654E	gaA	gaG	1	1	AY.9.2	0.000037
S	654	E654V	gAa	gTa	1	1	AY.9.2	0.000037
S	654	E654E	gaA	gaG	1	1	AY.95	0.000761
S	654	E654A	gAa	gCa	1	1	AY.98.1	0.000048
S	654	E654E	gaA	gaG	1	1	AY.98.1	0.000048
S	654	E654del	GAA	---	1	1	AY.99	0.001049
S	654	E654K	Gaa	Aaa	1	1	AY.99.2	0.000092
S	654	E654A	gAa	gCa	1	1	AZ.2	0.000821
S	654	E654Q	Gaa	Caa	1	1	B	0.000128
S	654	E654F	GAA	TTT	1	1	B.1	0.000009
S	654	E654A	gAa	gCa	1	1	B.1	0.000009
S	654	E654L	GAa	TTa	1	1	B.1	0.000009
S	654	E654Y	GaA	TaT	1	1	B.1	0.000009
S	654	E654V	gAa	gTa	1	1	B.1.1	0.000018
S	654	E654G	gAa	gGa	1	1	B.1.1.121	0.002427
S	654	E654K	Gaa	Aaa	1	1	B.1.1.13	0.035714
S	654	E654Q	Gaa	Caa	1	1	B.1.1.134	0.011364
S	654	E654K	Gaa	Aaa	1	1	B.1.1.214	0.000055
S	654	E654Q	Gaa	Caa	1	1	B.1.1.231	0.003096
S	654	E654V	gAa	gTa	1	1	B.1.1.25	0.000569
S	654	E654K	Gaa	Aaa	1	1	B.1.1.263	0.001558
S	654	E654E	gaA	gaG	1	1	B.1.1.277	0.000759
S	654	E654Q	Gaa	Caa	1	1	B.1.1.28	0.000311
S	654	E654D	gaA	gaT	1	1	B.1.1.306	0.000438
S	654	E654A	gAa	gCa	1	1	B.1.1.306	0.000438
S	654	E654G	gAa	gGa	1	1	B.1.1.317	0.000412
S	654	E654Q	Gaa	Caa	1	1	B.1.1.318	0.000302
S	654	E654V	gAa	gTa	1	1	B.1.1.348	0.000796
S	654	E654Q	Gaa	Caa	1	1	B.1.1.348	0.000796
S	654	E654G	gAa	gGa	1	1	B.1.1.349	0.010309
S	654	E654K	Gaa	Aaa	1	1	B.1.1.362	0.005618
S	654	E654V	gAa	gTa	1	1	B.1.1.37	0.000193
S	654	E654Q	Gaa	Caa	1	1	B.1.1.37	0.000193
S	654	E654del	GAA	---	1	1	B.1.1.372	0.000689
S	654	E654Q	Gaa	Caa	1	1	B.1.1.409	0.002833
S	654	E654G	gAa	gGa	1	1	B.1.1.409	0.002833
S	654	E654E	gaA	gaG	1	1	B.1.1.409	0.002833
S	654	E654Q	Gaa	Caa	1	1	B.1.1.424	0.045455
S	654	E654K	Gaa	Aaa	1	1	B.1.1.430	0.041667
S	654	E654K	Gaa	Aaa	1	1	B.1.1.486	0.001577
S	654	E654G	gAa	gGa	1	1	B.1.1.514	0.038462
S	654	E654V	gAa	gTa	1	1	B.1.1.519	0.00004
S	654	E654Q	Gaa	Caa	1	1	B.1.1.57	0.011494
S	654	E654Q	Gaa	Caa	1	1	B.1.1.59	0.006494
S	654	E654del2	gAA	g--	1	1	B.1.1.7	0.000001
S	654	E654E	gaA	gaG	1	1	B.1.1.70	0.000341
S	654	E654V	gAa	gTa	1	1	B.1.126	0.001276
S	654	E654D	gaA	gaC	1	1	B.1.160	0.000031
S	654	E654del	GAA	---	1	1	B.1.177	0.000013
S	654	E654V	gAa	gTa	1	1	B.1.177	0.000013
S	654	E654A	gAa	gCa	1	1	B.1.177	0.000013
S	654	E654E	gaA	gaG	1	1	B.1.177.23	0.003236
S	654	E654E	gaA	gaG	1	1	B.1.177.4	0.000211
S	654	E654K	Gaa	Aaa	1	1	B.1.177.60	0.000218
S	654	E654Q	Gaa	Caa	1	1	B.1.177.7	0.000165
S	654	E654del2	gAA	g--	1	1	B.1.2	0.000009
S	654	E654D	gaA	gaC	1	1	B.1.2	0.000009
S	654	E654F	GAA	TTT	1	1	B.1.2	0.000009
S	654	E654G	gAa	gGa	1	1	B.1.2	0.000009
S	654	E654E	gaA	gaG	1	1	B.1.221	0.000071
S	654	E654K	Gaa	Aaa	1	1	B.1.232	0.000537
S	654	E654Q	Gaa	Caa	1	1	B.1.243	0.00007
S	654	E654E	gaA	gaG	1	1	B.1.258	0.000067
S	654	E654K	Gaa	Aaa	1	1	B.1.258.17	0.000104
S	654	E654E	gaA	gaG	1	1	B.1.258.17	0.000104
S	654	E654E	gaA	gaG	1	1	B.1.258.22	0.002667
S	654	E654K	Gaa	Aaa	1	1	B.1.258.7	0.001912
S	654	E654X	Gaa	Taa	1	1	B.1.311	0.000275
S	654	E654Q	Gaa	Caa	1	1	B.1.336	0.002439
S	654	E654X	Gaa	Taa	1	1	B.1.351	0.00003
S	654	E654G	gAa	gGa	1	1	B.1.36	0.000146
S	654	E654K	Gaa	Aaa	1	1	B.1.36.10	0.004785
S	654	E654K	Gaa	Aaa	1	1	B.1.36.19	0.009259
S	654	E654del1	gAa	g-a	1	1	B.1.36.29	0.000517
S	654	E654Q	Gaa	Caa	1	1	B.1.36.31	0.001751
S	654	E654D	gaA	gaC	1	1	B.1.36.37	0.002778
S	654	E654V	gAa	gTa	1	1	B.1.369	0.000285
S	654	E654K	Gaa	Aaa	1	1	B.1.369	0.000285
S	654	E654Q	Gaa	Caa	1	1	B.1.369	0.000285
S	654	E654A	gAa	gCa	1	1	B.1.396	0.000706
S	654	E654K	Gaa	Aaa	1	1	B.1.427	0.00005
S	654	E654Q	Gaa	Caa	1	1	B.1.459	0.004082
S	654	E654G	gAa	gGa	1	1	B.1.474	0.001901
S	654	E654V	gAa	gTa	1	1	B.1.499.1	0.111111
S	654	E654Q	Gaa	Caa	1	1	B.1.524	0.001406
S	654	E654V	gAa	gTa	1	1	B.1.525	0.000113
S	654	E654K	Gaa	Aaa	1	1	B.1.525	0.000113
S	654	E654Q	Gaa	Caa	1	1	B.1.561	0.000397
S	654	E654G	gAa	gGa	1	1	B.1.564.1	0.001577
S	654	E654K	Gaa	Aaa	1	1	B.1.565	0.00081
S	654	E654V	gAa	gTa	1	1	B.1.575.1	0.002439
S	654	E654Q	Gaa	Caa	1	1	B.1.576	0.000907
S	654	E654V	gAa	gTa	1	1	B.1.582	0.000491
S	654	E654K	Gaa	Aaa	1	1	B.1.596	0.000087
S	654	E654del	GAA	---	1	1	B.1.596	0.000087
S	654	E654del1	gAa	g-a	1	1	B.1.617.1	0.000129
S	654	E654A	gAa	gCa	1	1	B.1.617.1	0.000129
S	654	E654del1	gAa	g-a	1	1	B.1.617.2	0.000004
S	654	E654D	gaA	gaC	1	1	B.1.617.2	0.000004
S	654	E654S	GAA	TCT	1	1	B.1.617.2	0.000004
S	654	E654V	gAa	gTa	1	1	B.1.620	0.000946
S	654	E654del	GAA	---	1	1	B.1.620	0.000946
S	654	E654E	gaA	gaG	1	1	B.1.621	0.000089
S	654	E654del	GAA	---	1	1	B.1.627	0.00202
S	654	E654Q	Gaa	Caa	1	1	B.1.637	0.000073
S	654	E654K	Gaa	Aaa	1	1	B.1.637	0.000073
S	654	E654del	GAA	---	1	1	B.1.638	0.052632
S	654	E654V	gAa	gTa	1	1	C.16	0.00106
S	654	E654del	GAA	---	1	1	C.37	0.000116
S	654	E654X	Gaa	Taa	1	1	D.2	0.000075
S	654	E654D	gaA	gaC	1	1	D.2	0.000075
S	654	E654A	gAa	gCa	1	1	D.2	0.000075
S	654	E654Q	Gaa	Caa	1	1	K.1	0.02381
S	654	E654X	Gaa	Taa	1	1	P.1	0.000016
S	654	E654del	GAA	---	1	1	P.1.13	0.000898
S	654	E654E	gaA	gaG	1	1	P.1.4	0.000977
S	654	E654V	gAa	gTa	1	1	P.2	0.000187
S	654	E654Q	Gaa	Caa	1	1	P.2	0.000187

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.