CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 796

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	796	D796H		nonsyn	Gat	Cat	7882	7882	1	23948-23950
S	796	D796Y		nonsyn	Gat	Tat	4204	4199	0.998811	23948-23950
S	796	D796Y		nonsyn	GaT	TaC	4204	5	0.00118934	23948-23950
S	796	D796D		syn	gaT	gaC	446	446	1	23948-23950
S	796	D796G		nonsyn	gAt	gGt	319	318	0.996865	23948-23950
S	796	D796G		nonsyn	gAT	gGG	319	1	0.0031348	23948-23950
S	796	D796N		nonsyn	Gat	Aat	257	256	0.996109	23948-23950
S	796	D796N		nonsyn	GaT	AaC	257	1	0.00389105	23948-23950
S	796	D796del		del	GAT	---	90	90	1	23948-23950
S	796	D796E		nonsyn	gaT	gaG	33	18	0.545455	23948-23950
S	796	D796E		nonsyn	gaT	gaA	33	15	0.454545	23948-23950
S	796	D796V		nonsyn	gAt	gTt	14	14	1	23948-23950
S	796	D796del1		del	gaT	ga-	14	12	0.857143	23948-23950
S	796	D796del1		del	GAT	AG-	14	1	0.0714286	23948-23950
S	796	D796del1		del	Gat	-at	14	1	0.0714286	23948-23950
S	796	D796A		nonsyn	gAt	gCt	7	7	1	23948-23950
S	796	D796I		nonsyn	GAT	ATA	2	2	1	23948-23950
S	796	D796T		nonsyn	GAT	ACA	2	2	1	23948-23950
S	796	D796R		nonsyn	GAT	AGA	2	2	1	23948-23950
S	796	D796del2		del	gAT	g--	2	2	1	23948-23950

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	796	D796H	Gat	Cat	7882	7882	All	0.001508
S	796	D796Y	Gat	Tat	4199	4204	All	0.000803
S	796	D796Y	GaT	TaC	5	4204	All	0.000001
S	796	D796H	Gat	Cat	3190	3190	B.1.1.318	0.962583
S	796	D796H	Gat	Cat	1213	1213	AZ.2	0.995895
S	796	D796H	Gat	Cat	1151	1151	AZ.1	0.998265
S	796	D796H	Gat	Cat	637	637	AZ.3	0.968085
S	796	D796Y	Gat	Tat	585	585	A.27	0.968543
S	796	D796Y	Gat	Tat	578	578	AY.4	0.0009
S	796	D796Y	Gat	Tat	499	499	B.1.474	0.948669
S	796	D796Y	Gat	Tat	484	484	B.1.1.7	0.000433
S	796	D796D	gaT	gaC	446	446	All	0.000085
S	796	D796G	gAt	gGt	318	319	All	0.000061
S	796	D796G	gAT	gGG	1	319	All	0
S	796	D796H	Gat	Cat	290	290	AZ.4	0.973154
S	796	D796H	Gat	Cat	279	279	AZ.5	0.978947
S	796	D796N	Gat	Aat	256	257	All	0.000049
S	796	D796N	GaT	AaC	1	257	All	0
S	796	D796H	Gat	Cat	181	181	B.1.1	0.003284
S	796	D796Y	Gat	Tat	159	159	AY.43	0.000704
S	796	D796Y	Gat	Tat	140	140	AY.25	0.000842
S	796	D796G	gAt	gGt	129	129	AY.4.5	0.013866
S	796	D796H	Gat	Cat	123	123	AZ.2.1	1
S	796	D796H	Gat	Cat	118	118	AZ.6	0.991597
S	796	D796Y	Gat	Tat	111	111	C.38	0.895161
S	796	D796G	gAt	gGt	106	106	B.1.443	0.495327
S	796	D796D	gaT	gaC	105	105	AY.3	0.001044
S	796	D796Y	Gat	Tat	99	99	B.1.617.2	0.000373
S	796	D796N	Gat	Aat	98	98	B.1.429	0.002306
S	796	D796Y	Gat	Tat	97	97	B.1.596	0.008452
S	796	D796del	GAT	---	90	90	All	0.000017
S	796	D796Y	Gat	Tat	86	86	AY.3	0.000855
S	796	D796Y	Gat	Tat	84	84	B.1	0.000769
S	796	D796Y	Gat	Tat	81	81	AY.103	0.000503
S	796	D796D	gaT	gaC	81	81	AY.44	0.000493
S	796	D796Y	Gat	Tat	81	81	AY.7	0.015876
S	796	D796Y	Gat	Tat	71	71	AY.113	0.01011
S	796	D796Y	Gat	Tat	70	70	B.1.629	0.933333
S	796	D796H	Gat	Cat	65	65	B.1.1.7	0.000058
S	796	D796Y	Gat	Tat	60	64	AY.44	0.000365
S	796	D796Y	GaT	TaC	4	64	AY.44	0.000024
S	796	D796H	Gat	Cat	58	58	B.1.177	0.000764
S	796	D796H	Gat	Cat	52	52	AY.4	0.000081
S	796	D796D	gaT	gaC	51	51	B.1.617.2	0.000192
S	796	D796Y	Gat	Tat	49	49	B.1.337	0.273743
S	796	D796H	Gat	Cat	47	47	AY.4.5	0.005052
S	796	D796Y	Gat	Tat	45	45	B.1.604	0.775862
S	796	D796H	Gat	Cat	43	43	B.1.177.6	0.041992
S	796	D796Y	Gat	Tat	38	38	B.1.2	0.000335
S	796	D796Y	Gat	Tat	34	34	AY.120	0.001264
S	796	D796Y	Gat	Tat	34	34	AY.4.2	0.000737
S	796	D796E	gaT	gaG	18	33	All	0.000003
S	796	D796E	gaT	gaA	15	33	All	0.000003
S	796	D796Y	Gat	Tat	32	32	B.1.1.318	0.009656
S	796	D796N	Gat	Aat	31	31	AY.25	0.000186
S	796	D796H	Gat	Cat	31	31	B.1	0.000284
S	796	D796Y	Gat	Tat	29	29	B.1.1	0.000526
S	796	D796H	Gat	Cat	29	29	B.1.617.2	0.000109
S	796	D796Y	Gat	Tat	28	28	AY.4.5	0.00301
S	796	D796D	gaT	gaC	28	28	B.1.1.7	0.000025
S	796	D796H	Gat	Cat	27	27	AY.25	0.000162
S	796	D796N	Gat	Aat	27	27	AY.4	0.000042
S	796	D796H	Gat	Cat	24	24	AY.116.1	0.007474
S	796	D796N	Gat	Aat	23	24	B.1.1.7	0.000021
S	796	D796N	GaT	AaC	1	24	B.1.1.7	0.000001
S	796	D796D	gaT	gaC	23	23	AY.4	0.000036
S	796	D796D	gaT	gaC	23	23	B.1.1.519	0.000913
S	796	D796H	Gat	Cat	23	23	B.1.525	0.002603
S	796	D796D	gaT	gaC	20	20	AY.61	0.002096
S	796	D796H	Gat	Cat	20	20	C.35	0.01548
S	796	D796Y	Gat	Tat	19	19	B.1.221	0.00135
S	796	D796Y	Gat	Tat	19	19	B.1.351	0.000565
S	796	D796Y	Gat	Tat	19	19	B.1.526	0.000447
S	796	D796H	Gat	Cat	18	18	AY.44	0.00011
S	796	D796Y	Gat	Tat	18	18	P.1.1	0.005718
S	796	D796Y	Gat	Tat	18	18	P.2	0.003359
S	796	D796Y	Gat	Tat	17	17	A	0.006579
S	796	D796H	Gat	Cat	17	17	B.1.633	0.708333
S	796	D796H	Gat	Cat	16	16	AY.120	0.000595
S	796	D796Y	Gat	Tat	16	16	AY.98.1	0.000775
S	796	D796Y	Gat	Tat	16	16	B.1.177	0.000211
S	796	D796E	gaT	gaG	12	15	B.1.1.7	0.000011
S	796	D796E	gaT	gaA	3	15	B.1.1.7	0.000003
S	796	D796Y	Gat	Tat	15	15	B.1.160	0.000468
S	796	D796V	gAt	gTt	14	14	All	0.000003
S	796	D796del1	gaT	ga-	12	14	All	0.000002
S	796	D796del1	Gat	-at	1	14	All	0
S	796	D796del1	GAT	AG-	1	14	All	0
S	796	D796N	Gat	Aat	13	13	AY.4.5	0.001397
S	796	D796H	Gat	Cat	13	13	AY.45	0.001582
S	796	D796Y	Gat	Tat	13	13	AY.74	0.001503
S	796	D796D	gaT	gaC	13	13	B.1.177.81	0.002461
S	796	D796H	Gat	Cat	13	13	B.1.429	0.000306
S	796	D796G	gAt	gGt	12	12	AY.4	0.000019
S	796	D796Y	Gat	Tat	12	12	AY.47	0.000373
S	796	D796Y	Gat	Tat	12	12	AY.61	0.001257
S	796	D796Y	Gat	Tat	12	12	P.1	0.000189
S	796	D796Y	Gat	Tat	11	11	AY.20	0.000428
S	796	D796del	GAT	---	11	11	B.1.1.7	0.00001
S	796	D796H	Gat	Cat	11	11	B.1.2	0.000097
S	796	D796H	Gat	Cat	11	11	B.1.526	0.000259
S	796	D796Y	Gat	Tat	10	10	AY.33	0.000668
S	796	D796Y	Gat	Tat	10	10	AY.36	0.001482
S	796	D796Y	Gat	Tat	10	10	B.1.258	0.000665
S	796	D796Y	Gat	Tat	10	10	B.1.369	0.002852
S	796	D796del	GAT	---	10	10	B.1.621	0.000885
S	796	D796D	gaT	gaC	9	9	AY.5.3	0.003036
S	796	D796Y	Gat	Tat	9	9	B	0.00115
S	796	D796G	gAt	gGt	9	9	B.1.1.7	0.000008
S	796	D796H	Gat	Cat	9	9	B.1.351	0.000268
S	796	D796Y	Gat	Tat	8	8	AY.39	0.000198
S	796	D796H	Gat	Cat	8	8	AY.9.2	0.000294
S	796	D796D	gaT	gaC	8	8	B.1.1.63	0.003086
S	796	D796H	Gat	Cat	8	8	B.1.452	0.109589
S	796	D796A	gAt	gCt	7	7	All	0.000001
S	796	D796Y	Gat	Tat	7	7	AY.100	0.000322
S	796	D796Y	Gat	Tat	7	7	AY.119	0.000247
S	796	D796D	gaT	gaC	7	7	AY.25	0.000042
S	796	D796H	Gat	Cat	7	7	AY.29	0.00011
S	796	D796H	Gat	Cat	7	7	AY.39	0.000173
S	796	D796N	Gat	Aat	7	7	B.1.2	0.000062
S	796	D796G	gAt	gGt	7	7	B.1.499	0.007353
S	796	D796G	gAt	gGt	7	7	B.1.596	0.00061
S	796	D796D	gaT	gaC	7	7	B.1.637	0.000512
S	796	D796H	Gat	Cat	7	7	B.1.9.5	0.039773
S	796	D796Y	Gat	Tat	6	6	AY.101	0.002943
S	796	D796Y	Gat	Tat	6	6	AY.102	0.000159
S	796	D796Y	Gat	Tat	6	6	AY.23	0.000418
S	796	D796Y	Gat	Tat	6	6	AY.27	0.000388
S	796	D796H	Gat	Cat	6	6	AY.3	0.00006
S	796	D796G	gAt	gGt	6	6	AY.3	0.00006
S	796	D796Y	Gat	Tat	6	6	AY.42	0.000241
S	796	D796H	Gat	Cat	6	6	AY.43	0.000027
S	796	D796Y	Gat	Tat	6	6	AY.46	0.000624
S	796	D796Y	Gat	Tat	6	6	AY.5	0.000124
S	796	D796Y	Gat	Tat	6	6	AY.75	0.000336
S	796	D796H	Gat	Cat	6	6	B.1.1.1	0.00196
S	796	D796Y	Gat	Tat	5	6	B.1.1.1	0.001633
S	796	D796Y	GaT	TaC	1	6	B.1.1.1	0.000327
S	796	D796N	Gat	Aat	6	6	B.1.617.2	0.000023
S	796	D796del	GAT	---	6	6	P.1.15	0.001394
S	796	D796G	gAt	gGt	5	5	AY.102	0.000133
S	796	D796G	gAt	gGt	5	5	AY.25	0.00003
S	796	D796Y	Gat	Tat	5	5	AY.29	0.000079
S	796	D796N	Gat	Aat	5	5	AY.43	0.000022
S	796	D796del	GAT	---	5	5	AY.43	0.000022
S	796	D796D	gaT	gaC	5	5	AY.43	0.000022
S	796	D796Y	Gat	Tat	5	5	AY.6	0.000206
S	796	D796Y	Gat	Tat	5	5	AY.9	0.000338
S	796	D796Y	Gat	Tat	5	5	AY.9.2	0.000184
S	796	D796G	gAt	gGt	5	5	B.1	0.000046
S	796	D796D	gaT	gaC	5	5	B.1	0.000046
S	796	D796del	GAT	---	5	5	B.1	0.000046
S	796	D796Y	Gat	Tat	5	5	B.1.1.396	0.227273
S	796	D796Y	Gat	Tat	5	5	B.1.1.519	0.000199
S	796	D796Y	Gat	Tat	5	5	B.1.243	0.000348
S	796	D796Y	Gat	Tat	5	5	B.1.401	0.040984
S	796	D796Y	Gat	Tat	5	5	B.1.404	0.00651
S	796	D796Y	Gat	Tat	5	5	B.1.405	0.061728
S	796	D796H	Gat	Cat	5	5	B.1.619	0.004355
S	796	D796del	GAT	---	5	5	P.1	0.000079
S	796	D796H	Gat	Cat	4	4	AT.1	0.020513
S	796	D796Y	Gat	Tat	4	4	AY.111	0.000733
S	796	D796Y	Gat	Tat	4	4	AY.121	0.000541
S	796	D796Y	Gat	Tat	4	4	AY.39.1	0.000158
S	796	D796V	gAt	gTt	4	4	AY.4	0.000006
S	796	D796G	gAt	gGt	4	4	AY.4.2	0.000087
S	796	D796Y	Gat	Tat	4	4	AY.45	0.000487
S	796	D796H	Gat	Cat	4	4	AY.5	0.000083
S	796	D796G	gAt	gGt	4	4	AY.75	0.000224
S	796	D796D	gaT	gaC	4	4	AY.75	0.000224
S	796	D796Y	Gat	Tat	4	4	AY.8	0.002424
S	796	D796Y	Gat	Tat	4	4	AY.9.1	0.000335
S	796	D796Y	Gat	Tat	4	4	B.1.1.220	0.007435
S	796	D796V	gAt	gTt	4	4	B.1.1.7	0.000004
S	796	D796N	Gat	Aat	4	4	B.1.110.3	0.002874
S	796	D796N	Gat	Aat	4	4	B.1.258.14	0.003922
S	796	D796N	Gat	Aat	4	4	B.1.369	0.001141
S	796	D796Y	Gat	Tat	4	4	B.1.525	0.000453
S	796	D796Y	Gat	Tat	4	4	B.1.588	0.00364
S	796	D796H	Gat	Cat	4	4	B.1.617.1	0.000516
S	796	D796Y	Gat	Tat	3	3	A.29	0.015957
S	796	D796H	Gat	Cat	3	3	AY.1	0.001187
S	796	D796D	gaT	gaC	3	3	AY.103	0.000019
S	796	D796Y	Gat	Tat	3	3	AY.114	0.000693
S	796	D796H	Gat	Cat	3	3	AY.118	0.000188
S	796	D796H	Gat	Cat	3	3	AY.20	0.000117
S	796	D796del	GAT	---	3	3	AY.25	0.000018
S	796	D796H	Gat	Cat	3	3	AY.26	0.000085
S	796	D796Y	Gat	Tat	3	3	AY.26	0.000085
S	796	D796Y	Gat	Tat	3	3	AY.3.1	0.000256
S	796	D796H	Gat	Cat	3	3	AY.33	0.0002
S	796	D796G	gAt	gGt	3	3	AY.43	0.000013
S	796	D796H	Gat	Cat	3	3	AY.47	0.000093
S	796	D796D	gaT	gaC	3	3	AY.5	0.000062
S	796	D796Y	Gat	Tat	3	3	AY.54	0.000286
S	796	D796Y	Gat	Tat	3	3	AY.67	0.001393
S	796	D796N	Gat	Aat	3	3	AY.9	0.000203
S	796	D796Y	Gat	Tat	3	3	AZ.5	0.010526
S	796	D796Y	Gat	Tat	3	3	B.1.1.161	0.010601
S	796	D796Y	Gat	Tat	3	3	B.1.1.311	0.001074
S	796	D796Y	Gat	Tat	3	3	B.1.1.523	0.004687
S	796	D796H	Gat	Cat	3	3	B.1.1.8	0.010753
S	796	D796G	gAt	gGt	3	3	B.1.160	0.000094
S	796	D796N	Gat	Aat	3	3	B.1.160	0.000094
S	796	D796H	Gat	Cat	3	3	B.1.160	0.000094
S	796	D796D	gaT	gaC	3	3	B.1.2	0.000026
S	796	D796H	Gat	Cat	3	3	B.1.403	0.009804
S	796	D796Y	Gat	Tat	3	3	B.1.416	0.003807
S	796	D796N	Gat	Aat	3	3	B.1.427	0.000151
S	796	D796Y	Gat	Tat	3	3	B.1.429	0.000071
S	796	D796H	Gat	Cat	3	3	B.1.576	0.00272
S	796	D796Y	Gat	Tat	3	3	B.1.576	0.00272
S	796	D796Y	Gat	Tat	3	3	B.1.609	0.001438
S	796	D796del	GAT	---	3	3	B.1.617.2	0.000011
S	796	D796G	gAt	gGt	3	3	B.1.617.2	0.000011
S	796	D796D	gaT	gaC	3	3	C.37	0.000348
S	796	D796E	gaT	gaA	3	3	P.1	0.000047
S	796	D796H	Gat	Cat	3	3	P.1	0.000047
S	796	D796Y	Gat	Tat	3	3	R.1	0.00027
S	796	D796T	GAT	ACA	2	2		0.111111
S	796	D796I	GAT	ATA	2	2		0.111111
S	796	D796R	GAT	AGA	2	2		0.111111
S	796	D796Y	Gat	Tat	2	2	A.2	0.001324
S	796	D796Y	Gat	Tat	2	2	AD.2	0.000438
S	796	D796del2	gAT	g--	2	2	All	0
S	796	D796T	GAT	ACA	2	2	All	0
S	796	D796R	GAT	AGA	2	2	All	0
S	796	D796I	GAT	ATA	2	2	All	0
S	796	D796Y	Gat	Tat	2	2	AU.2	0.004843
S	796	D796D	gaT	gaC	2	2	AY.100	0.000092
S	796	D796H	Gat	Cat	2	2	AY.102	0.000053
S	796	D796H	Gat	Cat	2	2	AY.103	0.000012
S	796	D796Y	Gat	Tat	2	2	AY.106	0.00067
S	796	D796D	gaT	gaC	2	2	AY.117	0.000169
S	796	D796Y	Gat	Tat	2	2	AY.118	0.000125
S	796	D796H	Gat	Cat	2	2	AY.121	0.000271
S	796	D796Y	Gat	Tat	2	2	AY.14	0.000176
S	796	D796H	Gat	Cat	2	2	AY.14	0.000176
S	796	D796D	gaT	gaC	2	2	AY.20	0.000078
S	796	D796N	Gat	Aat	2	2	AY.23	0.000139
S	796	D796del	GAT	---	2	2	AY.3	0.00002
S	796	D796Y	Gat	Tat	2	2	AY.34	0.000194
S	796	D796del	GAT	---	2	2	AY.34.1	0.00102
S	796	D796N	Gat	Aat	2	2	AY.39	0.000049
S	796	D796H	Gat	Cat	2	2	AY.4.2	0.000043
S	796	D796N	Gat	Aat	2	2	AY.4.2	0.000043
S	796	D796H	Gat	Cat	2	2	AY.42	0.00008
S	796	D796Y	Gat	Tat	2	2	AY.46.2	0.001271
S	796	D796Y	Gat	Tat	2	2	AY.46.4	0.000329
S	796	D796Y	Gat	Tat	2	2	AY.5.4	0.000553
S	796	D796H	Gat	Cat	2	2	AY.51	0.001818
S	796	D796Y	Gat	Tat	2	2	AY.53	0.000575
S	796	D796Y	Gat	Tat	2	2	AY.59	0.001059
S	796	D796H	Gat	Cat	2	2	AY.64	0.00119
S	796	D796del	GAT	---	2	2	AY.75	0.000112
S	796	D796N	Gat	Aat	2	2	AY.8	0.001212
S	796	D796Y	Gat	Tat	2	2	AY.84	0.000875
S	796	D796Y	Gat	Tat	2	2	AY.97	0.003401
S	796	D796Y	Gat	Tat	2	2	AY.99.1	0.003106
S	796	D796del1	gaT	ga-	2	2	B.1	0.000018
S	796	D796del	GAT	---	2	2	B.1.1	0.000036
S	796	D796D	gaT	gaC	2	2	B.1.1	0.000036
S	796	D796Y	Gat	Tat	2	2	B.1.1.273	0.013514
S	796	D796Y	Gat	Tat	2	2	B.1.1.28	0.000622
S	796	D796Y	Gat	Tat	2	2	B.1.1.317	0.000823
S	796	D796Y	Gat	Tat	2	2	B.1.1.346	0.058824
S	796	D796Y	Gat	Tat	2	2	B.1.1.4	0.005952
S	796	D796D	gaT	gaC	2	2	B.1.1.420	0.002012
S	796	D796D	gaT	gaC	2	2	B.1.1.517	0.013605
S	796	D796del2	gAT	g--	2	2	B.1.1.7	0.000002
S	796	D796del1	GAT	AG-	1	2	B.1.1.7	0.000001
S	796	D796del1	gaT	ga-	1	2	B.1.1.7	0.000001
S	796	D796D	gaT	gaC	2	2	B.1.177	0.000026
S	796	D796Y	Gat	Tat	2	2	B.1.177.4	0.000422
S	796	D796Y	Gat	Tat	2	2	B.1.177.81	0.000379
S	796	D796Y	Gat	Tat	2	2	B.1.234	0.000264
S	796	D796H	Gat	Cat	2	2	B.1.258.17	0.000208
S	796	D796Y	Gat	Tat	2	2	B.1.258.7	0.003824
S	796	D796Y	Gat	Tat	2	2	B.1.351.3	0.001753
S	796	D796H	Gat	Cat	2	2	B.1.36	0.000292
S	796	D796Y	Gat	Tat	2	2	B.1.36	0.000292
S	796	D796H	Gat	Cat	2	2	B.1.36.17	0.000988
S	796	D796Y	Gat	Tat	2	2	B.1.36.22	0.002415
S	796	D796H	Gat	Cat	2	2	B.1.36.24	0.012346
S	796	D796Y	Gat	Tat	2	2	B.1.36.31	0.003503
S	796	D796Y	Gat	Tat	2	2	B.1.389	0.002004
S	796	D796Y	Gat	Tat	2	2	B.1.396	0.001411
S	796	D796D	gaT	gaC	2	2	B.1.429	0.000047
S	796	D796H	Gat	Cat	2	2	B.1.438.1	0.000215
S	796	D796Y	Gat	Tat	2	2	B.1.507	0.022472
S	796	D796Y	Gat	Tat	2	2	B.1.527	0.007407
S	796	D796Y	Gat	Tat	2	2	B.1.595	0.000522
S	796	D796H	Gat	Cat	2	2	B.1.595	0.000522
S	796	D796H	Gat	Cat	2	2	B.1.596	0.000174
S	796	D796del1	gaT	ga-	2	2	B.1.617.1	0.000258
S	796	D796Y	Gat	Tat	2	2	B.1.625	0.004706
S	796	D796D	gaT	gaC	2	2	B.1.628	0.000705
S	796	D796Y	Gat	Tat	2	2	C.36	0.001821
S	796	D796Y	Gat	Tat	2	2	C.36.3.1	0.005435
S	796	D796H	Gat	Cat	2	2	C.37	0.000232
S	796	D796Y	Gat	Tat	2	2	D.2	0.00015
S	796	D796Y	Gat	Tat	2	2	N.5	0.003534
S	796	D796D	gaT	gaC	2	2	P.1	0.000032
S	796	D796H	Gat	Cat	2	2	P.1.12	0.000968
S	796	D796H	Gat	Cat	2	2	P.1.14	0.000096
S	796	D796Y	Gat	Tat	2	2	P.1.15	0.000465
S	796	D796del	GAT	---	2	2	P.1.7	0.000639
S	796	D796Y	Gat	Tat	2	2	Q.1	0.000253
S	796	D796D	gaT	gaC	1	1		0.055556
S	796	D796del	GAT	---	1	1	A	0.000387
S	796	D796A	gAt	gCt	1	1	A	0.000387
S	796	D796Y	Gat	Tat	1	1	A.1	0.000282
S	796	D796Y	Gat	Tat	1	1	A.18	0.05
S	796	D796D	gaT	gaC	1	1	A.2.4	0.003367
S	796	D796D	gaT	gaC	1	1	A.2.5	0.000499
S	796	D796del	GAT	---	1	1	AY.10	0.00053
S	796	D796E	gaT	gaA	1	1	AY.102	0.000027
S	796	D796D	gaT	gaC	1	1	AY.102	0.000027
S	796	D796N	Gat	Aat	1	1	AY.102	0.000027
S	796	D796del	GAT	---	1	1	AY.103	0.000006
S	796	D796H	Gat	Cat	1	1	AY.108	0.001103
S	796	D796D	gaT	gaC	1	1	AY.109	0.00074
S	796	D796H	Gat	Cat	1	1	AY.117	0.000085
S	796	D796Y	Gat	Tat	1	1	AY.117	0.000085
S	796	D796del	GAT	---	1	1	AY.120	0.000037
S	796	D796Y	Gat	Tat	1	1	AY.120.1	0.000321
S	796	D796H	Gat	Cat	1	1	AY.120.2	0.001285
S	796	D796H	Gat	Cat	1	1	AY.120.2.1	0.000498
S	796	D796D	gaT	gaC	1	1	AY.121	0.000135
S	796	D796H	Gat	Cat	1	1	AY.16.1	0.00047
S	796	D796H	Gat	Cat	1	1	AY.23	0.00007
S	796	D796Y	Gat	Tat	1	1	AY.23.1	0.000417
S	796	D796del	GAT	---	1	1	AY.24	0.000431
S	796	D796D	gaT	gaC	1	1	AY.26	0.000028
S	796	D796del	GAT	---	1	1	AY.29	0.000016
S	796	D796E	gaT	gaA	1	1	AY.3	0.00001
S	796	D796V	gAt	gTt	1	1	AY.3	0.00001
S	796	D796D	gaT	gaC	1	1	AY.32	0.000532
S	796	D796Y	Gat	Tat	1	1	AY.32	0.000532
S	796	D796G	gAT	gGG	1	1	AY.33	0.000067
S	796	D796A	gAt	gCt	1	1	AY.33	0.000067
S	796	D796E	gaT	gaA	1	1	AY.34	0.000097
S	796	D796G	gAt	gGt	1	1	AY.35	0.000233
S	796	D796Y	Gat	Tat	1	1	AY.38	0.000499
S	796	D796G	gAt	gGt	1	1	AY.39	0.000025
S	796	D796Y	Gat	Tat	1	1	AY.39.2	0.001541
S	796	D796E	gaT	gaG	1	1	AY.4	0.000002
S	796	D796Y	Gat	Tat	1	1	AY.41	0.000294
S	796	D796N	Gat	Aat	1	1	AY.42	0.00004
S	796	D796V	gAt	gTt	1	1	AY.43	0.000004
S	796	D796del	GAT	---	1	1	AY.44	0.000006
S	796	D796E	gaT	gaA	1	1	AY.44	0.000006
S	796	D796N	Gat	Aat	1	1	AY.47	0.000031
S	796	D796A	gAt	gCt	1	1	AY.5	0.000021
S	796	D796Y	Gat	Tat	1	1	AY.52	0.000814
S	796	D796N	Gat	Aat	1	1	AY.58	0.000907
S	796	D796Y	Gat	Tat	1	1	AY.58	0.000907
S	796	D796H	Gat	Cat	1	1	AY.59	0.00053
S	796	D796Y	Gat	Tat	1	1	AY.60	0.000938
S	796	D796Y	Gat	Tat	1	1	AY.63	0.000387
S	796	D796H	Gat	Cat	1	1	AY.63	0.000387
S	796	D796N	Gat	Aat	1	1	AY.67	0.000464
S	796	D796Y	Gat	Tat	1	1	AY.68	0.000274
S	796	D796del	GAT	---	1	1	AY.68	0.000274
S	796	D796Y	Gat	Tat	1	1	AY.69	0.000187
S	796	D796H	Gat	Cat	1	1	AY.69	0.000187
S	796	D796Y	Gat	Tat	1	1	AY.70	0.000209
S	796	D796H	Gat	Cat	1	1	AY.75	0.000056
S	796	D796E	gaT	gaG	1	1	AY.75	0.000056
S	796	D796Y	Gat	Tat	1	1	AY.75.1	0.00018
S	796	D796D	gaT	gaC	1	1	AY.84	0.000437
S	796	D796H	Gat	Cat	1	1	AY.85	0.000427
S	796	D796H	Gat	Cat	1	1	AY.86	0.00083
S	796	D796Y	Gat	Tat	1	1	AY.87	0.000833
S	796	D796N	Gat	Aat	1	1	AY.87	0.000833
S	796	D796D	gaT	gaC	1	1	AY.88	0.000884
S	796	D796del1	gaT	ga-	1	1	AY.9.2	0.000037
S	796	D796D	gaT	gaC	1	1	AY.9.2	0.000037
S	796	D796Y	Gat	Tat	1	1	AY.94	0.000443
S	796	D796D	gaT	gaC	1	1	AY.95	0.000761
S	796	D796Y	Gat	Tat	1	1	AY.98	0.000079
S	796	D796D	gaT	gaC	1	1	AY.98.1	0.000048
S	796	D796D	gaT	gaC	1	1	AY.99.2	0.000092
S	796	D796N	Gat	Aat	1	1	B.1	0.000009
S	796	D796E	gaT	gaA	1	1	B.1.1	0.000018
S	796	D796A	gAt	gCt	1	1	B.1.1	0.000018
S	796	D796del1	gaT	ga-	1	1	B.1.1	0.000018
S	796	D796N	Gat	Aat	1	1	B.1.1	0.000018
S	796	D796D	gaT	gaC	1	1	B.1.1.1	0.000327
S	796	D796del	GAT	---	1	1	B.1.1.139	0.022727
S	796	D796Y	Gat	Tat	1	1	B.1.1.174	0.003378
S	796	D796H	Gat	Cat	1	1	B.1.1.192	0.002309
S	796	D796D	gaT	gaC	1	1	B.1.1.214	0.000055
S	796	D796Y	Gat	Tat	1	1	B.1.1.216	0.00089
S	796	D796E	gaT	gaG	1	1	B.1.1.216	0.00089
S	796	D796N	Gat	Aat	1	1	B.1.1.222	0.000204
S	796	D796V	gAt	gTt	1	1	B.1.1.222	0.000204
S	796	D796Y	Gat	Tat	1	1	B.1.1.222	0.000204
S	796	D796Y	Gat	Tat	1	1	B.1.1.231	0.003096
S	796	D796del	GAT	---	1	1	B.1.1.236	0.006897
S	796	D796Y	Gat	Tat	1	1	B.1.1.241	0.00207
S	796	D796G	gAt	gGt	1	1	B.1.1.25	0.000569
S	796	D796Y	Gat	Tat	1	1	B.1.1.251	0.007937
S	796	D796E	gaT	gaG	1	1	B.1.1.277	0.000759
S	796	D796H	Gat	Cat	1	1	B.1.1.28	0.000311
S	796	D796del	GAT	---	1	1	B.1.1.291	0.000742
S	796	D796Y	Gat	Tat	1	1	B.1.1.306	0.000438
S	796	D796del	GAT	---	1	1	B.1.1.315	0.008475
S	796	D796D	gaT	gaC	1	1	B.1.1.322	0.008772
S	796	D796Y	Gat	Tat	1	1	B.1.1.348	0.000796
S	796	D796Y	Gat	Tat	1	1	B.1.1.37	0.000193
S	796	D796del	GAT	---	1	1	B.1.1.372	0.000689
S	796	D796Y	Gat	Tat	1	1	B.1.1.377	0.001381
S	796	D796Y	Gat	Tat	1	1	B.1.1.39	0.00051
S	796	D796del	GAT	---	1	1	B.1.1.409	0.002833
S	796	D796Y	Gat	Tat	1	1	B.1.1.409	0.002833
S	796	D796Y	Gat	Tat	1	1	B.1.1.432	0.001266
S	796	D796Y	Gat	Tat	1	1	B.1.1.44	0.00241
S	796	D796D	gaT	gaC	1	1	B.1.1.50	0.000679
S	796	D796H	Gat	Cat	1	1	B.1.1.50	0.000679
S	796	D796del	GAT	---	1	1	B.1.1.519	0.00004
S	796	D796E	gaT	gaA	1	1	B.1.1.519	0.00004
S	796	D796Y	Gat	Tat	1	1	B.1.1.521	0.005348
S	796	D796H	Gat	Cat	1	1	B.1.1.523	0.001563
S	796	D796Y	Gat	Tat	1	1	B.1.110.3	0.000718
S	796	D796del	GAT	---	1	1	B.1.140	0.018868
S	796	D796del	GAT	---	1	1	B.1.160	0.000031
S	796	D796Y	Gat	Tat	1	1	B.1.160.33	0.004425
S	796	D796Y	Gat	Tat	1	1	B.1.166	0.008475
S	796	D796H	Gat	Cat	1	1	B.1.170	0.00431
S	796	D796Y	Gat	Tat	1	1	B.1.170	0.00431
S	796	D796G	gAt	gGt	1	1	B.1.177	0.000013
S	796	D796N	Gat	Aat	1	1	B.1.177	0.000013
S	796	D796del1	gaT	ga-	1	1	B.1.177	0.000013
S	796	D796A	gAt	gCt	1	1	B.1.177	0.000013
S	796	D796Y	Gat	Tat	1	1	B.1.177.16	0.000664
S	796	D796H	Gat	Cat	1	1	B.1.177.16	0.000664
S	796	D796Y	Gat	Tat	1	1	B.1.177.21	0.000076
S	796	D796A	gAt	gCt	1	1	B.1.177.33	0.001645
S	796	D796H	Gat	Cat	1	1	B.1.177.4	0.000211
S	796	D796E	gaT	gaG	1	1	B.1.177.43	0.001477
S	796	D796E	gaT	gaA	1	1	B.1.177.44	0.000519
S	796	D796D	gaT	gaC	1	1	B.1.177.60	0.000218
S	796	D796H	Gat	Cat	1	1	B.1.177.73	0.000566
S	796	D796V	gAt	gTt	1	1	B.1.177.81	0.000189
S	796	D796H	Gat	Cat	1	1	B.1.177.86	0.000183
S	796	D796Y	Gat	Tat	1	1	B.1.177.87	0.000728
S	796	D796del	GAT	---	1	1	B.1.2	0.000009
S	796	D796E	gaT	gaG	1	1	B.1.2	0.000009
S	796	D796del1	gaT	ga-	1	1	B.1.2	0.000009
S	796	D796G	gAt	gGt	1	1	B.1.2	0.000009
S	796	D796Y	Gat	Tat	1	1	B.1.220	0.01087
S	796	D796N	Gat	Aat	1	1	B.1.221	0.000071
S	796	D796Y	Gat	Tat	1	1	B.1.222	0.001692
S	796	D796G	gAt	gGt	1	1	B.1.234	0.000132
S	796	D796N	Gat	Aat	1	1	B.1.236	0.002053
S	796	D796G	gAt	gGt	1	1	B.1.240	0.000216
S	796	D796H	Gat	Cat	1	1	B.1.243	0.00007
S	796	D796H	Gat	Cat	1	1	B.1.258	0.000067
S	796	D796del	GAT	---	1	1	B.1.258	0.000067
S	796	D796del	GAT	---	1	1	B.1.258.17	0.000104
S	796	D796Y	Gat	Tat	1	1	B.1.258.17	0.000104
S	796	D796H	Gat	Cat	1	1	B.1.267	0.018519
S	796	D796Y	Gat	Tat	1	1	B.1.293	0.0125
S	796	D796H	Gat	Cat	1	1	B.1.298	0.002114
S	796	D796Y	Gat	Tat	1	1	B.1.320	0.001245
S	796	D796Y	Gat	Tat	1	1	B.1.349	0.000715
S	796	D796del	GAT	---	1	1	B.1.351	0.00003
S	796	D796G	gAt	gGt	1	1	B.1.351	0.00003
S	796	D796H	Gat	Cat	1	1	B.1.351.2	0.000303
S	796	D796Y	Gat	Tat	1	1	B.1.351.2	0.000303
S	796	D796del1	gaT	ga-	1	1	B.1.36	0.000146
S	796	D796Y	Gat	Tat	1	1	B.1.36.16	0.001425
S	796	D796Y	Gat	Tat	1	1	B.1.36.17	0.000494
S	796	D796del	GAT	---	1	1	B.1.36.18	0.00042
S	796	D796Y	Gat	Tat	1	1	B.1.36.26	0.002857
S	796	D796Y	Gat	Tat	1	1	B.1.36.8	0.001
S	796	D796Y	Gat	Tat	1	1	B.1.399	0.001934
S	796	D796Y	Gat	Tat	1	1	B.1.427	0.00005
S	796	D796Y	Gat	Tat	1	1	B.1.436	0.001029
S	796	D796del	GAT	---	1	1	B.1.443	0.004673
S	796	D796Y	Gat	Tat	1	1	B.1.516	0.001957
S	796	D796D	gaT	gaC	1	1	B.1.523	0.002451
S	796	D796V	gAt	gTt	1	1	B.1.525	0.000113
S	796	D796del	GAT	---	1	1	B.1.526	0.000024
S	796	D796E	gaT	gaA	1	1	B.1.526	0.000024
S	796	D796H	Gat	Cat	1	1	B.1.540	0.009709
S	796	D796del	GAT	---	1	1	B.1.561	0.000397
S	796	D796H	Gat	Cat	1	1	B.1.575	0.000303
S	796	D796Y	Gat	Tat	1	1	B.1.577	0.000687
S	796	D796del1	gaT	ga-	1	1	B.1.581	0.009434
S	796	D796H	Gat	Cat	1	1	B.1.588	0.00091
S	796	D796D	gaT	gaC	1	1	B.1.595	0.000261
S	796	D796del	GAT	---	1	1	B.1.595	0.000261
S	796	D796Y	Gat	Tat	1	1	B.1.617.1	0.000129
S	796	D796N	Gat	Aat	1	1	B.1.617.1	0.000129
S	796	D796A	gAt	gCt	1	1	B.1.617.2	0.000004
S	796	D796del1	gaT	ga-	1	1	B.1.617.2	0.000004
S	796	D796Y	Gat	Tat	1	1	B.1.619	0.000871
S	796	D796del	GAT	---	1	1	B.1.620	0.000946
S	796	D796V	gAt	gTt	1	1	B.1.621	0.000089
S	796	D796Y	Gat	Tat	1	1	B.1.621	0.000089
S	796	D796H	Gat	Cat	1	1	B.1.623	0.000536
S	796	D796G	gAt	gGt	1	1	B.1.628	0.000352
S	796	D796del	GAT	---	1	1	B.1.638	0.052632
S	796	D796N	Gat	Aat	1	1	B.1.9	0.006173
S	796	D796Y	Gat	Tat	1	1	B.1.96	0.018868
S	796	D796Y	Gat	Tat	1	1	B.55	0.00295
S	796	D796Y	Gat	Tat	1	1	B.61	0.005747
S	796	D796Y	Gat	Tat	1	1	C.1	0.002392
S	796	D796D	gaT	gaC	1	1	C.30.1	0.006711
S	796	D796Y	Gat	Tat	1	1	C.32	0.023256
S	796	D796G	gAt	gGt	1	1	C.37	0.000116
S	796	D796del	GAT	---	1	1	C.37	0.000116
S	796	D796E	gaT	gaA	1	1	D.2	0.000075
S	796	D796del1	Gat	-at	1	1	K.3	0.006173
S	796	D796Y	Gat	Tat	1	1	N.9	0.005952
S	796	D796Y	Gat	Tat	1	1	P.1.12	0.000484
S	796	D796del	GAT	---	1	1	P.1.13	0.000898
S	796	D796N	Gat	Aat	1	1	P.1.14	0.000048
S	796	D796Y	Gat	Tat	1	1	P.1.14	0.000048
S	796	D796D	gaT	gaC	1	1	P.1.17	0.000162
S	796	D796Y	Gat	Tat	1	1	P.1.17	0.000162
S	796	D796H	Gat	Cat	1	1	P.1.17	0.000162
S	796	D796Y	Gat	Tat	1	1	P.1.7	0.000319
S	796	D796D	gaT	gaC	1	1	P.2	0.000187
S	796	D796N	Gat	Aat	1	1	P.2	0.000187
S	796	D796Y	Gat	Tat	1	1	P.6	0.003145
S	796	D796N	Gat	Aat	1	1	Q.1	0.000126
S	796	D796Y	Gat	Tat	1	1	Q.2	0.000613
S	796	D796del	GAT	---	1	1	Q.2	0.000613
S	796	D796H	Gat	Cat	1	1	Q.8	0.000165
S	796	D796del	GAT	---	1	1	Q.8	0.000165
S	796	D796D	gaT	gaC	1	1	R.1	0.00009

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.