CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1120

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
ORF1ab/nsp3	1120	A1120S	A1938S	nonsyn	Gct	Tct	1066	1063	0.997186	6077-6079
ORF1ab/nsp3	1120	A1120S	A1938S	nonsyn	GCT	AGC	1066	2	0.00187617	6077-6079
ORF1ab/nsp3	1120	A1120S	A1938S	nonsyn	GcT	TcA	1066	1	0.000938086	6077-6079
ORF1ab/nsp3	1120	A1120V	A1938V	nonsyn	gCt	gTt	421	421	1	6077-6079
ORF1ab/nsp3	1120	A1120A	A1938A	syn	gcT	gcC	371	282	0.760108	6077-6079
ORF1ab/nsp3	1120	A1120A	A1938A	syn	gcT	gcG	371	46	0.123989	6077-6079
ORF1ab/nsp3	1120	A1120A	A1938A	syn	gcT	gcA	371	43	0.115903	6077-6079
ORF1ab/nsp3	1120	A1120del	A1938del	del	GCT	---	75	75	1	6077-6079
ORF1ab/nsp3	1120	A1120T	A1938T	nonsyn	Gct	Act	41	37	0.902439	6077-6079
ORF1ab/nsp3	1120	A1120T	A1938T	nonsyn	GcT	AcG	41	2	0.0487805	6077-6079
ORF1ab/nsp3	1120	A1120T	A1938T	nonsyn	GcT	AcC	41	2	0.0487805	6077-6079
ORF1ab/nsp3	1120	A1120G	A1938G	nonsyn	gCt	gGt	9	5	0.555556	6077-6079
ORF1ab/nsp3	1120	A1120G	A1938G	nonsyn	gCT	gGG	9	2	0.222222	6077-6079
ORF1ab/nsp3	1120	A1120G	A1938G	nonsyn	gCT	gGC	9	2	0.222222	6077-6079
ORF1ab/nsp3	1120	A1120D	A1938D	nonsyn	gCt	gAt	5	5	1	6077-6079
ORF1ab/nsp3	1120	A1120del1	A1938del1	del	gcT	gc-	5	3	0.6	6077-6079
ORF1ab/nsp3	1120	A1120del1	A1938del1	del	gCt	g-t	5	1	0.2	6077-6079
ORF1ab/nsp3	1120	A1120del1	A1938del1	del	Gct	-ct	5	1	0.2	6077-6079
ORF1ab/nsp3	1120	A1120F	A1938F	nonsyn	GCt	TTt	3	3	1	6077-6079
ORF1ab/nsp3	1120	A1120del2	A1938del2	del	gCT	g--	3	2	0.666667	6077-6079
ORF1ab/nsp3	1120	A1120del2	A1938del2	del	GCt	--t	3	1	0.333333	6077-6079
ORF1ab/nsp3	1120	A1120P	A1938P	nonsyn	Gct	Cct	2	2	1	6077-6079
ORF1ab/nsp3	1120	A1120I	A1938I	nonsyn	GCt	ATt	2	2	1	6077-6079
ORF1ab/nsp3	1120	A1120R	A1938R	nonsyn	GCT	AGG	2	2	1	6077-6079
ORF1ab/nsp3	1120	A1120N	A1938N	nonsyn	GCt	AAt	1	1	1	6077-6079
ORF1ab/nsp3	1120	A1120Y	A1938Y	nonsyn	GCt	TAt	1	1	1	6077-6079

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
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1063	1066	All	0.000203
ORF1ab/nsp3	1120	A1120S	GCT	AGC	2	1066	All	0
ORF1ab/nsp3	1120	A1120S	GcT	TcA	1	1066	All	0
ORF1ab/nsp3	1120	A1120S	Gct	Tct	463	463	B.1.36.21	1
ORF1ab/nsp3	1120	A1120V	gCt	gTt	421	421	All	0.000081
ORF1ab/nsp3	1120	A1120A	gcT	gcC	282	371	All	0.000054
ORF1ab/nsp3	1120	A1120A	gcT	gcG	46	371	All	0.000009
ORF1ab/nsp3	1120	A1120A	gcT	gcA	43	371	All	0.000008
ORF1ab/nsp3	1120	A1120S	Gct	Tct	169	169	B.1.1.7	0.000151
ORF1ab/nsp3	1120	A1120V	gCt	gTt	151	151	B.1.1.7	0.000135
ORF1ab/nsp3	1120	A1120A	gcT	gcC	81	97	B.1.1.7	0.000073
ORF1ab/nsp3	1120	A1120A	gcT	gcG	10	97	B.1.1.7	0.000009
ORF1ab/nsp3	1120	A1120A	gcT	gcA	6	97	B.1.1.7	0.000005
ORF1ab/nsp3	1120	A1120S	Gct	Tct	86	86	AY.4	0.000134
ORF1ab/nsp3	1120	A1120del	GCT	---	75	75	All	0.000014
ORF1ab/nsp3	1120	A1120A	gcT	gcC	47	48	AY.25	0.000283
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	48	AY.25	0.000006
ORF1ab/nsp3	1120	A1120T	Gct	Act	37	41	All	0.000007
ORF1ab/nsp3	1120	A1120T	GcT	AcG	2	41	All	0
ORF1ab/nsp3	1120	A1120T	GcT	AcC	2	41	All	0
ORF1ab/nsp3	1120	A1120V	gCt	gTt	38	38	AY.59	0.020127
ORF1ab/nsp3	1120	A1120S	Gct	Tct	36	36	AY.43	0.000159
ORF1ab/nsp3	1120	A1120T	Gct	Act	31	31	B.1.1.7	0.000028
ORF1ab/nsp3	1120	A1120S	Gct	Tct	30	30	P.1	0.000473
ORF1ab/nsp3	1120	A1120A	gcT	gcC	25	28	AY.44	0.000152
ORF1ab/nsp3	1120	A1120A	gcT	gcG	3	28	AY.44	0.000018
ORF1ab/nsp3	1120	A1120S	Gct	Tct	26	26	B.1.617.2	0.000098
ORF1ab/nsp3	1120	A1120del	GCT	---	21	21	B.1.1.7	0.000019
ORF1ab/nsp3	1120	A1120V	gCt	gTt	21	21	B.1.617.2	0.000079
ORF1ab/nsp3	1120	A1120V	gCt	gTt	19	19	AY.4	0.00003
ORF1ab/nsp3	1120	A1120V	gCt	gTt	18	18	AY.39.1	0.000713
ORF1ab/nsp3	1120	A1120S	Gct	Tct	16	16	AY.25	0.000096
ORF1ab/nsp3	1120	A1120V	gCt	gTt	16	16	AY.43	0.000071
ORF1ab/nsp3	1120	A1120S	Gct	Tct	16	16	AY.44	0.000097
ORF1ab/nsp3	1120	A1120S	Gct	Tct	16	16	B.1.177	0.000211
ORF1ab/nsp3	1120	A1120S	Gct	Tct	15	15	B.1.1.326	0.026408
ORF1ab/nsp3	1120	A1120S	Gct	Tct	15	15	B.1.2	0.000132
ORF1ab/nsp3	1120	A1120A	gcT	gcA	15	15	B.1.221	0.001065
ORF1ab/nsp3	1120	A1120V	gCt	gTt	14	14	AY.96	0.029046
ORF1ab/nsp3	1120	A1120V	gCt	gTt	14	14	B.1	0.000128
ORF1ab/nsp3	1120	A1120A	gcT	gcC	13	13	A.2.5	0.006487
ORF1ab/nsp3	1120	A1120S	Gct	Tct	13	13	AY.103	0.000081
ORF1ab/nsp3	1120	A1120S	Gct	Tct	11	12	AY.3	0.000109
ORF1ab/nsp3	1120	A1120S	GcT	TcA	1	12	AY.3	0.00001
ORF1ab/nsp3	1120	A1120A	gcT	gcG	12	12	B.1.406	0.072727
ORF1ab/nsp3	1120	A1120A	gcT	gcC	11	11	AY.110	0.00124
ORF1ab/nsp3	1120	A1120S	Gct	Tct	11	11	B.1	0.000101
ORF1ab/nsp3	1120	A1120A	gcT	gcC	6	10	AY.4	0.000009
ORF1ab/nsp3	1120	A1120A	gcT	gcA	4	10	AY.4	0.000006
ORF1ab/nsp3	1120	A1120S	Gct	Tct	10	10	AY.67	0.004643
ORF1ab/nsp3	1120	A1120G	gCt	gGt	5	9	All	0.000001
ORF1ab/nsp3	1120	A1120G	gCT	gGC	2	9	All	0
ORF1ab/nsp3	1120	A1120G	gCT	gGG	2	9	All	0
ORF1ab/nsp3	1120	A1120A	gcT	gcC	9	9	AY.103	0.000056
ORF1ab/nsp3	1120	A1120A	gcT	gcC	9	9	AY.111	0.001648
ORF1ab/nsp3	1120	A1120A	gcT	gcC	9	9	AY.43	0.00004
ORF1ab/nsp3	1120	A1120V	gCt	gTt	8	8	AY.23	0.000558
ORF1ab/nsp3	1120	A1120S	Gct	Tct	8	8	AY.42	0.000322
ORF1ab/nsp3	1120	A1120V	gCt	gTt	8	8	AY.44	0.000049
ORF1ab/nsp3	1120	A1120V	gCt	gTt	8	8	AY.46.6	0.000578
ORF1ab/nsp3	1120	A1120A	gcT	gcC	8	8	B.1.539	0.140351
ORF1ab/nsp3	1120	A1120A	gcT	gcC	8	8	C.37	0.000929
ORF1ab/nsp3	1120	A1120S	Gct	Tct	7	7	AY.29	0.00011
ORF1ab/nsp3	1120	A1120A	gcT	gcC	7	7	AY.4.5	0.000752
ORF1ab/nsp3	1120	A1120V	gCt	gTt	7	7	B.1.351	0.000208
ORF1ab/nsp3	1120	A1120S	Gct	Tct	6	6	AY.20	0.000233
ORF1ab/nsp3	1120	A1120A	gcT	gcA	6	6	AY.26	0.00017
ORF1ab/nsp3	1120	A1120V	gCt	gTt	6	6	B.1.1.316	0.00555
ORF1ab/nsp3	1120	A1120A	gcT	gcA	5	6	B.1.561	0.001985
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	6	B.1.561	0.000397
ORF1ab/nsp3	1120	A1120D	gCt	gAt	5	5	All	0.000001
ORF1ab/nsp3	1120	A1120del1	gcT	gc-	3	5	All	0.000001
ORF1ab/nsp3	1120	A1120del1	Gct	-ct	1	5	All	0
ORF1ab/nsp3	1120	A1120del1	gCt	g-t	1	5	All	0
ORF1ab/nsp3	1120	A1120V	gCt	gTt	5	5	AY.45	0.000608
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	5	B.1	0.000018
ORF1ab/nsp3	1120	A1120A	gcT	gcA	2	5	B.1	0.000018
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	5	B.1	0.000009
ORF1ab/nsp3	1120	A1120V	gCt	gTt	5	5	B.1.2	0.000044
ORF1ab/nsp3	1120	A1120A	gcT	gcG	4	5	B.1.429	0.000094
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	5	B.1.429	0.000024
ORF1ab/nsp3	1120	A1120A	gcT	gcG	2	4		0.111111
ORF1ab/nsp3	1120	A1120T	GcT	AcG	2	4		0.111111
ORF1ab/nsp3	1120	A1120G	gCT	gGC	2	4		0.111111
ORF1ab/nsp3	1120	A1120G	gCT	gGG	2	4		0.111111
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	4		0.111111
ORF1ab/nsp3	1120	A1120T	GcT	AcC	2	4		0.111111
ORF1ab/nsp3	1120	A1120S	Gct	Tct	4	4	AY.118	0.000251
ORF1ab/nsp3	1120	A1120V	gCt	gTt	4	4	AY.120	0.000149
ORF1ab/nsp3	1120	A1120S	Gct	Tct	4	4	AY.4.2	0.000087
ORF1ab/nsp3	1120	A1120del	GCT	---	4	4	AY.43	0.000018
ORF1ab/nsp3	1120	A1120S	Gct	Tct	4	4	AY.5	0.000083
ORF1ab/nsp3	1120	A1120V	gCt	gTt	4	4	B.1.177	0.000053
ORF1ab/nsp3	1120	A1120S	Gct	Tct	4	4	B.1.177.58	0.005326
ORF1ab/nsp3	1120	A1120S	Gct	Tct	4	4	B.1.36	0.000584
ORF1ab/nsp3	1120	A1120S	Gct	Tct	4	4	B.1.36.26	0.011429
ORF1ab/nsp3	1120	A1120S	Gct	Tct	4	4	B.1.420	0.041667
ORF1ab/nsp3	1120	A1120del	GCT	---	4	4	B.1.617.2	0.000015
ORF1ab/nsp3	1120	A1120A	gcT	gcC	3	4	B.1.617.2	0.000011
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	4	B.1.617.2	0.000004
ORF1ab/nsp3	1120	A1120F	GCt	TTt	3	3	All	0.000001
ORF1ab/nsp3	1120	A1120del2	gCT	g--	2	3	All	0
ORF1ab/nsp3	1120	A1120del2	GCt	--t	1	3	All	0
ORF1ab/nsp3	1120	A1120A	gcT	gcG	3	3	AY.101	0.001471
ORF1ab/nsp3	1120	A1120V	gCt	gTt	3	3	AY.103	0.000019
ORF1ab/nsp3	1120	A1120A	gcT	gcC	3	3	AY.120	0.000112
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	AY.26	0.000085
ORF1ab/nsp3	1120	A1120A	gcT	gcC	3	3	AY.29	0.000047
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	3	AY.3	0.00002
ORF1ab/nsp3	1120	A1120A	gcT	gcA	1	3	AY.3	0.00001
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	AY.34	0.000291
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	AY.39	0.000074
ORF1ab/nsp3	1120	A1120V	gCt	gTt	3	3	AY.46	0.000312
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	AY.47	0.000093
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	AY.6	0.000123
ORF1ab/nsp3	1120	A1120V	gCt	gTt	3	3	AY.61	0.000314
ORF1ab/nsp3	1120	A1120V	gCt	gTt	3	3	AY.70	0.000626
ORF1ab/nsp3	1120	A1120V	gCt	gTt	3	3	AY.79	0.003632
ORF1ab/nsp3	1120	A1120del	GCT	---	3	3	B.1	0.000027
ORF1ab/nsp3	1120	A1120V	gCt	gTt	3	3	B.1.1	0.000054
ORF1ab/nsp3	1120	A1120del	GCT	---	3	3	B.1.1	0.000054
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	B.1.320	0.003736
ORF1ab/nsp3	1120	A1120A	gcT	gcC	3	3	B.1.526	0.000071
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	B.1.596	0.000261
ORF1ab/nsp3	1120	A1120V	gCt	gTt	3	3	B.1.617.1	0.000387
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	C.37	0.000348
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	P.1.15	0.000697
ORF1ab/nsp3	1120	A1120S	Gct	Tct	3	3	Q.8	0.000495
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2		0.111111
ORF1ab/nsp3	1120	A1120del2	gCT	g--	2	2		0.111111
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2		0.111111
ORF1ab/nsp3	1120	A1120R	GCT	AGG	2	2		0.111111
ORF1ab/nsp3	1120	A1120S	GCT	AGC	2	2		0.111111
ORF1ab/nsp3	1120	A1120R	GCT	AGG	2	2	All	0
ORF1ab/nsp3	1120	A1120P	Gct	Cct	2	2	All	0
ORF1ab/nsp3	1120	A1120I	GCt	ATt	2	2	All	0
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	AY.102	0.000053
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	2	AY.102	0.000027
ORF1ab/nsp3	1120	A1120A	gcT	gcA	1	2	AY.102	0.000027
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2	AY.25	0.000012
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	AY.26	0.000057
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	AY.3	0.00002
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	AY.39	0.000049
ORF1ab/nsp3	1120	A1120A	gcT	gcA	1	2	AY.4.2	0.000022
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	2	AY.4.2	0.000022
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2	AY.44	0.000012
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	AY.46	0.000208
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2	AY.53	0.000575
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	AY.61	0.00021
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	2	AY.61	0.00021
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	2	AY.69	0.000373
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	AY.75	0.000112
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	AY.9.1	0.000167
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2	AY.9.2	0.000073
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	B.1.1	0.000036
ORF1ab/nsp3	1120	A1120A	gcT	gcG	2	2	B.1.1.284	0.000215
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	2	B.1.1.519	0.000079
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	B.1.160	0.000062
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	2	B.1.177	0.000026
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	B.1.177.86	0.000367
ORF1ab/nsp3	1120	A1120G	gCt	gGt	2	2	B.1.2	0.000018
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2	B.1.2	0.000018
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	2	B.1.2	0.000009
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	2	B.1.2	0.000009
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2	B.1.258	0.000133
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	B.1.369	0.00057
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	B.1.429	0.000047
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	B.1.435	0.022727
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	2	B.1.509	0.001732
ORF1ab/nsp3	1120	A1120del1	gcT	gc-	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1120	A1120A	gcT	gcC	2	2	B.39	0.004662
ORF1ab/nsp3	1120	A1120V	gCt	gTt	2	2	B.6.6	0.001778
ORF1ab/nsp3	1120	A1120del	GCT	---	2	2	C.37	0.000232
ORF1ab/nsp3	1120	A1120S	Gct	Tct	2	2	Q.1	0.000253
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	A	0.000387
ORF1ab/nsp3	1120	A1120N	GCt	AAt	1	1	All	0
ORF1ab/nsp3	1120	A1120Y	GCt	TAt	1	1	All	0
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.100	0.000046
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.100	0.000046
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.102	0.000027
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.113	0.000142
ORF1ab/nsp3	1120	A1120F	GCt	TTt	1	1	AY.113	0.000142
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.116	0.000287
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.119	0.000035
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.119	0.000035
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.12	0.000316
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.120	0.000037
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.120.1	0.000321
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.120.2	0.001285
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.14	0.000088
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.2	0.000356
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.20	0.000039
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.20	0.000039
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.23.1	0.000417
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.24	0.000431
ORF1ab/nsp3	1120	A1120T	Gct	Act	1	1	AY.25	0.000006
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.25	0.000006
ORF1ab/nsp3	1120	A1120T	Gct	Act	1	1	AY.26	0.000028
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.27	0.000065
ORF1ab/nsp3	1120	A1120T	Gct	Act	1	1	AY.3	0.00001
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.32	0.000532
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.33	0.000067
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.33	0.000067
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.33	0.000067
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.36	0.000148
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.4	0.000002
ORF1ab/nsp3	1120	A1120T	Gct	Act	1	1	AY.4	0.000002
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.40	0.000964
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.45	0.000122
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.46	0.000104
ORF1ab/nsp3	1120	A1120T	Gct	Act	1	1	AY.46.6	0.000072
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.5.4	0.000277
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.52	0.000814
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.53	0.000288
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.54	0.000095
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.54	0.000095
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.59	0.00053
ORF1ab/nsp3	1120	A1120D	gCt	gAt	1	1	AY.59	0.00053
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.6	0.000041
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.61	0.000105
ORF1ab/nsp3	1120	A1120F	GCt	TTt	1	1	AY.62	0.000436
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.67	0.000464
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.7.1	0.000113
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.72	0.001361
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.84	0.000437
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.85	0.000427
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.91	0.00073
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	AY.94	0.000443
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.95	0.000761
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AY.98.1	0.000048
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	AY.99	0.001049
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	AY.99.2	0.000092
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	AZ.2	0.000821
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B	0.000128
ORF1ab/nsp3	1120	A1120D	gCt	gAt	1	1	B.1	0.000009
ORF1ab/nsp3	1120	A1120del1	Gct	-ct	1	1	B.1	0.000009
ORF1ab/nsp3	1120	A1120P	Gct	Cct	1	1	B.1	0.000009
ORF1ab/nsp3	1120	A1120G	gCt	gGt	1	1	B.1.1	0.000018
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.1.222	0.000204
ORF1ab/nsp3	1120	A1120A	gcT	gcA	1	1	B.1.1.226	0.005814
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	1120	A1120G	gCt	gGt	1	1	B.1.1.300	0.010753
ORF1ab/nsp3	1120	A1120P	Gct	Cct	1	1	B.1.1.318	0.000302
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.1.318	0.000302
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1120	A1120G	gCt	gGt	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.1.378	0.007299
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.1.417	0.002703
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	B.1.1.420	0.001006
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.1.50	0.000679
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1120	A1120I	GCt	ATt	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1120	A1120del1	gCt	g-t	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1120	A1120del2	GCt	--t	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.13	0.002375
ORF1ab/nsp3	1120	A1120D	gCt	gAt	1	1	B.1.13	0.002375
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.177.65	0.000665
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.177.77	0.000726
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.214.2	0.0006
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	B.1.234	0.000132
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.239	0.001221
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.240	0.000216
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.243	0.00007
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.243	0.00007
ORF1ab/nsp3	1120	A1120I	GCt	ATt	1	1	B.1.258	0.000067
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.258.11	0.000396
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.3	0.002618
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.344	0.008197
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.351	0.00003
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	B.1.351	0.00003
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.351.1	0.038462
ORF1ab/nsp3	1120	A1120D	gCt	gAt	1	1	B.1.351.2	0.000303
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	B.1.36	0.000146
ORF1ab/nsp3	1120	A1120F	GCt	TTt	1	1	B.1.36	0.000146
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.36	0.000146
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	1	B.1.36.16	0.001425
ORF1ab/nsp3	1120	A1120A	gcT	gcA	1	1	B.1.361	0.001289
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	1	B.1.398	0.002976
ORF1ab/nsp3	1120	A1120A	gcT	gcC	1	1	B.1.409	0.000781
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1120	A1120D	gCt	gAt	1	1	B.1.427	0.00005
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	1	B.1.427	0.00005
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.453	0.003236
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.517	0.000427
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.525	0.000113
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.525	0.000113
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.1.526	0.000024
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.537	0.02
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.1.596	0.000087
ORF1ab/nsp3	1120	A1120del1	gcT	gc-	1	1	B.1.596	0.000087
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.610	0.003546
ORF1ab/nsp3	1120	A1120T	Gct	Act	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1120	A1120A	gcT	gcG	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	B.1.625	0.002353
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	B.15	0.017544
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	B.55	0.00295
ORF1ab/nsp3	1120	A1120N	GCt	AAt	1	1	C.35	0.000774
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	D.2	0.000075
ORF1ab/nsp3	1120	A1120Y	GCt	TAt	1	1	P.1	0.000016
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	P.1	0.000016
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	P.1.12	0.000484
ORF1ab/nsp3	1120	A1120S	Gct	Tct	1	1	P.1.14	0.000048
ORF1ab/nsp3	1120	A1120V	gCt	gTt	1	1	P.1.16	0.000374
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	Q.1	0.000126
ORF1ab/nsp3	1120	A1120del	GCT	---	1	1	Q.8	0.000165
ORF1ab/nsp3	1120	A1120A	gcT	gcC	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.