CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1083

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	1083	H1083Y		nonsyn	Cat	Tat	1347	1347	1	24809-24811
S	1083	H1083H		syn	caT	caC	1011	1011	1	24809-24811
S	1083	H1083D		nonsyn	Cat	Gat	65	64	0.984615	24809-24811
S	1083	H1083D		nonsyn	CaT	GaC	65	1	0.0153846	24809-24811
S	1083	H1083Q		nonsyn	caT	caA	56	53	0.946429	24809-24811
S	1083	H1083Q		nonsyn	caT	caG	56	3	0.0535714	24809-24811
S	1083	H1083R		nonsyn	cAt	cGt	36	34	0.944444	24809-24811
S	1083	H1083R		nonsyn	cAT	cGC	36	1	0.0277778	24809-24811
S	1083	H1083R		nonsyn	cAT	cGA	36	1	0.0277778	24809-24811
S	1083	H1083N		nonsyn	Cat	Aat	33	33	1	24809-24811
S	1083	H1083del		del	CAT	---	27	27	1	24809-24811
S	1083	H1083P		nonsyn	cAt	cCt	3	3	1	24809-24811
S	1083	H1083G		nonsyn	CAT	GGC	3	2	0.666667	24809-24811
S	1083	H1083del2		del	CAt	--t	3	2	0.666667	24809-24811
S	1083	H1083G		nonsyn	CAT	GGA	3	1	0.333333	24809-24811
S	1083	H1083del2		del	cAT	c--	3	1	0.333333	24809-24811
S	1083	H1083S		nonsyn	CAt	AGt	2	1	0.5	24809-24811
S	1083	H1083S		nonsyn	CAt	TCt	2	1	0.5	24809-24811
S	1083	H1083del1		del	caT	ca-	1	1	1	24809-24811
S	1083	H1083L		nonsyn	cAt	cTt	1	1	1	24809-24811
S	1083	H1083E		nonsyn	CaT	GaA	1	1	1	24809-24811

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	1083	H1083Y	Cat	Tat	1347	1347	All	0.000258
S	1083	H1083H	caT	caC	1011	1011	All	0.000193
S	1083	H1083Y	Cat	Tat	402	402	AY.4.2	0.008719
S	1083	H1083H	caT	caC	329	329	C.36.3	0.186614
S	1083	H1083H	caT	caC	322	322	C.36.3.1	0.875
S	1083	H1083Y	Cat	Tat	294	294	B.1.1.7	0.000263
S	1083	H1083H	caT	caC	141	141	B.1.1.526	0.5
S	1083	H1083Y	Cat	Tat	96	96	AY.44	0.000584
S	1083	H1083D	Cat	Gat	64	65	All	0.000012
S	1083	H1083D	CaT	GaC	1	65	All	0
S	1083	H1083Y	Cat	Tat	65	65	AY.3	0.000647
S	1083	H1083D	Cat	Gat	59	59	B.1.1.7	0.000053
S	1083	H1083Q	caT	caA	53	56	All	0.00001
S	1083	H1083Q	caT	caG	3	56	All	0.000001
S	1083	H1083Y	Cat	Tat	47	47	AY.43	0.000208
S	1083	H1083Y	Cat	Tat	39	39	AY.4	0.000061
S	1083	H1083Y	Cat	Tat	39	39	B.1.617.2	0.000147
S	1083	H1083R	cAt	cGt	34	36	All	0.000007
S	1083	H1083R	cAT	cGA	1	36	All	0
S	1083	H1083R	cAT	cGC	1	36	All	0
S	1083	H1083N	Cat	Aat	33	33	All	0.000006
S	1083	H1083H	caT	caC	31	31	B.1.1.7	0.000028
S	1083	H1083Y	Cat	Tat	31	31	B.1.2	0.000273
S	1083	H1083H	caT	caC	30	30	B.1.617.2	0.000113
S	1083	H1083del	CAT	---	27	27	All	0.000005
S	1083	H1083H	caT	caC	24	24	AY.100	0.001104
S	1083	H1083Y	Cat	Tat	23	23	AY.26	0.000651
S	1083	H1083Y	Cat	Tat	21	21	B.1.36	0.003064
S	1083	H1083Y	Cat	Tat	19	19	B.1.177.10	0.016681
S	1083	H1083H	caT	caC	17	17	AY.44	0.000103
S	1083	H1083H	caT	caC	17	17	B.1	0.000156
S	1083	H1083Y	Cat	Tat	15	15	AY.25	0.00009
S	1083	H1083Y	Cat	Tat	15	15	B.1	0.000137
S	1083	H1083Y	Cat	Tat	14	14	AY.7.2	0.00783
S	1083	H1083Y	Cat	Tat	12	12	AY.120.1	0.003852
S	1083	H1083Q	caT	caA	12	12	B.1.36.8	0.012
S	1083	H1083H	caT	caC	11	11	AY.103	0.000068
S	1083	H1083Q	caT	caA	10	10	B.1.184	0.588235
S	1083	H1083Y	Cat	Tat	10	10	P.1	0.000158
S	1083	H1083R	cAt	cGt	9	9	B.1.1.7	0.000008
S	1083	H1083Y	Cat	Tat	9	9	P.1.1	0.002859
S	1083	H1083Y	Cat	Tat	9	9	P.1.15	0.002091
S	1083	H1083Y	Cat	Tat	8	8	A.27	0.013245
S	1083	H1083Y	Cat	Tat	8	8	AY.120	0.000297
S	1083	H1083N	Cat	Aat	8	8	B.1.1.7	0.000007
S	1083	H1083Y	Cat	Tat	7	7	AY.103	0.000043
S	1083	H1083Y	Cat	Tat	7	7	AY.119	0.000247
S	1083	H1083H	caT	caC	7	7	B.1.1	0.000127
S	1083	H1083Y	Cat	Tat	7	7	B.1.1.519	0.000278
S	1083	H1083Q	caT	caA	7	7	B.1.427	0.000353
S	1083	H1083Y	Cat	Tat	7	7	B.1.526	0.000165
S	1083	H1083H	caT	caC	7	7	B.1.621	0.00062
S	1083	H1083H	caT	caC	6	6	AY.116.1	0.001869
S	1083	H1083Y	Cat	Tat	6	6	AY.39	0.000148
S	1083	H1083Y	Cat	Tat	6	6	B.1.243	0.000418
S	1083	H1083Y	Cat	Tat	5	5	AY.20	0.000194
S	1083	H1083H	caT	caC	5	5	AY.4	0.000008
S	1083	H1083R	cAt	cGt	5	5	AY.4.2	0.000108
S	1083	H1083Y	Cat	Tat	5	5	AY.5	0.000103
S	1083	H1083Y	Cat	Tat	5	5	B.1.1	0.000091
S	1083	H1083Y	Cat	Tat	5	5	B.1.36.1	0.005701
S	1083	H1083Y	Cat	Tat	5	5	B.1.429	0.000118
S	1083	H1083Y	Cat	Tat	5	5	B.1.456	0.01634
S	1083	H1083N	Cat	Aat	5	5	B.1.617.2	0.000019
S	1083	H1083del	CAT	---	4	4		0.222222
S	1083	H1083Q	caT	caA	4	4	AU.3	0.008439
S	1083	H1083H	caT	caC	4	4	AY.20	0.000155
S	1083	H1083Q	caT	caA	4	4	AY.25	0.000024
S	1083	H1083Y	Cat	Tat	4	4	AY.29	0.000063
S	1083	H1083N	Cat	Aat	4	4	AY.4	0.000006
S	1083	H1083N	Cat	Aat	4	4	B.1	0.000037
S	1083	H1083Y	Cat	Tat	4	4	B.1.1.28	0.001245
S	1083	H1083del	CAT	---	4	4	B.1.1.7	0.000004
S	1083	H1083Y	Cat	Tat	4	4	B.1.177	0.000053
S	1083	H1083R	cAt	cGt	4	4	B.1.319	0.012195
S	1083	H1083H	caT	caC	4	4	B.1.351	0.000119
S	1083	H1083Y	Cat	Tat	4	4	B.1.596	0.000349
S	1083	H1083Y	Cat	Tat	4	4	Q.1	0.000505
S	1083	H1083P	cAt	cCt	3	3	All	0.000001
S	1083	H1083G	CAT	GGC	2	3	All	0
S	1083	H1083del2	CAt	--t	2	3	All	0
S	1083	H1083G	CAT	GGA	1	3	All	0
S	1083	H1083del2	cAT	c--	1	3	All	0
S	1083	H1083Y	Cat	Tat	3	3	AY.118	0.000188
S	1083	H1083H	caT	caC	3	3	AY.119	0.000106
S	1083	H1083del	CAT	---	3	3	AY.43	0.000013
S	1083	H1083R	cAT	cGA	1	3	AY.43	0.000004
S	1083	H1083R	cAT	cGC	1	3	AY.43	0.000004
S	1083	H1083R	cAt	cGt	1	3	AY.43	0.000004
S	1083	H1083Y	Cat	Tat	3	3	AY.7	0.000588
S	1083	H1083Y	Cat	Tat	3	3	B.1.1.382	0.107143
S	1083	H1083H	caT	caC	3	3	B.1.1.519	0.000119
S	1083	H1083Y	Cat	Tat	3	3	B.1.160	0.000094
S	1083	H1083H	caT	caC	3	3	B.1.160	0.000094
S	1083	H1083Y	Cat	Tat	3	3	C.16	0.003181
S	1083	H1083D	Cat	Gat	3	3	P.1.2	0.003468
S	1083	H1083del2	CAt	--t	2	2		0.111111
S	1083	H1083H	caT	caC	2	2	AD.2	0.000438
S	1083	H1083S	CAt	AGt	1	2	All	0
S	1083	H1083S	CAt	TCt	1	2	All	0
S	1083	H1083H	caT	caC	2	2	AY.102	0.000053
S	1083	H1083Q	caT	caA	2	2	AY.120	0.000074
S	1083	H1083del	CAT	---	2	2	AY.120	0.000074
S	1083	H1083Y	Cat	Tat	2	2	AY.121	0.000271
S	1083	H1083Y	Cat	Tat	2	2	AY.23	0.000139
S	1083	H1083H	caT	caC	2	2	AY.29	0.000032
S	1083	H1083R	cAt	cGt	2	2	AY.3	0.00002
S	1083	H1083Y	Cat	Tat	2	2	AY.34.1	0.00102
S	1083	H1083N	Cat	Aat	2	2	AY.39	0.000049
S	1083	H1083del	CAT	---	2	2	AY.4	0.000003
S	1083	H1083H	caT	caC	2	2	AY.4.2	0.000043
S	1083	H1083Y	Cat	Tat	2	2	AY.4.4	0.000818
S	1083	H1083Y	Cat	Tat	2	2	AY.42	0.00008
S	1083	H1083G	CAT	GGA	1	2	AY.43	0.000004
S	1083	H1083G	CAT	GGC	1	2	AY.43	0.000004
S	1083	H1083Q	caT	caG	1	2	AY.44	0.000006
S	1083	H1083Q	caT	caA	1	2	AY.44	0.000006
S	1083	H1083Y	Cat	Tat	2	2	AY.46.4	0.000329
S	1083	H1083H	caT	caC	2	2	AY.73	0.001331
S	1083	H1083H	caT	caC	2	2	AY.74	0.000231
S	1083	H1083H	caT	caC	2	2	AY.75	0.000112
S	1083	H1083H	caT	caC	2	2	AY.77	0.002255
S	1083	H1083H	caT	caC	2	2	AY.9.1	0.000167
S	1083	H1083H	caT	caC	2	2	AY.99.2	0.000184
S	1083	H1083Y	Cat	Tat	2	2	B	0.000256
S	1083	H1083N	Cat	Aat	2	2	B.1.1	0.000036
S	1083	H1083H	caT	caC	2	2	B.1.1.294	0.002532
S	1083	H1083R	cAt	cGt	2	2	B.1.1.305	0.007722
S	1083	H1083Y	Cat	Tat	2	2	B.1.1.39	0.001019
S	1083	H1083Y	Cat	Tat	2	2	B.1.1.397	0.004505
S	1083	H1083H	caT	caC	2	2	B.1.177	0.000026
S	1083	H1083Y	Cat	Tat	2	2	B.1.177.86	0.000367
S	1083	H1083Q	caT	caA	2	2	B.1.2	0.000018
S	1083	H1083Y	Cat	Tat	2	2	B.1.279	0.001027
S	1083	H1083Y	Cat	Tat	2	2	B.1.465	0.007605
S	1083	H1083Y	Cat	Tat	2	2	B.1.525	0.000226
S	1083	H1083del	CAT	---	2	2	B.1.617.2	0.000008
S	1083	H1083Q	caT	caA	2	2	B.1.617.2	0.000008
S	1083	H1083R	cAt	cGt	2	2	B.1.617.2	0.000008
S	1083	H1083Q	caT	caG	1	2	B.46	0.020833
S	1083	H1083Q	caT	caA	1	2	B.46	0.020833
S	1083	H1083Q	caT	caA	1	1		0.055556
S	1083	H1083E	CaT	GaA	1	1	All	0
S	1083	H1083del1	caT	ca-	1	1	All	0
S	1083	H1083L	cAt	cTt	1	1	All	0
S	1083	H1083H	caT	caC	1	1	AY.101	0.00049
S	1083	H1083Y	Cat	Tat	1	1	AY.102	0.000027
S	1083	H1083Y	Cat	Tat	1	1	AY.105	0.000643
S	1083	H1083H	caT	caC	1	1	AY.106	0.000335
S	1083	H1083H	caT	caC	1	1	AY.113	0.000142
S	1083	H1083R	cAt	cGt	1	1	AY.118	0.000063
S	1083	H1083Y	Cat	Tat	1	1	AY.13	0.000161
S	1083	H1083Y	Cat	Tat	1	1	AY.14	0.000088
S	1083	H1083R	cAt	cGt	1	1	AY.16.1	0.00047
S	1083	H1083H	caT	caC	1	1	AY.2	0.000356
S	1083	H1083N	Cat	Aat	1	1	AY.25	0.000006
S	1083	H1083R	cAt	cGt	1	1	AY.25	0.000006
S	1083	H1083H	caT	caC	1	1	AY.25	0.000006
S	1083	H1083H	caT	caC	1	1	AY.26	0.000028
S	1083	H1083Y	Cat	Tat	1	1	AY.27	0.000065
S	1083	H1083N	Cat	Aat	1	1	AY.3	0.00001
S	1083	H1083H	caT	caC	1	1	AY.3.1	0.000085
S	1083	H1083del	CAT	---	1	1	AY.36	0.000148
S	1083	H1083H	caT	caC	1	1	AY.36	0.000148
S	1083	H1083Y	Cat	Tat	1	1	AY.36	0.000148
S	1083	H1083D	Cat	Gat	1	1	AY.4	0.000002
S	1083	H1083R	cAt	cGt	1	1	AY.4	0.000002
S	1083	H1083Q	caT	caA	1	1	AY.4	0.000002
S	1083	H1083L	cAt	cTt	1	1	AY.4	0.000002
S	1083	H1083del	CAT	---	1	1	AY.4.5	0.000107
S	1083	H1083H	caT	caC	1	1	AY.43	0.000004
S	1083	H1083D	CaT	GaC	1	1	AY.43	0.000004
S	1083	H1083E	CaT	GaA	1	1	AY.43	0.000004
S	1083	H1083Q	caT	caA	1	1	AY.43	0.000004
S	1083	H1083del2	cAT	c--	1	1	AY.43	0.000004
S	1083	H1083R	cAt	cGt	1	1	AY.44	0.000006
S	1083	H1083H	caT	caC	1	1	AY.45	0.000122
S	1083	H1083H	caT	caC	1	1	AY.46	0.000104
S	1083	H1083Y	Cat	Tat	1	1	AY.46	0.000104
S	1083	H1083del	CAT	---	1	1	AY.46.2	0.000635
S	1083	H1083P	cAt	cCt	1	1	AY.47	0.000031
S	1083	H1083N	Cat	Aat	1	1	AY.47	0.000031
S	1083	H1083Y	Cat	Tat	1	1	AY.47	0.000031
S	1083	H1083Y	Cat	Tat	1	1	AY.6	0.000041
S	1083	H1083Y	Cat	Tat	1	1	AY.61	0.000105
S	1083	H1083del	CAT	---	1	1	AY.67	0.000464
S	1083	H1083G	CAT	GGC	1	1	AY.67	0.000464
S	1083	H1083H	caT	caC	1	1	AY.67	0.000464
S	1083	H1083Y	Cat	Tat	1	1	AY.69	0.000187
S	1083	H1083Y	Cat	Tat	1	1	AY.70	0.000209
S	1083	H1083H	caT	caC	1	1	AY.70	0.000209
S	1083	H1083N	Cat	Aat	1	1	AY.75	0.000056
S	1083	H1083del	CAT	---	1	1	AY.75	0.000056
S	1083	H1083Y	Cat	Tat	1	1	AY.78	0.001541
S	1083	H1083Y	Cat	Tat	1	1	AY.8	0.000606
S	1083	H1083H	caT	caC	1	1	AY.98.1	0.000048
S	1083	H1083Y	Cat	Tat	1	1	AZ.5	0.003509
S	1083	H1083R	cAt	cGt	1	1	B	0.000128
S	1083	H1083del	CAT	---	1	1	B.1	0.000009
S	1083	H1083Q	caT	caA	1	1	B.1	0.000009
S	1083	H1083R	cAt	cGt	1	1	B.1	0.000009
S	1083	H1083Q	caT	caA	1	1	B.1.1	0.000018
S	1083	H1083R	cAt	cGt	1	1	B.1.1	0.000018
S	1083	H1083S	CAt	TCt	1	1	B.1.1	0.000018
S	1083	H1083H	caT	caC	1	1	B.1.1.1	0.000327
S	1083	H1083R	cAt	cGt	1	1	B.1.1.214	0.000055
S	1083	H1083Y	Cat	Tat	1	1	B.1.1.25	0.000569
S	1083	H1083H	caT	caC	1	1	B.1.1.25	0.000569
S	1083	H1083Y	Cat	Tat	1	1	B.1.1.284	0.000107
S	1083	H1083P	cAt	cCt	1	1	B.1.1.300	0.010753
S	1083	H1083Y	Cat	Tat	1	1	B.1.1.329	0.003846
S	1083	H1083D	Cat	Gat	1	1	B.1.1.33	0.000421
S	1083	H1083H	caT	caC	1	1	B.1.1.39	0.00051
S	1083	H1083Y	Cat	Tat	1	1	B.1.1.523	0.001563
S	1083	H1083del1	caT	ca-	1	1	B.1.1.7	0.000001
S	1083	H1083P	cAt	cCt	1	1	B.1.1.7	0.000001
S	1083	H1083Y	Cat	Tat	1	1	B.1.1.70	0.000341
S	1083	H1083Y	Cat	Tat	1	1	B.1.146	0.004237
S	1083	H1083Y	Cat	Tat	1	1	B.1.147	0.000756
S	1083	H1083N	Cat	Aat	1	1	B.1.160.26	0.002421
S	1083	H1083N	Cat	Aat	1	1	B.1.177	0.000013
S	1083	H1083H	caT	caC	1	1	B.1.177.12	0.000152
S	1083	H1083Y	Cat	Tat	1	1	B.1.177.36	0.016129
S	1083	H1083Y	Cat	Tat	1	1	B.1.177.60	0.000218
S	1083	H1083Y	Cat	Tat	1	1	B.1.177.7	0.000165
S	1083	H1083Y	Cat	Tat	1	1	B.1.221	0.000071
S	1083	H1083Y	Cat	Tat	1	1	B.1.338	0.008621
S	1083	H1083del	CAT	---	1	1	B.1.351	0.00003
S	1083	H1083N	Cat	Aat	1	1	B.1.351	0.00003
S	1083	H1083Y	Cat	Tat	1	1	B.1.36.35	0.002604
S	1083	H1083Y	Cat	Tat	1	1	B.1.396	0.000706
S	1083	H1083Y	Cat	Tat	1	1	B.1.416	0.001269
S	1083	H1083H	caT	caC	1	1	B.1.429	0.000024
S	1083	H1083Y	Cat	Tat	1	1	B.1.459	0.004082
S	1083	H1083H	caT	caC	1	1	B.1.466.2	0.000391
S	1083	H1083Y	Cat	Tat	1	1	B.1.517	0.000427
S	1083	H1083Y	Cat	Tat	1	1	B.1.595	0.000261
S	1083	H1083Y	Cat	Tat	1	1	B.1.617.1	0.000129
S	1083	H1083S	CAt	AGt	1	1	B.1.617.2	0.000004
S	1083	H1083Y	Cat	Tat	1	1	B.1.621.1	0.000506
S	1083	H1083H	caT	caC	1	1	B.1.630	0.005236
S	1083	H1083Y	Cat	Tat	1	1	B.1.636	0.006711
S	1083	H1083Q	caT	caG	1	1	B.1.637	0.000073
S	1083	H1083Q	caT	caA	1	1	B.1.83	0.015385
S	1083	H1083Y	Cat	Tat	1	1	B.1.94	0.027027
S	1083	H1083Y	Cat	Tat	1	1	B.55	0.00295
S	1083	H1083H	caT	caC	1	1	C.36	0.000911
S	1083	H1083del	CAT	---	1	1	C.37	0.000116
S	1083	H1083Y	Cat	Tat	1	1	C.37	0.000116
S	1083	H1083H	caT	caC	1	1	C.39	0.018868
S	1083	H1083Q	caT	caA	1	1	D.2	0.000075
S	1083	H1083del	CAT	---	1	1	P.1	0.000016
S	1083	H1083del	CAT	---	1	1	P.1.15	0.000232
S	1083	H1083N	Cat	Aat	1	1	P.2	0.000187
S	1083	H1083Y	Cat	Tat	1	1	P.4	0.003802
S	1083	H1083Q	caT	caA	1	1	Q.8	0.000165

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.