CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1297

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	1297	R1297I	R2115I	nonsyn	aGa	aTa	1308	1308	1	6608-6610
ORF1ab/nsp3	1297	R1297R	R2115R	syn	agA	agG	454	436	0.960352	6608-6610
ORF1ab/nsp3	1297	R1297R	R2115R	syn	Aga	Cga	454	14	0.030837	6608-6610
ORF1ab/nsp3	1297	R1297R	R2115R	syn	AgA	CgT	454	3	0.00660793	6608-6610
ORF1ab/nsp3	1297	R1297R	R2115R	syn	AgA	CgC	454	1	0.00220264	6608-6610
ORF1ab/nsp3	1297	R1297S	R2115S	nonsyn	agA	agT	367	233	0.634877	6608-6610
ORF1ab/nsp3	1297	R1297S	R2115S	nonsyn	agA	agC	367	134	0.365123	6608-6610
ORF1ab/nsp3	1297	R1297del	R2115del	del	AGA	---	342	342	1	6608-6610
ORF1ab/nsp3	1297	R1297G	R2115G	nonsyn	Aga	Gga	207	206	0.995169	6608-6610
ORF1ab/nsp3	1297	R1297G	R2115G	nonsyn	AgA	GgC	207	1	0.00483092	6608-6610
ORF1ab/nsp3	1297	R1297K	R2115K	nonsyn	aGa	aAa	119	119	1	6608-6610
ORF1ab/nsp3	1297	R1297T	R2115T	nonsyn	aGa	aCa	81	81	1	6608-6610
ORF1ab/nsp3	1297	R1297del1	R2115del1	del	agA	ag-	9	5	0.555556	6608-6610
ORF1ab/nsp3	1297	R1297del1	R2115del1	del	Aga	-ga	9	4	0.444444	6608-6610
ORF1ab/nsp3	1297	R1297X	R2115X	nonsyn	Aga	Tga	7	7	1	6608-6610
ORF1ab/nsp3	1297	R1297L	R2115L	nonsyn	AGa	TTa	4	3	0.75	6608-6610
ORF1ab/nsp3	1297	R1297L	R2115L	nonsyn	AGa	CTa	4	1	0.25	6608-6610
ORF1ab/nsp3	1297	R1297N	R2115N	nonsyn	aGA	aAT	3	3	1	6608-6610
ORF1ab/nsp3	1297	R1297Q	R2115Q	nonsyn	AGa	CAa	2	2	1	6608-6610
ORF1ab/nsp3	1297	R1297del2	R2115del2	del	AGa	--a	2	2	1	6608-6610
ORF1ab/nsp3	1297	R1297H	R2115H	nonsyn	AGA	CAT	1	1	1	6608-6610
ORF1ab/nsp3	1297	R1297V	R2115V	nonsyn	AGa	GTa	1	1	1	6608-6610
ORF1ab/nsp3	1297	R1297E	R2115E	nonsyn	AGa	GAa	1	1	1	6608-6610

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	1297	R1297I	aGa	aTa	1308	1308	All	0.00025
ORF1ab/nsp3	1297	R1297I	aGa	aTa	620	620	B.1.1.523	0.96875
ORF1ab/nsp3	1297	R1297R	agA	agG	436	454	All	0.000083
ORF1ab/nsp3	1297	R1297R	Aga	Cga	14	454	All	0.000003
ORF1ab/nsp3	1297	R1297R	AgA	CgT	3	454	All	0.000001
ORF1ab/nsp3	1297	R1297R	AgA	CgC	1	454	All	0
ORF1ab/nsp3	1297	R1297S	agA	agT	233	367	All	0.000045
ORF1ab/nsp3	1297	R1297S	agA	agC	134	367	All	0.000026
ORF1ab/nsp3	1297	R1297del	AGA	---	342	342	All	0.000065
ORF1ab/nsp3	1297	R1297G	Aga	Gga	206	207	All	0.000039
ORF1ab/nsp3	1297	R1297G	AgA	GgC	1	207	All	0
ORF1ab/nsp3	1297	R1297R	agA	agG	202	202	AY.3	0.002009
ORF1ab/nsp3	1297	R1297del	AGA	---	166	166	B.1.1.7	0.000149
ORF1ab/nsp3	1297	R1297S	agA	agT	134	134	A	0.051858
ORF1ab/nsp3	1297	R1297I	aGa	aTa	131	131	B.1.1.7	0.000117
ORF1ab/nsp3	1297	R1297K	aGa	aAa	119	119	All	0.000023
ORF1ab/nsp3	1297	R1297I	aGa	aTa	117	117	C.38	0.943548
ORF1ab/nsp3	1297	R1297T	aGa	aCa	81	81	All	0.000015
ORF1ab/nsp3	1297	R1297T	aGa	aCa	61	61	B.1.1.50	0.041412
ORF1ab/nsp3	1297	R1297I	aGa	aTa	59	59	B.1.617.2	0.000222
ORF1ab/nsp3	1297	R1297del	AGA	---	53	53	AY.4	0.000082
ORF1ab/nsp3	1297	R1297S	agA	agC	30	49	B.1.1.7	0.000027
ORF1ab/nsp3	1297	R1297S	agA	agT	19	49	B.1.1.7	0.000017
ORF1ab/nsp3	1297	R1297I	aGa	aTa	48	48	B.1.604	0.827586
ORF1ab/nsp3	1297	R1297R	agA	agG	46	46	AY.75	0.002577
ORF1ab/nsp3	1297	R1297S	agA	agC	44	44	AY.44	0.000268
ORF1ab/nsp3	1297	R1297R	agA	agG	38	38	AY.4.2	0.000824
ORF1ab/nsp3	1297	R1297I	aGa	aTa	37	37	AY.4	0.000058
ORF1ab/nsp3	1297	R1297R	agA	agG	33	35	B.1.1.7	0.00003
ORF1ab/nsp3	1297	R1297R	AgA	CgC	1	35	B.1.1.7	0.000001
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	35	B.1.1.7	0.000001
ORF1ab/nsp3	1297	R1297K	aGa	aAa	32	32	B.1.2	0.000282
ORF1ab/nsp3	1297	R1297I	aGa	aTa	31	31	A.23.1	0.021831
ORF1ab/nsp3	1297	R1297G	Aga	Gga	31	31	AY.44	0.000189
ORF1ab/nsp3	1297	R1297S	agA	agT	27	29	B.1	0.000247
ORF1ab/nsp3	1297	R1297S	agA	agC	2	29	B.1	0.000018
ORF1ab/nsp3	1297	R1297S	agA	agT	26	26	B.1.36.1	0.029647
ORF1ab/nsp3	1297	R1297G	Aga	Gga	25	25	AY.4	0.000039
ORF1ab/nsp3	1297	R1297K	aGa	aAa	25	25	B.1.160	0.00078
ORF1ab/nsp3	1297	R1297G	Aga	Gga	25	25	B.1.462	0.181159
ORF1ab/nsp3	1297	R1297I	aGa	aTa	23	23	AY.4.5	0.002472
ORF1ab/nsp3	1297	R1297I	aGa	aTa	22	22	B.1.2	0.000194
ORF1ab/nsp3	1297	R1297I	aGa	aTa	19	19	B.1.1	0.000345
ORF1ab/nsp3	1297	R1297R	agA	agG	19	19	B.1.617.2	0.000072
ORF1ab/nsp3	1297	R1297G	Aga	Gga	19	19	C.37	0.002205
ORF1ab/nsp3	1297	R1297S	agA	agC	17	18	AY.4	0.000026
ORF1ab/nsp3	1297	R1297S	agA	agT	1	18	AY.4	0.000002
ORF1ab/nsp3	1297	R1297G	Aga	Gga	18	18	Q.2	0.011043
ORF1ab/nsp3	1297	R1297G	Aga	Gga	17	17	B.1	0.000156
ORF1ab/nsp3	1297	R1297I	aGa	aTa	17	17	B.1	0.000156
ORF1ab/nsp3	1297	R1297G	Aga	Gga	17	17	B.1.1.7	0.000015
ORF1ab/nsp3	1297	R1297I	aGa	aTa	16	16	AY.106	0.005358
ORF1ab/nsp3	1297	R1297K	aGa	aAa	16	16	AY.3	0.000159
ORF1ab/nsp3	1297	R1297R	agA	agG	16	16	B.1.2	0.000141
ORF1ab/nsp3	1297	R1297del	AGA	---	15	15	B.1.177	0.000198
ORF1ab/nsp3	1297	R1297R	agA	agG	13	13	AY.33	0.000868
ORF1ab/nsp3	1297	R1297R	Aga	Cga	6	11	AY.117	0.000507
ORF1ab/nsp3	1297	R1297R	agA	agG	5	11	AY.117	0.000423
ORF1ab/nsp3	1297	R1297R	agA	agG	10	10	AY.25	0.00006
ORF1ab/nsp3	1297	R1297del1	agA	ag-	5	9	All	0.000001
ORF1ab/nsp3	1297	R1297del1	Aga	-ga	4	9	All	0.000001
ORF1ab/nsp3	1297	R1297del	AGA	---	9	9	AY.25	0.000054
ORF1ab/nsp3	1297	R1297I	aGa	aTa	9	9	B.1.160	0.000281
ORF1ab/nsp3	1297	R1297del	AGA	---	9	9	B.1.617.2	0.000034
ORF1ab/nsp3	1297	R1297del	AGA	---	8	8	AY.43	0.000035
ORF1ab/nsp3	1297	R1297I	aGa	aTa	8	8	B.1.525	0.000905
ORF1ab/nsp3	1297	R1297X	Aga	Tga	7	7	All	0.000001
ORF1ab/nsp3	1297	R1297I	aGa	aTa	7	7	AY.3	0.00007
ORF1ab/nsp3	1297	R1297R	agA	agG	7	7	AY.4	0.000011
ORF1ab/nsp3	1297	R1297del	AGA	---	7	7	AY.4.5	0.000752
ORF1ab/nsp3	1297	R1297I	aGa	aTa	7	7	AY.43	0.000031
ORF1ab/nsp3	1297	R1297T	aGa	aCa	7	7	B.1.1.7	0.000006
ORF1ab/nsp3	1297	R1297I	aGa	aTa	7	7	B.1.131	0.061404
ORF1ab/nsp3	1297	R1297G	Aga	Gga	7	7	B.1.427	0.000353
ORF1ab/nsp3	1297	R1297K	aGa	aAa	7	7	B.1.636	0.04698
ORF1ab/nsp3	1297	R1297I	aGa	aTa	6	6	AY.102	0.000159
ORF1ab/nsp3	1297	R1297K	aGa	aAa	6	6	AY.36	0.000889
ORF1ab/nsp3	1297	R1297K	aGa	aAa	6	6	AY.4	0.000009
ORF1ab/nsp3	1297	R1297I	aGa	aTa	6	6	AY.9.2	0.00022
ORF1ab/nsp3	1297	R1297I	aGa	aTa	6	6	B.1.177	0.000079
ORF1ab/nsp3	1297	R1297R	agA	agG	6	6	P.1	0.000095
ORF1ab/nsp3	1297	R1297K	aGa	aAa	5	5		0.277778
ORF1ab/nsp3	1297	R1297I	aGa	aTa	5	5	AY.103	0.000031
ORF1ab/nsp3	1297	R1297G	Aga	Gga	5	5	AY.103	0.000031
ORF1ab/nsp3	1297	R1297G	Aga	Gga	5	5	AY.39	0.000124
ORF1ab/nsp3	1297	R1297I	aGa	aTa	5	5	AY.9	0.000338
ORF1ab/nsp3	1297	R1297I	aGa	aTa	5	5	B.1.1.519	0.000199
ORF1ab/nsp3	1297	R1297S	agA	agC	5	5	B.1.617.2	0.000019
ORF1ab/nsp3	1297	R1297K	aGa	aAa	5	5	P.1	0.000079
ORF1ab/nsp3	1297	R1297L	AGa	TTa	3	4	All	0.000001
ORF1ab/nsp3	1297	R1297L	AGa	CTa	1	4	All	0
ORF1ab/nsp3	1297	R1297S	agA	agT	4	4	AY.103	0.000025
ORF1ab/nsp3	1297	R1297I	aGa	aTa	4	4	AY.8	0.002424
ORF1ab/nsp3	1297	R1297I	aGa	aTa	4	4	AY.99.2	0.000369
ORF1ab/nsp3	1297	R1297del	AGA	---	4	4	B.1.1	0.000073
ORF1ab/nsp3	1297	R1297S	agA	agT	3	4	B.1.1	0.000054
ORF1ab/nsp3	1297	R1297S	agA	agC	1	4	B.1.1	0.000018
ORF1ab/nsp3	1297	R1297K	aGa	aAa	4	4	B.1.1.7	0.000004
ORF1ab/nsp3	1297	R1297S	agA	agC	4	4	B.1.177.12	0.000607
ORF1ab/nsp3	1297	R1297del	AGA	---	4	4	B.1.597	0.018519
ORF1ab/nsp3	1297	R1297I	aGa	aTa	4	4	C.14	0.017316
ORF1ab/nsp3	1297	R1297N	aGA	aAT	3	3	All	0.000001
ORF1ab/nsp3	1297	R1297R	agA	agG	3	3	AY.103	0.000019
ORF1ab/nsp3	1297	R1297R	agA	agG	3	3	AY.116	0.00086
ORF1ab/nsp3	1297	R1297S	agA	agT	2	3	AY.3	0.00002
ORF1ab/nsp3	1297	R1297S	agA	agC	1	3	AY.3	0.00001
ORF1ab/nsp3	1297	R1297R	agA	agG	3	3	AY.44	0.000018
ORF1ab/nsp3	1297	R1297I	aGa	aTa	3	3	AY.47	0.000093
ORF1ab/nsp3	1297	R1297del	AGA	---	3	3	B.1	0.000027
ORF1ab/nsp3	1297	R1297S	agA	agT	3	3	B.1.177	0.00004
ORF1ab/nsp3	1297	R1297R	agA	agG	3	3	B.1.243	0.000209
ORF1ab/nsp3	1297	R1297R	agA	agG	3	3	B.1.526	0.000071
ORF1ab/nsp3	1297	R1297G	Aga	Gga	3	3	B.1.617.2	0.000011
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2		0.111111
ORF1ab/nsp3	1297	R1297T	aGa	aCa	2	2		0.111111
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	2		0.055556
ORF1ab/nsp3	1297	R1297R	AgA	CgT	1	2		0.055556
ORF1ab/nsp3	1297	R1297del2	AGa	--a	2	2	All	0
ORF1ab/nsp3	1297	R1297Q	AGa	CAa	2	2	All	0
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	AU.2	0.004843
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	AY.1	0.000791
ORF1ab/nsp3	1297	R1297G	Aga	Gga	2	2	AY.102	0.000053
ORF1ab/nsp3	1297	R1297G	Aga	Gga	2	2	AY.119	0.000071
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	AY.120	0.000074
ORF1ab/nsp3	1297	R1297R	agA	agG	2	2	AY.14	0.000176
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	AY.14	0.000176
ORF1ab/nsp3	1297	R1297G	Aga	Gga	2	2	AY.23	0.000139
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	AY.29	0.000032
ORF1ab/nsp3	1297	R1297R	agA	agG	1	2	AY.29	0.000016
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	2	AY.29	0.000016
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	AY.39	0.000049
ORF1ab/nsp3	1297	R1297S	agA	agC	2	2	AY.43	0.000009
ORF1ab/nsp3	1297	R1297G	Aga	Gga	2	2	AY.43	0.000009
ORF1ab/nsp3	1297	R1297R	AgA	CgT	1	2	AY.43	0.000004
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	2	AY.43	0.000004
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	AY.44	0.000012
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	AY.5	0.000041
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	AY.58	0.001815
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	AY.75.1	0.000361
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	AY.98.1	0.000097
ORF1ab/nsp3	1297	R1297S	agA	agC	2	2	AY.99.2	0.000184
ORF1ab/nsp3	1297	R1297T	aGa	aCa	2	2	B.1	0.000018
ORF1ab/nsp3	1297	R1297T	aGa	aCa	2	2	B.1.1	0.000036
ORF1ab/nsp3	1297	R1297K	aGa	aAa	2	2	B.1.1	0.000036
ORF1ab/nsp3	1297	R1297R	agA	agG	1	2	B.1.1	0.000018
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	2	B.1.1	0.000018
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.1.294	0.002532
ORF1ab/nsp3	1297	R1297S	agA	agC	2	2	B.1.1.382	0.071429
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.1.39	0.001019
ORF1ab/nsp3	1297	R1297del1	Aga	-ga	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.160.16	0.001859
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.160.20	0.017857
ORF1ab/nsp3	1297	R1297R	agA	agG	2	2	B.1.177	0.000026
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.177.23	0.006472
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	B.1.177.4	0.000422
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.177.44	0.001038
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	B.1.177.7	0.00033
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	B.1.177.87	0.001456
ORF1ab/nsp3	1297	R1297T	aGa	aCa	2	2	B.1.2	0.000018
ORF1ab/nsp3	1297	R1297S	agA	agC	1	2	B.1.2	0.000009
ORF1ab/nsp3	1297	R1297S	agA	agT	1	2	B.1.2	0.000009
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.221	0.000142
ORF1ab/nsp3	1297	R1297S	agA	agT	2	2	B.1.221	0.000142
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.236	0.004107
ORF1ab/nsp3	1297	R1297S	agA	agC	2	2	B.1.241	0.001623
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	B.1.243	0.000139
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	B.1.351	0.000059
ORF1ab/nsp3	1297	R1297del	AGA	---	2	2	B.1.36.17	0.000988
ORF1ab/nsp3	1297	R1297R	agA	agG	2	2	B.1.427	0.000101
ORF1ab/nsp3	1297	R1297G	Aga	Gga	2	2	B.1.429	0.000047
ORF1ab/nsp3	1297	R1297G	Aga	Gga	2	2	B.1.466.2	0.000782
ORF1ab/nsp3	1297	R1297X	Aga	Tga	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1297	R1297S	agA	agC	2	2	B.1.621	0.000177
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	C.36.3.1	0.005435
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	D.2	0.00015
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	P.1	0.000032
ORF1ab/nsp3	1297	R1297S	agA	agC	2	2	P.1	0.000032
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	2	P.1	0.000016
ORF1ab/nsp3	1297	R1297G	AgA	GgC	1	2	P.1	0.000016
ORF1ab/nsp3	1297	R1297I	aGa	aTa	2	2	P.1.7	0.000639
ORF1ab/nsp3	1297	R1297G	Aga	Gga	2	2	P.2	0.000373
ORF1ab/nsp3	1297	R1297N	aGA	aAT	1	1		0.055556
ORF1ab/nsp3	1297	R1297H	AGA	CAT	1	1		0.055556
ORF1ab/nsp3	1297	R1297Q	AGa	CAa	1	1		0.055556
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1		0.055556
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	A	0.000387
ORF1ab/nsp3	1297	R1297T	aGa	aCa	1	1	A.1	0.000282
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	A.2.5.3	0.010309
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	1	A.5	0.001923
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AD.2	0.000219
ORF1ab/nsp3	1297	R1297V	AGa	GTa	1	1	All	0
ORF1ab/nsp3	1297	R1297E	AGa	GAa	1	1	All	0
ORF1ab/nsp3	1297	R1297H	AGA	CAT	1	1	All	0
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AU.2	0.002421
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	1	AY.100	0.000046
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.100	0.000046
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.102	0.000027
ORF1ab/nsp3	1297	R1297del1	agA	ag-	1	1	AY.103	0.000006
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.110	0.000113
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.113	0.000142
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.114	0.000231
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.115	0.005208
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.116	0.000287
ORF1ab/nsp3	1297	R1297V	AGa	GTa	1	1	AY.119	0.000035
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.119	0.000035
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.119	0.000035
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.12	0.000316
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.12	0.000316
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.120	0.000037
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.120	0.000037
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.14	0.000088
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.16	0.00038
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.17	0.008197
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.19	0.00114
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.19	0.00114
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.20	0.000039
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.20	0.000039
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.24	0.000431
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.25	0.000006
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	AY.25	0.000006
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.3	0.00001
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.30	0.000396
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	AY.33	0.000067
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.37	0.000316
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	AY.39	0.000025
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.39	0.000025
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.39	0.000025
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.39	0.000025
ORF1ab/nsp3	1297	R1297del1	Aga	-ga	1	1	AY.4	0.000002
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1297	R1297del1	Aga	-ga	1	1	AY.43	0.000004
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	AY.44	0.000006
ORF1ab/nsp3	1297	R1297del1	agA	ag-	1	1	AY.44	0.000006
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.45	0.000122
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.45	0.000122
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.46	0.000104
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.46	0.000104
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.46.1	0.001027
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.47	0.000031
ORF1ab/nsp3	1297	R1297E	AGa	GAa	1	1	AY.48	0.000465
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.5	0.000021
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.51	0.000909
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	AY.54	0.000095
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.6	0.000041
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.60	0.000938
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.67	0.000464
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	AY.70	0.000209
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.75	0.000056
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	AY.75.1	0.00018
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.84	0.000437
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.84	0.000437
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	AY.85	0.000427
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	AY.87	0.000833
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1297	R1297del2	AGa	--a	1	1	AY.9	0.000068
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	AY.9.1	0.000084
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AY.95	0.000761
ORF1ab/nsp3	1297	R1297R	Aga	Cga	1	1	AY.98	0.000079
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	AY.99	0.001049
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	AZ.2	0.000821
ORF1ab/nsp3	1297	R1297del1	agA	ag-	1	1	B.1	0.000009
ORF1ab/nsp3	1297	R1297N	aGA	aAT	1	1	B.1	0.000009
ORF1ab/nsp3	1297	R1297R	AgA	CgT	1	1	B.1	0.000009
ORF1ab/nsp3	1297	R1297X	Aga	Tga	1	1	B.1.1	0.000018
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	B.1.1.16	0.055556
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.1.161	0.003534
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.1.176	0.000439
ORF1ab/nsp3	1297	R1297L	AGa	TTa	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.1.236	0.006897
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1297	R1297del1	agA	ag-	1	1	B.1.1.301	0.001179
ORF1ab/nsp3	1297	R1297Q	AGa	CAa	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	B.1.1.354	0.004386
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.1.398	0.003226
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	1297	R1297T	aGa	aCa	1	1	B.1.1.420	0.001006
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.1.44	0.00241
ORF1ab/nsp3	1297	R1297del2	AGa	--a	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1297	R1297X	Aga	Tga	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1297	R1297T	aGa	aCa	1	1	B.1.110.3	0.000718
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.111	0.001175
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	B.1.124	0.007812
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.146	0.004237
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	B.1.157	0.002985
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.160.29	0.004219
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.160.31	0.008065
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	B.1.173	0.026316
ORF1ab/nsp3	1297	R1297T	aGa	aCa	1	1	B.1.177	0.000013
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.11	0.001698
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.177.28	0.007407
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.177.31	0.011494
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.177.43	0.001477
ORF1ab/nsp3	1297	R1297X	Aga	Tga	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.56	0.000668
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.58	0.001332
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.6	0.000977
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	B.1.195	0.005025
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	B.1.2	0.000009
ORF1ab/nsp3	1297	R1297X	Aga	Tga	1	1	B.1.2	0.000009
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	B.1.218	0.005155
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.221	0.000071
ORF1ab/nsp3	1297	R1297T	aGa	aCa	1	1	B.1.243	0.00007
ORF1ab/nsp3	1297	R1297X	Aga	Tga	1	1	B.1.258	0.000067
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	B.1.258	0.000067
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.258	0.000067
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.258.10	0.011364
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.258.11	0.000396
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	B.1.351	0.00003
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	B.1.36	0.000146
ORF1ab/nsp3	1297	R1297L	AGa	TTa	1	1	B.1.36	0.000146
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.36.1	0.00114
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.36.18	0.00042
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.36.35	0.002604
ORF1ab/nsp3	1297	R1297L	AGa	CTa	1	1	B.1.36.8	0.001
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	B.1.398	0.002976
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.409	0.000781
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.456	0.003268
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.459	0.004082
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	B.1.459	0.004082
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	B.1.470	0.001404
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	B.1.526	0.000024
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.526	0.000024
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	B.1.546	0.003704
ORF1ab/nsp3	1297	R1297S	agA	agC	1	1	B.1.551	0.00129
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	B.1.561	0.000397
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.564	0.000426
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.568	0.001111
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.577	0.000687
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	B.1.595	0.000261
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	B.1.595	0.000261
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	B.1.595	0.000261
ORF1ab/nsp3	1297	R1297N	aGA	aAT	1	1	B.1.595	0.000261
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.596	0.000087
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.599	0.00365
ORF1ab/nsp3	1297	R1297del1	agA	ag-	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.617.3	0.002985
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	B.1.621	0.000089
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.621	0.000089
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.1.630	0.005236
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.636	0.006711
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	B.1.637	0.000073
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	B.34	0.013699
ORF1ab/nsp3	1297	R1297K	aGa	aAa	1	1	B.40	0.000364
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	B.6	0.00091
ORF1ab/nsp3	1297	R1297L	AGa	TTa	1	1	C.35	0.000774
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	C.37	0.000116
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	C.37.1	0.002618
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	N.6	0.007092
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	P.1	0.000016
ORF1ab/nsp3	1297	R1297S	agA	agT	1	1	P.1.14	0.000048
ORF1ab/nsp3	1297	R1297R	agA	agG	1	1	P.1.14	0.000048
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	P.1.15	0.000232
ORF1ab/nsp3	1297	R1297I	aGa	aTa	1	1	P.2	0.000187
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	Q.1	0.000126
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	Q.4	0.000455
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	Q.8	0.000165
ORF1ab/nsp3	1297	R1297G	Aga	Gga	1	1	R.1	0.00009
ORF1ab/nsp3	1297	R1297del	AGA	---	1	1	U.3	0.003861

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.