CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 819

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	819	E819E		syn	gaA	gaG	368	368	1	24017-24019
S	819	E819del		del	GAA	---	123	123	1	24017-24019
S	819	E819K		nonsyn	Gaa	Aaa	9	8	0.888889	24017-24019
S	819	E819K		nonsyn	GaA	AaG	9	1	0.111111	24017-24019
S	819	E819X		nonsyn	Gaa	Taa	8	8	1	24017-24019
S	819	E819D		nonsyn	gaA	gaC	7	7	1	24017-24019
S	819	E819del2		del	gAA	g--	6	6	1	24017-24019
S	819	E819G		nonsyn	gAa	gGa	6	6	1	24017-24019
S	819	E819Q		nonsyn	Gaa	Caa	5	5	1	24017-24019
S	819	E819V		nonsyn	gAa	gTa	3	3	1	24017-24019
S	819	E819del1		del	gAa	g-a	3	2	0.666667	24017-24019
S	819	E819del1		del	GaA	-aN	3	1	0.333333	24017-24019
S	819	E819R		nonsyn	GAa	CGa	1	1	1	24017-24019

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	819	E819E	gaA	gaG	368	368	All	0.00007
S	819	E819del	GAA	---	123	123	All	0.000024
S	819	E819E	gaA	gaG	80	80	B.1.617.2	0.000301
S	819	E819E	gaA	gaG	40	40	B.1.1.394	0.97561
S	819	E819E	gaA	gaG	38	38	B.1.1.7	0.000034
S	819	E819E	gaA	gaG	25	25	AY.42	0.001006
S	819	E819E	gaA	gaG	23	23	AY.102	0.00061
S	819	E819del	GAA	---	21	21	B.1.1.7	0.000019
S	819	E819E	gaA	gaG	20	20	AY.44	0.000122
S	819	E819E	gaA	gaG	18	18	AY.25	0.000108
S	819	E819E	gaA	gaG	16	16	AY.43	0.000071
S	819	E819E	gaA	gaG	15	15	AY.4	0.000023
S	819	E819del	GAA	---	10	10	B.1	0.000092
S	819	E819K	Gaa	Aaa	8	9	All	0.000002
S	819	E819K	GaA	AaG	1	9	All	0
S	819	E819E	gaA	gaG	9	9	P.1	0.000142
S	819	E819X	Gaa	Taa	8	8	All	0.000002
S	819	E819del	GAA	---	8	8	AY.43	0.000035
S	819	E819E	gaA	gaG	8	8	AY.95	0.006088
S	819	E819D	gaA	gaC	7	7	All	0.000001
S	819	E819del	GAA	---	7	7	B.1.621	0.00062
S	819	E819del2	gAA	g--	6	6	All	0.000001
S	819	E819G	gAa	gGa	6	6	All	0.000001
S	819	E819Q	Gaa	Caa	5	5	All	0.000001
S	819	E819E	gaA	gaG	5	5	AY.100	0.00023
S	819	E819E	gaA	gaG	5	5	AY.54	0.000477
S	819	E819E	gaA	gaG	5	5	B.1.2	0.000044
S	819	E819del	GAA	---	5	5	P.1	0.000079
S	819	E819del	GAA	---	5	5	P.1.15	0.001162
S	819	E819del	GAA	---	4	4	AY.4.5	0.00043
S	819	E819del	GAA	---	4	4	B.1.1	0.000073
S	819	E819del	GAA	---	4	4	B.1.2	0.000035
S	819	E819D	gaA	gaC	4	4	C.21	0.571429
S	819	E819V	gAa	gTa	3	3	All	0.000001
S	819	E819del1	gAa	g-a	2	3	All	0
S	819	E819del1	GaA	-aN	1	3	All	0
S	819	E819E	gaA	gaG	3	3	AY.23	0.000209
S	819	E819del	GAA	---	3	3	AY.25	0.000018
S	819	E819E	gaA	gaG	3	3	AY.39	0.000074
S	819	E819E	gaA	gaG	3	3	AY.4.4	0.001227
S	819	E819del	GAA	---	3	3	AY.44	0.000018
S	819	E819E	gaA	gaG	3	3	AY.82	0.004071
S	819	E819E	gaA	gaG	3	3	B.1	0.000027
S	819	E819E	gaA	gaG	2	2	AY.103	0.000012
S	819	E819E	gaA	gaG	2	2	AY.118	0.000125
S	819	E819E	gaA	gaG	2	2	AY.119	0.000071
S	819	E819E	gaA	gaG	2	2	AY.3	0.00002
S	819	E819del	GAA	---	2	2	AY.4	0.000003
S	819	E819del2	gAA	g--	2	2	AY.75	0.000112
S	819	E819del	GAA	---	2	2	AY.9.2	0.000073
S	819	E819del	GAA	---	2	2	AY.99.2	0.000184
S	819	E819K	Gaa	Aaa	2	2	B.1	0.000018
S	819	E819D	gaA	gaC	2	2	B.1	0.000018
S	819	E819E	gaA	gaG	2	2	B.1.1.232	0.00363
S	819	E819del	GAA	---	2	2	B.1.1.236	0.013793
S	819	E819E	gaA	gaG	2	2	B.1.1.28	0.000622
S	819	E819del	GAA	---	2	2	B.1.177.63	0.005405
S	819	E819E	gaA	gaG	2	2	B.1.36	0.000292
S	819	E819del	GAA	---	2	2	B.1.526	0.000047
S	819	E819E	gaA	gaG	2	2	B.1.582	0.000981
S	819	E819del	GAA	---	2	2	B.1.617.2	0.000008
S	819	E819E	gaA	gaG	2	2	R.1	0.00018
S	819	E819del	GAA	---	1	1	A	0.000387
S	819	E819R	GAa	CGa	1	1	All	0
S	819	E819E	gaA	gaG	1	1	AW.1	0.003049
S	819	E819del	GAA	---	1	1	AY.10	0.00053
S	819	E819E	gaA	gaG	1	1	AY.10	0.00053
S	819	E819del	GAA	---	1	1	AY.100	0.000046
S	819	E819del2	gAA	g--	1	1	AY.103	0.000006
S	819	E819del	GAA	---	1	1	AY.103	0.000006
S	819	E819Q	Gaa	Caa	1	1	AY.103	0.000006
S	819	E819G	gAa	gGa	1	1	AY.103	0.000006
S	819	E819E	gaA	gaG	1	1	AY.108	0.001103
S	819	E819del2	gAA	g--	1	1	AY.117	0.000085
S	819	E819del2	gAA	g--	1	1	AY.119	0.000035
S	819	E819E	gaA	gaG	1	1	AY.12	0.000316
S	819	E819del	GAA	---	1	1	AY.120	0.000037
S	819	E819Q	Gaa	Caa	1	1	AY.120	0.000037
S	819	E819G	gAa	gGa	1	1	AY.120	0.000037
S	819	E819E	gaA	gaG	1	1	AY.13	0.000161
S	819	E819del	GAA	---	1	1	AY.14	0.000088
S	819	E819del	GAA	---	1	1	AY.24	0.000431
S	819	E819G	gAa	gGa	1	1	AY.25	0.000006
S	819	E819E	gaA	gaG	1	1	AY.26	0.000028
S	819	E819del	GAA	---	1	1	AY.26	0.000028
S	819	E819E	gaA	gaG	1	1	AY.36	0.000148
S	819	E819E	gaA	gaG	1	1	AY.4.2	0.000022
S	819	E819E	gaA	gaG	1	1	AY.4.3	0.000842
S	819	E819del1	gAa	g-a	1	1	AY.43	0.000004
S	819	E819K	Gaa	Aaa	1	1	AY.43	0.000004
S	819	E819V	gAa	gTa	1	1	AY.43	0.000004
S	819	E819X	Gaa	Taa	1	1	AY.43	0.000004
S	819	E819K	Gaa	Aaa	1	1	AY.44	0.000006
S	819	E819Q	Gaa	Caa	1	1	AY.45	0.000122
S	819	E819Q	Gaa	Caa	1	1	AY.46	0.000104
S	819	E819del	GAA	---	1	1	AY.46.2	0.000635
S	819	E819E	gaA	gaG	1	1	AY.46.6	0.000072
S	819	E819X	Gaa	Taa	1	1	AY.47	0.000031
S	819	E819del	GAA	---	1	1	AY.61	0.000105
S	819	E819E	gaA	gaG	1	1	AY.61	0.000105
S	819	E819del	GAA	---	1	1	AY.68	0.000274
S	819	E819E	gaA	gaG	1	1	AY.7	0.000196
S	819	E819E	gaA	gaG	1	1	AY.75	0.000056
S	819	E819del	GAA	---	1	1	AY.98.1	0.000048
S	819	E819K	Gaa	Aaa	1	1	AY.98.1	0.000048
S	819	E819del	GAA	---	1	1	B	0.000128
S	819	E819del2	gAA	g--	1	1	B.1	0.000009
S	819	E819Q	Gaa	Caa	1	1	B.1	0.000009
S	819	E819V	gAa	gTa	1	1	B.1	0.000009
S	819	E819X	Gaa	Taa	1	1	B.1	0.000009
S	819	E819E	gaA	gaG	1	1	B.1.1	0.000018
S	819	E819X	Gaa	Taa	1	1	B.1.1	0.000018
S	819	E819del	GAA	---	1	1	B.1.1.161	0.003534
S	819	E819D	gaA	gaC	1	1	B.1.1.269	0.001353
S	819	E819G	gAa	gGa	1	1	B.1.1.289	0.002083
S	819	E819E	gaA	gaG	1	1	B.1.1.31	0.066667
S	819	E819del	GAA	---	1	1	B.1.1.315	0.008475
S	819	E819del	GAA	---	1	1	B.1.1.409	0.002833
S	819	E819del1	GaA	-aN	1	1	B.1.1.519	0.00004
S	819	E819E	gaA	gaG	1	1	B.1.1.523	0.001563
S	819	E819K	Gaa	Aaa	1	1	B.1.1.7	0.000001
S	819	E819R	GAa	CGa	1	1	B.1.1.7	0.000001
S	819	E819G	gAa	gGa	1	1	B.1.1.7	0.000001
S	819	E819E	gaA	gaG	1	1	B.1.147	0.000756
S	819	E819del	GAA	---	1	1	B.1.160	0.000031
S	819	E819V	gAa	gTa	1	1	B.1.177	0.000013
S	819	E819del	GAA	---	1	1	B.1.177	0.000013
S	819	E819E	gaA	gaG	1	1	B.1.177	0.000013
S	819	E819del	GAA	---	1	1	B.1.177.17	0.000821
S	819	E819K	Gaa	Aaa	1	1	B.1.177.21	0.000076
S	819	E819del	GAA	---	1	1	B.1.177.44	0.000519
S	819	E819del	GAA	---	1	1	B.1.177.51	0.004566
S	819	E819E	gaA	gaG	1	1	B.1.177.53	0.002392
S	819	E819G	gAa	gGa	1	1	B.1.2	0.000009
S	819	E819E	gaA	gaG	1	1	B.1.221	0.000071
S	819	E819del	GAA	---	1	1	B.1.234	0.000132
S	819	E819del	GAA	---	1	1	B.1.258	0.000067
S	819	E819X	Gaa	Taa	1	1	B.1.258.21	0.007752
S	819	E819del	GAA	---	1	1	B.1.311	0.000275
S	819	E819del	GAA	---	1	1	B.1.369	0.000285
S	819	E819E	gaA	gaG	1	1	B.1.427	0.00005
S	819	E819E	gaA	gaG	1	1	B.1.429	0.000024
S	819	E819E	gaA	gaG	1	1	B.1.456	0.003268
S	819	E819del	GAA	---	1	1	B.1.466.2	0.000391
S	819	E819E	gaA	gaG	1	1	B.1.517	0.000427
S	819	E819del1	gAa	g-a	1	1	B.1.526	0.000024
S	819	E819E	gaA	gaG	1	1	B.1.575.1	0.002439
S	819	E819del	GAA	---	1	1	B.1.582	0.000491
S	819	E819E	gaA	gaG	1	1	B.1.595	0.000261
S	819	E819del	GAA	---	1	1	B.1.596	0.000087
S	819	E819del	GAA	---	1	1	B.1.606	0.006024
S	819	E819K	GaA	AaG	1	1	B.1.617.2	0.000004
S	819	E819del	GAA	---	1	1	B.1.638	0.052632
S	819	E819del	GAA	---	1	1	B.3	0.000831
S	819	E819X	Gaa	Taa	1	1	B.6	0.00091
S	819	E819X	Gaa	Taa	1	1	B.6.6	0.000889
S	819	E819E	gaA	gaG	1	1	C.35	0.000774
S	819	E819del	GAA	---	1	1	C.37	0.000116
S	819	E819del	GAA	---	1	1	D.2	0.000075
S	819	E819K	Gaa	Aaa	1	1	P.1	0.000016
S	819	E819del	GAA	---	1	1	P.1.13	0.000898
S	819	E819del	GAA	---	1	1	P.1.7	0.000319
S	819	E819E	gaA	gaG	1	1	Q.4	0.000455
S	819	E819X	Gaa	Taa	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.