CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = E : CodonNum = 3

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
E	3	S3S		syn	tcA	tcT	239	97	0.405858	26251-26253
E	3	S3S		syn	tcA	tcC	239	92	0.384937	26251-26253
E	3	S3S		syn	tcA	tcG	239	50	0.209205	26251-26253
E	3	S3L		nonsyn	tCa	tTa	140	140	1	26251-26253
E	3	S3P		nonsyn	Tca	Cca	123	123	1	26251-26253
E	3	S3X		nonsyn	tCa	tGa	26	21	0.807692	26251-26253
E	3	S3X		nonsyn	tCa	tAa	26	5	0.192308	26251-26253
E	3	S3del		del	TCA	---	11	11	1	26251-26253
E	3	S3A		nonsyn	Tca	Gca	7	7	1	26251-26253
E	3	S3T		nonsyn	Tca	Aca	4	4	1	26251-26253
E	3	S3H		nonsyn	TCA	CAT	2	2	1	26251-26253
E	3	S3del1		del	Tca	-ca	1	1	1	26251-26253

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
E	3	S3S	tcA	tcT	97	239	All	0.000019
E	3	S3S	tcA	tcC	92	239	All	0.000018
E	3	S3S	tcA	tcG	50	239	All	0.00001
E	3	S3L	tCa	tTa	140	140	All	0.000027
E	3	S3P	Tca	Cca	123	123	All	0.000024
E	3	S3S	tcA	tcC	51	62	B.1.617.2	0.000192
E	3	S3S	tcA	tcT	10	62	B.1.617.2	0.000038
E	3	S3S	tcA	tcG	1	62	B.1.617.2	0.000004
E	3	S3P	Tca	Cca	48	48	B.1.1.7	0.000043
E	3	S3P	Tca	Cca	32	32	AY.44	0.000195
E	3	S3X	tCa	tGa	21	26	All	0.000004
E	3	S3X	tCa	tAa	5	26	All	0.000001
E	3	S3L	tCa	tTa	23	23	AY.4	0.000036
E	3	S3S	tcA	tcT	11	23	B.1.1.7	0.00001
E	3	S3S	tcA	tcC	6	23	B.1.1.7	0.000005
E	3	S3S	tcA	tcG	6	23	B.1.1.7	0.000005
E	3	S3S	tcA	tcG	13	17	AY.4	0.00002
E	3	S3S	tcA	tcT	3	17	AY.4	0.000005
E	3	S3S	tcA	tcC	1	17	AY.4	0.000002
E	3	S3L	tCa	tTa	16	16	B.1.1.434	0.005577
E	3	S3S	tcA	tcT	15	15	B.1.177	0.000198
E	3	S3L	tCa	tTa	13	13	B.1.617.1	0.001677
E	3	S3L	tCa	tTa	12	12	B.1.1.7	0.000011
E	3	S3del	TCA	---	11	11	All	0.000002
E	3	S3P	Tca	Cca	11	11	AY.4	0.000017
E	3	S3S	tcA	tcC	7	11	AY.5	0.000145
E	3	S3S	tcA	tcT	4	11	AY.5	0.000083
E	3	S3S	tcA	tcT	8	10	AY.25	0.000048
E	3	S3S	tcA	tcG	2	10	AY.25	0.000012
E	3	S3L	tCa	tTa	10	10	B.1.617.2	0.000038
E	3	S3S	tcA	tcC	5	9	AY.103	0.000031
E	3	S3S	tcA	tcG	3	9	AY.103	0.000019
E	3	S3S	tcA	tcT	1	9	AY.103	0.000006
E	3	S3X	tCa	tGa	9	9	B.1.1.7	0.000008
E	3	S3X	tCa	tGa	9	9	B.1.525	0.001018
E	3	S3A	Tca	Gca	7	7	All	0.000001
E	3	S3S	tcA	tcT	6	7	AY.44	0.000037
E	3	S3S	tcA	tcG	1	7	AY.44	0.000006
E	3	S3S	tcA	tcT	4	7	B.1.1	0.000073
E	3	S3S	tcA	tcG	2	7	B.1.1	0.000036
E	3	S3S	tcA	tcC	1	7	B.1.1	0.000018
E	3	S3S	tcA	tcG	4	7	B.1.2	0.000035
E	3	S3S	tcA	tcT	3	7	B.1.2	0.000026
E	3	S3S	tcA	tcC	7	7	D.2	0.000525
E	3	S3S	tcA	tcT	6	6	AH.1	0.857143
E	3	S3P	Tca	Cca	6	6	B.1.427	0.000303
E	3	S3L	tCa	tTa	6	6	P.1	0.000095
E	3	S3L	tCa	tTa	5	5	AY.4.2	0.000108
E	3	S3S	tcA	tcT	4	5	AY.43	0.000018
E	3	S3S	tcA	tcG	1	5	AY.43	0.000004
E	3	S3T	Tca	Aca	4	4	All	0.000001
E	3	S3L	tCa	tTa	4	4	AY.20	0.000155
E	3	S3A	Tca	Gca	4	4	AY.26	0.000113
E	3	S3L	tCa	tTa	4	4	AY.44	0.000024
E	3	S3X	tCa	tAa	3	4	B.1	0.000027
E	3	S3X	tCa	tGa	1	4	B.1	0.000009
E	3	S3L	tCa	tTa	3	3	AY.102	0.00008
E	3	S3S	tcA	tcC	3	3	AY.16	0.001139
E	3	S3L	tCa	tTa	3	3	AY.25	0.000018
E	3	S3L	tCa	tTa	3	3	AY.39	0.000074
E	3	S3S	tcA	tcC	2	3	AY.39	0.000049
E	3	S3S	tcA	tcT	1	3	AY.39	0.000025
E	3	S3L	tCa	tTa	3	3	AY.43	0.000013
E	3	S3L	tCa	tTa	3	3	B.1.177.81	0.000568
E	3	S3L	tCa	tTa	3	3	B.1.2	0.000026
E	3	S3S	tcA	tcC	3	3	B.1.235	0.007557
E	3	S3T	Tca	Aca	3	3	B.1.427	0.000151
E	3	S3del	TCA	---	2	2		0.111111
E	3	S3H	TCA	CAT	2	2		0.111111
E	3	S3H	TCA	CAT	2	2	All	0
E	3	S3P	Tca	Cca	2	2	AY.102	0.000053
E	3	S3S	tcA	tcT	2	2	AY.117	0.000169
E	3	S3S	tcA	tcG	2	2	AY.20	0.000078
E	3	S3L	tCa	tTa	2	2	AY.26	0.000057
E	3	S3S	tcA	tcT	2	2	AY.27	0.000129
E	3	S3P	Tca	Cca	2	2	AY.4.5	0.000215
E	3	S3P	Tca	Cca	2	2	AY.6	0.000082
E	3	S3S	tcA	tcT	2	2	AY.74	0.000231
E	3	S3L	tCa	tTa	2	2	AY.93	0.000546
E	3	S3S	tcA	tcT	1	2	B.1	0.000009
E	3	S3S	tcA	tcG	1	2	B.1	0.000009
E	3	S3S	tcA	tcG	2	2	B.1.1.28	0.000622
E	3	S3del	TCA	---	2	2	B.1.1.7	0.000002
E	3	S3P	Tca	Cca	2	2	B.1.2	0.000018
E	3	S3L	tCa	tTa	2	2	B.1.351.3	0.001753
E	3	S3S	tcA	tcG	2	2	B.1.427	0.000101
E	3	S3L	tCa	tTa	2	2	B.1.595	0.000522
E	3	S3P	Tca	Cca	2	2	B.1.617.2	0.000008
E	3	S3S	tcA	tcT	2	2	P.1	0.000032
E	3	S3X	tCa	tAa	1	1	A	0.000387
E	3	S3del1	Tca	-ca	1	1	All	0
E	3	S3L	tCa	tTa	1	1	AY.100	0.000046
E	3	S3S	tcA	tcC	1	1	AY.100	0.000046
E	3	S3P	Tca	Cca	1	1	AY.100	0.000046
E	3	S3S	tcA	tcT	1	1	AY.102	0.000027
E	3	S3P	Tca	Cca	1	1	AY.103	0.000006
E	3	S3L	tCa	tTa	1	1	AY.103	0.000006
E	3	S3A	Tca	Gca	1	1	AY.113	0.000142
E	3	S3S	tcA	tcT	1	1	AY.113	0.000142
E	3	S3del	TCA	---	1	1	AY.118	0.000063
E	3	S3P	Tca	Cca	1	1	AY.119	0.000035
E	3	S3S	tcA	tcG	1	1	AY.119	0.000035
E	3	S3L	tCa	tTa	1	1	AY.119	0.000035
E	3	S3S	tcA	tcG	1	1	AY.120	0.000037
E	3	S3T	Tca	Aca	1	1	AY.120	0.000037
E	3	S3S	tcA	tcC	1	1	AY.121	0.000135
E	3	S3S	tcA	tcC	1	1	AY.14	0.000088
E	3	S3P	Tca	Cca	1	1	AY.23	0.00007
E	3	S3P	Tca	Cca	1	1	AY.25	0.000006
E	3	S3S	tcA	tcC	1	1	AY.29	0.000016
E	3	S3del	TCA	---	1	1	AY.39	0.000025
E	3	S3S	tcA	tcG	1	1	AY.39.1	0.00004
E	3	S3X	tCa	tGa	1	1	AY.4	0.000002
E	3	S3del	TCA	---	1	1	AY.4.5	0.000107
E	3	S3P	Tca	Cca	1	1	AY.43	0.000004
E	3	S3del	TCA	---	1	1	AY.43	0.000004
E	3	S3S	tcA	tcG	1	1	AY.45	0.000122
E	3	S3P	Tca	Cca	1	1	AY.46.6	0.000072
E	3	S3P	Tca	Cca	1	1	AY.47	0.000031
E	3	S3L	tCa	tTa	1	1	AY.47	0.000031
E	3	S3P	Tca	Cca	1	1	AY.5	0.000021
E	3	S3S	tcA	tcG	1	1	AY.59	0.00053
E	3	S3L	tCa	tTa	1	1	AY.61	0.000105
E	3	S3S	tcA	tcC	1	1	AY.61	0.000105
E	3	S3del	TCA	---	1	1	AY.68	0.000274
E	3	S3S	tcA	tcT	1	1	AY.72	0.001361
E	3	S3L	tCa	tTa	1	1	AY.73	0.000665
E	3	S3A	Tca	Gca	1	1	AY.74	0.000116
E	3	S3L	tCa	tTa	1	1	AY.75	0.000056
E	3	S3del	TCA	---	1	1	AY.75	0.000056
E	3	S3S	tcA	tcT	1	1	AY.91	0.00073
E	3	S3S	tcA	tcT	1	1	AY.92	0.000287
E	3	S3L	tCa	tTa	1	1	AZ.6	0.008403
E	3	S3S	tcA	tcT	1	1	B	0.000128
E	3	S3P	Tca	Cca	1	1	B.1	0.000009
E	3	S3L	tCa	tTa	1	1	B.1	0.000009
E	3	S3L	tCa	tTa	1	1	B.1.1	0.000018
E	3	S3P	Tca	Cca	1	1	B.1.1	0.000018
E	3	S3X	tCa	tAa	1	1	B.1.1	0.000018
E	3	S3L	tCa	tTa	1	1	B.1.1.153	0.001095
E	3	S3S	tcA	tcG	1	1	B.1.1.214	0.000055
E	3	S3L	tCa	tTa	1	1	B.1.1.222	0.000204
E	3	S3S	tcA	tcG	1	1	B.1.1.236	0.006897
E	3	S3L	tCa	tTa	1	1	B.1.1.291	0.000742
E	3	S3S	tcA	tcG	1	1	B.1.1.519	0.00004
E	3	S3L	tCa	tTa	1	1	B.1.1.63	0.000386
E	3	S3L	tCa	tTa	1	1	B.1.1.70	0.000341
E	3	S3S	tcA	tcC	1	1	B.1.111	0.001175
E	3	S3del1	Tca	-ca	1	1	B.1.127	0.002198
E	3	S3L	tCa	tTa	1	1	B.1.177	0.000013
E	3	S3S	tcA	tcG	1	1	B.1.177.60	0.000218
E	3	S3L	tCa	tTa	1	1	B.1.177.7	0.000165
E	3	S3L	tCa	tTa	1	1	B.1.177.72	0.00339
E	3	S3del	TCA	---	1	1	B.1.218	0.005155
E	3	S3P	Tca	Cca	1	1	B.1.221.1	0.002907
E	3	S3S	tcA	tcG	1	1	B.1.243	0.00007
E	3	S3P	Tca	Cca	1	1	B.1.258.17	0.000104
E	3	S3P	Tca	Cca	1	1	B.1.279	0.000514
E	3	S3X	tCa	tGa	1	1	B.1.311	0.000275
E	3	S3S	tcA	tcT	1	1	B.1.351	0.00003
E	3	S3P	Tca	Cca	1	1	B.1.429	0.000024
E	3	S3L	tCa	tTa	1	1	B.1.596	0.000087
E	3	S3L	tCa	tTa	1	1	B.1.621	0.000089
E	3	S3S	tcA	tcT	1	1	B.1.621.1	0.000506
E	3	S3A	Tca	Gca	1	1	B.23	0.002924
E	3	S3S	tcA	tcT	1	1	C.37	0.000116
E	3	S3P	Tca	Cca	1	1	D.2	0.000075
E	3	S3S	tcA	tcT	1	1	P.1.1	0.000318
E	3	S3L	tCa	tTa	1	1	P.1.2	0.001156
E	3	S3S	tcA	tcT	1	1	P.1.6	0.001946
E	3	S3S	tcA	tcT	1	1	P.2	0.000187

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.