CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 661

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	661	E661D		nonsyn	gaG	gaT	5158	5152	0.998837	23543-23545
S	661	E661D		nonsyn	gaG	gaC	5158	6	0.00116324	23543-23545
S	661	E661E		syn	gaG	gaA	185	185	1	23543-23545
S	661	E661del		del	GAG	---	56	56	1	23543-23545
S	661	E661V		nonsyn	gAg	gTg	30	29	0.966667	23543-23545
S	661	E661V		nonsyn	gAG	gTC	30	1	0.0333333	23543-23545
S	661	E661A		nonsyn	gAg	gCg	24	23	0.958333	23543-23545
S	661	E661A		nonsyn	gAG	gCT	24	1	0.0416667	23543-23545
S	661	E661G		nonsyn	gAg	gGg	23	23	1	23543-23545
S	661	E661K		nonsyn	Gag	Aag	18	18	1	23543-23545
S	661	E661Q		nonsyn	Gag	Cag	18	18	1	23543-23545
S	661	E661X		nonsyn	Gag	Tag	12	12	1	23543-23545
S	661	E661T		nonsyn	GAG	ACA	6	6	1	23543-23545
S	661	E661R		nonsyn	GAG	CGC	5	3	0.6	23543-23545
S	661	E661R		nonsyn	GAG	AGA	5	1	0.2	23543-23545
S	661	E661R		nonsyn	GAg	AGg	5	1	0.2	23543-23545
S	661	E661H		nonsyn	GaG	CaC	4	3	0.75	23543-23545
S	661	E661del1		del	gaG	ga-	4	2	0.5	23543-23545
S	661	E661del1		del	Gag	-ag	4	2	0.5	23543-23545
S	661	E661H		nonsyn	GaG	CaT	4	1	0.25	23543-23545
S	661	E661S		nonsyn	GAG	AGC	2	2	1	23543-23545
S	661	E661N		nonsyn	GaG	AaC	2	2	1	23543-23545
S	661	E661Y		nonsyn	GaG	TaC	1	1	1	23543-23545
S	661	E661P		nonsyn	GAG	CCA	1	1	1	23543-23545
S	661	E661L		nonsyn	GAG	CTC	1	1	1	23543-23545
S	661	E661C		nonsyn	GAG	TGC	1	1	1	23543-23545

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	661	E661D	gaG	gaT	5152	5158	All	0.000985
S	661	E661D	gaG	gaC	6	5158	All	0.000001
S	661	E661D	gaG	gaT	4134	4134	AY.46.4	0.680046
S	661	E661D	gaG	gaT	472	472	P.1	0.007436
S	661	E661E	gaG	gaA	185	185	All	0.000035
S	661	E661E	gaG	gaA	100	100	P.1.1	0.031766
S	661	E661del	GAG	---	56	56	All	0.000011
S	661	E661D	gaG	gaT	41	44	B.1.1.7	0.000037
S	661	E661D	gaG	gaC	3	44	B.1.1.7	0.000003
S	661	E661D	gaG	gaT	43	43	B.1.617.2	0.000162
S	661	E661D	gaG	gaT	32	32	AY.46	0.003331
S	661	E661D	gaG	gaT	31	31	AY.44	0.000189
S	661	E661V	gAg	gTg	29	30	All	0.000006
S	661	E661V	gAG	gTC	1	30	All	0
S	661	E661D	gaG	gaT	28	28	B.1.177.81	0.005301
S	661	E661E	gaG	gaA	27	27	B.1.595	0.007046
S	661	E661D	gaG	gaT	26	26	AY.117	0.002197
S	661	E661D	gaG	gaT	26	26	AY.4	0.00004
S	661	E661D	gaG	gaT	25	25	B.1.258.17	0.002599
S	661	E661A	gAg	gCg	23	24	All	0.000004
S	661	E661A	gAG	gCT	1	24	All	0
S	661	E661D	gaG	gaT	24	24	AY.75	0.001345
S	661	E661G	gAg	gGg	23	23	All	0.000004
S	661	E661D	gaG	gaT	22	22	AY.120	0.000818
S	661	E661D	gaG	gaT	19	19	B.1.637	0.001388
S	661	E661Q	Gag	Cag	18	18	All	0.000003
S	661	E661K	Gag	Aag	18	18	All	0.000003
S	661	E661D	gaG	gaT	17	17	AY.103	0.000106
S	661	E661E	gaG	gaA	16	16	B.1.526	0.000376
S	661	E661D	gaG	gaT	15	15	AY.43	0.000066
S	661	E661D	gaG	gaT	14	14	B.1.177.54	0.00849
S	661	E661X	Gag	Tag	12	12	All	0.000002
S	661	E661D	gaG	gaT	11	11	AY.39	0.000272
S	661	E661D	gaG	gaT	11	11	P.1.14	0.000526
S	661	E661D	gaG	gaT	10	10	B.1	0.000092
S	661	E661D	gaG	gaT	10	10	B.1.1	0.000181
S	661	E661del	GAG	---	8	8	B.1	0.000073
S	661	E661del	GAG	---	8	8	B.1.1.7	0.000007
S	661	E661D	gaG	gaT	8	8	B.1.429	0.000188
S	661	E661D	gaG	gaT	7	7	AY.25	0.000042
S	661	E661E	gaG	gaA	7	7	AY.4	0.000011
S	661	E661D	gaG	gaT	7	7	AY.45	0.000852
S	661	E661V	gAg	gTg	7	7	P.1	0.00011
S	661	E661T	GAG	ACA	6	6	All	0.000001
S	661	E661D	gaG	gaT	6	6	AY.118	0.000376
S	661	E661V	gAg	gTg	6	6	AY.4	0.000009
S	661	E661R	GAG	CGC	3	5	All	0.000001
S	661	E661R	GAg	AGg	1	5	All	0
S	661	E661R	GAG	AGA	1	5	All	0
S	661	E661X	Gag	Tag	5	5	B.1	0.000046
S	661	E661E	gaG	gaA	5	5	B.1.1	0.000091
S	661	E661D	gaG	gaT	5	5	B.1.1.368	0.015432
S	661	E661V	gAg	gTg	4	5	B.1.1.7	0.000004
S	661	E661V	gAG	gTC	1	5	B.1.1.7	0.000001
S	661	E661H	GaG	CaC	3	4	All	0.000001
S	661	E661del1	Gag	-ag	2	4	All	0
S	661	E661del1	gaG	ga-	2	4	All	0
S	661	E661H	GaG	CaT	1	4	All	0
S	661	E661D	gaG	gaT	4	4	AY.20	0.000155
S	661	E661K	Gag	Aag	4	4	AY.4	0.000006
S	661	E661D	gaG	gaT	4	4	AY.4.2	0.000087
S	661	E661D	gaG	gaT	4	4	B.1.1.317	0.001647
S	661	E661D	gaG	gaT	4	4	B.1.1.519	0.000159
S	661	E661G	gAg	gGg	4	4	B.1.1.7	0.000004
S	661	E661D	gaG	gaT	4	4	B.1.177	0.000053
S	661	E661A	gAg	gCg	4	4	B.1.351	0.000119
S	661	E661D	gaG	gaT	4	4	B.1.466.2	0.001565
S	661	E661del	GAG	---	4	4	P.1	0.000063
S	661	E661D	gaG	gaT	4	4	P.1.12	0.001936
S	661	E661K	Gag	Aag	4	4	Q.2	0.002454
S	661	E661D	gaG	gaT	3	3	AY.23	0.000209
S	661	E661del	GAG	---	3	3	AY.25	0.000018
S	661	E661D	gaG	gaT	3	3	AY.26	0.000085
S	661	E661Q	Gag	Cag	3	3	AY.29	0.000047
S	661	E661D	gaG	gaT	3	3	AY.36	0.000445
S	661	E661del	GAG	---	3	3	AY.43	0.000013
S	661	E661del1	Gag	-ag	2	3	B.1	0.000018
S	661	E661del1	gaG	ga-	1	3	B.1	0.000009
S	661	E661A	gAg	gCg	3	3	B.1.429	0.000071
S	661	E661E	gaG	gaA	3	3	B.1.617.2	0.000011
S	661	E661V	gAg	gTg	3	3	B.1.617.2	0.000011
S	661	E661del	GAG	---	3	3	B.1.617.2	0.000011
S	661	E661A	gAg	gCg	3	3	B.1.617.2	0.000011
S	661	E661E	gaG	gaA	3	3	B.1.621	0.000266
S	661	E661del	GAG	---	3	3	B.1.621	0.000266
S	661	E661del	GAG	---	3	3	P.1.15	0.000697
S	661	E661G	gAg	gGg	2	2		0.111111
S	661	E661X	Gag	Tag	2	2		0.111111
S	661	E661K	Gag	Aag	2	2		0.111111
S	661	E661R	GAG	CGC	2	2		0.111111
S	661	E661H	GaG	CaC	2	2		0.111111
S	661	E661S	GAG	AGC	2	2		0.111111
S	661	E661N	GaG	AaC	2	2		0.111111
S	661	E661E	gaG	gaA	2	2	A.23.1	0.001408
S	661	E661N	GaG	AaC	2	2	All	0
S	661	E661S	GAG	AGC	2	2	All	0
S	661	E661D	gaG	gaT	2	2	AY.113	0.000285
S	661	E661D	gaG	gaT	2	2	AY.119	0.000071
S	661	E661Q	Gag	Cag	2	2	AY.20	0.000078
S	661	E661D	gaG	gaT	2	2	AY.29	0.000032
S	661	E661E	gaG	gaA	2	2	AY.3	0.00002
S	661	E661G	gAg	gGg	2	2	AY.3	0.00002
S	661	E661T	GAG	ACA	2	2	AY.43	0.000009
S	661	E661A	gAg	gCg	2	2	AY.44	0.000012
S	661	E661D	gaG	gaT	2	2	AY.47	0.000062
S	661	E661D	gaG	gaT	2	2	AY.5	0.000041
S	661	E661D	gaG	gaT	2	2	AY.98.1	0.000097
S	661	E661D	gaG	gaT	2	2	AY.99.2	0.000184
S	661	E661K	Gag	Aag	2	2	B.1	0.000018
S	661	E661G	gAg	gGg	2	2	B.1	0.000018
S	661	E661Q	Gag	Cag	2	2	B.1	0.000018
S	661	E661A	gAg	gCg	2	2	B.1.1	0.000036
S	661	E661del	GAG	---	2	2	B.1.1	0.000036
S	661	E661D	gaG	gaT	2	2	B.1.1.365	0.011173
S	661	E661D	gaG	gaT	2	2	B.1.1.39	0.001019
S	661	E661D	gaG	gaT	2	2	B.1.1.466	0.017391
S	661	E661E	gaG	gaA	2	2	B.1.1.7	0.000002
S	661	E661A	gAg	gCg	2	2	B.1.1.7	0.000002
S	661	E661D	gaG	gaT	2	2	B.1.160	0.000062
S	661	E661G	gAg	gGg	2	2	B.1.177	0.000026
S	661	E661Q	Gag	Cag	2	2	B.1.2	0.000018
S	661	E661D	gaG	gaT	2	2	B.1.2	0.000018
S	661	E661G	gAg	gGg	2	2	B.1.2	0.000018
S	661	E661del	GAG	---	2	2	B.1.2	0.000018
S	661	E661D	gaG	gaT	2	2	B.1.234	0.000264
S	661	E661D	gaG	gaT	2	2	B.1.351.3	0.001753
S	661	E661E	gaG	gaA	2	2	B.1.36.31	0.003503
S	661	E661D	gaG	gaT	2	2	B.1.427	0.000101
S	661	E661K	Gag	Aag	2	2	B.1.526	0.000047
S	661	E661del	GAG	---	2	2	B.1.596	0.000174
S	661	E661D	gaG	gaT	2	2	B.1.596	0.000174
S	661	E661D	gaG	gaT	2	2	B.1.617.1	0.000258
S	661	E661Q	Gag	Cag	2	2	B.1.617.2	0.000008
S	661	E661D	gaG	gaT	2	2	C.36.3	0.001134
S	661	E661Q	Gag	Cag	2	2	D.2	0.00015
S	661	E661D	gaG	gaT	2	2	D.2	0.00015
S	661	E661A	gAg	gCg	1	2	D.2	0.000075
S	661	E661A	gAG	gCT	1	2	D.2	0.000075
S	661	E661E	gaG	gaA	2	2	P.1	0.000032
S	661	E661D	gaG	gaT	2	2	P.1.15	0.000465
S	661	E661D	gaG	gaT	2	2	Q.1	0.000253
S	661	E661del	GAG	---	1	1	A.2.2	0.001689
S	661	E661D	gaG	gaT	1	1	A.21	0.00277
S	661	E661X	Gag	Tag	1	1	A.27	0.001656
S	661	E661Y	GaG	TaC	1	1	All	0
S	661	E661C	GAG	TGC	1	1	All	0
S	661	E661L	GAG	CTC	1	1	All	0
S	661	E661P	GAG	CCA	1	1	All	0
S	661	E661E	gaG	gaA	1	1	AY.103	0.000006
S	661	E661del	GAG	---	1	1	AY.103	0.000006
S	661	E661D	gaG	gaT	1	1	AY.110	0.000113
S	661	E661D	gaG	gaT	1	1	AY.116	0.000287
S	661	E661E	gaG	gaA	1	1	AY.117	0.000085
S	661	E661K	Gag	Aag	1	1	AY.120	0.000037
S	661	E661D	gaG	gaT	1	1	AY.13	0.000161
S	661	E661D	gaG	gaT	1	1	AY.17	0.008197
S	661	E661D	gaG	gaT	1	1	AY.22	0.002092
S	661	E661G	gAg	gGg	1	1	AY.23	0.00007
S	661	E661D	gaG	gaT	1	1	AY.24	0.000431
S	661	E661V	gAg	gTg	1	1	AY.25	0.000006
S	661	E661V	gAg	gTg	1	1	AY.29	0.000016
S	661	E661D	gaG	gaT	1	1	AY.29.1	0.000221
S	661	E661C	GAG	TGC	1	1	AY.3	0.00001
S	661	E661H	GaG	CaC	1	1	AY.3	0.00001
S	661	E661T	GAG	ACA	1	1	AY.3	0.00001
S	661	E661Y	GaG	TaC	1	1	AY.3	0.00001
S	661	E661R	GAG	CGC	1	1	AY.3	0.00001
S	661	E661A	gAg	gCg	1	1	AY.32	0.000532
S	661	E661V	gAg	gTg	1	1	AY.33	0.000067
S	661	E661D	gaG	gaT	1	1	AY.34	0.000097
S	661	E661E	gaG	gaA	1	1	AY.39	0.000025
S	661	E661A	gAg	gCg	1	1	AY.4	0.000002
S	661	E661V	gAg	gTg	1	1	AY.4.2	0.000022
S	661	E661D	gaG	gaT	1	1	AY.4.2.1	0.000149
S	661	E661D	gaG	gaT	1	1	AY.42	0.00004
S	661	E661E	gaG	gaA	1	1	AY.43	0.000004
S	661	E661del1	gaG	ga-	1	1	AY.43	0.000004
S	661	E661V	gAg	gTg	1	1	AY.44	0.000006
S	661	E661Q	Gag	Cag	1	1	AY.44	0.000006
S	661	E661T	GAG	ACA	1	1	AY.44	0.000006
S	661	E661del	GAG	---	1	1	AY.44	0.000006
S	661	E661del	GAG	---	1	1	AY.46	0.000104
S	661	E661E	gaG	gaA	1	1	AY.46.4	0.000165
S	661	E661D	gaG	gaT	1	1	AY.46.5	0.000198
S	661	E661del	GAG	---	1	1	AY.46.6	0.000072
S	661	E661H	GaG	CaT	1	1	AY.59	0.00053
S	661	E661D	gaG	gaC	1	1	AY.6	0.000041
S	661	E661G	gAg	gGg	1	1	AY.6	0.000041
S	661	E661K	Gag	Aag	1	1	AY.62	0.000436
S	661	E661D	gaG	gaC	1	1	AY.67	0.000464
S	661	E661V	gAg	gTg	1	1	AY.7.2	0.000559
S	661	E661E	gaG	gaA	1	1	AY.73	0.000665
S	661	E661D	gaG	gaT	1	1	AY.77	0.001127
S	661	E661Q	Gag	Cag	1	1	AY.79	0.001211
S	661	E661del	GAG	---	1	1	AY.84	0.000437
S	661	E661D	gaG	gaT	1	1	AY.85	0.000427
S	661	E661del	GAG	---	1	1	AY.85	0.000427
S	661	E661D	gaG	gaT	1	1	AY.9	0.000068
S	661	E661E	gaG	gaA	1	1	AY.9.1	0.000084
S	661	E661D	gaG	gaT	1	1	AY.9.2	0.000037
S	661	E661T	GAG	ACA	1	1	AY.9.2	0.000037
S	661	E661E	gaG	gaA	1	1	AY.92	0.000287
S	661	E661D	gaG	gaT	1	1	AY.92	0.000287
S	661	E661D	gaG	gaT	1	1	AY.98	0.000079
S	661	E661G	gAg	gGg	1	1	AY.98.1	0.000048
S	661	E661del	GAG	---	1	1	AY.99	0.001049
S	661	E661V	gAg	gTg	1	1	AZ.2	0.000821
S	661	E661E	gaG	gaA	1	1	B.1	0.000009
S	661	E661R	GAG	AGA	1	1	B.1	0.000009
S	661	E661V	gAg	gTg	1	1	B.1.1	0.000018
S	661	E661Q	Gag	Cag	1	1	B.1.1	0.000018
S	661	E661D	gaG	gaT	1	1	B.1.1.220	0.001859
S	661	E661K	Gag	Aag	1	1	B.1.1.243	0.004082
S	661	E661D	gaG	gaT	1	1	B.1.1.303	0.002762
S	661	E661D	gaG	gaC	1	1	B.1.1.37	0.000193
S	661	E661del	GAG	---	1	1	B.1.1.372	0.000689
S	661	E661D	gaG	gaT	1	1	B.1.1.448	0.002033
S	661	E661G	gAg	gGg	1	1	B.1.1.50	0.000679
S	661	E661X	Gag	Tag	1	1	B.1.1.7	0.000001
S	661	E661R	GAg	AGg	1	1	B.1.1.7	0.000001
S	661	E661Q	Gag	Cag	1	1	B.1.1.7	0.000001
S	661	E661A	gAg	gCg	1	1	B.1.117	0.0125
S	661	E661del	GAG	---	1	1	B.1.177	0.000013
S	661	E661A	gAg	gCg	1	1	B.1.177	0.000013
S	661	E661D	gaG	gaT	1	1	B.1.177.12	0.000152
S	661	E661A	gAg	gCg	1	1	B.1.177.86	0.000183
S	661	E661X	Gag	Tag	1	1	B.1.2	0.000009
S	661	E661V	gAg	gTg	1	1	B.1.2	0.000009
S	661	E661X	Gag	Tag	1	1	B.1.201	0.005682
S	661	E661D	gaG	gaT	1	1	B.1.210	0.002132
S	661	E661D	gaG	gaT	1	1	B.1.221	0.000071
S	661	E661E	gaG	gaA	1	1	B.1.221	0.000071
S	661	E661D	gaG	gaT	1	1	B.1.258	0.000067
S	661	E661X	Gag	Tag	1	1	B.1.329	0.000608
S	661	E661D	gaG	gaT	1	1	B.1.351	0.00003
S	661	E661L	GAG	CTC	1	1	B.1.351	0.00003
S	661	E661D	gaG	gaT	1	1	B.1.36	0.000146
S	661	E661A	gAg	gCg	1	1	B.1.36.10	0.004785
S	661	E661G	gAg	gGg	1	1	B.1.429	0.000024
S	661	E661E	gaG	gaA	1	1	B.1.429	0.000024
S	661	E661G	gAg	gGg	1	1	B.1.438.1	0.000107
S	661	E661Q	Gag	Cag	1	1	B.1.565	0.00081
S	661	E661D	gaG	gaT	1	1	B.1.595	0.000261
S	661	E661E	gaG	gaA	1	1	B.1.604	0.017241
S	661	E661G	gAg	gGg	1	1	B.1.617.2	0.000004
S	661	E661P	GAG	CCA	1	1	B.1.617.2	0.000004
S	661	E661T	GAG	ACA	1	1	B.1.617.2	0.000004
S	661	E661del	GAG	---	1	1	B.1.620	0.000946
S	661	E661D	gaG	gaT	1	1	B.1.621	0.000089
S	661	E661K	Gag	Aag	1	1	B.1.621	0.000089
S	661	E661del	GAG	---	1	1	B.1.627	0.00202
S	661	E661del	GAG	---	1	1	B.1.638	0.052632
S	661	E661del	GAG	---	1	1	C.37	0.000116
S	661	E661E	gaG	gaA	1	1	C.37	0.000116
S	661	E661E	gaG	gaA	1	1	D.2	0.000075
S	661	E661G	gAg	gGg	1	1	P.1	0.000016
S	661	E661del	GAG	---	1	1	P.1.13	0.000898
S	661	E661G	gAg	gGg	1	1	P.1.14	0.000048

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.