CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = E : CodonNum = 60

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	60	S60S		syn	tcT	tcC	6947	6693	0.963437	26422-26424
E	60	S60S		syn	tcT	tcG	6947	237	0.0341154	26422-26424
E	60	S60S		syn	tcT	tcA	6947	17	0.0024471	26422-26424
E	60	S60del		del	TCT	---	69	69	1	26422-26424
E	60	S60A		nonsyn	Tct	Gct	44	44	1	26422-26424
E	60	S60Y		nonsyn	tCt	tAt	44	43	0.977273	26422-26424
E	60	S60Y		nonsyn	tCT	tAC	44	1	0.0227273	26422-26424
E	60	S60T		nonsyn	Tct	Act	39	38	0.974359	26422-26424
E	60	S60T		nonsyn	TcT	AcC	39	1	0.025641	26422-26424
E	60	S60F		nonsyn	tCt	tTt	36	32	0.888889	26422-26424
E	60	S60F		nonsyn	tCT	tTC	36	4	0.111111	26422-26424
E	60	S60P		nonsyn	Tct	Cct	11	9	0.818182	26422-26424
E	60	S60P		nonsyn	TcT	CcA	11	2	0.181818	26422-26424
E	60	S60del1		del	Tct	-ct	9	5	0.555556	26422-26424
E	60	S60del1		del	TCT	-YY	9	2	0.222222	26422-26424
E	60	S60del1		del	tCt	t-t	9	1	0.111111	26422-26424
E	60	S60del1		del	tcT	tc-	9	1	0.111111	26422-26424
E	60	S60I		nonsyn	TCt	ATt	7	3	0.428571	26422-26424
E	60	S60I		nonsyn	TCT	ATC	7	3	0.428571	26422-26424
E	60	S60I		nonsyn	TCT	ATA	7	1	0.142857	26422-26424
E	60	S60N		nonsyn	TCt	AAt	1	1	1	26422-26424
E	60	S60L		nonsyn	TCT	CTC	1	1	1	26422-26424

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	60	S60S	tcT	tcC	6693	6947	All	0.00128
E	60	S60S	tcT	tcG	237	6947	All	0.000045
E	60	S60S	tcT	tcA	17	6947	All	0.000003
E	60	S60S	tcT	tcC	6176	6176	B.1.177	0.081323
E	60	S60S	tcT	tcC	354	354	B.1.177.63	0.956757
E	60	S60S	tcT	tcG	188	188	B.1.517.1	0.989474
E	60	S60del	TCT	---	69	69	All	0.000013
E	60	S60A	Tct	Gct	44	44	All	0.000008
E	60	S60Y	tCt	tAt	43	44	All	0.000008
E	60	S60Y	tCT	tAC	1	44	All	0
E	60	S60S	tcT	tcG	18	41	B.1.1.7	0.000016
E	60	S60S	tcT	tcC	17	41	B.1.1.7	0.000015
E	60	S60S	tcT	tcA	6	41	B.1.1.7	0.000005
E	60	S60T	Tct	Act	38	39	All	0.000007
E	60	S60T	TcT	AcC	1	39	All	0
E	60	S60F	tCt	tTt	32	36	All	0.000006
E	60	S60F	tCT	tTC	4	36	All	0.000001
E	60	S60S	tcT	tcC	24	30	B.1	0.00022
E	60	S60S	tcT	tcG	4	30	B.1	0.000037
E	60	S60S	tcT	tcA	2	30	B.1	0.000018
E	60	S60S	tcT	tcC	16	16	AY.114	0.003698
E	60	S60A	Tct	Gct	15	15	AY.25	0.00009
E	60	S60P	Tct	Cct	9	11	All	0.000002
E	60	S60P	TcT	CcA	2	11	All	0
E	60	S60S	tcT	tcG	8	11	AY.4	0.000012
E	60	S60S	tcT	tcC	3	11	AY.4	0.000005
E	60	S60S	tcT	tcC	11	11	B.1.177.64	1
E	60	S60del	TCT	---	10	10	P.1	0.000158
E	60	S60del1	Tct	-ct	5	9	All	0.000001
E	60	S60del1	TCT	-YY	2	9	All	0
E	60	S60del1	tCt	t-t	1	9	All	0
E	60	S60del1	tcT	tc-	1	9	All	0
E	60	S60T	Tct	Act	9	9	AY.119	0.000318
E	60	S60del	TCT	---	9	9	B.1	0.000082
E	60	S60T	Tct	Act	9	9	B.1.1.7	0.000008
E	60	S60S	tcT	tcC	7	8	AY.120	0.00026
E	60	S60S	tcT	tcG	1	8	AY.120	0.000037
E	60	S60F	tCt	tTt	8	8	B.1.1.7	0.000007
E	60	S60I	TCt	ATt	3	7	All	0.000001
E	60	S60I	TCT	ATC	3	7	All	0.000001
E	60	S60I	TCT	ATA	1	7	All	0
E	60	S60A	Tct	Gct	7	7	AY.103	0.000043
E	60	S60Y	tCt	tAt	7	7	B.1.1.521	0.037433
E	60	S60T	Tct	Act	7	7	B.1.258.14	0.006863
E	60	S60del	TCT	---	7	7	P.1.15	0.001626
E	60	S60Y	tCt	tAt	6	6	B.1.1.7	0.000005
E	60	S60F	tCt	tTt	3	5		0.166667
E	60	S60F	tCT	tTC	2	5		0.111111
E	60	S60S	tcT	tcC	5	5	AY.103	0.000031
E	60	S60F	tCt	tTt	5	5	B.1.2	0.000044
E	60	S60S	tcT	tcG	3	5	B.1.2	0.000026
E	60	S60S	tcT	tcC	2	5	B.1.2	0.000018
E	60	S60S	tcT	tcA	5	5	B.1.206	0.004078
E	60	S60S	tcT	tcC	5	5	B.1.617.2	0.000019
E	60	S60I	TCT	ATC	2	4		0.111111
E	60	S60I	TCt	ATt	2	4		0.111111
E	60	S60S	tcT	tcC	2	4	AY.20	0.000078
E	60	S60S	tcT	tcG	2	4	AY.20	0.000078
E	60	S60Y	tCt	tAt	4	4	AY.4	0.000006
E	60	S60S	tcT	tcC	4	4	AY.98.1	0.000194
E	60	S60F	tCt	tTt	3	4	B.1	0.000027
E	60	S60F	tCT	tTC	1	4	B.1	0.000009
E	60	S60S	tcT	tcC	2	4	B.1.1	0.000036
E	60	S60S	tcT	tcG	1	4	B.1.1	0.000018
E	60	S60S	tcT	tcA	1	4	B.1.1	0.000018
E	60	S60del	TCT	---	4	4	B.1.1.7	0.000004
E	60	S60Y	tCt	tAt	4	4	B.1.2	0.000035
E	60	S60Y	tCt	tAt	3	3	AY.100	0.000138
E	60	S60S	tcT	tcG	2	3	AY.23	0.000139
E	60	S60S	tcT	tcC	1	3	AY.23	0.00007
E	60	S60del	TCT	---	3	3	AY.25	0.000018
E	60	S60S	tcT	tcC	3	3	AY.25	0.000018
E	60	S60del	TCT	---	3	3	AY.43	0.000013
E	60	S60S	tcT	tcC	3	3	AY.44	0.000018
E	60	S60S	tcT	tcC	3	3	AY.6	0.000123
E	60	S60Y	tCt	tAt	3	3	B.1	0.000027
E	60	S60P	Tct	Cct	3	3	B.1	0.000027
E	60	S60S	tcT	tcC	3	3	B.1.1.162	0.088235
E	60	S60Y	tCt	tAt	3	3	B.1.1.297	0.006711
E	60	S60T	Tct	Act	3	3	B.1.1.526	0.010638
E	60	S60S	tcT	tcC	3	3	B.1.177.57	0.000843
E	60	S60A	Tct	Gct	3	3	B.1.221	0.000213
E	60	S60S	tcT	tcC	3	3	B.1.351	0.000089
E	60	S60T	Tct	Act	3	3	B.1.617.2	0.000011
E	60	S60del	TCT	---	3	3	B.1.621	0.000266
E	60	S60del	TCT	---	3	3	C.37	0.000348
E	60	S60S	tcT	tcC	3	3	P.1	0.000047
E	60	S60del	TCT	---	2	2		0.111111
E	60	S60P	TcT	CcA	2	2		0.111111
E	60	S60del1	TCT	-YY	2	2		0.111111
E	60	S60A	Tct	Gct	2	2	AY.33	0.000134
E	60	S60del	TCT	---	2	2	AY.4	0.000003
E	60	S60A	Tct	Gct	2	2	AY.41	0.000588
E	60	S60S	tcT	tcC	1	2	AY.43	0.000004
E	60	S60S	tcT	tcG	1	2	AY.43	0.000004
E	60	S60del	TCT	---	2	2	AY.44	0.000012
E	60	S60T	Tct	Act	2	2	AY.47	0.000062
E	60	S60S	tcT	tcC	2	2	AY.47	0.000062
E	60	S60S	tcT	tcC	2	2	AY.5	0.000041
E	60	S60S	tcT	tcC	2	2	AY.99.2	0.000184
E	60	S60I	TCt	ATt	1	2	B.1	0.000009
E	60	S60T	TcT	AcC	1	2	B.1	0.000009
E	60	S60T	Tct	Act	1	2	B.1	0.000009
E	60	S60I	TCT	ATC	1	2	B.1	0.000009
E	60	S60F	tCt	tTt	2	2	B.1.1	0.000036
E	60	S60S	tcT	tcG	2	2	B.1.1.222	0.000408
E	60	S60S	tcT	tcC	2	2	B.1.1.315	0.016949
E	60	S60P	Tct	Cct	2	2	B.1.1.7	0.000002
E	60	S60S	tcT	tcC	2	2	B.1.177.21	0.000153
E	60	S60S	tcT	tcC	2	2	B.1.177.5	0.002484
E	60	S60S	tcT	tcC	2	2	B.1.177.6	0.001953
E	60	S60S	tcT	tcC	2	2	B.1.177.7	0.00033
E	60	S60T	Tct	Act	2	2	B.1.258	0.000133
E	60	S60S	tcT	tcC	2	2	B.1.258	0.000133
E	60	S60A	Tct	Gct	2	2	B.1.362	0.003082
E	60	S60S	tcT	tcC	2	2	B.1.525	0.000226
E	60	S60S	tcT	tcC	2	2	B.1.526	0.000047
E	60	S60A	Tct	Gct	2	2	B.1.617.2	0.000008
E	60	S60Y	tCt	tAt	2	2	B.1.617.2	0.000008
E	60	S60S	tcT	tcC	2	2	P.1.14	0.000096
E	60	S60del1	Tct	-ct	1	1	A	0.000387
E	60	S60S	tcT	tcG	1	1	A.21	0.00277
E	60	S60S	tcT	tcC	1	1	AA.5	0.016129
E	60	S60L	TCT	CTC	1	1	All	0
E	60	S60N	TCt	AAt	1	1	All	0
E	60	S60del	TCT	---	1	1	AY.10	0.00053
E	60	S60A	Tct	Gct	1	1	AY.100	0.000046
E	60	S60del1	Tct	-ct	1	1	AY.103	0.000006
E	60	S60F	tCt	tTt	1	1	AY.103	0.000006
E	60	S60A	Tct	Gct	1	1	AY.105	0.000643
E	60	S60F	tCt	tTt	1	1	AY.117	0.000085
E	60	S60S	tcT	tcC	1	1	AY.118	0.000063
E	60	S60del	TCT	---	1	1	AY.118	0.000063
E	60	S60S	tcT	tcA	1	1	AY.119	0.000035
E	60	S60del	TCT	---	1	1	AY.120	0.000037
E	60	S60S	tcT	tcC	1	1	AY.120.1	0.000321
E	60	S60I	TCT	ATA	1	1	AY.120.1	0.000321
E	60	S60S	tcT	tcG	1	1	AY.121	0.000135
E	60	S60Y	tCt	tAt	1	1	AY.14	0.000088
E	60	S60del	TCT	---	1	1	AY.23	0.00007
E	60	S60P	Tct	Cct	1	1	AY.23	0.00007
E	60	S60F	tCt	tTt	1	1	AY.23.1	0.000417
E	60	S60Y	tCt	tAt	1	1	AY.25	0.000006
E	60	S60del	TCT	---	1	1	AY.26	0.000028
E	60	S60S	tcT	tcA	1	1	AY.39	0.000025
E	60	S60del	TCT	---	1	1	AY.39	0.000025
E	60	S60S	tcT	tcC	1	1	AY.39.1	0.00004
E	60	S60A	Tct	Gct	1	1	AY.4	0.000002
E	60	S60Y	tCt	tAt	1	1	AY.4.2	0.000022
E	60	S60S	tcT	tcG	1	1	AY.41	0.000294
E	60	S60A	Tct	Gct	1	1	AY.43	0.000004
E	60	S60F	tCt	tTt	1	1	AY.43	0.000004
E	60	S60F	tCT	tTC	1	1	AY.44	0.000006
E	60	S60T	Tct	Act	1	1	AY.44	0.000006
E	60	S60del1	tCt	t-t	1	1	AY.44	0.000006
E	60	S60P	Tct	Cct	1	1	AY.44	0.000006
E	60	S60F	tCt	tTt	1	1	AY.46.3	0.000934
E	60	S60S	tcT	tcG	1	1	AY.46.6	0.000072
E	60	S60del	TCT	---	1	1	AY.54	0.000095
E	60	S60Y	tCt	tAt	1	1	AY.58	0.000907
E	60	S60S	tcT	tcC	1	1	AY.61	0.000105
E	60	S60del	TCT	---	1	1	AY.68	0.000274
E	60	S60del	TCT	---	1	1	AY.75.1	0.00018
E	60	S60del	TCT	---	1	1	AY.85	0.000427
E	60	S60S	tcT	tcG	1	1	AY.92	0.000287
E	60	S60del	TCT	---	1	1	AY.95	0.000761
E	60	S60Y	tCt	tAt	1	1	AY.99	0.001049
E	60	S60del	TCT	---	1	1	B	0.000128
E	60	S60N	TCt	AAt	1	1	B.1	0.000009
E	60	S60del1	Tct	-ct	1	1	B.1	0.000009
E	60	S60A	Tct	Gct	1	1	B.1	0.000009
E	60	S60S	tcT	tcC	1	1	B.1.1.214	0.000055
E	60	S60S	tcT	tcA	1	1	B.1.1.241	0.00207
E	60	S60S	tcT	tcC	1	1	B.1.1.316	0.000925
E	60	S60S	tcT	tcC	1	1	B.1.1.317	0.000412
E	60	S60P	Tct	Cct	1	1	B.1.1.335	0.012987
E	60	S60F	tCt	tTt	1	1	B.1.1.368	0.003086
E	60	S60S	tcT	tcC	1	1	B.1.1.37	0.000193
E	60	S60L	TCT	CTC	1	1	B.1.1.409	0.002833
E	60	S60A	Tct	Gct	1	1	B.1.1.7	0.000001
E	60	S60del1	Tct	-ct	1	1	B.1.1.7	0.000001
E	60	S60T	Tct	Act	1	1	B.1.160.12	0.00641
E	60	S60del	TCT	---	1	1	B.1.161	0.017241
E	60	S60S	tcT	tcC	1	1	B.1.177.44	0.000519
E	60	S60Y	tCt	tAt	1	1	B.1.177.44	0.000519
E	60	S60del1	tcT	tc-	1	1	B.1.177.44	0.000519
E	60	S60S	tcT	tcC	1	1	B.1.177.56	0.000668
E	60	S60A	Tct	Gct	1	1	B.1.2	0.000009
E	60	S60del	TCT	---	1	1	B.1.218	0.005155
E	60	S60S	tcT	tcC	1	1	B.1.221	0.000071
E	60	S60Y	tCt	tAt	1	1	B.1.234	0.000132
E	60	S60S	tcT	tcC	1	1	B.1.236	0.002053
E	60	S60A	Tct	Gct	1	1	B.1.243	0.00007
E	60	S60S	tcT	tcC	1	1	B.1.243	0.00007
E	60	S60del	TCT	---	1	1	B.1.36	0.000146
E	60	S60S	tcT	tcG	1	1	B.1.362	0.001541
E	60	S60Y	tCt	tAt	1	1	B.1.427	0.00005
E	60	S60S	tcT	tcC	1	1	B.1.429	0.000024
E	60	S60A	Tct	Gct	1	1	B.1.429	0.000024
E	60	S60S	tcT	tcC	1	1	B.1.448	0.002625
E	60	S60Y	tCT	tAC	1	1	B.1.497	0.000315
E	60	S60Y	tCt	tAt	1	1	B.1.526	0.000024
E	60	S60S	tcT	tcG	1	1	B.1.543	0.01
E	60	S60S	tcT	tcC	1	1	B.1.561	0.000397
E	60	S60F	tCt	tTt	1	1	B.1.564	0.000426
E	60	S60F	tCt	tTt	1	1	B.1.596	0.000087
E	60	S60S	tcT	tcC	1	1	B.1.596	0.000087
E	60	S60del	TCT	---	1	1	B.1.617.1	0.000129
E	60	S60P	Tct	Cct	1	1	B.1.617.1	0.000129
E	60	S60del1	Tct	-ct	1	1	B.1.617.2	0.000004
E	60	S60F	tCt	tTt	1	1	B.1.617.2	0.000004
E	60	S60del	TCT	---	1	1	B.1.627	0.00202
E	60	S60del	TCT	---	1	1	B.1.638	0.052632
E	60	S60Y	tCt	tAt	1	1	B.6	0.00091
E	60	S60F	tCt	tTt	1	1	B.6.6	0.000889
E	60	S60A	Tct	Gct	1	1	C.37	0.000116
E	60	S60del	TCT	---	1	1	C.37.1	0.002618
E	60	S60F	tCt	tTt	1	1	P.1	0.000016
E	60	S60A	Tct	Gct	1	1	P.1	0.000016
E	60	S60Y	tCt	tAt	1	1	P.1.1	0.000318
E	60	S60del	TCT	---	1	1	P.1.13	0.000898
E	60	S60del	TCT	---	1	1	P.1.7	0.000319

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.