CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 616

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	616	L616I	L1434I	nonsyn	Ctt	Att	161	161	1	4565-4567
ORF1ab/nsp3	616	L616L	L1434L	syn	ctT	ctC	158	134	0.848101	4565-4567
ORF1ab/nsp3	616	L616L	L1434L	syn	ctT	ctA	158	22	0.139241	4565-4567
ORF1ab/nsp3	616	L616L	L1434L	syn	ctT	ctG	158	2	0.0126582	4565-4567
ORF1ab/nsp3	616	L616del	L1434del	del	CTT	---	62	62	1	4565-4567
ORF1ab/nsp3	616	L616F	L1434F	nonsyn	Ctt	Ttt	26	26	1	4565-4567
ORF1ab/nsp3	616	L616R	L1434R	nonsyn	cTt	cGt	10	10	1	4565-4567
ORF1ab/nsp3	616	L616V	L1434V	nonsyn	Ctt	Gtt	5	5	1	4565-4567
ORF1ab/nsp3	616	L616del1	L1434del1	del	cTt	c-t	3	2	0.666667	4565-4567
ORF1ab/nsp3	616	L616del1	L1434del1	del	cTT	c-C	3	1	0.333333	4565-4567
ORF1ab/nsp3	616	L616P	L1434P	nonsyn	cTt	cCt	2	1	0.5	4565-4567
ORF1ab/nsp3	616	L616P	L1434P	nonsyn	cTT	cCC	2	1	0.5	4565-4567
ORF1ab/nsp3	616	L616S	L1434S	nonsyn	CTT	TCC	1	1	1	4565-4567
ORF1ab/nsp3	616	L616del2	L1434del2	del	CTt	--t	1	1	1	4565-4567

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	616	L616I	Ctt	Att	161	161	All	0.000031
ORF1ab/nsp3	616	L616L	ctT	ctC	134	158	All	0.000026
ORF1ab/nsp3	616	L616L	ctT	ctA	22	158	All	0.000004
ORF1ab/nsp3	616	L616L	ctT	ctG	2	158	All	0
ORF1ab/nsp3	616	L616del	CTT	---	62	62	All	0.000012
ORF1ab/nsp3	616	L616F	Ctt	Ttt	26	26	All	0.000005
ORF1ab/nsp3	616	L616L	ctT	ctA	14	26	B.1.1.7	0.000013
ORF1ab/nsp3	616	L616L	ctT	ctC	12	26	B.1.1.7	0.000011
ORF1ab/nsp3	616	L616I	Ctt	Att	22	22	AY.100	0.001012
ORF1ab/nsp3	616	L616I	Ctt	Att	22	22	B.1.1.7	0.00002
ORF1ab/nsp3	616	L616I	Ctt	Att	21	21	AY.44	0.000128
ORF1ab/nsp3	616	L616del	CTT	---	20	20	B.1.1.7	0.000018
ORF1ab/nsp3	616	L616L	ctT	ctC	19	19	B.1.177.80	0.036329
ORF1ab/nsp3	616	L616I	Ctt	Att	17	17	B.1.1.341	1
ORF1ab/nsp3	616	L616I	Ctt	Att	16	16	AY.29	0.000252
ORF1ab/nsp3	616	L616L	ctT	ctC	15	16	B.1.429	0.000353
ORF1ab/nsp3	616	L616L	ctT	ctG	1	16	B.1.429	0.000024
ORF1ab/nsp3	616	L616L	ctT	ctC	15	15	B.1.609	0.007191
ORF1ab/nsp3	616	L616I	Ctt	Att	14	14	B.1.1.432	0.017722
ORF1ab/nsp3	616	L616L	ctT	ctC	10	12	AY.103	0.000062
ORF1ab/nsp3	616	L616L	ctT	ctA	1	12	AY.103	0.000006
ORF1ab/nsp3	616	L616L	ctT	ctG	1	12	AY.103	0.000006
ORF1ab/nsp3	616	L616L	ctT	ctC	12	12	B.1.2	0.000106
ORF1ab/nsp3	616	L616I	Ctt	Att	11	11	B.1.617.2	0.000041
ORF1ab/nsp3	616	L616R	cTt	cGt	10	10	All	0.000002
ORF1ab/nsp3	616	L616I	Ctt	Att	9	9	B.1.1	0.000163
ORF1ab/nsp3	616	L616I	Ctt	Att	7	7	AY.4	0.000011
ORF1ab/nsp3	616	L616L	ctT	ctC	6	7	B.1	0.000055
ORF1ab/nsp3	616	L616L	ctT	ctA	1	7	B.1	0.000009
ORF1ab/nsp3	616	L616R	cTt	cGt	7	7	B.1.1.7	0.000006
ORF1ab/nsp3	616	L616V	Ctt	Gtt	5	5	All	0.000001
ORF1ab/nsp3	616	L616L	ctT	ctC	3	5	AY.44	0.000018
ORF1ab/nsp3	616	L616L	ctT	ctA	2	5	AY.44	0.000012
ORF1ab/nsp3	616	L616L	ctT	ctC	4	5	B.1.177	0.000053
ORF1ab/nsp3	616	L616L	ctT	ctA	1	5	B.1.177	0.000013
ORF1ab/nsp3	616	L616I	Ctt	Att	5	5	B.1.429	0.000118
ORF1ab/nsp3	616	L616L	ctT	ctC	4	4	AY.3	0.00004
ORF1ab/nsp3	616	L616del	CTT	---	4	4	AY.4	0.000006
ORF1ab/nsp3	616	L616L	ctT	ctC	4	4	AY.4	0.000006
ORF1ab/nsp3	616	L616F	Ctt	Ttt	4	4	B.1	0.000037
ORF1ab/nsp3	616	L616L	ctT	ctC	4	4	B.1.1	0.000073
ORF1ab/nsp3	616	L616L	ctT	ctC	2	4	B.1.617.2	0.000008
ORF1ab/nsp3	616	L616L	ctT	ctA	2	4	B.1.617.2	0.000008
ORF1ab/nsp3	616	L616del1	cTt	c-t	2	3	All	0
ORF1ab/nsp3	616	L616del1	cTT	c-C	1	3	All	0
ORF1ab/nsp3	616	L616I	Ctt	Att	3	3	AY.26	0.000085
ORF1ab/nsp3	616	L616del	CTT	---	3	3	AY.42	0.000121
ORF1ab/nsp3	616	L616L	ctT	ctC	3	3	AY.54	0.000286
ORF1ab/nsp3	616	L616L	ctT	ctC	2	3	P.1	0.000032
ORF1ab/nsp3	616	L616L	ctT	ctA	1	3	P.1	0.000016
ORF1ab/nsp3	616	L616P	cTT	cCC	1	2	All	0
ORF1ab/nsp3	616	L616P	cTt	cCt	1	2	All	0
ORF1ab/nsp3	616	L616L	ctT	ctC	2	2	AY.120	0.000074
ORF1ab/nsp3	616	L616L	ctT	ctC	2	2	AY.23	0.000139
ORF1ab/nsp3	616	L616L	ctT	ctC	2	2	AY.25	0.000012
ORF1ab/nsp3	616	L616V	Ctt	Gtt	2	2	AY.42	0.00008
ORF1ab/nsp3	616	L616F	Ctt	Ttt	2	2	AY.44	0.000012
ORF1ab/nsp3	616	L616del1	cTT	c-C	1	2	AY.44	0.000006
ORF1ab/nsp3	616	L616del1	cTt	c-t	1	2	AY.44	0.000006
ORF1ab/nsp3	616	L616I	Ctt	Att	2	2	AY.47	0.000062
ORF1ab/nsp3	616	L616del	CTT	---	2	2	AY.9.1	0.000167
ORF1ab/nsp3	616	L616F	Ctt	Ttt	2	2	B	0.000256
ORF1ab/nsp3	616	L616del	CTT	---	2	2	B.1	0.000018
ORF1ab/nsp3	616	L616I	Ctt	Att	2	2	B.1.1.244	0.030769
ORF1ab/nsp3	616	L616L	ctT	ctC	2	2	B.1.1.354	0.008772
ORF1ab/nsp3	616	L616del	CTT	---	2	2	B.1.1.519	0.000079
ORF1ab/nsp3	616	L616F	Ctt	Ttt	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	616	L616del	CTT	---	2	2	B.1.177	0.000026
ORF1ab/nsp3	616	L616I	Ctt	Att	2	2	B.1.178	0.047619
ORF1ab/nsp3	616	L616R	cTt	cGt	2	2	B.1.525	0.000226
ORF1ab/nsp3	616	L616del	CTT	---	2	2	P.1	0.000032
ORF1ab/nsp3	616	L616del	CTT	---	1	1	A	0.000387
ORF1ab/nsp3	616	L616del	CTT	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	616	L616V	Ctt	Gtt	1	1	A.2.5	0.000499
ORF1ab/nsp3	616	L616S	CTT	TCC	1	1	All	0
ORF1ab/nsp3	616	L616del2	CTt	--t	1	1	All	0
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	AY.102	0.000027
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	AY.109	0.00074
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	AY.117	0.000085
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	AY.121	0.000135
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	AY.25	0.000006
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	AY.27	0.000065
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	AY.28	0.00189
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	AY.33	0.000067
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	AY.39.1	0.00004
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	AY.4	0.000002
ORF1ab/nsp3	616	L616V	Ctt	Gtt	1	1	AY.43	0.000004
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	AY.43	0.000004
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	AY.43	0.000004
ORF1ab/nsp3	616	L616del	CTT	---	1	1	AY.43	0.000004
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	AY.43	0.000004
ORF1ab/nsp3	616	L616del	CTT	---	1	1	AY.5	0.000021
ORF1ab/nsp3	616	L616del	CTT	---	1	1	AY.52	0.000814
ORF1ab/nsp3	616	L616S	CTT	TCC	1	1	AY.52	0.000814
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	AY.59	0.00053
ORF1ab/nsp3	616	L616del	CTT	---	1	1	AY.67	0.000464
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	AY.7	0.000196
ORF1ab/nsp3	616	L616del	CTT	---	1	1	AY.85	0.000427
ORF1ab/nsp3	616	L616V	Ctt	Gtt	1	1	AY.98.1	0.000048
ORF1ab/nsp3	616	L616del	CTT	---	1	1	AY.99	0.001049
ORF1ab/nsp3	616	L616P	cTT	cCC	1	1	B	0.000128
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	B.1	0.000009
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.1	0.000018
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.1.220	0.001859
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.1.315	0.008475
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.1.61	0.008772
ORF1ab/nsp3	616	L616del1	cTt	c-t	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	616	L616del2	CTt	--t	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.157	0.002985
ORF1ab/nsp3	616	L616P	cTt	cCt	1	1	B.1.160	0.000031
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	B.1.160	0.000031
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.160.14	0.002119
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	B.1.177	0.000013
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.177.76	0.002494
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	B.1.177.77	0.000726
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	B.1.177.8	0.000752
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.2	0.000009
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.2	0.000009
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	B.1.276	0.016949
ORF1ab/nsp3	616	L616R	cTt	cGt	1	1	B.1.311	0.000275
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.36	0.000146
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	B.1.427	0.00005
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.429	0.000024
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.576	0.000907
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.580	0.004065
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.609	0.000479
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	616	L616del	CTT	---	1	1	B.15	0.017544
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	B.36	0.076923
ORF1ab/nsp3	616	L616F	Ctt	Ttt	1	1	D.2	0.000075
ORF1ab/nsp3	616	L616L	ctT	ctC	1	1	P.1.15	0.000232
ORF1ab/nsp3	616	L616del	CTT	---	1	1	P.1.4	0.000977
ORF1ab/nsp3	616	L616I	Ctt	Att	1	1	P.1.6	0.001946
ORF1ab/nsp3	616	L616del	CTT	---	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.