CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 663

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	663	D663D		syn	gaC	gaT	1506	1506	1	23549-23551
S	663	D663del		del	GAC	---	54	54	1	23549-23551
S	663	D663P		nonsyn	GAc	CCc	10	7	0.7	23549-23551
S	663	D663A		nonsyn	gAc	gCc	10	5	0.5	23549-23551
S	663	D663A		nonsyn	gAC	gCT	10	3	0.3	23549-23551
S	663	D663A		nonsyn	gAC	gCG	10	2	0.2	23549-23551
S	663	D663P		nonsyn	GAC	CCG	10	2	0.2	23549-23551
S	663	D663P		nonsyn	GAC	CCA	10	1	0.1	23549-23551
S	663	D663Y		nonsyn	Gac	Tac	9	9	1	23549-23551
S	663	D663H		nonsyn	Gac	Cac	7	7	1	23549-23551
S	663	D663T		nonsyn	GAc	ACc	7	5	0.714286	23549-23551
S	663	D663E		nonsyn	gaC	gaG	7	4	0.571429	23549-23551
S	663	D663E		nonsyn	gaC	gaA	7	3	0.428571	23549-23551
S	663	D663T		nonsyn	GAC	ACA	7	1	0.142857	23549-23551
S	663	D663T		nonsyn	GAC	ACG	7	1	0.142857	23549-23551
S	663	D663G		nonsyn	gAc	gGc	6	5	0.833333	23549-23551
S	663	D663G		nonsyn	gAC	gGA	6	1	0.166667	23549-23551
S	663	D663N		nonsyn	Gac	Aac	5	5	1	23549-23551
S	663	D663R		nonsyn	GAC	CGA	4	2	0.5	23549-23551
S	663	D663R		nonsyn	GAc	CGc	4	1	0.25	23549-23551
S	663	D663R		nonsyn	GAC	AGA	4	1	0.25	23549-23551
S	663	D663del2		del	gAC	g--	3	3	1	23549-23551
S	663	D663X		nonsyn	GAC	TGA	3	2	0.666667	23549-23551
S	663	D663L		nonsyn	GAc	CTc	3	2	0.666667	23549-23551
S	663	D663X		nonsyn	GaC	TaA	3	1	0.333333	23549-23551
S	663	D663L		nonsyn	GAC	CTG	3	1	0.333333	23549-23551
S	663	D663del1		del	Gac	-ac	2	2	1	23549-23551
S	663	D663Q		nonsyn	GaC	CaG	2	2	1	23549-23551
S	663	D663I		nonsyn	GAc	ATc	1	1	1	23549-23551
S	663	D663S		nonsyn	GAc	AGc	1	1	1	23549-23551
S	663	D663C		nonsyn	GAc	TGc	1	1	1	23549-23551

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	663	D663D	gaC	gaT	1506	1506	All	0.000288
S	663	D663D	gaC	gaT	379	379	B.1.448	0.994751
S	663	D663D	gaC	gaT	270	270	AY.44	0.001643
S	663	D663D	gaC	gaT	67	67	B.1.2	0.00059
S	663	D663D	gaC	gaT	62	62	B.1	0.000568
S	663	D663D	gaC	gaT	59	59	B.1.408	0.217712
S	663	D663D	gaC	gaT	55	55	B.1.177.87	0.040029
S	663	D663del	GAC	---	54	54	All	0.00001
S	663	D663D	gaC	gaT	54	54	B.1.177	0.000711
S	663	D663D	gaC	gaT	51	51	B.1.637	0.003727
S	663	D663D	gaC	gaT	47	47	B.1.617.2	0.000177
S	663	D663D	gaC	gaT	40	40	C.36.3	0.022689
S	663	D663D	gaC	gaT	37	37	B.1.221	0.002628
S	663	D663D	gaC	gaT	33	33	AY.103	0.000205
S	663	D663D	gaC	gaT	30	30	B.1.1.7	0.000027
S	663	D663D	gaC	gaT	24	24	B.1.429	0.000565
S	663	D663D	gaC	gaT	23	23	AY.4	0.000036
S	663	D663D	gaC	gaT	20	20	P.1	0.000315
S	663	D663D	gaC	gaT	17	17	AY.25	0.000102
S	663	D663D	gaC	gaT	16	16	B.1.351	0.000476
S	663	D663D	gaC	gaT	12	12	P.1.16	0.004489
S	663	D663D	gaC	gaT	11	11	AY.119	0.000388
S	663	D663D	gaC	gaT	11	11	B.1.1	0.0002
S	663	D663P	GAc	CCc	7	10	All	0.000001
S	663	D663A	gAc	gCc	5	10	All	0.000001
S	663	D663A	gAC	gCT	3	10	All	0.000001
S	663	D663P	GAC	CCG	2	10	All	0
S	663	D663A	gAC	gCG	2	10	All	0
S	663	D663P	GAC	CCA	1	10	All	0
S	663	D663D	gaC	gaT	10	10	B.1.36	0.001459
S	663	D663Y	Gac	Tac	9	9	All	0.000002
S	663	D663D	gaC	gaT	9	9	AY.20	0.00035
S	663	D663D	gaC	gaT	9	9	B.1.160	0.000281
S	663	D663D	gaC	gaT	9	9	B.1.160.14	0.019068
S	663	D663del	GAC	---	8	8	B.1	0.000073
S	663	D663D	gaC	gaT	8	8	B.1.258	0.000532
S	663	D663D	gaC	gaT	8	8	B.1.576	0.007253
S	663	D663H	Gac	Cac	7	7	All	0.000001
S	663	D663T	GAc	ACc	5	7	All	0.000001
S	663	D663E	gaC	gaG	4	7	All	0.000001
S	663	D663E	gaC	gaA	3	7	All	0.000001
S	663	D663T	GAC	ACG	1	7	All	0
S	663	D663T	GAC	ACA	1	7	All	0
S	663	D663del	GAC	---	7	7	B.1.1.7	0.000006
S	663	D663G	gAc	gGc	5	6	All	0.000001
S	663	D663G	gAC	gGA	1	6	All	0
S	663	D663D	gaC	gaT	6	6	B.1.1.241	0.012422
S	663	D663N	Gac	Aac	5	5	All	0.000001
S	663	D663D	gaC	gaT	5	5	B.1.1.432	0.006329
S	663	D663N	Gac	Aac	4	4		0.222222
S	663	D663P	GAc	CCc	4	4		0.222222
S	663	D663A	gAC	gCT	2	4		0.111111
S	663	D663A	gAc	gCc	2	4		0.111111
S	663	D663R	GAC	CGA	2	4	All	0
S	663	D663R	GAC	AGA	1	4	All	0
S	663	D663R	GAc	CGc	1	4	All	0
S	663	D663del	GAC	---	4	4	AY.43	0.000018
S	663	D663D	gaC	gaT	4	4	AY.43	0.000018
S	663	D663D	gaC	gaT	4	4	B.1.1.362	0.022472
S	663	D663del	GAC	---	4	4	P.1	0.000063
S	663	D663D	gaC	gaT	4	4	P.1.15	0.000929
S	663	D663D	gaC	gaT	4	4	P.2	0.000747
S	663	D663del2	gAC	g--	3	3	All	0.000001
S	663	D663L	GAc	CTc	2	3	All	0
S	663	D663X	GAC	TGA	2	3	All	0
S	663	D663X	GaC	TaA	1	3	All	0
S	663	D663L	GAC	CTG	1	3	All	0
S	663	D663del	GAC	---	3	3	AY.25	0.000018
S	663	D663R	GAC	CGA	1	3	AY.3	0.00001
S	663	D663R	GAC	AGA	1	3	AY.3	0.00001
S	663	D663R	GAc	CGc	1	3	AY.3	0.00001
S	663	D663D	gaC	gaT	3	3	AY.9.2	0.00011
S	663	D663Y	Gac	Tac	3	3	B.1.1	0.000054
S	663	D663D	gaC	gaT	3	3	B.1.1.326	0.005282
S	663	D663D	gaC	gaT	3	3	B.1.177.7	0.000495
S	663	D663D	gaC	gaT	3	3	B.1.596	0.000261
S	663	D663del	GAC	---	3	3	B.1.621	0.000266
S	663	D663D	gaC	gaT	3	3	C.37	0.000348
S	663	D663del	GAC	---	3	3	P.1.15	0.000697
S	663	D663H	Gac	Cac	2	2		0.111111
S	663	D663T	GAc	ACc	2	2		0.111111
S	663	D663del1	Gac	-ac	2	2	All	0
S	663	D663Q	GaC	CaG	2	2	All	0
S	663	D663D	gaC	gaT	2	2	AY.100	0.000092
S	663	D663D	gaC	gaT	2	2	AY.102	0.000053
S	663	D663D	gaC	gaT	2	2	AY.118	0.000125
S	663	D663D	gaC	gaT	2	2	AY.120	0.000074
S	663	D663D	gaC	gaT	2	2	AY.121	0.000271
S	663	D663T	GAC	ACA	1	2	AY.3	0.00001
S	663	D663T	GAc	ACc	1	2	AY.3	0.00001
S	663	D663P	GAc	CCc	1	2	AY.3	0.00001
S	663	D663P	GAC	CCA	1	2	AY.3	0.00001
S	663	D663D	gaC	gaT	2	2	AY.39	0.000049
S	663	D663L	GAC	CTG	1	2	AY.43	0.000004
S	663	D663P	GAC	CCG	1	2	AY.43	0.000004
S	663	D663L	GAc	CTc	1	2	AY.43	0.000004
S	663	D663P	GAc	CCc	1	2	AY.43	0.000004
S	663	D663A	gAc	gCc	1	2	AY.43	0.000004
S	663	D663A	gAC	gCG	1	2	AY.43	0.000004
S	663	D663E	gaC	gaG	2	2	AY.44	0.000012
S	663	D663D	gaC	gaT	2	2	AY.47	0.000062
S	663	D663G	gAc	gGc	2	2	B	0.000256
S	663	D663D	gaC	gaT	2	2	B	0.000256
S	663	D663G	gAC	gGA	1	2	B.1.1	0.000018
S	663	D663X	GAC	TGA	1	2	B.1.1	0.000018
S	663	D663X	GaC	TaA	1	2	B.1.1	0.000018
S	663	D663G	gAc	gGc	1	2	B.1.1	0.000018
S	663	D663D	gaC	gaT	2	2	B.1.1.297	0.004474
S	663	D663D	gaC	gaT	2	2	B.1.1.306	0.000877
S	663	D663D	gaC	gaT	2	2	B.1.1.311	0.000716
S	663	D663D	gaC	gaT	2	2	B.1.1.39	0.001019
S	663	D663D	gaC	gaT	2	2	B.1.110	0.00905
S	663	D663D	gaC	gaT	2	2	B.1.177.12	0.000303
S	663	D663D	gaC	gaT	2	2	B.1.177.46	0.001837
S	663	D663D	gaC	gaT	2	2	B.1.177.73	0.001133
S	663	D663D	gaC	gaT	2	2	B.1.177.86	0.000367
S	663	D663del	GAC	---	2	2	B.1.2	0.000018
S	663	D663D	gaC	gaT	2	2	B.1.232	0.001075
S	663	D663D	gaC	gaT	2	2	B.1.265	0.002541
S	663	D663D	gaC	gaT	2	2	B.1.311	0.000549
S	663	D663D	gaC	gaT	2	2	B.1.369	0.00057
S	663	D663D	gaC	gaT	2	2	B.1.427	0.000101
S	663	D663D	gaC	gaT	2	2	B.1.478	0.023529
S	663	D663del	GAC	---	2	2	B.1.596	0.000174
S	663	D663D	gaC	gaT	2	2	B.1.609	0.000959
S	663	D663del	GAC	---	2	2	B.1.617.2	0.000008
S	663	D663A	gAc	gCc	1	2	B.1.617.2	0.000004
S	663	D663A	gAC	gCG	1	2	B.1.617.2	0.000004
S	663	D663P	GAC	CCG	1	2	B.1.617.2	0.000004
S	663	D663P	GAc	CCc	1	2	B.1.617.2	0.000004
S	663	D663del	GAC	---	1	1	A.2.2	0.001689
S	663	D663D	gaC	gaT	1	1	AD.2	0.000219
S	663	D663I	GAc	ATc	1	1	All	0
S	663	D663S	GAc	AGc	1	1	All	0
S	663	D663C	GAc	TGc	1	1	All	0
S	663	D663del	GAC	---	1	1	AY.103	0.000006
S	663	D663R	GAC	CGA	1	1	AY.113	0.000142
S	663	D663D	gaC	gaT	1	1	AY.113	0.000142
S	663	D663H	Gac	Cac	1	1	AY.23	0.00007
S	663	D663D	gaC	gaT	1	1	AY.23	0.00007
S	663	D663T	GAc	ACc	1	1	AY.24	0.000431
S	663	D663D	gaC	gaT	1	1	AY.29	0.000016
S	663	D663S	GAc	AGc	1	1	AY.3	0.00001
S	663	D663L	GAc	CTc	1	1	AY.3	0.00001
S	663	D663del1	Gac	-ac	1	1	AY.38	0.000499
S	663	D663T	GAC	ACG	1	1	AY.39.1	0.00004
S	663	D663E	gaC	gaG	1	1	AY.43	0.000004
S	663	D663H	Gac	Cac	1	1	AY.43	0.000004
S	663	D663Q	GaC	CaG	1	1	AY.43	0.000004
S	663	D663del	GAC	---	1	1	AY.44	0.000006
S	663	D663Y	Gac	Tac	1	1	AY.45	0.000122
S	663	D663del	GAC	---	1	1	AY.46	0.000104
S	663	D663D	gaC	gaT	1	1	AY.55	0.000917
S	663	D663D	gaC	gaT	1	1	AY.64	0.000595
S	663	D663I	GAc	ATc	1	1	AY.67	0.000464
S	663	D663del	GAC	---	1	1	AY.84	0.000437
S	663	D663D	gaC	gaT	1	1	AY.85	0.000427
S	663	D663del	GAC	---	1	1	AY.85	0.000427
S	663	D663D	gaC	gaT	1	1	AY.87	0.000833
S	663	D663G	gAc	gGc	1	1	AY.9.2	0.000037
S	663	D663del	GAC	---	1	1	AY.99	0.001049
S	663	D663A	gAc	gCc	1	1	B.1	0.000009
S	663	D663Y	Gac	Tac	1	1	B.1	0.000009
S	663	D663G	gAc	gGc	1	1	B.1	0.000009
S	663	D663del2	gAC	g--	1	1	B.1	0.000009
S	663	D663del	GAC	---	1	1	B.1.1	0.000018
S	663	D663C	GAc	TGc	1	1	B.1.1	0.000018
S	663	D663A	gAC	gCT	1	1	B.1.1	0.000018
S	663	D663E	gaC	gaA	1	1	B.1.1	0.000018
S	663	D663del2	gAC	g--	1	1	B.1.1.197	0.037037
S	663	D663D	gaC	gaT	1	1	B.1.1.214	0.000055
S	663	D663D	gaC	gaT	1	1	B.1.1.216	0.00089
S	663	D663D	gaC	gaT	1	1	B.1.1.222	0.000204
S	663	D663D	gaC	gaT	1	1	B.1.1.25	0.000569
S	663	D663D	gaC	gaT	1	1	B.1.1.263	0.001558
S	663	D663D	gaC	gaT	1	1	B.1.1.28	0.000311
S	663	D663D	gaC	gaT	1	1	B.1.1.317	0.000412
S	663	D663H	Gac	Cac	1	1	B.1.1.37	0.000193
S	663	D663D	gaC	gaT	1	1	B.1.1.37	0.000193
S	663	D663del	GAC	---	1	1	B.1.1.372	0.000689
S	663	D663D	gaC	gaT	1	1	B.1.1.425	0.045455
S	663	D663H	Gac	Cac	1	1	B.1.1.7	0.000001
S	663	D663T	GAc	ACc	1	1	B.1.1.7	0.000001
S	663	D663D	gaC	gaT	1	1	B.1.1.71	0.006061
S	663	D663D	gaC	gaT	1	1	B.1.140	0.018868
S	663	D663D	gaC	gaT	1	1	B.1.160.31	0.008065
S	663	D663del	GAC	---	1	1	B.1.177	0.000013
S	663	D663D	gaC	gaT	1	1	B.1.177.17	0.000821
S	663	D663D	gaC	gaT	1	1	B.1.177.21	0.000076
S	663	D663D	gaC	gaT	1	1	B.1.177.35	0.000691
S	663	D663D	gaC	gaT	1	1	B.1.177.44	0.000519
S	663	D663D	gaC	gaT	1	1	B.1.177.54	0.000606
S	663	D663D	gaC	gaT	1	1	B.1.177.60	0.000218
S	663	D663D	gaC	gaT	1	1	B.1.177.81	0.000189
S	663	D663D	gaC	gaT	1	1	B.1.177.82	0.000477
S	663	D663Y	Gac	Tac	1	1	B.1.2	0.000009
S	663	D663del	GAC	---	1	1	B.1.234	0.000132
S	663	D663D	gaC	gaT	1	1	B.1.258.14	0.00098
S	663	D663D	gaC	gaT	1	1	B.1.258.2	0.004505
S	663	D663Y	Gac	Tac	1	1	B.1.311	0.000275
S	663	D663D	gaC	gaT	1	1	B.1.313	0.006579
S	663	D663D	gaC	gaT	1	1	B.1.325	0.006897
S	663	D663E	gaC	gaA	1	1	B.1.36.8	0.001
S	663	D663D	gaC	gaT	1	1	B.1.367	0.000792
S	663	D663D	gaC	gaT	1	1	B.1.371	0.001122
S	663	D663del2	gAC	g--	1	1	B.1.429	0.000024
S	663	D663D	gaC	gaT	1	1	B.1.438.1	0.000107
S	663	D663D	gaC	gaT	1	1	B.1.497	0.000315
S	663	D663D	gaC	gaT	1	1	B.1.595	0.000261
S	663	D663D	gaC	gaT	1	1	B.1.602	0.006536
S	663	D663D	gaC	gaT	1	1	B.1.617.1	0.000129
S	663	D663Y	Gac	Tac	1	1	B.1.617.2	0.000004
S	663	D663E	gaC	gaG	1	1	B.1.617.2	0.000004
S	663	D663H	Gac	Cac	1	1	B.1.617.2	0.000004
S	663	D663X	GAC	TGA	1	1	B.1.617.2	0.000004
S	663	D663Q	GaC	CaG	1	1	B.1.617.2	0.000004
S	663	D663del1	Gac	-ac	1	1	B.1.617.2	0.000004
S	663	D663del	GAC	---	1	1	B.1.620	0.000946
S	663	D663del	GAC	---	1	1	B.1.627	0.00202
S	663	D663del	GAC	---	1	1	B.1.638	0.052632
S	663	D663Y	Gac	Tac	1	1	B.3	0.000831
S	663	D663D	gaC	gaT	1	1	B.6	0.00091
S	663	D663del	GAC	---	1	1	C.37	0.000116
S	663	D663D	gaC	gaT	1	1	D.2	0.000075
S	663	D663E	gaC	gaA	1	1	D.2	0.000075
S	663	D663N	Gac	Aac	1	1	P.1	0.000016
S	663	D663D	gaC	gaT	1	1	P.1.12	0.000484
S	663	D663del	GAC	---	1	1	P.1.13	0.000898
S	663	D663D	gaC	gaT	1	1	P.1.14	0.000048
S	663	D663D	gaC	gaT	1	1	P.1.2	0.001156
S	663	D663D	gaC	gaT	1	1	Q.8	0.000165

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.