CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 612

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	612	Y612Y		syn	taT	taC	1281	1281	1	23396-23398
S	612	Y612F		nonsyn	tAt	tTt	87	87	1	23396-23398
S	612	Y612H		nonsyn	Tat	Cat	9	9	1	23396-23398
S	612	Y612del		del	TAT	---	5	5	1	23396-23398
S	612	Y612C		nonsyn	tAt	tGt	3	3	1	23396-23398
S	612	Y612X		nonsyn	taT	taA	2	1	0.5	23396-23398
S	612	Y612X		nonsyn	taT	taG	2	1	0.5	23396-23398
S	612	Y612N		nonsyn	Tat	Aat	1	1	1	23396-23398
S	612	Y612S		nonsyn	tAt	tCt	1	1	1	23396-23398

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	612	Y612Y	taT	taC	1281	1281	All	0.000245
S	612	Y612Y	taT	taC	529	529	AY.97	0.89966
S	612	Y612Y	taT	taC	194	194	AY.4	0.000302
S	612	Y612F	tAt	tTt	87	87	All	0.000017
S	612	Y612F	tAt	tTt	65	65	B.1.396	0.045872
S	612	Y612Y	taT	taC	62	62	B.1.1.7	0.000056
S	612	Y612Y	taT	taC	55	55	AY.44	0.000335
S	612	Y612Y	taT	taC	49	49	AY.103	0.000304
S	612	Y612Y	taT	taC	48	48	B.1.1.214	0.002662
S	612	Y612Y	taT	taC	36	36	AY.3.1	0.003069
S	612	Y612Y	taT	taC	32	32	B.1.617.2	0.00012
S	612	Y612Y	taT	taC	25	25	AY.3	0.000249
S	612	Y612Y	taT	taC	25	25	AY.43	0.000111
S	612	Y612Y	taT	taC	23	23	B.1.596	0.002004
S	612	Y612Y	taT	taC	20	20	B.1.2	0.000176
S	612	Y612Y	taT	taC	12	12	AY.25	0.000072
S	612	Y612Y	taT	taC	11	11	AY.35	0.002564
S	612	Y612Y	taT	taC	11	11	B.1.351	0.000327
S	612	Y612Y	taT	taC	10	10	AY.5	0.000206
S	612	Y612Y	taT	taC	10	10	B.1.1.519	0.000397
S	612	Y612H	Tat	Cat	9	9	All	0.000002
S	612	Y612Y	taT	taC	9	9	B.1.1.284	0.000967
S	612	Y612F	tAt	tTt	8	8	AY.4	0.000012
S	612	Y612Y	taT	taC	8	8	B.1	0.000073
S	612	Y612Y	taT	taC	7	7	B.1.1	0.000127
S	612	Y612Y	taT	taC	7	7	P.1	0.00011
S	612	Y612Y	taT	taC	6	6	AY.46	0.000624
S	612	Y612del	TAT	---	5	5	All	0.000001
S	612	Y612F	tAt	tTt	5	5	B.1	0.000046
S	612	Y612Y	taT	taC	5	5	B.1.1.348	0.003981
S	612	Y612Y	taT	taC	4	4	B.1.160	0.000125
S	612	Y612Y	taT	taC	4	4	B.1.177	0.000053
S	612	Y612Y	taT	taC	4	4	B.1.258.7	0.007648
S	612	Y612C	tAt	tGt	3	3	All	0.000001
S	612	Y612Y	taT	taC	3	3	AY.115	0.015625
S	612	Y612Y	taT	taC	3	3	AY.20	0.000117
S	612	Y612Y	taT	taC	3	3	AY.26	0.000085
S	612	Y612Y	taT	taC	3	3	AY.39.1	0.000119
S	612	Y612Y	taT	taC	3	3	B.1.582	0.001472
S	612	Y612Y	taT	taC	3	3	B.1.621	0.000266
S	612	Y612Y	taT	taC	3	3	P.1.14	0.000143
S	612	Y612Y	taT	taC	3	3	Q.1	0.000379
S	612	Y612F	tAt	tTt	2	2		0.111111
S	612	Y612X	taT	taA	1	2	All	0
S	612	Y612X	taT	taG	1	2	All	0
S	612	Y612Y	taT	taC	2	2	AY.100	0.000092
S	612	Y612Y	taT	taC	2	2	AY.102	0.000053
S	612	Y612Y	taT	taC	2	2	AY.119	0.000071
S	612	Y612Y	taT	taC	2	2	AY.29	0.000032
S	612	Y612Y	taT	taC	2	2	AY.4.2	0.000043
S	612	Y612Y	taT	taC	2	2	AY.46.6	0.000144
S	612	Y612Y	taT	taC	2	2	B.1.1.222	0.000408
S	612	Y612Y	taT	taC	2	2	B.1.1.28	0.000622
S	612	Y612Y	taT	taC	2	2	B.1.239	0.002442
S	612	Y612Y	taT	taC	2	2	B.1.517	0.000854
S	612	Y612Y	taT	taC	2	2	B.1.526	0.000047
S	612	Y612Y	taT	taC	2	2	L.3	0.007092
S	612	Y612S	tAt	tCt	1	1		0.055556
S	612	Y612S	tAt	tCt	1	1	All	0
S	612	Y612N	Tat	Aat	1	1	All	0
S	612	Y612C	tAt	tGt	1	1	AY.117	0.000085
S	612	Y612Y	taT	taC	1	1	AY.118	0.000063
S	612	Y612Y	taT	taC	1	1	AY.120	0.000037
S	612	Y612Y	taT	taC	1	1	AY.120.1	0.000321
S	612	Y612Y	taT	taC	1	1	AY.14	0.000088
S	612	Y612F	tAt	tTt	1	1	AY.29	0.000016
S	612	Y612F	tAt	tTt	1	1	AY.3	0.00001
S	612	Y612Y	taT	taC	1	1	AY.34	0.000097
S	612	Y612F	tAt	tTt	1	1	AY.36	0.000148
S	612	Y612del	TAT	---	1	1	AY.38	0.000499
S	612	Y612F	tAt	tTt	1	1	AY.4.5	0.000107
S	612	Y612Y	taT	taC	1	1	AY.42	0.00004
S	612	Y612F	tAt	tTt	1	1	AY.43	0.000004
S	612	Y612del	TAT	---	1	1	AY.43	0.000004
S	612	Y612H	Tat	Cat	1	1	AY.44	0.000006
S	612	Y612H	Tat	Cat	1	1	AY.46.6	0.000072
S	612	Y612Y	taT	taC	1	1	AY.47	0.000031
S	612	Y612X	taT	taA	1	1	AY.55	0.000917
S	612	Y612Y	taT	taC	1	1	AY.6	0.000041
S	612	Y612Y	taT	taC	1	1	AY.74	0.000116
S	612	Y612Y	taT	taC	1	1	AY.77	0.001127
S	612	Y612Y	taT	taC	1	1	AY.79	0.001211
S	612	Y612del	TAT	---	1	1	AY.99.2	0.000092
S	612	Y612Y	taT	taC	1	1	B	0.000128
S	612	Y612C	tAt	tGt	1	1	B.1.1	0.000018
S	612	Y612X	taT	taG	1	1	B.1.1	0.000018
S	612	Y612Y	taT	taC	1	1	B.1.1.1	0.000327
S	612	Y612Y	taT	taC	1	1	B.1.1.153	0.001095
S	612	Y612Y	taT	taC	1	1	B.1.1.198	0.001468
S	612	Y612H	Tat	Cat	1	1	B.1.1.205	0.003717
S	612	Y612Y	taT	taC	1	1	B.1.1.291	0.000742
S	612	Y612Y	taT	taC	1	1	B.1.1.419	0.007407
S	612	Y612Y	taT	taC	1	1	B.1.1.487	0.005587
S	612	Y612H	Tat	Cat	1	1	B.1.1.519	0.00004
S	612	Y612H	Tat	Cat	1	1	B.1.1.7	0.000001
S	612	Y612Y	taT	taC	1	1	B.1.1.70	0.000341
S	612	Y612H	Tat	Cat	1	1	B.1.177	0.000013
S	612	Y612F	tAt	tTt	1	1	B.1.177	0.000013
S	612	Y612Y	taT	taC	1	1	B.1.177.17	0.000821
S	612	Y612Y	taT	taC	1	1	B.1.177.86	0.000183
S	612	Y612C	tAt	tGt	1	1	B.1.2	0.000009
S	612	Y612H	Tat	Cat	1	1	B.1.2	0.000009
S	612	Y612Y	taT	taC	1	1	B.1.427	0.00005
S	612	Y612N	Tat	Aat	1	1	B.1.427	0.00005
S	612	Y612Y	taT	taC	1	1	B.1.429	0.000024
S	612	Y612Y	taT	taC	1	1	B.1.509	0.000866
S	612	Y612del	TAT	---	1	1	B.1.564	0.000426
S	612	Y612Y	taT	taC	1	1	B.1.595	0.000261
S	612	Y612H	Tat	Cat	1	1	B.1.617.2	0.000004
S	612	Y612del	TAT	---	1	1	B.1.620	0.000946
S	612	Y612H	Tat	Cat	1	1	C.37	0.000116
S	612	Y612Y	taT	taC	1	1	N.9	0.005952
S	612	Y612F	tAt	tTt	1	1	P.1	0.000016
S	612	Y612Y	taT	taC	1	1	P.1.12	0.000484

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.