CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 449

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	449	Y449S		nonsyn	tAt	tCt	986	979	0.992901	22907-22909
S	449	Y449S		nonsyn	tAT	tCA	986	6	0.00608519	22907-22909
S	449	Y449S		nonsyn	tAT	tCG	986	1	0.0010142	22907-22909
S	449	Y449H		nonsyn	Tat	Cat	852	848	0.995305	22907-22909
S	449	Y449H		nonsyn	TaT	CaC	852	4	0.00469484	22907-22909
S	449	Y449N		nonsyn	Tat	Aat	560	560	1	22907-22909
S	449	Y449Y		syn	taT	taC	451	451	1	22907-22909
S	449	Y449del		del	TAT	---	49	49	1	22907-22909
S	449	Y449D		nonsyn	Tat	Gat	35	35	1	22907-22909
S	449	Y449F		nonsyn	tAt	tTt	30	29	0.966667	22907-22909
S	449	Y449F		nonsyn	tAT	tTC	30	1	0.0333333	22907-22909
S	449	Y449T		nonsyn	TAT	ACA	27	18	0.666667	22907-22909
S	449	Y449T		nonsyn	TAt	ACt	27	8	0.296296	22907-22909
S	449	Y449T		nonsyn	TAT	ACC	27	1	0.037037	22907-22909
S	449	Y449V		nonsyn	TAT	GTA	20	18	0.9	22907-22909
S	449	Y449V		nonsyn	TAt	GTt	20	2	0.1	22907-22909
S	449	Y449X		nonsyn	taT	taA	18	13	0.722222	22907-22909
S	449	Y449X		nonsyn	taT	taG	18	5	0.277778	22907-22909
S	449	Y449K		nonsyn	TaT	AaA	10	10	1	22907-22909
S	449	Y449C		nonsyn	tAt	tGt	8	8	1	22907-22909
S	449	Y449L		nonsyn	TAt	CTt	6	3	0.5	22907-22909
S	449	Y449L		nonsyn	TAT	CTC	6	1	0.166667	22907-22909
S	449	Y449L		nonsyn	TAT	CTG	6	1	0.166667	22907-22909
S	449	Y449L		nonsyn	tAT	tTG	6	1	0.166667	22907-22909
S	449	Y449I		nonsyn	TAT	ATA	2	2	1	22907-22909
S	449	Y449R		nonsyn	TAt	CGt	1	1	1	22907-22909
S	449	Y449A		nonsyn	TAT	GCC	1	1	1	22907-22909
S	449	Y449Q		nonsyn	TaT	CaG	1	1	1	22907-22909
S	449	Y449E		nonsyn	TaT	GaG	1	1	1	22907-22909

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	449	Y449S	tAt	tCt	979	986	All	0.000187
S	449	Y449S	tAT	tCA	6	986	All	0.000001
S	449	Y449S	tAT	tCG	1	986	All	0
S	449	Y449S	tAt	tCt	952	952	B.1.1.7	0.000852
S	449	Y449H	Tat	Cat	848	852	All	0.000162
S	449	Y449H	TaT	CaC	4	852	All	0.000001
S	449	Y449N	Tat	Aat	560	560	All	0.000107
S	449	Y449N	Tat	Aat	456	456	B.1.621	0.040365
S	449	Y449Y	taT	taC	451	451	All	0.000086
S	449	Y449H	Tat	Cat	333	334	B.1.1.7	0.000298
S	449	Y449H	TaT	CaC	1	334	B.1.1.7	0.000001
S	449	Y449H	Tat	Cat	207	207	C.1.2	0.880851
S	449	Y449H	Tat	Cat	178	178	A.29	0.946809
S	449	Y449Y	taT	taC	149	149	B.1.1.7	0.000133
S	449	Y449Y	taT	taC	111	111	AY.4	0.000173
S	449	Y449del	TAT	---	49	49	All	0.000009
S	449	Y449Y	taT	taC	45	45	B.1.221	0.003196
S	449	Y449D	Tat	Gat	35	35	All	0.000007
S	449	Y449Y	taT	taC	35	35	AY.25	0.000211
S	449	Y449N	Tat	Aat	33	33	B.1	0.000302
S	449	Y449D	Tat	Gat	32	32	B.1.1.7	0.000029
S	449	Y449F	tAt	tTt	29	30	All	0.000006
S	449	Y449F	tAT	tTC	1	30	All	0
S	449	Y449N	Tat	Aat	29	29	B.1.1.7	0.000026
S	449	Y449T	TAT	ACA	18	27	All	0.000003
S	449	Y449T	TAt	ACt	8	27	All	0.000002
S	449	Y449T	TAT	ACC	1	27	All	0
S	449	Y449H	Tat	Cat	25	25	C.36.3.1	0.067935
S	449	Y449H	Tat	Cat	21	21	B.1.214.2	0.01259
S	449	Y449V	TAT	GTA	18	20	All	0.000003
S	449	Y449V	TAt	GTt	2	20	All	0
S	449	Y449N	Tat	Aat	20	20	B.1.576	0.018132
S	449	Y449Y	taT	taC	19	19	B.1.2	0.000167
S	449	Y449X	taT	taA	13	18	All	0.000002
S	449	Y449X	taT	taG	5	18	All	0.000001
S	449	Y449H	Tat	Cat	17	17	Q.7	0.018889
S	449	Y449S	tAt	tCt	16	16	P.1.15	0.003717
S	449	Y449Y	taT	taC	14	14	B.1.1.294	0.017722
S	449	Y449T	TAT	ACA	8	13	AY.43	0.000035
S	449	Y449T	TAt	ACt	5	13	AY.43	0.000022
S	449	Y449del	TAT	---	11	11	AY.43	0.000049
S	449	Y449K	TaT	AaA	10	10	All	0.000002
S	449	Y449H	Tat	Cat	10	10	P.1	0.000158
S	449	Y449V	TAT	GTA	9	9	AY.20	0.00035
S	449	Y449S	tAt	tCt	5	9	AY.43	0.000022
S	449	Y449S	tAT	tCA	4	9	AY.43	0.000018
S	449	Y449C	tAt	tGt	8	8	All	0.000002
S	449	Y449Y	taT	taC	8	8	B.1.617.2	0.00003
S	449	Y449N	Tat	Aat	7	7	AY.43	0.000031
S	449	Y449Y	taT	taC	7	7	B.1	0.000064
S	449	Y449F	tAt	tTt	7	7	B.1.1	0.000127
S	449	Y449F	tAt	tTt	7	7	B.1.1.7	0.000006
S	449	Y449H	Tat	Cat	7	7	B.1.351	0.000208
S	449	Y449L	TAt	CTt	3	6	All	0.000001
S	449	Y449L	tAT	tTG	1	6	All	0
S	449	Y449L	TAT	CTG	1	6	All	0
S	449	Y449L	TAT	CTC	1	6	All	0
S	449	Y449K	TaT	AaA	6	6	AY.43	0.000027
S	449	Y449X	taT	taA	5	6	AY.43	0.000022
S	449	Y449X	taT	taG	1	6	AY.43	0.000004
S	449	Y449del	TAT	---	6	6	B.1.1.7	0.000005
S	449	Y449Y	taT	taC	6	6	B.1.526	0.000141
S	449	Y449T	TAT	ACA	4	6	B.1.617.2	0.000015
S	449	Y449T	TAt	ACt	2	6	B.1.617.2	0.000008
S	449	Y449Y	taT	taC	5	5	AY.44	0.00003
S	449	Y449H	Tat	Cat	5	5	B	0.000639
S	449	Y449H	Tat	Cat	5	5	B.1	0.000046
S	449	Y449H	Tat	Cat	5	5	P.1.14	0.000239
S	449	Y449Y	taT	taC	4	4		0.222222
S	449	Y449L	TAt	CTt	1	4		0.055556
S	449	Y449L	TAT	CTC	1	4		0.055556
S	449	Y449L	tAT	tTG	1	4		0.055556
S	449	Y449L	TAT	CTG	1	4		0.055556
S	449	Y449Y	taT	taC	4	4	AY.3	0.00004
S	449	Y449T	TAT	ACA	4	4	AY.45	0.000487
S	449	Y449del	TAT	---	4	4	B.1.617.2	0.000015
S	449	Y449S	tAT	tCA	2	4	B.1.617.2	0.000008
S	449	Y449S	tAt	tCt	2	4	B.1.617.2	0.000008
S	449	Y449H	Tat	Cat	3	3	A	0.001161
S	449	Y449Y	taT	taC	3	3	A.2.5.3	0.030928
S	449	Y449Y	taT	taC	3	3	AY.113	0.000427
S	449	Y449Y	taT	taC	3	3	AY.33	0.0002
S	449	Y449H	TaT	CaC	2	3	AY.42	0.00008
S	449	Y449H	Tat	Cat	1	3	AY.42	0.00004
S	449	Y449Y	taT	taC	3	3	AY.43	0.000013
S	449	Y449H	Tat	Cat	3	3	AY.68	0.000821
S	449	Y449F	tAt	tTt	3	3	B.1	0.000027
S	449	Y449N	Tat	Aat	3	3	B.1.351	0.000089
S	449	Y449K	TaT	AaA	3	3	B.1.617.2	0.000011
S	449	Y449N	Tat	Aat	3	3	B.1.617.2	0.000011
S	449	Y449X	taT	taA	3	3	B.1.617.2	0.000011
S	449	Y449del	TAT	---	2	2		0.111111
S	449	Y449I	TAT	ATA	2	2		0.111111
S	449	Y449F	tAt	tTt	1	2		0.055556
S	449	Y449H	TaT	CaC	1	2		0.055556
S	449	Y449H	Tat	Cat	1	2		0.055556
S	449	Y449F	tAT	tTC	1	2		0.055556
S	449	Y449N	Tat	Aat	2	2	A.2	0.001324
S	449	Y449I	TAT	ATA	2	2	All	0
S	449	Y449V	TAT	GTA	2	2	AY.119	0.000071
S	449	Y449V	TAT	GTA	2	2	AY.26	0.000057
S	449	Y449V	TAT	GTA	2	2	AY.3	0.00002
S	449	Y449Y	taT	taC	2	2	AY.42	0.00008
S	449	Y449del	TAT	---	2	2	AY.42	0.00008
S	449	Y449Y	taT	taC	2	2	AY.46	0.000208
S	449	Y449del	TAT	---	2	2	AY.9.2	0.000073
S	449	Y449del	TAT	---	2	2	B.1	0.000018
S	449	Y449H	Tat	Cat	2	2	B.1.1	0.000036
S	449	Y449Y	taT	taC	2	2	B.1.1.284	0.000215
S	449	Y449V	TAt	GTt	2	2	B.1.1.7	0.000002
S	449	Y449Y	taT	taC	2	2	B.1.177	0.000026
S	449	Y449Y	taT	taC	2	2	B.1.258.14	0.001961
S	449	Y449del	TAT	---	2	2	B.1.351	0.000059
S	449	Y449Y	taT	taC	2	2	B.1.427	0.000101
S	449	Y449Y	taT	taC	2	2	B.1.429	0.000047
S	449	Y449Y	taT	taC	2	2	B.1.617.1	0.000258
S	449	Y449H	Tat	Cat	2	2	B.1.617.2	0.000008
S	449	Y449H	Tat	Cat	2	2	B.1.621	0.000177
S	449	Y449H	Tat	Cat	2	2	C.1	0.004785
S	449	Y449Q	TaT	CaG	1	1		0.055556
S	449	Y449X	taT	taG	1	1		0.055556
S	449	Y449del	TAT	---	1	1	A	0.000387
S	449	Y449F	tAt	tTt	1	1	A.2	0.000662
S	449	Y449H	Tat	Cat	1	1	A.2	0.000662
S	449	Y449H	Tat	Cat	1	1	A.27	0.001656
S	449	Y449Y	taT	taC	1	1	A.27	0.001656
S	449	Y449E	TaT	GaG	1	1	All	0
S	449	Y449A	TAT	GCC	1	1	All	0
S	449	Y449R	TAt	CGt	1	1	All	0
S	449	Y449Q	TaT	CaG	1	1	All	0
S	449	Y449V	TAT	GTA	1	1	AY.100	0.000046
S	449	Y449Y	taT	taC	1	1	AY.100	0.000046
S	449	Y449del	TAT	---	1	1	AY.102	0.000027
S	449	Y449N	Tat	Aat	1	1	AY.102	0.000027
S	449	Y449S	tAt	tCt	1	1	AY.102	0.000027
S	449	Y449X	taT	taA	1	1	AY.102	0.000027
S	449	Y449V	TAT	GTA	1	1	AY.102	0.000027
S	449	Y449T	TAt	ACt	1	1	AY.102	0.000027
S	449	Y449F	tAt	tTt	1	1	AY.102	0.000027
S	449	Y449C	tAt	tGt	1	1	AY.103	0.000006
S	449	Y449H	Tat	Cat	1	1	AY.103	0.000006
S	449	Y449del	TAT	---	1	1	AY.107	0.000466
S	449	Y449del	TAT	---	1	1	AY.108	0.001103
S	449	Y449T	TAT	ACA	1	1	AY.110	0.000113
S	449	Y449del	TAT	---	1	1	AY.113	0.000142
S	449	Y449H	Tat	Cat	1	1	AY.120	0.000037
S	449	Y449Y	taT	taC	1	1	AY.21	0.001898
S	449	Y449N	Tat	Aat	1	1	AY.25	0.000006
S	449	Y449H	Tat	Cat	1	1	AY.25	0.000006
S	449	Y449X	taT	taA	1	1	AY.3	0.00001
S	449	Y449F	tAt	tTt	1	1	AY.34	0.000097
S	449	Y449Y	taT	taC	1	1	AY.39	0.000025
S	449	Y449F	tAt	tTt	1	1	AY.39	0.000025
S	449	Y449Y	taT	taC	1	1	AY.39.1	0.00004
S	449	Y449H	Tat	Cat	1	1	AY.4	0.000002
S	449	Y449K	TaT	AaA	1	1	AY.42	0.00004
S	449	Y449H	Tat	Cat	1	1	AY.43	0.000004
S	449	Y449V	TAT	GTA	1	1	AY.44	0.000006
S	449	Y449del	TAT	---	1	1	AY.44	0.000006
S	449	Y449del	TAT	---	1	1	AY.45	0.000122
S	449	Y449Y	taT	taC	1	1	AY.46.1	0.001027
S	449	Y449T	TAT	ACA	1	1	AY.46.6	0.000072
S	449	Y449Y	taT	taC	1	1	AY.46.6	0.000072
S	449	Y449X	taT	taG	1	1	AY.5	0.000021
S	449	Y449Y	taT	taC	1	1	AY.5	0.000021
S	449	Y449N	Tat	Aat	1	1	AY.52	0.000814
S	449	Y449T	TAT	ACC	1	1	AY.67	0.000464
S	449	Y449del	TAT	---	1	1	AY.84	0.000437
S	449	Y449C	tAt	tGt	1	1	AY.9.2	0.000037
S	449	Y449del	TAT	---	1	1	AY.99	0.001049
S	449	Y449N	Tat	Aat	1	1	B	0.000128
S	449	Y449F	tAt	tTt	1	1	B	0.000128
S	449	Y449S	tAT	tCG	1	1	B.1	0.000009
S	449	Y449C	tAt	tGt	1	1	B.1	0.000009
S	449	Y449E	TaT	GaG	1	1	B.1.1	0.000018
S	449	Y449Y	taT	taC	1	1	B.1.1	0.000018
S	449	Y449D	Tat	Gat	1	1	B.1.1	0.000018
S	449	Y449X	taT	taG	1	1	B.1.1	0.000018
S	449	Y449F	tAt	tTt	1	1	B.1.1.161	0.003534
S	449	Y449X	taT	taA	1	1	B.1.1.289	0.002083
S	449	Y449H	Tat	Cat	1	1	B.1.1.294	0.001266
S	449	Y449del	TAT	---	1	1	B.1.1.306	0.000438
S	449	Y449D	Tat	Gat	1	1	B.1.1.372	0.000689
S	449	Y449H	Tat	Cat	1	1	B.1.1.402	0.011111
S	449	Y449F	tAt	tTt	1	1	B.1.1.409	0.002833
S	449	Y449L	TAt	CTt	1	1	B.1.1.7	0.000001
S	449	Y449C	tAt	tGt	1	1	B.1.1.7	0.000001
S	449	Y449F	tAt	tTt	1	1	B.1.1.70	0.000341
S	449	Y449del	TAT	---	1	1	B.1.177	0.000013
S	449	Y449H	Tat	Cat	1	1	B.1.177.34	0.052632
S	449	Y449del	TAT	---	1	1	B.1.177.4	0.000211
S	449	Y449H	Tat	Cat	1	1	B.1.2	0.000009
S	449	Y449del	TAT	---	1	1	B.1.2	0.000009
S	449	Y449N	Tat	Aat	1	1	B.1.2	0.000009
S	449	Y449del	TAT	---	1	1	B.1.214.2	0.0006
S	449	Y449Y	taT	taC	1	1	B.1.240	0.000216
S	449	Y449H	Tat	Cat	1	1	B.1.243	0.00007
S	449	Y449D	Tat	Gat	1	1	B.1.243	0.00007
S	449	Y449L	TAt	CTt	1	1	B.1.258	0.000067
S	449	Y449H	Tat	Cat	1	1	B.1.268	0.010417
S	449	Y449Y	taT	taC	1	1	B.1.351	0.00003
S	449	Y449C	tAt	tGt	1	1	B.1.36.16	0.001425
S	449	Y449X	taT	taG	1	1	B.1.362	0.001541
S	449	Y449H	Tat	Cat	1	1	B.1.429	0.000024
S	449	Y449X	taT	taA	1	1	B.1.470	0.001404
S	449	Y449C	tAt	tGt	1	1	B.1.501	0.007353
S	449	Y449S	tAt	tCt	1	1	B.1.508	0.025641
S	449	Y449C	tAt	tGt	1	1	B.1.526	0.000024
S	449	Y449del	TAT	---	1	1	B.1.526	0.000024
S	449	Y449N	Tat	Aat	1	1	B.1.582	0.000491
S	449	Y449X	taT	taA	1	1	B.1.596	0.000087
S	449	Y449H	Tat	Cat	1	1	B.1.617.1	0.000129
S	449	Y449R	TAt	CGt	1	1	B.1.617.2	0.000004
S	449	Y449A	TAT	GCC	1	1	B.1.617.2	0.000004
S	449	Y449F	tAt	tTt	1	1	B.1.617.2	0.000004
S	449	Y449del	TAT	---	1	1	B.1.620	0.000946
S	449	Y449Y	taT	taC	1	1	B.1.630	0.005236
S	449	Y449F	tAt	tTt	1	1	B.55	0.00295
S	449	Y449H	Tat	Cat	1	1	C.35	0.000774
S	449	Y449Y	taT	taC	1	1	D.2	0.000075
S	449	Y449C	tAt	tGt	1	1	D.2	0.000075
S	449	Y449Y	taT	taC	1	1	P.1	0.000016
S	449	Y449S	tAt	tCt	1	1	P.1	0.000016
S	449	Y449N	Tat	Aat	1	1	P.1	0.000016
S	449	Y449del	TAT	---	1	1	P.1.1	0.000318
S	449	Y449F	tAt	tTt	1	1	P.1.1	0.000318
S	449	Y449del	TAT	---	1	1	P.1.15	0.000232
S	449	Y449H	Tat	Cat	1	1	P.1.7	0.000319
S	449	Y449Y	taT	taC	1	1	P.2	0.000187
S	449	Y449H	Tat	Cat	1	1	P.3	0.001595
S	449	Y449Y	taT	taC	1	1	Q.1	0.000126
S	449	Y449S	tAt	tCt	1	1	Q.1	0.000126
S	449	Y449H	Tat	Cat	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.