CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 549

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	549	T549I		nonsyn	aCa	aTa	1161	1114	0.959518	23207-23209
S	549	T549I		nonsyn	aCA	aTT	1161	46	0.039621	23207-23209
S	549	T549I		nonsyn	aCA	aTC	1161	1	0.000861326	23207-23209
S	549	T549T		syn	acA	acG	245	144	0.587755	23207-23209
S	549	T549T		syn	acA	acT	245	54	0.220408	23207-23209
S	549	T549T		syn	acA	acC	245	47	0.191837	23207-23209
S	549	T549S		nonsyn	Aca	Tca	194	174	0.896907	23207-23209
S	549	T549S		nonsyn	aCA	aGT	194	17	0.0876289	23207-23209
S	549	T549S		nonsyn	aCA	aGC	194	2	0.0103093	23207-23209
S	549	T549S		nonsyn	AcA	TcT	194	1	0.00515464	23207-23209
S	549	T549A		nonsyn	Aca	Gca	180	180	1	23207-23209
S	549	T549L		nonsyn	ACa	TTa	62	38	0.612903	23207-23209
S	549	T549L		nonsyn	ACA	TTG	62	16	0.258065	23207-23209
S	549	T549L		nonsyn	ACa	CTa	62	3	0.0483871	23207-23209
S	549	T549L		nonsyn	ACA	CTG	62	2	0.0322581	23207-23209
S	549	T549L		nonsyn	ACA	CTT	62	2	0.0322581	23207-23209
S	549	T549L		nonsyn	ACA	CTC	62	1	0.016129	23207-23209
S	549	T549F		nonsyn	ACA	TTT	48	46	0.958333	23207-23209
S	549	T549K		nonsyn	aCa	aAa	48	41	0.854167	23207-23209
S	549	T549K		nonsyn	aCA	aAG	48	7	0.145833	23207-23209
S	549	T549F		nonsyn	ACA	TTC	48	2	0.0416667	23207-23209
S	549	T549X		nonsyn	ACa	TAa	47	27	0.574468	23207-23209
S	549	T549X		nonsyn	ACa	TGa	47	12	0.255319	23207-23209
S	549	T549X		nonsyn	ACA	TAG	47	8	0.170213	23207-23209
S	549	T549Y		nonsyn	ACA	TAT	37	34	0.918919	23207-23209
S	549	T549Y		nonsyn	ACA	TAC	37	3	0.0810811	23207-23209
S	549	T549V		nonsyn	ACA	GTT	35	16	0.457143	23207-23209
S	549	T549V		nonsyn	ACa	GTa	35	10	0.285714	23207-23209
S	549	T549V		nonsyn	ACA	GTG	35	8	0.228571	23207-23209
S	549	T549V		nonsyn	ACA	GTC	35	1	0.0285714	23207-23209
S	549	T549N		nonsyn	aCA	aAT	34	32	0.941176	23207-23209
S	549	T549N		nonsyn	aCA	aAC	34	2	0.0588235	23207-23209
S	549	T549G		nonsyn	ACA	GGT	33	16	0.484848	23207-23209
S	549	T549G		nonsyn	ACa	GGa	33	9	0.272727	23207-23209
S	549	T549G		nonsyn	ACA	GGG	33	7	0.212121	23207-23209
S	549	T549G		nonsyn	ACA	GGC	33	1	0.030303	23207-23209
S	549	T549R		nonsyn	aCa	aGa	21	12	0.571429	23207-23209
S	549	T549R		nonsyn	aCA	aGG	21	7	0.333333	23207-23209
S	549	T549R		nonsyn	ACA	CGT	21	1	0.047619	23207-23209
S	549	T549R		nonsyn	ACa	CGa	21	1	0.047619	23207-23209
S	549	T549C		nonsyn	ACA	TGT	19	17	0.894737	23207-23209
S	549	T549C		nonsyn	ACA	TGC	19	2	0.105263	23207-23209
S	549	T549del		del	ACA	---	15	15	1	23207-23209
S	549	T549M		nonsyn	aCA	aTG	14	14	1	23207-23209
S	549	T549W		nonsyn	ACA	TGG	8	8	1	23207-23209
S	549	T549E		nonsyn	ACa	GAa	5	4	0.8	23207-23209
S	549	T549D		nonsyn	ACA	GAT	5	4	0.8	23207-23209
S	549	T549Q		nonsyn	ACa	CAa	5	3	0.6	23207-23209
S	549	T549Q		nonsyn	ACA	CAG	5	2	0.4	23207-23209
S	549	T549D		nonsyn	ACA	GAC	5	1	0.2	23207-23209
S	549	T549E		nonsyn	ACA	GAG	5	1	0.2	23207-23209
S	549	T549H		nonsyn	ACA	CAT	3	2	0.666667	23207-23209
S	549	T549H		nonsyn	ACA	CAC	3	1	0.333333	23207-23209
S	549	T549del1		del	Aca	-ca	2	1	0.5	23207-23209
S	549	T549del1		del	acA	ac-	2	1	0.5	23207-23209
S	549	T549P		nonsyn	Aca	Cca	1	1	1	23207-23209
S	549	T549del2		del	aCA	a--	1	1	1	23207-23209

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	549	T549I	aCa	aTa	1114	1161	All	0.000213
S	549	T549I	aCA	aTT	46	1161	All	0.000009
S	549	T549I	aCA	aTC	1	1161	All	0
S	549	T549I	aCa	aTa	854	897	B.1.1.7	0.000765
S	549	T549I	aCA	aTT	42	897	B.1.1.7	0.000038
S	549	T549I	aCA	aTC	1	897	B.1.1.7	0.000001
S	549	T549T	acA	acG	144	245	All	0.000028
S	549	T549T	acA	acT	54	245	All	0.00001
S	549	T549T	acA	acC	47	245	All	0.000009
S	549	T549S	Aca	Tca	174	194	All	0.000033
S	549	T549S	aCA	aGT	17	194	All	0.000003
S	549	T549S	aCA	aGC	2	194	All	0
S	549	T549S	AcA	TcT	1	194	All	0
S	549	T549A	Aca	Gca	180	180	All	0.000034
S	549	T549S	Aca	Tca	80	100	B.1.1.7	0.000072
S	549	T549S	aCA	aGT	17	100	B.1.1.7	0.000015
S	549	T549S	aCA	aGC	2	100	B.1.1.7	0.000002
S	549	T549S	AcA	TcT	1	100	B.1.1.7	0.000001
S	549	T549A	Aca	Gca	80	80	B.1.1.299	0.97561
S	549	T549L	ACa	TTa	38	62	All	0.000007
S	549	T549L	ACA	TTG	16	62	All	0.000003
S	549	T549L	ACa	CTa	3	62	All	0.000001
S	549	T549L	ACA	CTT	2	62	All	0
S	549	T549L	ACA	CTG	2	62	All	0
S	549	T549L	ACA	CTC	1	62	All	0
S	549	T549L	ACa	TTa	34	58	B.1.1.7	0.00003
S	549	T549L	ACA	TTG	16	58	B.1.1.7	0.000014
S	549	T549L	ACa	CTa	3	58	B.1.1.7	0.000003
S	549	T549L	ACA	CTG	2	58	B.1.1.7	0.000002
S	549	T549L	ACA	CTT	2	58	B.1.1.7	0.000002
S	549	T549L	ACA	CTC	1	58	B.1.1.7	0.000001
S	549	T549T	acA	acG	53	56	AY.44	0.000323
S	549	T549T	acA	acC	3	56	AY.44	0.000018
S	549	T549F	ACA	TTT	46	48	All	0.000009
S	549	T549K	aCa	aAa	41	48	All	0.000008
S	549	T549K	aCA	aAG	7	48	All	0.000001
S	549	T549F	ACA	TTC	2	48	All	0
S	549	T549X	ACa	TAa	27	47	All	0.000005
S	549	T549X	ACa	TGa	12	47	All	0.000002
S	549	T549X	ACA	TAG	8	47	All	0.000002
S	549	T549I	aCa	aTa	45	45	XA	1
S	549	T549F	ACA	TTT	42	44	B.1.1.7	0.000038
S	549	T549F	ACA	TTC	2	44	B.1.1.7	0.000002
S	549	T549X	ACa	TAa	22	41	B.1.1.7	0.00002
S	549	T549X	ACa	TGa	11	41	B.1.1.7	0.00001
S	549	T549X	ACA	TAG	8	41	B.1.1.7	0.000007
S	549	T549Y	ACA	TAT	34	37	All	0.000007
S	549	T549Y	ACA	TAC	3	37	All	0.000001
S	549	T549I	aCa	aTa	36	37	AY.25	0.000217
S	549	T549I	aCA	aTT	1	37	AY.25	0.000006
S	549	T549V	ACA	GTT	16	35	All	0.000003
S	549	T549V	ACa	GTa	10	35	All	0.000002
S	549	T549V	ACA	GTG	8	35	All	0.000002
S	549	T549V	ACA	GTC	1	35	All	0
S	549	T549V	ACA	GTT	16	35	B.1.1.7	0.000014
S	549	T549V	ACa	GTa	10	35	B.1.1.7	0.000009
S	549	T549V	ACA	GTG	8	35	B.1.1.7	0.000007
S	549	T549V	ACA	GTC	1	35	B.1.1.7	0.000001
S	549	T549N	aCA	aAT	32	34	All	0.000006
S	549	T549N	aCA	aAC	2	34	All	0
S	549	T549A	Aca	Gca	34	34	B.1.1.7	0.00003
S	549	T549S	Aca	Tca	34	34	B.1.617.2	0.000128
S	549	T549G	ACA	GGT	16	33	All	0.000003
S	549	T549G	ACa	GGa	9	33	All	0.000002
S	549	T549G	ACA	GGG	7	33	All	0.000001
S	549	T549G	ACA	GGC	1	33	All	0
S	549	T549Y	ACA	TAT	29	32	B.1.1.7	0.000026
S	549	T549Y	ACA	TAC	3	32	B.1.1.7	0.000003
S	549	T549G	ACA	GGT	15	31	B.1.1.7	0.000013
S	549	T549G	ACa	GGa	8	31	B.1.1.7	0.000007
S	549	T549G	ACA	GGG	7	31	B.1.1.7	0.000006
S	549	T549G	ACA	GGC	1	31	B.1.1.7	0.000001
S	549	T549N	aCA	aAT	28	30	B.1.1.7	0.000025
S	549	T549N	aCA	aAC	2	30	B.1.1.7	0.000002
S	549	T549I	aCa	aTa	29	29	AY.43	0.000128
S	549	T549K	aCa	aAa	22	29	B.1.1.7	0.00002
S	549	T549K	aCA	aAG	7	29	B.1.1.7	0.000006
S	549	T549I	aCa	aTa	28	28	AY.4	0.000044
S	549	T549T	acA	acG	26	27	AY.4	0.00004
S	549	T549T	acA	acT	1	27	AY.4	0.000002
S	549	T549S	Aca	Tca	23	23	AY.25	0.000138
S	549	T549R	aCa	aGa	12	21	All	0.000002
S	549	T549R	aCA	aGG	7	21	All	0.000001
S	549	T549R	ACa	CGa	1	21	All	0
S	549	T549R	ACA	CGT	1	21	All	0
S	549	T549T	acA	acG	21	21	AY.25	0.000126
S	549	T549R	aCa	aGa	12	21	B.1.1.7	0.000011
S	549	T549R	aCA	aGG	7	21	B.1.1.7	0.000006
S	549	T549R	ACA	CGT	1	21	B.1.1.7	0.000001
S	549	T549R	ACa	CGa	1	21	B.1.1.7	0.000001
S	549	T549C	ACA	TGT	17	19	All	0.000003
S	549	T549C	ACA	TGC	2	19	All	0
S	549	T549T	acA	acC	11	19	B.1.617.2	0.000041
S	549	T549T	acA	acG	8	19	B.1.617.2	0.00003
S	549	T549C	ACA	TGT	16	18	B.1.1.7	0.000014
S	549	T549C	ACA	TGC	2	18	B.1.1.7	0.000002
S	549	T549del	ACA	---	15	15	All	0.000003
S	549	T549T	acA	acT	15	15	AY.113	0.002136
S	549	T549T	acA	acC	8	15	AY.43	0.000035
S	549	T549T	acA	acT	7	15	AY.43	0.000031
S	549	T549M	aCA	aTG	14	14	All	0.000003
S	549	T549A	Aca	Gca	14	14	AY.111	0.002564
S	549	T549M	aCA	aTG	14	14	B.1.1.7	0.000013
S	549	T549T	acA	acG	8	13	B.1.1.7	0.000007
S	549	T549T	acA	acT	4	13	B.1.1.7	0.000004
S	549	T549T	acA	acC	1	13	B.1.1.7	0.000001
S	549	T549I	aCa	aTa	12	12	B.1.1	0.000218
S	549	T549K	aCa	aAa	9	9	AY.24	0.003879
S	549	T549T	acA	acC	9	9	B.1.177.86	0.001651
S	549	T549W	ACA	TGG	8	8	All	0.000002
S	549	T549T	acA	acT	7	8	AY.34	0.000679
S	549	T549T	acA	acC	1	8	AY.34	0.000097
S	549	T549I	aCa	aTa	8	8	AY.39	0.000198
S	549	T549W	ACA	TGG	8	8	B.1.1.7	0.000007
S	549	T549A	Aca	Gca	8	8	P.1	0.000126
S	549	T549T	acA	acT	7	7	AY.26	0.000198
S	549	T549S	Aca	Tca	7	7	AY.39	0.000173
S	549	T549I	aCa	aTa	7	7	AY.4.3	0.005892
S	549	T549A	Aca	Gca	7	7	B.1.160	0.000218
S	549	T549I	aCa	aTa	5	6	B.1	0.000046
S	549	T549I	aCA	aTT	1	6	B.1	0.000009
S	549	T549T	acA	acG	6	6	B.1.177.5	0.007453
S	549	T549I	aCa	aTa	6	6	B.1.177.52	0.010545
S	549	T549I	aCa	aTa	6	6	B.1.234	0.000792
S	549	T549A	Aca	Gca	6	6	B.1.617.2	0.000023
S	549	T549E	ACa	GAa	4	5	All	0.000001
S	549	T549D	ACA	GAT	4	5	All	0.000001
S	549	T549Q	ACa	CAa	3	5	All	0.000001
S	549	T549Q	ACA	CAG	2	5	All	0
S	549	T549E	ACA	GAG	1	5	All	0
S	549	T549D	ACA	GAC	1	5	All	0
S	549	T549S	Aca	Tca	5	5	AY.4	0.000008
S	549	T549I	aCa	aTa	5	5	AY.46.6	0.000361
S	549	T549Q	ACa	CAa	3	5	B.1.1.7	0.000003
S	549	T549Q	ACA	CAG	2	5	B.1.1.7	0.000002
S	549	T549I	aCa	aTa	4	5	P.1	0.000063
S	549	T549I	aCA	aTT	1	5	P.1	0.000016
S	549	T549I	aCa	aTa	4	4	AY.103	0.000025
S	549	T549del	ACA	---	4	4	AY.25	0.000024
S	549	T549A	Aca	Gca	4	4	AY.4	0.000006
S	549	T549I	aCa	aTa	4	4	AY.44	0.000024
S	549	T549T	acA	acC	4	4	AY.6	0.000165
S	549	T549I	aCa	aTa	4	4	AY.72	0.005442
S	549	T549I	aCa	aTa	4	4	B.1.1.265	0.012618
S	549	T549T	acA	acG	4	4	B.1.1.412	0.030534
S	549	T549E	ACa	GAa	3	4	B.1.1.7	0.000003
S	549	T549D	ACA	GAT	3	4	B.1.1.7	0.000003
S	549	T549D	ACA	GAC	1	4	B.1.1.7	0.000001
S	549	T549E	ACA	GAG	1	4	B.1.1.7	0.000001
S	549	T549T	acA	acC	4	4	B.1.177	0.000053
S	549	T549I	aCa	aTa	4	4	B.1.617.2	0.000015
S	549	T549H	ACA	CAT	2	3	All	0
S	549	T549H	ACA	CAC	1	3	All	0
S	549	T549A	Aca	Gca	3	3	AY.26	0.000085
S	549	T549I	aCa	aTa	3	3	AY.3	0.00003
S	549	T549S	Aca	Tca	3	3	AY.43	0.000013
S	549	T549I	aCa	aTa	3	3	AY.47	0.000093
S	549	T549I	aCa	aTa	3	3	AY.5	0.000062
S	549	T549S	Aca	Tca	3	3	AY.51	0.002727
S	549	T549I	aCa	aTa	3	3	B.1.1.39	0.001529
S	549	T549H	ACA	CAT	2	3	B.1.1.7	0.000002
S	549	T549H	ACA	CAC	1	3	B.1.1.7	0.000001
S	549	T549I	aCa	aTa	3	3	B.1.2	0.000026
S	549	T549A	Aca	Gca	3	3	B.1.2	0.000026
S	549	T549T	acA	acG	3	3	B.1.351	0.000089
S	549	T549T	acA	acG	3	3	B.1.36.35	0.007812
S	549	T549del1	Aca	-ca	1	2	All	0
S	549	T549del1	acA	ac-	1	2	All	0
S	549	T549S	Aca	Tca	2	2	AY.102	0.000053
S	549	T549I	aCa	aTa	2	2	AY.111	0.000366
S	549	T549K	aCa	aAa	2	2	AY.26	0.000057
S	549	T549I	aCa	aTa	2	2	AY.34	0.000194
S	549	T549S	Aca	Tca	2	2	AY.36	0.000296
S	549	T549A	Aca	Gca	2	2	AY.43	0.000009
S	549	T549S	Aca	Tca	2	2	AY.5	0.000041
S	549	T549A	Aca	Gca	2	2	AY.64	0.00119
S	549	T549I	aCa	aTa	2	2	AY.92	0.000575
S	549	T549K	aCa	aAa	2	2	B.1	0.000018
S	549	T549A	Aca	Gca	2	2	B.1	0.000018
S	549	T549G	ACA	GGT	1	2	B.1.1	0.000018
S	549	T549X	ACa	TAa	1	2	B.1.1	0.000018
S	549	T549G	ACa	GGa	1	2	B.1.1	0.000018
S	549	T549X	ACa	TGa	1	2	B.1.1	0.000018
S	549	T549T	acA	acT	2	2	B.1.1.25	0.001137
S	549	T549S	Aca	Tca	2	2	B.1.1.299	0.02439
S	549	T549I	aCa	aTa	2	2	B.1.177	0.000026
S	549	T549S	Aca	Tca	2	2	B.1.2	0.000018
S	549	T549T	acA	acC	2	2	B.1.243	0.000139
S	549	T549A	Aca	Gca	2	2	B.1.243	0.000139
S	549	T549T	acA	acC	2	2	B.1.258	0.000133
S	549	T549I	aCA	aTT	1	2	B.1.576	0.000907
S	549	T549I	aCa	aTa	1	2	B.1.576	0.000907
S	549	T549I	aCa	aTa	2	2	D.2	0.00015
S	549	T549T	acA	acT	2	2	P.1	0.000032
S	549	T549P	Aca	Cca	1	1	All	0
S	549	T549del2	aCA	a--	1	1	All	0
S	549	T549S	Aca	Tca	1	1	AY.100	0.000046
S	549	T549A	Aca	Gca	1	1	AY.102	0.000027
S	549	T549S	Aca	Tca	1	1	AY.103	0.000006
S	549	T549A	Aca	Gca	1	1	AY.103	0.000006
S	549	T549T	acA	acT	1	1	AY.103	0.000006
S	549	T549I	aCa	aTa	1	1	AY.106	0.000335
S	549	T549I	aCa	aTa	1	1	AY.115	0.005208
S	549	T549del2	aCA	a--	1	1	AY.117	0.000085
S	549	T549I	aCa	aTa	1	1	AY.117	0.000085
S	549	T549T	acA	acG	1	1	AY.119	0.000035
S	549	T549T	acA	acG	1	1	AY.13	0.000161
S	549	T549T	acA	acG	1	1	AY.16.1	0.00047
S	549	T549I	aCa	aTa	1	1	AY.20	0.000039
S	549	T549T	acA	acG	1	1	AY.23.1	0.000417
S	549	T549A	Aca	Gca	1	1	AY.25	0.000006
S	549	T549X	ACa	TAa	1	1	AY.25	0.000006
S	549	T549N	aCA	aAT	1	1	AY.25	0.000006
S	549	T549F	ACA	TTT	1	1	AY.25	0.000006
S	549	T549L	ACa	TTa	1	1	AY.25	0.000006
S	549	T549Y	ACA	TAT	1	1	AY.25	0.000006
S	549	T549K	aCa	aAa	1	1	AY.25	0.000006
S	549	T549I	aCa	aTa	1	1	AY.26	0.000028
S	549	T549S	Aca	Tca	1	1	AY.29	0.000016
S	549	T549A	Aca	Gca	1	1	AY.29	0.000016
S	549	T549K	aCa	aAa	1	1	AY.3	0.00001
S	549	T549T	acA	acG	1	1	AY.3	0.00001
S	549	T549del	ACA	---	1	1	AY.33	0.000067
S	549	T549del	ACA	---	1	1	AY.35	0.000233
S	549	T549del	ACA	---	1	1	AY.38	0.000499
S	549	T549del	ACA	---	1	1	AY.4	0.000002
S	549	T549I	aCa	aTa	1	1	AY.4.2	0.000022
S	549	T549A	Aca	Gca	1	1	AY.4.2	0.000022
S	549	T549S	Aca	Tca	1	1	AY.40	0.000964
S	549	T549del	ACA	---	1	1	AY.43	0.000004
S	549	T549A	Aca	Gca	1	1	AY.44	0.000006
S	549	T549S	Aca	Tca	1	1	AY.44	0.000006
S	549	T549del	ACA	---	1	1	AY.46.4	0.000165
S	549	T549A	Aca	Gca	1	1	AY.5.4	0.000277
S	549	T549T	acA	acT	1	1	AY.55	0.000917
S	549	T549T	acA	acT	1	1	AY.56	0.001605
S	549	T549I	aCa	aTa	1	1	AY.75	0.000056
S	549	T549T	acA	acG	1	1	AY.75.1	0.00018
S	549	T549del	ACA	---	1	1	AY.75.1	0.00018
S	549	T549A	Aca	Gca	1	1	AY.79	0.001211
S	549	T549I	aCa	aTa	1	1	AY.96	0.002075
S	549	T549T	acA	acC	1	1	AY.98	0.000079
S	549	T549I	aCa	aTa	1	1	AY.98.1	0.000048
S	549	T549S	Aca	Tca	1	1	AY.98.1	0.000048
S	549	T549del	ACA	---	1	1	AY.99	0.001049
S	549	T549T	acA	acT	1	1	AY.99.2	0.000092
S	549	T549L	ACa	TTa	1	1	B.1	0.000009
S	549	T549N	aCA	aAT	1	1	B.1	0.000009
S	549	T549Y	ACA	TAT	1	1	B.1	0.000009
S	549	T549X	ACa	TAa	1	1	B.1	0.000009
S	549	T549F	ACA	TTT	1	1	B.1	0.000009
S	549	T549P	Aca	Cca	1	1	B.1	0.000009
S	549	T549T	acA	acG	1	1	B.1	0.000009
S	549	T549S	Aca	Tca	1	1	B.1	0.000009
S	549	T549del1	acA	ac-	1	1	B.1	0.000009
S	549	T549C	ACA	TGT	1	1	B.1.1	0.000018
S	549	T549S	Aca	Tca	1	1	B.1.1	0.000018
S	549	T549E	ACa	GAa	1	1	B.1.1	0.000018
S	549	T549D	ACA	GAT	1	1	B.1.1	0.000018
S	549	T549Y	ACA	TAT	1	1	B.1.1	0.000018
S	549	T549I	aCa	aTa	1	1	B.1.1.222	0.000204
S	549	T549T	acA	acT	1	1	B.1.1.277	0.000759
S	549	T549I	aCa	aTa	1	1	B.1.1.280	0.003086
S	549	T549T	acA	acG	1	1	B.1.1.284	0.000107
S	549	T549I	aCa	aTa	1	1	B.1.1.284	0.000107
S	549	T549I	aCa	aTa	1	1	B.1.1.33	0.000421
S	549	T549K	aCa	aAa	1	1	B.1.1.409	0.002833
S	549	T549I	aCa	aTa	1	1	B.1.1.47	0.005348
S	549	T549T	acA	acG	1	1	B.1.1.519	0.00004
S	549	T549I	aCa	aTa	1	1	B.1.160	0.000031
S	549	T549T	acA	acG	1	1	B.1.160	0.000031
S	549	T549A	Aca	Gca	1	1	B.1.177.76	0.002494
S	549	T549T	acA	acT	1	1	B.1.2	0.000009
S	549	T549I	aCa	aTa	1	1	B.1.258	0.000067
S	549	T549I	aCa	aTa	1	1	B.1.336	0.002439
S	549	T549A	Aca	Gca	1	1	B.1.36	0.000146
S	549	T549I	aCa	aTa	1	1	B.1.362	0.001541
S	549	T549del	ACA	---	1	1	B.1.415	0.014286
S	549	T549I	aCa	aTa	1	1	B.1.429	0.000024
S	549	T549T	acA	acT	1	1	B.1.429	0.000024
S	549	T549A	Aca	Gca	1	1	B.1.525	0.000113
S	549	T549I	aCa	aTa	1	1	B.1.525	0.000113
S	549	T549S	Aca	Tca	1	1	B.1.526	0.000024
S	549	T549I	aCa	aTa	1	1	B.1.527	0.003704
S	549	T549Y	ACA	TAT	1	1	B.1.576	0.000907
S	549	T549F	ACA	TTT	1	1	B.1.576	0.000907
S	549	T549N	aCA	aAT	1	1	B.1.576	0.000907
S	549	T549X	ACa	TAa	1	1	B.1.576	0.000907
S	549	T549L	ACa	TTa	1	1	B.1.576	0.000907
S	549	T549K	aCa	aAa	1	1	B.1.576	0.000907
S	549	T549T	acA	acG	1	1	B.1.580	0.004065
S	549	T549K	aCa	aAa	1	1	B.1.582	0.000491
S	549	T549I	aCa	aTa	1	1	B.1.596	0.000087
S	549	T549T	acA	acC	1	1	B.1.596	0.000087
S	549	T549T	acA	acG	1	1	B.1.600	0.005848
S	549	T549A	Aca	Gca	1	1	B.1.617.1	0.000129
S	549	T549del	ACA	---	1	1	B.1.617.2	0.000004
S	549	T549del	ACA	---	1	1	B.1.620	0.000946
S	549	T549T	acA	acT	1	1	B.1.621	0.000089
S	549	T549del1	Aca	-ca	1	1	D.2	0.000075
S	549	T549K	aCa	aAa	1	1	P.1	0.000016
S	549	T549F	ACA	TTT	1	1	P.1	0.000016
S	549	T549Y	ACA	TAT	1	1	P.1	0.000016
S	549	T549X	ACa	TAa	1	1	P.1	0.000016
S	549	T549L	ACa	TTa	1	1	P.1	0.000016
S	549	T549N	aCA	aAT	1	1	P.1	0.000016
S	549	T549T	acA	acT	1	1	P.1.15	0.000232
S	549	T549I	aCa	aTa	1	1	Q.3	0.000145
S	549	T549A	Aca	Gca	1	1	R.2	0.014493

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.