CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 216

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	216	L216F		nonsyn	Ctc	Ttc	6017	6015	0.999668	22208-22210
S	216	L216F		nonsyn	CtC	TtT	6017	2	0.000332392	22208-22210
S	216	L216L		syn	ctC	ctT	1068	1011	0.946629	22208-22210
S	216	L216L		syn	ctC	ctA	1068	54	0.0505618	22208-22210
S	216	L216L		syn	ctC	ctG	1068	3	0.00280899	22208-22210
S	216	L216del1		del	ctC	ct-	193	185	0.958549	22208-22210
S	216	L216del1		del	Ctc	-tc	193	5	0.0259067	22208-22210
S	216	L216del1		del	cTc	c-c	193	3	0.015544	22208-22210
S	216	L216del		del	CTC	---	173	173	1	22208-22210
S	216	L216I		nonsyn	Ctc	Atc	97	87	0.896907	22208-22210
S	216	L216I		nonsyn	CtC	AtA	97	8	0.0824742	22208-22210
S	216	L216I		nonsyn	CtC	AtT	97	2	0.0206186	22208-22210
S	216	L216P		nonsyn	cTc	cCc	46	42	0.913043	22208-22210
S	216	L216P		nonsyn	cTC	cCA	46	3	0.0652174	22208-22210
S	216	L216P		nonsyn	cTC	cCT	46	1	0.0217391	22208-22210
S	216	L216V		nonsyn	CtC	GtG	12	5	0.416667	22208-22210
S	216	L216V		nonsyn	Ctc	Gtc	12	4	0.333333	22208-22210
S	216	L216V		nonsyn	CtC	GtA	12	3	0.25	22208-22210
S	216	L216H		nonsyn	cTc	cAc	10	10	1	22208-22210
S	216	L216A		nonsyn	CTC	GCA	9	5	0.555556	22208-22210
S	216	L216A		nonsyn	CTc	GCc	9	3	0.333333	22208-22210
S	216	L216A		nonsyn	CTC	GCT	9	1	0.111111	22208-22210
S	216	L216R		nonsyn	cTc	cGc	5	4	0.8	22208-22210
S	216	L216R		nonsyn	cTC	cGT	5	1	0.2	22208-22210
S	216	L216del2		del	CTc	--c	4	3	0.75	22208-22210
S	216	L216del2		del	cTC	c--	4	1	0.25	22208-22210
S	216	L216S		nonsyn	CTC	TCT	3	2	0.666667	22208-22210
S	216	L216S		nonsyn	CTc	TCc	3	1	0.333333	22208-22210
S	216	L216D		nonsyn	CTC	GAT	2	2	1	22208-22210
S	216	L216C		nonsyn	CTc	TGc	1	1	1	22208-22210
S	216	L216Q		nonsyn	cTC	cAG	1	1	1	22208-22210
S	216	L216X		nonsyn	CTC	TAG	1	1	1	22208-22210
S	216	L216Y		nonsyn	CTc	TAc	1	1	1	22208-22210
S	216	L216G		nonsyn	CTc	GGc	1	1	1	22208-22210

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	216	L216F	Ctc	Ttc	6015	6017	All	0.00115
S	216	L216F	CtC	TtT	2	6017	All	0
S	216	L216F	Ctc	Ttc	2362	2362	AY.4	0.003676
S	216	L216F	Ctc	Ttc	1753	1754	B.1.1.7	0.001569
S	216	L216F	CtC	TtT	1	1754	B.1.1.7	0.000001
S	216	L216L	ctC	ctT	1011	1068	All	0.000193
S	216	L216L	ctC	ctA	54	1068	All	0.00001
S	216	L216L	ctC	ctG	3	1068	All	0.000001
S	216	L216L	ctC	ctT	225	225	C.1.2	0.957447
S	216	L216del1	ctC	ct-	185	193	All	0.000035
S	216	L216del1	Ctc	-tc	5	193	All	0.000001
S	216	L216del1	cTc	c-c	3	193	All	0.000001
S	216	L216L	ctC	ctT	186	186	B.1.1.58	1
S	216	L216del	CTC	---	173	173	All	0.000033
S	216	L216L	ctC	ctT	171	171	B.1.1.7	0.000153
S	216	L216F	Ctc	Ttc	150	150	AY.103	0.000931
S	216	L216F	Ctc	Ttc	135	135	B.1.617.2	0.000508
S	216	L216F	Ctc	Ttc	130	130	AY.44	0.000791
S	216	L216del1	ctC	ct-	114	114	B.1.1.7	0.000102
S	216	L216F	Ctc	Ttc	114	114	P.1	0.001796
S	216	L216F	Ctc	Ttc	110	110	AY.43	0.000487
S	216	L216F	Ctc	Ttc	105	105	B.1.1	0.001905
S	216	L216I	Ctc	Atc	87	97	All	0.000017
S	216	L216I	CtC	AtA	8	97	All	0.000002
S	216	L216I	CtC	AtT	2	97	All	0
S	216	L216L	ctC	ctT	81	81	B.1.526	0.001904
S	216	L216F	Ctc	Ttc	77	77	P.1.14	0.003681
S	216	L216F	Ctc	Ttc	73	73	B.1.526	0.001716
S	216	L216F	Ctc	Ttc	66	66	AY.3	0.000656
S	216	L216F	Ctc	Ttc	53	53	AY.25	0.000319
S	216	L216L	ctC	ctT	49	49	B.1.2	0.000431
S	216	L216P	cTc	cCc	42	46	All	0.000008
S	216	L216P	cTC	cCA	3	46	All	0.000001
S	216	L216P	cTC	cCT	1	46	All	0
S	216	L216F	Ctc	Ttc	42	42	AY.32	0.022364
S	216	L216F	Ctc	Ttc	42	42	B.1.177	0.000553
S	216	L216F	Ctc	Ttc	38	38	AY.36	0.005632
S	216	L216F	Ctc	Ttc	37	37	AY.102	0.000981
S	216	L216F	Ctc	Ttc	35	35	B.1	0.000321
S	216	L216F	Ctc	Ttc	35	35	B.1.258	0.002329
S	216	L216del	CTC	---	33	33	B.1.1.7	0.00003
S	216	L216F	Ctc	Ttc	32	32	AY.42	0.001287
S	216	L216L	ctC	ctT	30	30	AY.119	0.001059
S	216	L216L	ctC	ctT	30	30	C.36.3.1	0.081522
S	216	L216L	ctC	ctT	28	29	AY.4	0.000044
S	216	L216L	ctC	ctG	1	29	AY.4	0.000002
S	216	L216F	Ctc	Ttc	27	27	B.1.2	0.000238
S	216	L216L	ctC	ctT	26	26	P.1	0.00041
S	216	L216F	Ctc	Ttc	24	24	AY.4.2	0.000521
S	216	L216L	ctC	ctA	22	24	AY.44	0.000134
S	216	L216L	ctC	ctT	2	24	AY.44	0.000012
S	216	L216F	Ctc	Ttc	23	23	AY.53	0.006613
S	216	L216F	Ctc	Ttc	23	23	B.1.637	0.001681
S	216	L216F	Ctc	Ttc	21	21	AY.9	0.001419
S	216	L216F	Ctc	Ttc	19	19	AY.3.1	0.00162
S	216	L216F	Ctc	Ttc	18	18	AY.61	0.001886
S	216	L216L	ctC	ctA	10	17	B.1.617.2	0.000038
S	216	L216L	ctC	ctT	7	17	B.1.617.2	0.000026
S	216	L216del1	ctC	ct-	15	16	P.1	0.000236
S	216	L216del1	Ctc	-tc	1	16	P.1	0.000016
S	216	L216L	ctC	ctT	9	15	AY.43	0.00004
S	216	L216L	ctC	ctA	6	15	AY.43	0.000027
S	216	L216L	ctC	ctT	12	15	B.1	0.00011
S	216	L216L	ctC	ctA	3	15	B.1	0.000027
S	216	L216L	ctC	ctT	15	15	B.1.214.2	0.008993
S	216	L216F	Ctc	Ttc	15	15	Q.1	0.001895
S	216	L216F	Ctc	Ttc	14	14	AY.20	0.000544
S	216	L216F	Ctc	Ttc	14	14	AY.39	0.000346
S	216	L216F	Ctc	Ttc	14	14	AY.6	0.000576
S	216	L216F	Ctc	Ttc	14	14	AY.81	0.027888
S	216	L216L	ctC	ctT	14	14	B.1.1	0.000254
S	216	L216L	ctC	ctT	14	14	B.1.1.398	0.045161
S	216	L216I	Ctc	Atc	14	14	B.1.1.7	0.000013
S	216	L216V	CtC	GtG	5	12	All	0.000001
S	216	L216V	Ctc	Gtc	4	12	All	0.000001
S	216	L216V	CtC	GtA	3	12	All	0.000001
S	216	L216F	Ctc	Ttc	12	12	AY.101	0.005885
S	216	L216L	ctC	ctT	12	12	AY.103	0.000075
S	216	L216F	Ctc	Ttc	12	12	AY.41	0.003527
S	216	L216del	CTC	---	12	12	AY.43	0.000053
S	216	L216F	Ctc	Ttc	12	12	AY.47	0.000373
S	216	L216F	Ctc	Ttc	12	12	Q.8	0.001979
S	216	L216H	cTc	cAc	10	10	All	0.000002
S	216	L216del	CTC	---	10	10	B.1	0.000092
S	216	L216L	ctC	ctT	10	10	B.1.177.81	0.001893
S	216	L216I	Ctc	Atc	10	10	B.1.214.2	0.005995
S	216	L216del	CTC	---	10	10	P.1.15	0.002323
S	216	L216F	Ctc	Ttc	10	10	P.1.7	0.003193
S	216	L216A	CTC	GCA	5	9	All	0.000001
S	216	L216A	CTc	GCc	3	9	All	0.000001
S	216	L216A	CTC	GCT	1	9	All	0
S	216	L216del1	ctC	ct-	9	9	AY.43	0.00004
S	216	L216I	Ctc	Atc	6	9	AY.43	0.000027
S	216	L216I	CtC	AtA	3	9	AY.43	0.000013
S	216	L216I	Ctc	Atc	7	9	B.1	0.000064
S	216	L216I	CtC	AtT	1	9	B.1	0.000009
S	216	L216I	CtC	AtA	1	9	B.1	0.000009
S	216	L216F	Ctc	Ttc	9	9	B.1.258.17	0.000936
S	216	L216F	Ctc	Ttc	9	9	B.1.311	0.002471
S	216	L216F	Ctc	Ttc	8	8	AY.5	0.000165
S	216	L216F	Ctc	Ttc	8	8	B.1.160	0.00025
S	216	L216I	Ctc	Atc	8	8	B.1.617.2	0.00003
S	216	L216del	CTC	---	8	8	B.1.617.2	0.00003
S	216	L216del	CTC	---	8	8	C.37	0.000929
S	216	L216del	CTC	---	8	8	P.1	0.000126
S	216	L216F	Ctc	Ttc	7	7	AY.26	0.000198
S	216	L216L	ctC	ctT	7	7	AY.3	0.00007
S	216	L216F	Ctc	Ttc	7	7	AY.46	0.000729
S	216	L216F	Ctc	Ttc	7	7	AY.85	0.00299
S	216	L216del	CTC	---	7	7	B.1.177	0.000092
S	216	L216F	Ctc	Ttc	7	7	B.1.349	0.005004
S	216	L216del1	ctC	ct-	7	7	P.1.14	0.000335
S	216	L216A	CTc	GCc	3	6	A.2.5.1	0.014423
S	216	L216V	CtC	GtA	3	6	A.2.5.1	0.014423
S	216	L216V	Ctc	Gtc	3	6	A.2.5.1	0.014423
S	216	L216P	cTc	cCc	3	6	A.2.5.1	0.014423
S	216	L216A	CTC	GCA	3	6	A.2.5.1	0.014423
S	216	L216P	cTC	cCA	3	6	A.2.5.1	0.014423
S	216	L216F	Ctc	Ttc	6	6	AY.100	0.000276
S	216	L216F	Ctc	Ttc	6	6	AY.120	0.000223
S	216	L216del	CTC	---	6	6	AY.25	0.000036
S	216	L216I	Ctc	Atc	6	6	AY.4	0.000009
S	216	L216F	Ctc	Ttc	6	6	AY.98.1	0.000291
S	216	L216L	ctC	ctT	6	6	AY.99.2	0.000553
S	216	L216F	Ctc	Ttc	6	6	B.1.561	0.002382
S	216	L216F	Ctc	Ttc	6	6	P.1.12	0.002904
S	216	L216L	ctC	ctT	6	6	P.1.7	0.001916
S	216	L216L	ctC	ctT	6	6	Q.8	0.000989
S	216	L216R	cTc	cGc	4	5	All	0.000001
S	216	L216R	cTC	cGT	1	5	All	0
S	216	L216F	Ctc	Ttc	5	5	AY.119	0.000177
S	216	L216L	ctC	ctT	5	5	AY.25	0.00003
S	216	L216P	cTc	cCc	5	5	AY.4	0.000008
S	216	L216F	Ctc	Ttc	5	5	AY.75	0.00028
S	216	L216F	Ctc	Ttc	5	5	AY.9.2	0.000184
S	216	L216V	CtC	GtG	5	5	B.1.351	0.000149
S	216	L216F	Ctc	Ttc	5	5	B.1.36	0.00073
S	216	L216F	Ctc	Ttc	5	5	B.1.429	0.000118
S	216	L216F	Ctc	Ttc	5	5	P.1.15	0.001162
S	216	L216del2	CTc	--c	3	4	All	0.000001
S	216	L216del2	cTC	c--	1	4	All	0
S	216	L216F	Ctc	Ttc	4	4	AY.106	0.00134
S	216	L216F	Ctc	Ttc	4	4	AY.29	0.000063
S	216	L216I	Ctc	Atc	4	4	AY.3	0.00004
S	216	L216F	Ctc	Ttc	4	4	AY.70	0.000834
S	216	L216del1	ctC	ct-	4	4	AY.9.2	0.000147
S	216	L216F	Ctc	Ttc	4	4	AY.99.2	0.000369
S	216	L216F	Ctc	Ttc	4	4	B.1.1.304	0.011236
S	216	L216P	cTc	cCc	4	4	B.1.1.7	0.000004
S	216	L216L	ctC	ctT	4	4	B.1.177	0.000053
S	216	L216F	Ctc	Ttc	4	4	B.1.177.42	0.003578
S	216	L216L	ctC	ctT	4	4	B.1.177.87	0.002911
S	216	L216del1	ctC	ct-	2	4	B.1.2	0.000018
S	216	L216del1	Ctc	-tc	1	4	B.1.2	0.000009
S	216	L216del1	cTc	c-c	1	4	B.1.2	0.000009
S	216	L216del1	ctC	ct-	4	4	B.1.351	0.000119
S	216	L216F	Ctc	Ttc	4	4	B.1.517	0.001708
S	216	L216F	Ctc	Ttc	4	4	D.2	0.0003
S	216	L216F	Ctc	Ttc	4	4	P.1.17	0.000647
S	216	L216L	ctC	ctA	3	3	A.2.5.1	0.014423
S	216	L216S	CTC	TCT	2	3	All	0
S	216	L216S	CTc	TCc	1	3	All	0
S	216	L216F	Ctc	Ttc	3	3	AY.114	0.000693
S	216	L216F	Ctc	Ttc	3	3	AY.121	0.000406
S	216	L216F	Ctc	Ttc	3	3	AY.19	0.003421
S	216	L216F	Ctc	Ttc	3	3	AY.23	0.000209
S	216	L216F	Ctc	Ttc	3	3	AY.30	0.001187
S	216	L216F	Ctc	Ttc	3	3	AY.4.4	0.001227
S	216	L216del	CTC	---	3	3	AY.4.5	0.000322
S	216	L216del	CTC	---	3	3	AY.44	0.000018
S	216	L216F	Ctc	Ttc	3	3	AY.46.4	0.000494
S	216	L216del1	ctC	ct-	3	3	AY.46.6	0.000217
S	216	L216F	Ctc	Ttc	3	3	AY.54	0.000286
S	216	L216F	Ctc	Ttc	3	3	AY.55	0.002752
S	216	L216F	Ctc	Ttc	3	3	AY.98	0.000237
S	216	L216del1	ctC	ct-	3	3	B.1.1	0.000054
S	216	L216F	Ctc	Ttc	3	3	B.1.1.214	0.000166
S	216	L216F	Ctc	Ttc	3	3	B.1.1.519	0.000119
S	216	L216del	CTC	---	3	3	B.1.214.1	0.06
S	216	L216F	Ctc	Ttc	3	3	B.1.320	0.003736
S	216	L216L	ctC	ctT	3	3	B.1.351	0.000089
S	216	L216I	Ctc	Atc	3	3	B.1.36	0.000438
S	216	L216F	Ctc	Ttc	3	3	B.1.577	0.002062
S	216	L216F	Ctc	Ttc	3	3	B.1.596	0.000261
S	216	L216L	ctC	ctT	3	3	C.37	0.000348
S	216	L216L	ctC	ctT	3	3	D.2	0.000225
S	216	L216L	ctC	ctT	3	3	P.1.14	0.000143
S	216	L216del	CTC	---	2	2		0.111111
S	216	L216del1	ctC	ct-	2	2		0.111111
S	216	L216L	ctC	ctT	1	2	A	0.000387
S	216	L216I	Ctc	Atc	1	2	A	0.000387
S	216	L216I	CtC	AtA	1	2	A	0.000387
S	216	L216L	ctC	ctA	1	2	A	0.000387
S	216	L216A	CTC	GCA	2	2	A.2.5	0.000998
S	216	L216D	CTC	GAT	2	2	All	0
S	216	L216del	CTC	---	2	2	AY.100	0.000092
S	216	L216I	Ctc	Atc	2	2	AY.100	0.000092
S	216	L216I	Ctc	Atc	2	2	AY.102	0.000053
S	216	L216H	cTc	cAc	2	2	AY.102	0.000053
S	216	L216del	CTC	---	2	2	AY.120	0.000074
S	216	L216F	Ctc	Ttc	2	2	AY.13	0.000322
S	216	L216F	Ctc	Ttc	2	2	AY.16.1	0.00094
S	216	L216I	CtC	AtA	1	2	AY.23	0.00007
S	216	L216I	Ctc	Atc	1	2	AY.23	0.00007
S	216	L216P	cTc	cCc	2	2	AY.26	0.000057
S	216	L216F	Ctc	Ttc	2	2	AY.27	0.000129
S	216	L216I	Ctc	Atc	2	2	AY.33	0.000134
S	216	L216F	Ctc	Ttc	2	2	AY.39.1	0.000079
S	216	L216H	cTc	cAc	2	2	AY.4	0.000003
S	216	L216del	CTC	---	2	2	AY.4	0.000003
S	216	L216del1	Ctc	-tc	1	2	AY.4.5	0.000107
S	216	L216del1	ctC	ct-	1	2	AY.4.5	0.000107
S	216	L216I	Ctc	Atc	2	2	AY.42	0.00008
S	216	L216P	cTc	cCc	2	2	AY.43	0.000009
S	216	L216F	Ctc	Ttc	2	2	AY.45	0.000243
S	216	L216del1	ctC	ct-	2	2	AY.46	0.000208
S	216	L216F	Ctc	Ttc	2	2	AY.46.6	0.000144
S	216	L216F	Ctc	Ttc	2	2	AY.52	0.001629
S	216	L216F	Ctc	Ttc	2	2	AY.56	0.00321
S	216	L216F	Ctc	Ttc	2	2	AY.64	0.00119
S	216	L216F	Ctc	Ttc	2	2	AY.7	0.000392
S	216	L216F	Ctc	Ttc	2	2	AY.74	0.000231
S	216	L216L	ctC	ctT	2	2	AY.75	0.000112
S	216	L216F	Ctc	Ttc	2	2	AY.93	0.000546
S	216	L216del	CTC	---	2	2	AY.95	0.001522
S	216	L216F	Ctc	Ttc	2	2	AY.97	0.003401
S	216	L216del	CTC	---	2	2	AY.98.1	0.000097
S	216	L216F	Ctc	Ttc	2	2	AY.99	0.002099
S	216	L216L	ctC	ctA	2	2	B	0.000256
S	216	L216I	CtC	AtA	1	2	B	0.000128
S	216	L216I	Ctc	Atc	1	2	B	0.000128
S	216	L216P	cTc	cCc	2	2	B.1	0.000018
S	216	L216del1	ctC	ct-	1	2	B.1	0.000009
S	216	L216del1	cTc	c-c	1	2	B.1	0.000009
S	216	L216del	CTC	---	2	2	B.1.1	0.000036
S	216	L216F	Ctc	Ttc	2	2	B.1.1.170	0.002494
S	216	L216F	Ctc	Ttc	2	2	B.1.1.222	0.000408
S	216	L216F	Ctc	Ttc	2	2	B.1.1.291	0.001485
S	216	L216F	Ctc	Ttc	2	2	B.1.1.306	0.000877
S	216	L216F	Ctc	Ttc	2	2	B.1.1.316	0.00185
S	216	L216P	cTc	cCc	2	2	B.1.177	0.000026
S	216	L216F	Ctc	Ttc	2	2	B.1.177.40	0.010309
S	216	L216I	Ctc	Atc	2	2	B.1.177.75	0.002081
S	216	L216P	cTc	cCc	2	2	B.1.2	0.000018
S	216	L216F	Ctc	Ttc	2	2	B.1.214.2	0.001199
S	216	L216D	CTC	GAT	2	2	B.1.214.2	0.001199
S	216	L216F	Ctc	Ttc	2	2	B.1.221	0.000142
S	216	L216del	CTC	---	2	2	B.1.258	0.000133
S	216	L216I	CtC	AtA	1	2	B.1.301	0.005917
S	216	L216I	Ctc	Atc	1	2	B.1.301	0.005917
S	216	L216F	Ctc	Ttc	2	2	B.1.351	0.000059
S	216	L216H	cTc	cAc	2	2	B.1.36.8	0.002
S	216	L216P	cTc	cCc	1	2	B.1.391	0.001127
S	216	L216S	CTC	TCT	1	2	B.1.391	0.001127
S	216	L216F	CtC	TtT	1	2	B.1.391	0.001127
S	216	L216F	Ctc	Ttc	1	2	B.1.391	0.001127
S	216	L216S	CTc	TCc	1	2	B.1.391	0.001127
S	216	L216P	cTC	cCT	1	2	B.1.391	0.001127
S	216	L216F	Ctc	Ttc	2	2	B.1.470	0.002809
S	216	L216F	Ctc	Ttc	2	2	B.1.474	0.003802
S	216	L216F	Ctc	Ttc	2	2	B.1.525	0.000226
S	216	L216F	Ctc	Ttc	2	2	B.1.575	0.000607
S	216	L216F	Ctc	Ttc	2	2	B.1.617.1	0.000258
S	216	L216P	cTc	cCc	2	2	B.1.617.2	0.000008
S	216	L216del1	ctC	ct-	2	2	B.1.627	0.00404
S	216	L216F	Ctc	Ttc	2	2	B.1.69	0.071429
S	216	L216L	ctC	ctT	2	2	B.1.9	0.012346
S	216	L216L	ctC	ctT	2	2	C.1	0.004785
S	216	L216F	Ctc	Ttc	2	2	C.30	0.003454
S	216	L216F	Ctc	Ttc	2	2	C.36.3	0.001134
S	216	L216del	CTC	---	2	2	P.1.1	0.000635
S	216	L216del1	ctC	ct-	1	2	P.1.12	0.000484
S	216	L216del1	Ctc	-tc	1	2	P.1.12	0.000484
S	216	L216F	Ctc	Ttc	2	2	P.1.13	0.001797
S	216	L216H	cTc	cAc	2	2	P.1.14	0.000096
S	216	L216del1	ctC	ct-	2	2	P.1.7	0.000639
S	216	L216F	Ctc	Ttc	2	2	P.2	0.000373
S	216	L216I	Ctc	Atc	2	2	Q.1	0.000253
S	216	L216del1	ctC	ct-	2	2	Q.4	0.00091
S	216	L216I	Ctc	Atc	1	1	A.2.4	0.003367
S	216	L216del	CTC	---	1	1	A.2.5	0.000499
S	216	L216L	ctC	ctT	1	1	A.2.5	0.000499
S	216	L216F	Ctc	Ttc	1	1	A.2.5.2	0.001572
S	216	L216F	Ctc	Ttc	1	1	AD.2	0.000219
S	216	L216F	Ctc	Ttc	1	1	AE.8	0.000489
S	216	L216G	CTc	GGc	1	1	All	0
S	216	L216C	CTc	TGc	1	1	All	0
S	216	L216Q	cTC	cAG	1	1	All	0
S	216	L216X	CTC	TAG	1	1	All	0
S	216	L216Y	CTc	TAc	1	1	All	0
S	216	L216P	cTc	cCc	1	1	AN.1	0.02
S	216	L216F	Ctc	Ttc	1	1	AY.10	0.00053
S	216	L216L	ctC	ctT	1	1	AY.100	0.000046
S	216	L216del	CTC	---	1	1	AY.101	0.00049
S	216	L216P	cTc	cCc	1	1	AY.102	0.000027
S	216	L216del	CTC	---	1	1	AY.102	0.000027
S	216	L216L	ctC	ctG	1	1	AY.102	0.000027
S	216	L216I	Ctc	Atc	1	1	AY.103	0.000006
S	216	L216P	cTc	cCc	1	1	AY.103	0.000006
S	216	L216F	Ctc	Ttc	1	1	AY.107	0.000466
S	216	L216F	Ctc	Ttc	1	1	AY.113	0.000142
S	216	L216L	ctC	ctT	1	1	AY.116	0.000287
S	216	L216L	ctC	ctA	1	1	AY.118	0.000063
S	216	L216F	Ctc	Ttc	1	1	AY.118	0.000063
S	216	L216del	CTC	---	1	1	AY.118	0.000063
S	216	L216H	cTc	cAc	1	1	AY.120	0.000037
S	216	L216L	ctC	ctT	1	1	AY.120	0.000037
S	216	L216del1	ctC	ct-	1	1	AY.121	0.000135
S	216	L216I	Ctc	Atc	1	1	AY.121	0.000135
S	216	L216L	ctC	ctT	1	1	AY.121	0.000135
S	216	L216F	Ctc	Ttc	1	1	AY.14	0.000088
S	216	L216F	Ctc	Ttc	1	1	AY.16	0.00038
S	216	L216del	CTC	---	1	1	AY.20	0.000039
S	216	L216P	cTc	cCc	1	1	AY.23	0.00007
S	216	L216L	ctC	ctA	1	1	AY.23	0.00007
S	216	L216F	Ctc	Ttc	1	1	AY.24	0.000431
S	216	L216del	CTC	---	1	1	AY.24	0.000431
S	216	L216I	Ctc	Atc	1	1	AY.25	0.000006
S	216	L216P	cTc	cCc	1	1	AY.25	0.000006
S	216	L216del1	ctC	ct-	1	1	AY.25	0.000006
S	216	L216I	Ctc	Atc	1	1	AY.26	0.000028
S	216	L216L	ctC	ctT	1	1	AY.26	0.000028
S	216	L216del	CTC	---	1	1	AY.26	0.000028
S	216	L216L	ctC	ctT	1	1	AY.29	0.000016
S	216	L216del	CTC	---	1	1	AY.29	0.000016
S	216	L216del	CTC	---	1	1	AY.3	0.00001
S	216	L216L	ctC	ctT	1	1	AY.30	0.000396
S	216	L216del	CTC	---	1	1	AY.30	0.000396
S	216	L216del1	ctC	ct-	1	1	AY.32	0.000532
S	216	L216L	ctC	ctA	1	1	AY.33	0.000067
S	216	L216F	Ctc	Ttc	1	1	AY.34	0.000097
S	216	L216L	ctC	ctT	1	1	AY.34.1	0.00051
S	216	L216F	Ctc	Ttc	1	1	AY.35	0.000233
S	216	L216L	ctC	ctT	1	1	AY.36	0.000148
S	216	L216L	ctC	ctA	1	1	AY.39	0.000025
S	216	L216Y	CTc	TAc	1	1	AY.4	0.000002
S	216	L216del1	ctC	ct-	1	1	AY.4	0.000002
S	216	L216P	cTc	cCc	1	1	AY.4.2	0.000022
S	216	L216L	ctC	ctT	1	1	AY.4.2	0.000022
S	216	L216F	Ctc	Ttc	1	1	AY.4.5	0.000107
S	216	L216del2	CTc	--c	1	1	AY.4.5	0.000107
S	216	L216del1	ctC	ct-	1	1	AY.41	0.000294
S	216	L216I	Ctc	Atc	1	1	AY.41	0.000294
S	216	L216R	cTc	cGc	1	1	AY.43	0.000004
S	216	L216A	CTC	GCT	1	1	AY.43	0.000004
S	216	L216P	cTc	cCc	1	1	AY.44	0.000006
S	216	L216del1	ctC	ct-	1	1	AY.45	0.000122
S	216	L216L	ctC	ctT	1	1	AY.45	0.000122
S	216	L216F	Ctc	Ttc	1	1	AY.46.2	0.000635
S	216	L216del	CTC	---	1	1	AY.46.2	0.000635
S	216	L216L	ctC	ctT	1	1	AY.46.6	0.000072
S	216	L216R	cTc	cGc	1	1	AY.46.6	0.000072
S	216	L216del	CTC	---	1	1	AY.46.6	0.000072
S	216	L216del	CTC	---	1	1	AY.47	0.000031
S	216	L216del1	ctC	ct-	1	1	AY.47	0.000031
S	216	L216del1	ctC	ct-	1	1	AY.48	0.000465
S	216	L216F	Ctc	Ttc	1	1	AY.49	0.003195
S	216	L216F	Ctc	Ttc	1	1	AY.5.3	0.000337
S	216	L216del	CTC	---	1	1	AY.5.3	0.000337
S	216	L216L	ctC	ctA	1	1	AY.52	0.000814
S	216	L216P	cTc	cCc	1	1	AY.6	0.000041
S	216	L216F	Ctc	Ttc	1	1	AY.62	0.000436
S	216	L216del	CTC	---	1	1	AY.65	0.000533
S	216	L216del1	ctC	ct-	1	1	AY.68	0.000274
S	216	L216P	cTc	cCc	1	1	AY.69	0.000187
S	216	L216F	Ctc	Ttc	1	1	AY.69	0.000187
S	216	L216F	Ctc	Ttc	1	1	AY.84	0.000437
S	216	L216F	Ctc	Ttc	1	1	AY.86	0.00083
S	216	L216F	Ctc	Ttc	1	1	AY.9.1	0.000084
S	216	L216I	Ctc	Atc	1	1	AY.9.2	0.000037
S	216	L216F	Ctc	Ttc	1	1	AY.92	0.000287
S	216	L216F	Ctc	Ttc	1	1	AY.94	0.000443
S	216	L216L	ctC	ctT	1	1	AY.94	0.000443
S	216	L216del	CTC	---	1	1	AY.96	0.002075
S	216	L216del	CTC	---	1	1	AY.98	0.000079
S	216	L216L	ctC	ctT	1	1	AY.98.1	0.000048
S	216	L216F	Ctc	Ttc	1	1	AZ.1	0.000867
S	216	L216del	CTC	---	1	1	B	0.000128
S	216	L216I	Ctc	Atc	1	1	B.1.1	0.000018
S	216	L216L	ctC	ctT	1	1	B.1.1.1	0.000327
S	216	L216del1	Ctc	-tc	1	1	B.1.1.121	0.002427
S	216	L216del	CTC	---	1	1	B.1.1.159	0.004673
S	216	L216F	Ctc	Ttc	1	1	B.1.1.176	0.000439
S	216	L216F	Ctc	Ttc	1	1	B.1.1.220	0.001859
S	216	L216F	Ctc	Ttc	1	1	B.1.1.284	0.000107
S	216	L216del	CTC	---	1	1	B.1.1.315	0.008475
S	216	L216F	Ctc	Ttc	1	1	B.1.1.325	0.025641
S	216	L216L	ctC	ctT	1	1	B.1.1.33	0.000421
S	216	L216F	Ctc	Ttc	1	1	B.1.1.37	0.000193
S	216	L216L	ctC	ctT	1	1	B.1.1.39	0.00051
S	216	L216del	CTC	---	1	1	B.1.1.39	0.00051
S	216	L216F	Ctc	Ttc	1	1	B.1.1.409	0.002833
S	216	L216F	Ctc	Ttc	1	1	B.1.1.423	0.0625
S	216	L216F	Ctc	Ttc	1	1	B.1.1.432	0.001266
S	216	L216F	Ctc	Ttc	1	1	B.1.1.434	0.000349
S	216	L216F	Ctc	Ttc	1	1	B.1.1.486	0.001577
S	216	L216P	cTc	cCc	1	1	B.1.1.519	0.00004
S	216	L216L	ctC	ctT	1	1	B.1.1.519	0.00004
S	216	L216I	Ctc	Atc	1	1	B.1.1.63	0.000386
S	216	L216del2	CTc	--c	1	1	B.1.1.7	0.000001
S	216	L216Q	cTC	cAG	1	1	B.1.1.7	0.000001
S	216	L216del	CTC	---	1	1	B.1.1.70	0.000341
S	216	L216F	Ctc	Ttc	1	1	B.1.110.3	0.000718
S	216	L216F	Ctc	Ttc	1	1	B.1.139	0.000733
S	216	L216del	CTC	---	1	1	B.1.140	0.018868
S	216	L216F	Ctc	Ttc	1	1	B.1.151	0.011111
S	216	L216F	Ctc	Ttc	1	1	B.1.157	0.002985
S	216	L216P	cTc	cCc	1	1	B.1.160	0.000031
S	216	L216L	ctC	ctT	1	1	B.1.160	0.000031
S	216	L216L	ctC	ctT	1	1	B.1.160.16	0.000929
S	216	L216del	CTC	---	1	1	B.1.160.23	0.004831
S	216	L216I	CtC	AtT	1	1	B.1.167	0.007812
S	216	L216F	Ctc	Ttc	1	1	B.1.177.12	0.000152
S	216	L216P	cTc	cCc	1	1	B.1.177.15	0.000631
S	216	L216del	CTC	---	1	1	B.1.177.16	0.000664
S	216	L216P	cTc	cCc	1	1	B.1.177.21	0.000076
S	216	L216L	ctC	ctT	1	1	B.1.177.21	0.000076
S	216	L216F	Ctc	Ttc	1	1	B.1.177.4	0.000211
S	216	L216del	CTC	---	1	1	B.1.177.51	0.004566
S	216	L216F	Ctc	Ttc	1	1	B.1.177.56	0.000668
S	216	L216F	Ctc	Ttc	1	1	B.1.177.57	0.000281
S	216	L216del	CTC	---	1	1	B.1.177.6	0.000977
S	216	L216del	CTC	---	1	1	B.1.177.62	0.001192
S	216	L216del	CTC	---	1	1	B.1.177.69	0.001484
S	216	L216F	Ctc	Ttc	1	1	B.1.177.7	0.000165
S	216	L216F	Ctc	Ttc	1	1	B.1.177.79	0.002342
S	216	L216del1	ctC	ct-	1	1	B.1.177.81	0.000189
S	216	L216F	Ctc	Ttc	1	1	B.1.177.9	0.001332
S	216	L216del	CTC	---	1	1	B.1.2	0.000009
S	216	L216I	Ctc	Atc	1	1	B.1.2	0.000009
S	216	L216S	CTC	TCT	1	1	B.1.214.2	0.0006
S	216	L216del	CTC	---	1	1	B.1.218	0.005155
S	216	L216L	ctC	ctT	1	1	B.1.221	0.000071
S	216	L216F	Ctc	Ttc	1	1	B.1.243	0.00007
S	216	L216L	ctC	ctT	1	1	B.1.243	0.00007
S	216	L216P	cTc	cCc	1	1	B.1.243	0.00007
S	216	L216F	Ctc	Ttc	1	1	B.1.258.7	0.001912
S	216	L216L	ctC	ctA	1	1	B.1.301	0.005917
S	216	L216R	cTc	cGc	1	1	B.1.311	0.000275
S	216	L216F	Ctc	Ttc	1	1	B.1.319	0.003049
S	216	L216del	CTC	---	1	1	B.1.351	0.00003
S	216	L216F	Ctc	Ttc	1	1	B.1.356	0.001727
S	216	L216del1	cTc	c-c	1	1	B.1.36	0.000146
S	216	L216del	CTC	---	1	1	B.1.36.18	0.00042
S	216	L216F	Ctc	Ttc	1	1	B.1.36.26	0.002857
S	216	L216F	Ctc	Ttc	1	1	B.1.36.28	0.005747
S	216	L216del	CTC	---	1	1	B.1.36.29	0.000517
S	216	L216F	Ctc	Ttc	1	1	B.1.369	0.000285
S	216	L216I	Ctc	Atc	1	1	B.1.370	0.008
S	216	L216L	ctC	ctT	1	1	B.1.391	0.001127
S	216	L216L	ctC	ctT	1	1	B.1.396	0.000706
S	216	L216del2	CTc	--c	1	1	B.1.409	0.000781
S	216	L216L	ctC	ctT	1	1	B.1.429	0.000024
S	216	L216P	cTc	cCc	1	1	B.1.429	0.000024
S	216	L216L	ctC	ctA	1	1	B.1.438.1	0.000107
S	216	L216F	Ctc	Ttc	1	1	B.1.438.1	0.000107
S	216	L216L	ctC	ctT	1	1	B.1.466.2	0.000391
S	216	L216del	CTC	---	1	1	B.1.525	0.000113
S	216	L216F	Ctc	Ttc	1	1	B.1.558	0.004566
S	216	L216del	CTC	---	1	1	B.1.561	0.000397
S	216	L216L	ctC	ctT	1	1	B.1.561	0.000397
S	216	L216F	Ctc	Ttc	1	1	B.1.564	0.000426
S	216	L216F	Ctc	Ttc	1	1	B.1.565	0.00081
S	216	L216L	ctC	ctT	1	1	B.1.575	0.000303
S	216	L216F	Ctc	Ttc	1	1	B.1.580	0.004065
S	216	L216R	cTC	cGT	1	1	B.1.582	0.000491
S	216	L216F	Ctc	Ttc	1	1	B.1.609	0.000479
S	216	L216del	CTC	---	1	1	B.1.617.1	0.000129
S	216	L216R	cTc	cGc	1	1	B.1.617.2	0.000004
S	216	L216del	CTC	---	1	1	B.1.620	0.000946
S	216	L216X	CTC	TAG	1	1	B.1.621	0.000089
S	216	L216del	CTC	---	1	1	B.1.621	0.000089
S	216	L216F	Ctc	Ttc	1	1	B.1.623	0.000536
S	216	L216I	Ctc	Atc	1	1	B.1.623	0.000536
S	216	L216F	Ctc	Ttc	1	1	B.1.628	0.000352
S	216	L216F	Ctc	Ttc	1	1	B.1.629	0.013333
S	216	L216F	Ctc	Ttc	1	1	B.1.630	0.005236
S	216	L216del	CTC	---	1	1	B.1.630	0.005236
S	216	L216L	ctC	ctG	1	1	B.1.637	0.000073
S	216	L216del	CTC	---	1	1	B.1.638	0.052632
S	216	L216I	Ctc	Atc	1	1	B.6	0.00091
S	216	L216C	CTc	TGc	1	1	B.6	0.00091
S	216	L216del	CTC	---	1	1	C.16	0.00106
S	216	L216F	Ctc	Ttc	1	1	C.35	0.000774
S	216	L216L	ctC	ctT	1	1	C.35	0.000774
S	216	L216F	Ctc	Ttc	1	1	C.36	0.000911
S	216	L216F	Ctc	Ttc	1	1	C.37	0.000116
S	216	L216H	cTc	cAc	1	1	D.2	0.000075
S	216	L216G	CTc	GGc	1	1	P.1	0.000016
S	216	L216F	Ctc	Ttc	1	1	P.1.1	0.000318
S	216	L216F	Ctc	Ttc	1	1	P.1.11	0.010204
S	216	L216V	Ctc	Gtc	1	1	P.1.14	0.000048
S	216	L216P	cTc	cCc	1	1	P.1.16	0.000374
S	216	L216L	ctC	ctT	1	1	P.1.17	0.000162
S	216	L216F	Ctc	Ttc	1	1	P.1.2	0.001156
S	216	L216P	cTc	cCc	1	1	P.1.4	0.000977
S	216	L216F	Ctc	Ttc	1	1	P.1.4	0.000977
S	216	L216F	Ctc	Ttc	1	1	P.3	0.001595
S	216	L216L	ctC	ctT	1	1	Q.1	0.000126
S	216	L216del1	ctC	ct-	1	1	Q.1	0.000126
S	216	L216F	Ctc	Ttc	1	1	Q.2	0.000613
S	216	L216del	CTC	---	1	1	Q.2	0.000613
S	216	L216F	Ctc	Ttc	1	1	Q.3	0.000145
S	216	L216del2	cTC	c--	1	1	Q.3	0.000145
S	216	L216del	CTC	---	1	1	U.3	0.003861

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.