CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 884

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	884	S884F		nonsyn	tCt	tTt	1096	1096	1	24212-24214
S	884	S884S		syn	tcT	tcC	510	340	0.666667	24212-24214
S	884	S884S		syn	tcT	tcA	510	128	0.25098	24212-24214
S	884	S884S		syn	tcT	tcG	510	41	0.0803922	24212-24214
S	884	S884S		syn	TCt	AGt	510	1	0.00196078	24212-24214
S	884	S884A		nonsyn	Tct	Gct	144	144	1	24212-24214
S	884	S884del		del	TCT	---	132	132	1	24212-24214
S	884	S884C		nonsyn	tCt	tGt	46	46	1	24212-24214
S	884	S884T		nonsyn	Tct	Act	12	11	0.916667	24212-24214
S	884	S884T		nonsyn	TcT	AcG	12	1	0.0833333	24212-24214
S	884	S884P		nonsyn	Tct	Cct	11	11	1	24212-24214
S	884	S884Y		nonsyn	tCt	tAt	7	7	1	24212-24214
S	884	S884del1		del	tCt	t-t	4	2	0.5	24212-24214
S	884	S884del1		del	tcT	tc-	4	1	0.25	24212-24214
S	884	S884del1		del	Tct	-ct	4	1	0.25	24212-24214
S	884	S884N		nonsyn	TCt	AAt	3	3	1	24212-24214
S	884	S884del2		del	TCt	--t	3	3	1	24212-24214
S	884	S884L		nonsyn	TCt	CTt	3	2	0.666667	24212-24214
S	884	S884L		nonsyn	TCT	CTC	3	1	0.333333	24212-24214
S	884	S884V		nonsyn	TCT	GTG	1	1	1	24212-24214

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	884	S884F	tCt	tTt	1096	1096	All	0.00021
S	884	S884S	tcT	tcC	340	510	All	0.000065
S	884	S884S	tcT	tcA	128	510	All	0.000024
S	884	S884S	tcT	tcG	41	510	All	0.000008
S	884	S884S	TCt	AGt	1	510	All	0
S	884	S884F	tCt	tTt	363	363	B.1.1.7	0.000325
S	884	S884A	Tct	Gct	144	144	All	0.000028
S	884	S884del	TCT	---	132	132	All	0.000025
S	884	S884F	tCt	tTt	125	125	AY.4	0.000195
S	884	S884S	tcT	tcC	43	73	B.1.1.7	0.000038
S	884	S884S	tcT	tcA	29	73	B.1.1.7	0.000026
S	884	S884S	tcT	tcG	1	73	B.1.1.7	0.000001
S	884	S884A	Tct	Gct	70	70	B.1.369	0.019966
S	884	S884S	tcT	tcC	50	51	AY.26	0.001416
S	884	S884S	tcT	tcA	1	51	AY.26	0.000028
S	884	S884S	tcT	tcC	47	49	AY.43	0.000208
S	884	S884S	tcT	tcA	2	49	AY.43	0.000009
S	884	S884del	TCT	---	47	47	B.1.1.7	0.000042
S	884	S884C	tCt	tGt	46	46	All	0.000009
S	884	S884F	tCt	tTt	46	46	B.1.177	0.000606
S	884	S884F	tCt	tTt	36	36	B.1.2	0.000317
S	884	S884S	tcT	tcA	29	33	AY.25	0.000174
S	884	S884S	tcT	tcC	4	33	AY.25	0.000024
S	884	S884S	tcT	tcG	19	31	AY.4	0.00003
S	884	S884S	tcT	tcC	8	31	AY.4	0.000012
S	884	S884S	tcT	tcA	4	31	AY.4	0.000006
S	884	S884F	tCt	tTt	30	30	B.1	0.000275
S	884	S884S	tcT	tcC	25	26	B.1.160	0.00078
S	884	S884S	tcT	tcA	1	26	B.1.160	0.000031
S	884	S884F	tCt	tTt	23	23	AY.25	0.000138
S	884	S884A	Tct	Gct	23	23	Q.2	0.01411
S	884	S884F	tCt	tTt	22	22	AY.43	0.000097
S	884	S884F	tCt	tTt	22	22	AY.44	0.000134
S	884	S884F	tCt	tTt	22	22	B.1.617.2	0.000083
S	884	S884S	tcT	tcC	19	22	B.1.617.2	0.000072
S	884	S884S	tcT	tcG	2	22	B.1.617.2	0.000008
S	884	S884S	tcT	tcA	1	22	B.1.617.2	0.000004
S	884	S884S	tcT	tcC	17	20	B.1.2	0.00015
S	884	S884S	tcT	tcA	3	20	B.1.2	0.000026
S	884	S884F	tCt	tTt	20	20	B.1.429	0.000471
S	884	S884S	tcT	tcC	20	20	B.1.621	0.00177
S	884	S884F	tCt	tTt	20	20	D.2	0.001501
S	884	S884F	tCt	tTt	17	17	B.1.1	0.000308
S	884	S884S	tcT	tcC	17	17	B.1.1.112	1
S	884	S884S	tcT	tcC	13	15	B.1.526	0.000306
S	884	S884S	tcT	tcG	2	15	B.1.526	0.000047
S	884	S884F	tCt	tTt	14	14	AY.103	0.000087
S	884	S884C	tCt	tGt	13	13	B.1.1.7	0.000012
S	884	S884T	Tct	Act	11	12	All	0.000002
S	884	S884T	TcT	AcG	1	12	All	0
S	884	S884A	Tct	Gct	12	12	B.1.1.7	0.000011
S	884	S884P	Tct	Cct	11	11	All	0.000002
S	884	S884F	tCt	tTt	11	11	AY.120	0.000409
S	884	S884S	tcT	tcC	11	11	AY.39	0.000272
S	884	S884S	tcT	tcA	8	11	B.1	0.000073
S	884	S884S	tcT	tcC	3	11	B.1	0.000027
S	884	S884F	tCt	tTt	9	9	AY.3	0.00009
S	884	S884S	tcT	tcC	6	8	AY.44	0.000037
S	884	S884S	tcT	tcA	1	8	AY.44	0.000006
S	884	S884S	tcT	tcG	1	8	AY.44	0.000006
S	884	S884A	Tct	Gct	8	8	B.1	0.000073
S	884	S884S	tcT	tcA	7	8	B.1.351	0.000208
S	884	S884S	tcT	tcC	1	8	B.1.351	0.00003
S	884	S884Y	tCt	tAt	7	7	All	0.000001
S	884	S884F	tCt	tTt	7	7	AY.39	0.000173
S	884	S884F	tCt	tTt	7	7	B	0.000895
S	884	S884S	tcT	tcC	7	7	B.1.1.70	0.002387
S	884	S884F	tCt	tTt	7	7	B.1.177.21	0.000535
S	884	S884del	TCT	---	7	7	B.1.617.2	0.000026
S	884	S884F	tCt	tTt	6	6	AY.102	0.000159
S	884	S884S	tcT	tcC	6	6	AY.29	0.000095
S	884	S884F	tCt	tTt	6	6	AY.29	0.000095
S	884	S884del	TCT	---	6	6	AY.4	0.000009
S	884	S884S	tcT	tcA	6	6	AY.47	0.000187
S	884	S884F	tCt	tTt	6	6	AY.5	0.000124
S	884	S884S	tcT	tcG	6	6	AY.74	0.000694
S	884	S884F	tCt	tTt	6	6	B.1.160	0.000187
S	884	S884del	TCT	---	6	6	B.1.177	0.000079
S	884	S884S	tcT	tcC	5	6	B.1.36	0.00073
S	884	S884S	tcT	tcA	1	6	B.1.36	0.000146
S	884	S884F	tCt	tTt	5	5	AY.34	0.000485
S	884	S884F	tCt	tTt	5	5	AY.39.1	0.000198
S	884	S884S	tcT	tcC	5	5	AY.6	0.000206
S	884	S884F	tCt	tTt	5	5	B.1.1.214	0.000277
S	884	S884F	tCt	tTt	5	5	B.1.1.33	0.002104
S	884	S884F	tCt	tTt	5	5	B.1.1.519	0.000199
S	884	S884S	tcT	tcA	4	5	B.1.177	0.000053
S	884	S884S	tcT	tcC	1	5	B.1.177	0.000013
S	884	S884S	tcT	tcA	5	5	B.1.177.46	0.004591
S	884	S884A	Tct	Gct	5	5	B.1.2	0.000044
S	884	S884F	tCt	tTt	5	5	B.1.427	0.000252
S	884	S884S	tcT	tcC	2	5	P.1	0.000032
S	884	S884S	tcT	tcA	2	5	P.1	0.000032
S	884	S884S	tcT	tcG	1	5	P.1	0.000016
S	884	S884del	TCT	---	4	4		0.222222
S	884	S884del1	tCt	t-t	2	4	All	0
S	884	S884del1	Tct	-ct	1	4	All	0
S	884	S884del1	tcT	tc-	1	4	All	0
S	884	S884S	tcT	tcA	4	4	AY.101	0.001962
S	884	S884S	tcT	tcA	2	4	AY.103	0.000012
S	884	S884S	tcT	tcC	2	4	AY.103	0.000012
S	884	S884C	tCt	tGt	4	4	AY.4	0.000006
S	884	S884F	tCt	tTt	4	4	AY.42	0.000161
S	884	S884del	TCT	---	4	4	AY.43	0.000018
S	884	S884F	tCt	tTt	4	4	AY.47	0.000124
S	884	S884F	tCt	tTt	4	4	AY.98	0.000316
S	884	S884C	tCt	tGt	4	4	AY.98.1	0.000194
S	884	S884F	tCt	tTt	4	4	AZ.5	0.014035
S	884	S884del	TCT	---	4	4	B.1.2	0.000035
S	884	S884F	tCt	tTt	4	4	B.1.258	0.000266
S	884	S884F	tCt	tTt	4	4	B.1.351	0.000119
S	884	S884A	Tct	Gct	4	4	B.1.36.21	0.008639
S	884	S884F	tCt	tTt	4	4	P.1.14	0.000191
S	884	S884N	TCt	AAt	3	3	All	0.000001
S	884	S884del2	TCt	--t	3	3	All	0.000001
S	884	S884L	TCt	CTt	2	3	All	0
S	884	S884L	TCT	CTC	1	3	All	0
S	884	S884F	tCt	tTt	3	3	AY.110	0.000338
S	884	S884S	tcT	tcC	3	3	AY.121	0.000406
S	884	S884F	tCt	tTt	3	3	AY.23	0.000209
S	884	S884F	tCt	tTt	3	3	AY.3.1	0.000256
S	884	S884F	tCt	tTt	3	3	AY.33	0.0002
S	884	S884A	Tct	Gct	3	3	AY.4	0.000005
S	884	S884F	tCt	tTt	3	3	AY.4.2	0.000065
S	884	S884S	tcT	tcG	3	3	AY.4.2	0.000065
S	884	S884del	TCT	---	3	3	AY.4.5	0.000322
S	884	S884F	tCt	tTt	3	3	AY.7.1	0.000338
S	884	S884F	tCt	tTt	3	3	AY.9.2	0.00011
S	884	S884del	TCT	---	3	3	B.1	0.000027
S	884	S884F	tCt	tTt	3	3	B.1.1.222	0.000612
S	884	S884F	tCt	tTt	3	3	B.1.1.50	0.002037
S	884	S884F	tCt	tTt	3	3	B.1.177.7	0.000495
S	884	S884C	tCt	tGt	3	3	B.1.177.83	0.004444
S	884	S884del1	tCt	t-t	2	3	B.1.2	0.000018
S	884	S884del1	tcT	tc-	1	3	B.1.2	0.000009
S	884	S884F	tCt	tTt	3	3	B.1.311	0.000824
S	884	S884F	tCt	tTt	3	3	B.1.351.5	0.001799
S	884	S884F	tCt	tTt	3	3	B.1.416.1	0.004687
S	884	S884S	tcT	tcC	3	3	B.1.429	0.000071
S	884	S884F	tCt	tTt	3	3	B.1.438.1	0.000322
S	884	S884A	Tct	Gct	3	3	B.1.564	0.001278
S	884	S884S	tcT	tcA	3	3	C.36	0.002732
S	884	S884F	tCt	tTt	3	3	P.1	0.000047
S	884	S884F	tCt	tTt	3	3	Q.1	0.000379
S	884	S884S	tcT	tcG	3	3	R.1	0.00027
S	884	S884N	TCt	AAt	2	2		0.111111
S	884	S884L	TCt	CTt	2	2		0.111111
S	884	S884F	tCt	tTt	2	2	AD.2	0.000438
S	884	S884F	tCt	tTt	2	2	AY.100	0.000092
S	884	S884S	tcT	tcA	1	2	AY.100	0.000046
S	884	S884S	tcT	tcC	1	2	AY.100	0.000046
S	884	S884C	tCt	tGt	2	2	AY.103	0.000012
S	884	S884F	tCt	tTt	2	2	AY.113	0.000285
S	884	S884F	tCt	tTt	2	2	AY.116	0.000574
S	884	S884del	TCT	---	2	2	AY.120	0.000074
S	884	S884F	tCt	tTt	2	2	AY.20	0.000078
S	884	S884S	tcT	tcC	2	2	AY.20	0.000078
S	884	S884C	tCt	tGt	2	2	AY.25	0.000012
S	884	S884F	tCt	tTt	2	2	AY.26	0.000057
S	884	S884F	tCt	tTt	2	2	AY.27	0.000129
S	884	S884S	tcT	tcC	2	2	AY.3	0.00002
S	884	S884F	tCt	tTt	2	2	AY.36	0.000296
S	884	S884S	tcT	tcA	1	2	AY.39.1	0.00004
S	884	S884S	tcT	tcC	1	2	AY.39.1	0.00004
S	884	S884A	Tct	Gct	2	2	AY.43	0.000009
S	884	S884C	tCt	tGt	2	2	AY.43	0.000009
S	884	S884T	Tct	Act	1	2	AY.43	0.000004
S	884	S884T	TcT	AcG	1	2	AY.43	0.000004
S	884	S884F	tCt	tTt	2	2	AY.46	0.000208
S	884	S884F	tCt	tTt	2	2	AY.46.6	0.000144
S	884	S884F	tCt	tTt	2	2	AY.9	0.000135
S	884	S884F	tCt	tTt	2	2	AY.90	0.001369
S	884	S884F	tCt	tTt	2	2	AY.98.1	0.000097
S	884	S884C	tCt	tGt	2	2	B.1.1	0.000036
S	884	S884F	tCt	tTt	2	2	B.1.1.176	0.000879
S	884	S884F	tCt	tTt	2	2	B.1.1.269	0.002706
S	884	S884F	tCt	tTt	2	2	B.1.1.277	0.001517
S	884	S884F	tCt	tTt	2	2	B.1.1.37	0.000386
S	884	S884F	tCt	tTt	2	2	B.1.1.434	0.000697
S	884	S884P	Tct	Cct	2	2	B.1.1.7	0.000002
S	884	S884T	Tct	Act	2	2	B.1.1.7	0.000002
S	884	S884Y	tCt	tAt	2	2	B.1.1.7	0.000002
S	884	S884F	tCt	tTt	2	2	B.1.1.70	0.000682
S	884	S884F	tCt	tTt	2	2	B.1.177.12	0.000303
S	884	S884A	Tct	Gct	2	2	B.1.177.12	0.000303
S	884	S884F	tCt	tTt	2	2	B.1.177.57	0.000562
S	884	S884F	tCt	tTt	2	2	B.1.177.86	0.000367
S	884	S884C	tCt	tGt	2	2	B.1.2	0.000018
S	884	S884F	tCt	tTt	2	2	B.1.206	0.001631
S	884	S884F	tCt	tTt	2	2	B.1.234	0.000264
S	884	S884F	tCt	tTt	2	2	B.1.243	0.000139
S	884	S884F	tCt	tTt	2	2	B.1.36	0.000292
S	884	S884A	Tct	Gct	2	2	B.1.361	0.002577
S	884	S884F	tCt	tTt	2	2	B.1.448	0.005249
S	884	S884F	tCt	tTt	2	2	B.1.517.1	0.010526
S	884	S884del	TCT	---	2	2	B.1.526	0.000047
S	884	S884F	tCt	tTt	2	2	B.1.617.1	0.000258
S	884	S884A	Tct	Gct	2	2	B.1.617.2	0.000008
S	884	S884F	tCt	tTt	2	2	B.1.637	0.000146
S	884	S884S	tcT	tcA	2	2	P.1.1	0.000635
S	884	S884F	tCt	tTt	2	2	P.1.10	0.000539
S	884	S884F	tCt	tTt	2	2	P.1.16	0.000748
S	884	S884F	tCt	tTt	2	2	Q.3	0.00029
S	884	S884del	TCT	---	1	1	A	0.000387
S	884	S884F	tCt	tTt	1	1	A.1	0.000282
S	884	S884P	Tct	Cct	1	1	A.1	0.000282
S	884	S884S	tcT	tcC	1	1	A.2.5.2	0.001572
S	884	S884F	tCt	tTt	1	1	AE.8	0.000489
S	884	S884del	TCT	---	1	1	AH.3	0.003802
S	884	S884F	tCt	tTt	1	1	AL.1	0.012987
S	884	S884V	TCT	GTG	1	1	All	0
S	884	S884A	Tct	Gct	1	1	AY.100	0.000046
S	884	S884C	tCt	tGt	1	1	AY.102	0.000027
S	884	S884Y	tCt	tAt	1	1	AY.103	0.000006
S	884	S884C	tCt	tGt	1	1	AY.106	0.000335
S	884	S884F	tCt	tTt	1	1	AY.107	0.000466
S	884	S884F	tCt	tTt	1	1	AY.11	0.001339
S	884	S884F	tCt	tTt	1	1	AY.111	0.000183
S	884	S884del	TCT	---	1	1	AY.111	0.000183
S	884	S884T	Tct	Act	1	1	AY.117	0.000085
S	884	S884S	tcT	tcC	1	1	AY.118	0.000063
S	884	S884C	tCt	tGt	1	1	AY.119	0.000035
S	884	S884P	Tct	Cct	1	1	AY.119	0.000035
S	884	S884F	tCt	tTt	1	1	AY.119	0.000035
S	884	S884S	tcT	tcA	1	1	AY.120	0.000037
S	884	S884S	tcT	tcA	1	1	AY.120.1	0.000321
S	884	S884F	tCt	tTt	1	1	AY.120.2	0.001285
S	884	S884F	tCt	tTt	1	1	AY.120.2.1	0.000498
S	884	S884F	tCt	tTt	1	1	AY.121	0.000135
S	884	S884del	TCT	---	1	1	AY.19	0.00114
S	884	S884F	tCt	tTt	1	1	AY.2	0.000356
S	884	S884S	tcT	tcA	1	1	AY.2	0.000356
S	884	S884F	tCt	tTt	1	1	AY.22	0.002092
S	884	S884del	TCT	---	1	1	AY.25	0.000006
S	884	S884V	TCT	GTG	1	1	AY.25	0.000006
S	884	S884C	tCt	tGt	1	1	AY.29	0.000016
S	884	S884A	Tct	Gct	1	1	AY.3	0.00001
S	884	S884C	tCt	tGt	1	1	AY.3	0.00001
S	884	S884F	tCt	tTt	1	1	AY.32	0.000532
S	884	S884S	tcT	tcC	1	1	AY.33	0.000067
S	884	S884S	tcT	tcC	1	1	AY.34	0.000097
S	884	S884del	TCT	---	1	1	AY.36	0.000148
S	884	S884del2	TCt	--t	1	1	AY.4	0.000002
S	884	S884P	Tct	Cct	1	1	AY.4	0.000002
S	884	S884T	Tct	Act	1	1	AY.4.2.1	0.000149
S	884	S884F	tCt	tTt	1	1	AY.4.4	0.000409
S	884	S884del1	Tct	-ct	1	1	AY.4.5	0.000107
S	884	S884S	tcT	tcG	1	1	AY.42	0.00004
S	884	S884T	Tct	Act	1	1	AY.44	0.000006
S	884	S884C	tCt	tGt	1	1	AY.44	0.000006
S	884	S884del	TCT	---	1	1	AY.44	0.000006
S	884	S884P	Tct	Cct	1	1	AY.44	0.000006
S	884	S884del	TCT	---	1	1	AY.46.2	0.000635
S	884	S884F	tCt	tTt	1	1	AY.46.5	0.000198
S	884	S884F	tCt	tTt	1	1	AY.48	0.000465
S	884	S884T	Tct	Act	1	1	AY.5	0.000021
S	884	S884del	TCT	---	1	1	AY.5	0.000021
S	884	S884F	tCt	tTt	1	1	AY.5.3	0.000337
S	884	S884Y	tCt	tAt	1	1	AY.55	0.000917
S	884	S884F	tCt	tTt	1	1	AY.6	0.000041
S	884	S884C	tCt	tGt	1	1	AY.6	0.000041
S	884	S884F	tCt	tTt	1	1	AY.61	0.000105
S	884	S884del	TCT	---	1	1	AY.67	0.000464
S	884	S884T	Tct	Act	1	1	AY.71	0.000475
S	884	S884del	TCT	---	1	1	AY.72	0.001361
S	884	S884F	tCt	tTt	1	1	AY.73	0.000665
S	884	S884F	tCt	tTt	1	1	AY.74	0.000116
S	884	S884del	TCT	---	1	1	AY.75	0.000056
S	884	S884F	tCt	tTt	1	1	AY.77	0.001127
S	884	S884C	tCt	tGt	1	1	AY.77	0.001127
S	884	S884F	tCt	tTt	1	1	AY.78	0.001541
S	884	S884del	TCT	---	1	1	AY.81	0.001992
S	884	S884S	tcT	tcA	1	1	AY.85	0.000427
S	884	S884F	tCt	tTt	1	1	AY.85	0.000427
S	884	S884del	TCT	---	1	1	AY.9	0.000068
S	884	S884F	tCt	tTt	1	1	AY.92	0.000287
S	884	S884F	tCt	tTt	1	1	AY.93	0.000273
S	884	S884F	tCt	tTt	1	1	AY.97	0.001701
S	884	S884del	TCT	---	1	1	AY.99	0.001049
S	884	S884del	TCT	---	1	1	AY.99.1	0.001553
S	884	S884S	tcT	tcC	1	1	AY.99.2	0.000092
S	884	S884Y	tCt	tAt	1	1	B	0.000128
S	884	S884S	tcT	tcC	1	1	B	0.000128
S	884	S884P	Tct	Cct	1	1	B	0.000128
S	884	S884del2	TCt	--t	1	1	B.1	0.000009
S	884	S884P	Tct	Cct	1	1	B.1	0.000009
S	884	S884del	TCT	---	1	1	B.1.1	0.000018
S	884	S884L	TCT	CTC	1	1	B.1.1	0.000018
S	884	S884S	tcT	tcC	1	1	B.1.1	0.000018
S	884	S884F	tCt	tTt	1	1	B.1.1.122	0.045455
S	884	S884F	tCt	tTt	1	1	B.1.1.186	0.003436
S	884	S884A	Tct	Gct	1	1	B.1.1.194	0.00495
S	884	S884F	tCt	tTt	1	1	B.1.1.198	0.001468
S	884	S884S	tcT	tcA	1	1	B.1.1.214	0.000055
S	884	S884F	tCt	tTt	1	1	B.1.1.216	0.00089
S	884	S884del	TCT	---	1	1	B.1.1.236	0.006897
S	884	S884F	tCt	tTt	1	1	B.1.1.25	0.000569
S	884	S884F	tCt	tTt	1	1	B.1.1.280	0.003086
S	884	S884F	tCt	tTt	1	1	B.1.1.284	0.000107
S	884	S884F	tCt	tTt	1	1	B.1.1.291	0.000742
S	884	S884S	tcT	tcA	1	1	B.1.1.294	0.001266
S	884	S884F	tCt	tTt	1	1	B.1.1.306	0.000438
S	884	S884del	TCT	---	1	1	B.1.1.311	0.000358
S	884	S884del	TCT	---	1	1	B.1.1.312	0.001912
S	884	S884F	tCt	tTt	1	1	B.1.1.316	0.000925
S	884	S884F	tCt	tTt	1	1	B.1.1.317	0.000412
S	884	S884F	tCt	tTt	1	1	B.1.1.318	0.000302
S	884	S884F	tCt	tTt	1	1	B.1.1.322	0.008772
S	884	S884S	tcT	tcC	1	1	B.1.1.322	0.008772
S	884	S884F	tCt	tTt	1	1	B.1.1.368	0.003086
S	884	S884F	tCt	tTt	1	1	B.1.1.369	0.000446
S	884	S884F	tCt	tTt	1	1	B.1.1.39	0.00051
S	884	S884S	tcT	tcC	1	1	B.1.1.416	0.000905
S	884	S884F	tCt	tTt	1	1	B.1.1.47	0.005348
S	884	S884F	tCt	tTt	1	1	B.1.1.51	0.001718
S	884	S884F	tCt	tTt	1	1	B.1.1.513	0.012346
S	884	S884C	tCt	tGt	1	1	B.1.1.519	0.00004
S	884	S884A	Tct	Gct	1	1	B.1.1.519	0.00004
S	884	S884S	tcT	tcA	1	1	B.1.1.523	0.001563
S	884	S884P	Tct	Cct	1	1	B.1.1.54	0.003021
S	884	S884N	TCt	AAt	1	1	B.1.1.7	0.000001
S	884	S884Y	tCt	tAt	1	1	B.1.128	0.000635
S	884	S884T	Tct	Act	1	1	B.1.160	0.000031
S	884	S884F	tCt	tTt	1	1	B.1.160.22	0.006757
S	884	S884F	tCt	tTt	1	1	B.1.160.32	0.004292
S	884	S884del	TCT	---	1	1	B.1.177.10	0.000878
S	884	S884F	tCt	tTt	1	1	B.1.177.15	0.000631
S	884	S884del	TCT	---	1	1	B.1.177.17	0.000821
S	884	S884S	tcT	tcG	1	1	B.1.177.19	0.001431
S	884	S884del	TCT	---	1	1	B.1.177.21	0.000076
S	884	S884F	tCt	tTt	1	1	B.1.177.4	0.000211
S	884	S884F	tCt	tTt	1	1	B.1.177.41	0.0025
S	884	S884F	tCt	tTt	1	1	B.1.177.45	0.000381
S	884	S884del	TCT	---	1	1	B.1.177.48	0.003125
S	884	S884F	tCt	tTt	1	1	B.1.177.48	0.003125
S	884	S884del	TCT	---	1	1	B.1.177.54	0.000606
S	884	S884del	TCT	---	1	1	B.1.177.56	0.000668
S	884	S884del	TCT	---	1	1	B.1.177.60	0.000218
S	884	S884F	tCt	tTt	1	1	B.1.177.60	0.000218
S	884	S884del	TCT	---	1	1	B.1.177.63	0.002703
S	884	S884F	tCt	tTt	1	1	B.1.177.65	0.000665
S	884	S884S	tcT	tcA	1	1	B.1.177.7	0.000165
S	884	S884F	tCt	tTt	1	1	B.1.177.74	0.015152
S	884	S884F	tCt	tTt	1	1	B.1.177.75	0.001041
S	884	S884F	tCt	tTt	1	1	B.1.177.77	0.000726
S	884	S884F	tCt	tTt	1	1	B.1.177.8	0.000752
S	884	S884F	tCt	tTt	1	1	B.1.177.80	0.001912
S	884	S884del	TCT	---	1	1	B.1.177.87	0.000728
S	884	S884del	TCT	---	1	1	B.1.179	0.003759
S	884	S884Y	tCt	tAt	1	1	B.1.2	0.000009
S	884	S884T	Tct	Act	1	1	B.1.2	0.000009
S	884	S884P	Tct	Cct	1	1	B.1.201	0.005682
S	884	S884S	tcT	tcA	1	1	B.1.218	0.005155
S	884	S884del	TCT	---	1	1	B.1.221	0.000071
S	884	S884F	tCt	tTt	1	1	B.1.221	0.000071
S	884	S884F	tCt	tTt	1	1	B.1.23	0.006061
S	884	S884A	Tct	Gct	1	1	B.1.234	0.000132
S	884	S884S	tcT	tcG	1	1	B.1.240	0.000216
S	884	S884F	tCt	tTt	1	1	B.1.240	0.000216
S	884	S884S	tcT	tcC	1	1	B.1.243	0.00007
S	884	S884del	TCT	---	1	1	B.1.258	0.000067
S	884	S884S	tcT	tcC	1	1	B.1.258.17	0.000104
S	884	S884F	tCt	tTt	1	1	B.1.258.17	0.000104
S	884	S884F	tCt	tTt	1	1	B.1.258.7	0.001912
S	884	S884del	TCT	---	1	1	B.1.279	0.000514
S	884	S884F	tCt	tTt	1	1	B.1.282	0.014925
S	884	S884F	tCt	tTt	1	1	B.1.338	0.008621
S	884	S884C	tCt	tGt	1	1	B.1.351	0.00003
S	884	S884F	tCt	tTt	1	1	B.1.351.1	0.038462
S	884	S884del	TCT	---	1	1	B.1.36	0.000146
S	884	S884del	TCT	---	1	1	B.1.36.17	0.000494
S	884	S884F	tCt	tTt	1	1	B.1.36.17	0.000494
S	884	S884del	TCT	---	1	1	B.1.36.18	0.00042
S	884	S884F	tCt	tTt	1	1	B.1.36.18	0.00042
S	884	S884F	tCt	tTt	1	1	B.1.36.31	0.001751
S	884	S884F	tCt	tTt	1	1	B.1.389	0.001002
S	884	S884C	tCt	tGt	1	1	B.1.391	0.001127
S	884	S884F	tCt	tTt	1	1	B.1.397	0.004854
S	884	S884S	tcT	tcC	1	1	B.1.398	0.002976
S	884	S884F	tCt	tTt	1	1	B.1.400	0.000429
S	884	S884F	tCt	tTt	1	1	B.1.413	0.004255
S	884	S884F	tCt	tTt	1	1	B.1.422	0.000812
S	884	S884F	tCt	tTt	1	1	B.1.426	0.001009
S	884	S884S	tcT	tcC	1	1	B.1.427	0.00005
S	884	S884F	tCt	tTt	1	1	B.1.428	0.00102
S	884	S884A	Tct	Gct	1	1	B.1.429	0.000024
S	884	S884F	tCt	tTt	1	1	B.1.436	0.001029
S	884	S884S	tcT	tcC	1	1	B.1.438.1	0.000107
S	884	S884F	tCt	tTt	1	1	B.1.469	0.00361
S	884	S884F	tCt	tTt	1	1	B.1.471	0.002732
S	884	S884F	tCt	tTt	1	1	B.1.497	0.000315
S	884	S884F	tCt	tTt	1	1	B.1.503	0.002488
S	884	S884F	tCt	tTt	1	1	B.1.524	0.001406
S	884	S884F	tCt	tTt	1	1	B.1.525	0.000113
S	884	S884F	tCt	tTt	1	1	B.1.526	0.000024
S	884	S884F	tCt	tTt	1	1	B.1.532	0.006211
S	884	S884F	tCt	tTt	1	1	B.1.538	0.008065
S	884	S884F	tCt	tTt	1	1	B.1.564.1	0.001577
S	884	S884P	Tct	Cct	1	1	B.1.567	0.003333
S	884	S884F	tCt	tTt	1	1	B.1.575	0.000303
S	884	S884del	TCT	---	1	1	B.1.577	0.000687
S	884	S884S	tcT	tcC	1	1	B.1.596	0.000087
S	884	S884F	tCt	tTt	1	1	B.1.596	0.000087
S	884	S884del2	TCt	--t	1	1	B.1.617.2	0.000004
S	884	S884F	tCt	tTt	1	1	B.1.621	0.000089
S	884	S884S	tcT	tcA	1	1	B.1.627	0.00202
S	884	S884F	tCt	tTt	1	1	B.1.628	0.000352
S	884	S884del	TCT	---	1	1	B.1.630	0.005236
S	884	S884S	tcT	tcA	1	1	B.1.637	0.000073
S	884	S884F	tCt	tTt	1	1	B.4.5	0.011905
S	884	S884S	tcT	tcC	1	1	B.57	0.015152
S	884	S884A	Tct	Gct	1	1	B.6	0.00091
S	884	S884F	tCt	tTt	1	1	B.6	0.00091
S	884	S884F	tCt	tTt	1	1	B.6.3	0.026316
S	884	S884F	tCt	tTt	1	1	C.3	0.007634
S	884	S884F	tCt	tTt	1	1	C.37	0.000116
S	884	S884C	tCt	tGt	1	1	P.1	0.000016
S	884	S884T	Tct	Act	1	1	P.1.1	0.000318
S	884	S884A	Tct	Gct	1	1	P.1.1	0.000318
S	884	S884del	TCT	---	1	1	P.1.10	0.000269
S	884	S884del	TCT	---	1	1	P.1.13	0.000898
S	884	S884del	TCT	---	1	1	Q.1	0.000126
S	884	S884S	TCt	AGt	1	1	Q.3	0.000145
S	884	S884del	TCT	---	1	1	Q.8	0.000165
S	884	S884F	tCt	tTt	1	1	Q.8	0.000165
S	884	S884del	TCT	---	1	1	U.3	0.003861
S	884	S884del	TCT	---	1	1	W.4	0.001351

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.