CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp9 : CodonNum = 46

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
ORF1ab/nsp9	46	S46S	S4186S	syn	tcC	tcT	5744	5395	0.939241	12821-12823
ORF1ab/nsp9	46	S46S	S4186S	syn	tcC	tcA	5744	329	0.0572772	12821-12823
ORF1ab/nsp9	46	S46S	S4186S	syn	tcC	tcG	5744	20	0.00348189	12821-12823
ORF1ab/nsp9	46	S46A	S4186A	nonsyn	Tcc	Gcc	102	102	1	12821-12823
ORF1ab/nsp9	46	S46del	S4186del	del	TCC	---	36	36	1	12821-12823
ORF1ab/nsp9	46	S46F	S4186F	nonsyn	tCc	tTc	21	21	1	12821-12823
ORF1ab/nsp9	46	S46P	S4186P	nonsyn	Tcc	Ccc	9	9	1	12821-12823
ORF1ab/nsp9	46	S46T	S4186T	nonsyn	Tcc	Acc	5	5	1	12821-12823
ORF1ab/nsp9	46	S46Y	S4186Y	nonsyn	tCc	tAc	4	4	1	12821-12823
ORF1ab/nsp9	46	S46del1	S4186del1	del	tCc	t-c	2	2	1	12821-12823
ORF1ab/nsp9	46	S46C	S4186C	nonsyn	tCc	tGc	2	2	1	12821-12823

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
ORF1ab/nsp9	46	S46S	tcC	tcT	5395	5744	All	0.001032
ORF1ab/nsp9	46	S46S	tcC	tcA	329	5744	All	0.000063
ORF1ab/nsp9	46	S46S	tcC	tcG	20	5744	All	0.000004
ORF1ab/nsp9	46	S46S	tcC	tcT	1874	1904	AY.4	0.002917
ORF1ab/nsp9	46	S46S	tcC	tcA	30	1904	AY.4	0.000047
ORF1ab/nsp9	46	S46S	tcC	tcT	608	608	B.1.1.189	0.919818
ORF1ab/nsp9	46	S46S	tcC	tcT	385	394	P.1	0.006065
ORF1ab/nsp9	46	S46S	tcC	tcA	9	394	P.1	0.000142
ORF1ab/nsp9	46	S46S	tcC	tcT	275	326	B.1.1.7	0.000246
ORF1ab/nsp9	46	S46S	tcC	tcA	51	326	B.1.1.7	0.000046
ORF1ab/nsp9	46	S46S	tcC	tcT	246	246	AY.9.2	0.009035
ORF1ab/nsp9	46	S46S	tcC	tcT	234	234	B.1.351.2	0.070802
ORF1ab/nsp9	46	S46S	tcC	tcT	199	219	B.1.2	0.001752
ORF1ab/nsp9	46	S46S	tcC	tcG	19	219	B.1.2	0.000167
ORF1ab/nsp9	46	S46S	tcC	tcA	1	219	B.1.2	0.000009
ORF1ab/nsp9	46	S46S	tcC	tcT	154	172	B.1.617.2	0.00058
ORF1ab/nsp9	46	S46S	tcC	tcA	18	172	B.1.617.2	0.000068
ORF1ab/nsp9	46	S46S	tcC	tcA	166	166	AY.2	0.059117
ORF1ab/nsp9	46	S46S	tcC	tcT	135	137	AY.43	0.000598
ORF1ab/nsp9	46	S46S	tcC	tcA	1	137	AY.43	0.000004
ORF1ab/nsp9	46	S46S	tcC	tcG	1	137	AY.43	0.000004
ORF1ab/nsp9	46	S46S	tcC	tcT	126	126	AT.1	0.646154
ORF1ab/nsp9	46	S46A	Tcc	Gcc	102	102	All	0.00002
ORF1ab/nsp9	46	S46S	tcC	tcT	64	64	Q.7	0.071111
ORF1ab/nsp9	46	S46S	tcC	tcT	62	62	B.1.177	0.000816
ORF1ab/nsp9	46	S46S	tcC	tcT	58	59	B.1.1	0.001052
ORF1ab/nsp9	46	S46S	tcC	tcA	1	59	B.1.1	0.000018
ORF1ab/nsp9	46	S46S	tcC	tcT	57	58	AY.44	0.000347
ORF1ab/nsp9	46	S46S	tcC	tcA	1	58	AY.44	0.000006
ORF1ab/nsp9	46	S46A	Tcc	Gcc	56	56	AY.54	0.005339
ORF1ab/nsp9	46	S46S	tcC	tcT	54	54	B.1	0.000495
ORF1ab/nsp9	46	S46S	tcC	tcT	45	45	B.1.526	0.001058
ORF1ab/nsp9	46	S46S	tcC	tcT	40	40	B.1.429	0.000941
ORF1ab/nsp9	46	S46S	tcC	tcT	26	38	AY.25	0.000156
ORF1ab/nsp9	46	S46S	tcC	tcA	12	38	AY.25	0.000072
ORF1ab/nsp9	46	S46del	TCC	---	36	36	All	0.000007
ORF1ab/nsp9	46	S46S	tcC	tcT	33	33	AY.39	0.000815
ORF1ab/nsp9	46	S46S	tcC	tcT	33	33	B.1.160	0.001029
ORF1ab/nsp9	46	S46S	tcC	tcT	32	32	B.1.258.17	0.003327
ORF1ab/nsp9	46	S46S	tcC	tcT	27	29	AY.3	0.000269
ORF1ab/nsp9	46	S46S	tcC	tcA	2	29	AY.3	0.00002
ORF1ab/nsp9	46	S46S	tcC	tcT	25	28	AY.102	0.000663
ORF1ab/nsp9	46	S46S	tcC	tcA	3	28	AY.102	0.00008
ORF1ab/nsp9	46	S46S	tcC	tcT	28	28	AY.46.6	0.002022
ORF1ab/nsp9	46	S46S	tcC	tcT	28	28	B.1.396	0.01976
ORF1ab/nsp9	46	S46S	tcC	tcT	24	25	AY.47	0.000747
ORF1ab/nsp9	46	S46S	tcC	tcA	1	25	AY.47	0.000031
ORF1ab/nsp9	46	S46F	tCc	tTc	21	21	All	0.000004
ORF1ab/nsp9	46	S46S	tcC	tcT	21	21	AY.103	0.00013
ORF1ab/nsp9	46	S46S	tcC	tcT	18	19	AY.26	0.00051
ORF1ab/nsp9	46	S46S	tcC	tcA	1	19	AY.26	0.000028
ORF1ab/nsp9	46	S46S	tcC	tcT	19	19	AY.4.2	0.000412
ORF1ab/nsp9	46	S46S	tcC	tcT	14	14	AY.46.2	0.008895
ORF1ab/nsp9	46	S46S	tcC	tcT	13	13	AY.27	0.000841
ORF1ab/nsp9	46	S46S	tcC	tcT	13	13	B.1.254	0.325
ORF1ab/nsp9	46	S46A	Tcc	Gcc	12	12	AY.43	0.000053
ORF1ab/nsp9	46	S46del	TCC	---	12	12	B.1.1.7	0.000011
ORF1ab/nsp9	46	S46S	tcC	tcT	12	12	B.1.369	0.003423
ORF1ab/nsp9	46	S46S	tcC	tcT	11	11	AY.119	0.000388
ORF1ab/nsp9	46	S46S	tcC	tcT	11	11	AY.42	0.000443
ORF1ab/nsp9	46	S46S	tcC	tcT	11	11	B.1.337	0.061453
ORF1ab/nsp9	46	S46P	Tcc	Ccc	9	9	All	0.000002
ORF1ab/nsp9	46	S46S	tcC	tcT	8	9	B	0.001022
ORF1ab/nsp9	46	S46S	tcC	tcA	1	9	B	0.000128
ORF1ab/nsp9	46	S46S	tcC	tcT	9	9	B.50	1
ORF1ab/nsp9	46	S46S	tcC	tcT	9	9	P.1.14	0.00043
ORF1ab/nsp9	46	S46S	tcC	tcT	8	8	AY.45	0.000973
ORF1ab/nsp9	46	S46S	tcC	tcT	8	8	B.1.36.1	0.009122
ORF1ab/nsp9	46	S46S	tcC	tcT	7	7	AY.120	0.00026
ORF1ab/nsp9	46	S46S	tcC	tcT	7	7	AY.30	0.00277
ORF1ab/nsp9	46	S46S	tcC	tcT	7	7	AY.39.1	0.000277
ORF1ab/nsp9	46	S46S	tcC	tcT	7	7	AY.4.4	0.002864
ORF1ab/nsp9	46	S46S	tcC	tcT	7	7	B.1.177.81	0.001325
ORF1ab/nsp9	46	S46S	tcC	tcT	6	7	B.1.596	0.000523
ORF1ab/nsp9	46	S46S	tcC	tcA	1	7	B.1.596	0.000087
ORF1ab/nsp9	46	S46S	tcC	tcT	4	7	C.37	0.000464
ORF1ab/nsp9	46	S46S	tcC	tcA	3	7	C.37	0.000348
ORF1ab/nsp9	46	S46S	tcC	tcA	5	6	AY.117	0.000423
ORF1ab/nsp9	46	S46S	tcC	tcT	1	6	AY.117	0.000085
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	AY.20	0.000233
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	AY.23	0.000418
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	AY.33	0.000401
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	AY.5	0.000124
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	AY.75	0.000336
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	B.1.1.198	0.008811
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	B.1.1.306	0.00263
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	B.1.1.326	0.010563
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	B.1.1.519	0.000238
ORF1ab/nsp9	46	S46A	Tcc	Gcc	6	6	B.1.177	0.000079
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	B.1.177.52	0.010545
ORF1ab/nsp9	46	S46S	tcC	tcT	6	6	B.1.609	0.002876
ORF1ab/nsp9	46	S46A	Tcc	Gcc	6	6	B.1.627	0.012121
ORF1ab/nsp9	46	S46T	Tcc	Acc	5	5	All	0.000001
ORF1ab/nsp9	46	S46S	tcC	tcT	4	5	AY.100	0.000184
ORF1ab/nsp9	46	S46S	tcC	tcA	1	5	AY.100	0.000046
ORF1ab/nsp9	46	S46S	tcC	tcT	5	5	AY.28	0.009452
ORF1ab/nsp9	46	S46S	tcC	tcT	5	5	AY.34	0.000485
ORF1ab/nsp9	46	S46S	tcC	tcT	5	5	AY.99.2	0.000461
ORF1ab/nsp9	46	S46A	Tcc	Gcc	5	5	B.1.1.7	0.000004
ORF1ab/nsp9	46	S46S	tcC	tcT	5	5	B.1.177.21	0.000382
ORF1ab/nsp9	46	S46S	tcC	tcT	4	5	B.1.351	0.000119
ORF1ab/nsp9	46	S46S	tcC	tcA	1	5	B.1.351	0.00003
ORF1ab/nsp9	46	S46S	tcC	tcT	5	5	B.1.362	0.007704
ORF1ab/nsp9	46	S46S	tcC	tcT	5	5	P.1.13	0.004492
ORF1ab/nsp9	46	S46S	tcC	tcT	5	5	P.1.15	0.001162
ORF1ab/nsp9	46	S46Y	tCc	tAc	4	4	All	0.000001
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	AY.118	0.000251
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	AY.29	0.000063
ORF1ab/nsp9	46	S46S	tcC	tcA	4	4	AY.37	0.001264
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	AY.4.2.1	0.000596
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	AY.97	0.006803
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	AZ.2	0.003284
ORF1ab/nsp9	46	S46F	tCc	tTc	4	4	B.1.1.7	0.000004
ORF1ab/nsp9	46	S46T	Tcc	Acc	4	4	B.1.409	0.003125
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	B.1.565	0.003241
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	B.1.576	0.003626
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	D.2	0.0003
ORF1ab/nsp9	46	S46S	tcC	tcT	4	4	P.2	0.000747
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	AY.106	0.001005
ORF1ab/nsp9	46	S46S	tcC	tcA	3	3	AY.116.1	0.000934
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	AY.3.1	0.000256
ORF1ab/nsp9	46	S46A	Tcc	Gcc	3	3	AY.4	0.000005
ORF1ab/nsp9	46	S46A	Tcc	Gcc	3	3	AY.44	0.000018
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	AY.6	0.000123
ORF1ab/nsp9	46	S46S	tcC	tcA	3	3	AY.71	0.001425
ORF1ab/nsp9	46	S46F	tCc	tTc	3	3	B.1	0.000027
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.1.312	0.005736
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.1.318	0.000905
ORF1ab/nsp9	46	S46A	Tcc	Gcc	3	3	B.1.1.63	0.001157
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.177.12	0.000455
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.177.44	0.001557
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.177.77	0.002179
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.258	0.0002
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.427	0.000151
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.575	0.00091
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	B.1.617.1	0.000387
ORF1ab/nsp9	46	S46P	Tcc	Ccc	3	3	D.2	0.000225
ORF1ab/nsp9	46	S46S	tcC	tcT	3	3	N.4	0.012766
ORF1ab/nsp9	46	S46C	tCc	tGc	2	2	All	0
ORF1ab/nsp9	46	S46del1	tCc	t-c	2	2	All	0
ORF1ab/nsp9	46	S46S	tcC	tcA	1	2	AY.10	0.00053
ORF1ab/nsp9	46	S46S	tcC	tcT	1	2	AY.10	0.00053
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.113	0.000285
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.114	0.000462
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.116	0.000574
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.14	0.000176
ORF1ab/nsp9	46	S46del	TCC	---	2	2	AY.4	0.000003
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.4.5	0.000215
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.59	0.001059
ORF1ab/nsp9	46	S46S	tcC	tcA	1	2	AY.75.1	0.00018
ORF1ab/nsp9	46	S46S	tcC	tcT	1	2	AY.75.1	0.00018
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.82	0.002714
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.85	0.000854
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AY.92	0.000575
ORF1ab/nsp9	46	S46A	Tcc	Gcc	2	2	AY.99.2	0.000184
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	AZ.1	0.001735
ORF1ab/nsp9	46	S46F	tCc	tTc	2	2	B	0.000256
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	B.1.1.28	0.000622
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	B.1.1.416	0.00181
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	B.1.1.512	0.057143
ORF1ab/nsp9	46	S46P	Tcc	Ccc	2	2	B.1.1.7	0.000002
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	B.1.177.35	0.001382
ORF1ab/nsp9	46	S46P	Tcc	Ccc	2	2	B.1.2	0.000018
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	B.1.243	0.000139
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	B.1.36.33	0.015152
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	B.1.628	0.000705
ORF1ab/nsp9	46	S46S	tcC	tcA	2	2	B.6.6	0.001778
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	P.1.12	0.000968
ORF1ab/nsp9	46	S46S	tcC	tcT	2	2	P.3	0.00319
ORF1ab/nsp9	46	S46Y	tCc	tAc	1	1	A	0.000387
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	A.27	0.001656
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AE.8	0.000489
ORF1ab/nsp9	46	S46S	tcC	tcA	1	1	AY.1	0.000396
ORF1ab/nsp9	46	S46A	Tcc	Gcc	1	1	AY.103	0.000006
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.108	0.001103
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.111	0.000183
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.12	0.000316
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	AY.120	0.000037
ORF1ab/nsp9	46	S46C	tCc	tGc	1	1	AY.120.1	0.000321
ORF1ab/nsp9	46	S46S	tcC	tcA	1	1	AY.121	0.000135
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.13	0.000161
ORF1ab/nsp9	46	S46S	tcC	tcA	1	1	AY.23.1	0.000417
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.24	0.000431
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.32	0.000532
ORF1ab/nsp9	46	S46del	TCC	---	1	1	AY.34	0.000097
ORF1ab/nsp9	46	S46C	tCc	tGc	1	1	AY.4	0.000002
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	AY.4	0.000002
ORF1ab/nsp9	46	S46A	Tcc	Gcc	1	1	AY.4.2	0.000022
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.4.3	0.000842
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.40	0.000964
ORF1ab/nsp9	46	S46del	TCC	---	1	1	AY.43	0.000004
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	AY.44	0.000006
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.46.4	0.000165
ORF1ab/nsp9	46	S46S	tcC	tcA	1	1	AY.46.5	0.000198
ORF1ab/nsp9	46	S46del	TCC	---	1	1	AY.5.3	0.000337
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.5.3	0.000337
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.5.4	0.000277
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.51	0.000909
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.52	0.000814
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.57	0.000656
ORF1ab/nsp9	46	S46A	Tcc	Gcc	1	1	AY.61	0.000105
ORF1ab/nsp9	46	S46S	tcC	tcA	1	1	AY.62	0.000436
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.63	0.000387
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.67	0.000464
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.7	0.000196
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.7.1	0.000113
ORF1ab/nsp9	46	S46del	TCC	---	1	1	AY.72	0.001361
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.74	0.000116
ORF1ab/nsp9	46	S46del	TCC	---	1	1	AY.75.1	0.00018
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.84	0.000437
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.88	0.000884
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.9.1	0.000084
ORF1ab/nsp9	46	S46A	Tcc	Gcc	1	1	AY.9.2	0.000037
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	AY.98.1	0.000048
ORF1ab/nsp9	46	S46P	Tcc	Ccc	1	1	B.1	0.000009
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1	0.000009
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.1	0.000018
ORF1ab/nsp9	46	S46Y	tCc	tAc	1	1	B.1.1.1	0.000327
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.1.1	0.000327
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.1	0.000327
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.170	0.001247
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.204	0.00304
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.207	0.001182
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.1.28	0.000311
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.298	0.000862
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.1.301	0.001179
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.305	0.003861
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.33	0.000421
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.39	0.00051
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.40	0.034483
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.1.432	0.001266
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.1.519	0.00004
ORF1ab/nsp9	46	S46Y	tCc	tAc	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	46	S46T	Tcc	Acc	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.104	0.00369
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.110.3	0.000718
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.111	0.001175
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.126	0.001276
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.139	0.000733
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.162	0.005025
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.177	0.000013
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.177	0.000013
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.177.6	0.000977
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.177.60	0.000218
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.177.60	0.000218
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.177.7	0.000165
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.177.7	0.000165
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.177.73	0.000566
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.177.81	0.000189
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.2	0.000009
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.22	0.001318
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.221	0.000071
ORF1ab/nsp9	46	S46P	Tcc	Ccc	1	1	B.1.234	0.000132
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.234	0.000132
ORF1ab/nsp9	46	S46S	tcC	tcA	1	1	B.1.258.11	0.000396
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.258.16	0.001637
ORF1ab/nsp9	46	S46A	Tcc	Gcc	1	1	B.1.258.17	0.000104
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.258.3	0.001675
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.260	0.003344
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.311	0.000275
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.311	0.000275
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.340	0.004292
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.351.3	0.000876
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.351.5	0.0006
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.36.29	0.000517
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.36.36	0.000602
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.370	0.008
ORF1ab/nsp9	46	S46A	Tcc	Gcc	1	1	B.1.438.1	0.000107
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.521	0.004975
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.525	0.000113
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.564	0.000426
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.577	0.000687
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.595	0.000261
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.597	0.00463
ORF1ab/nsp9	46	S46del1	tCc	t-c	1	1	B.1.617.1	0.000129
ORF1ab/nsp9	46	S46del	TCC	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp9	46	S46del1	tCc	t-c	1	1	B.1.617.2	0.000004
ORF1ab/nsp9	46	S46F	tCc	tTc	1	1	B.1.621	0.000089
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	B.1.621.1	0.000506
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	C.14	0.004329
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	C.33	0.058824
ORF1ab/nsp9	46	S46del	TCC	---	1	1	D.2	0.000075
ORF1ab/nsp9	46	S46del	TCC	---	1	1	N.4	0.004255
ORF1ab/nsp9	46	S46Y	tCc	tAc	1	1	P.1.15	0.000232
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	P.1.17	0.000162
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	P.1.7	0.000319
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	Q.1	0.000126
ORF1ab/nsp9	46	S46S	tcC	tcT	1	1	Q.3	0.000145
ORF1ab/nsp9	46	S46del	TCC	---	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.