CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 689

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/nsp3	689	L689F	L1507F	nonsyn	Ctt	Ttt	10481	10481	1	4784-4786
ORF1ab/nsp3	689	L689I	L1507I	nonsyn	Ctt	Att	311	311	1	4784-4786
ORF1ab/nsp3	689	L689L	L1507L	syn	ctT	ctC	307	207	0.674267	4784-4786
ORF1ab/nsp3	689	L689L	L1507L	syn	ctT	ctA	307	56	0.18241	4784-4786
ORF1ab/nsp3	689	L689L	L1507L	syn	ctT	ctG	307	43	0.140065	4784-4786
ORF1ab/nsp3	689	L689L	L1507L	syn	CtT	TtA	307	1	0.00325733	4784-4786
ORF1ab/nsp3	689	L689del	L1507del	del	CTT	---	83	83	1	4784-4786
ORF1ab/nsp3	689	L689V	L1507V	nonsyn	Ctt	Gtt	9	9	1	4784-4786
ORF1ab/nsp3	689	L689P	L1507P	nonsyn	cTt	cCt	7	7	1	4784-4786
ORF1ab/nsp3	689	L689H	L1507H	nonsyn	cTt	cAt	5	5	1	4784-4786
ORF1ab/nsp3	689	L689R	L1507R	nonsyn	cTt	cGt	4	3	0.75	4784-4786
ORF1ab/nsp3	689	L689R	L1507R	nonsyn	cTT	cGA	4	1	0.25	4784-4786
ORF1ab/nsp3	689	L689del1	L1507del1	del	Ctt	-tt	2	1	0.5	4784-4786
ORF1ab/nsp3	689	L689del1	L1507del1	del	cTt	c-t	2	1	0.5	4784-4786
ORF1ab/nsp3	689	L689G	L1507G	nonsyn	CTt	GGt	1	1	1	4784-4786
ORF1ab/nsp3	689	L689Y	L1507Y	nonsyn	CTt	TAt	1	1	1	4784-4786
ORF1ab/nsp3	689	L689A	L1507A	nonsyn	CTt	GCt	1	1	1	4784-4786
ORF1ab/nsp3	689	L689C	L1507C	nonsyn	CTt	TGt	1	1	1	4784-4786
ORF1ab/nsp3	689	L689X	L1507X	nonsyn	CTT	TGA	1	1	1	4784-4786
ORF1ab/nsp3	689	L689S	L1507S	nonsyn	CTt	TCt	1	1	1	4784-4786

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/nsp3	689	L689F	Ctt	Ttt	10481	10481	All	0.002005
ORF1ab/nsp3	689	L689F	Ctt	Ttt	7681	7681	B.1.1.7	0.006876
ORF1ab/nsp3	689	L689F	Ctt	Ttt	386	386	AY.4	0.000601
ORF1ab/nsp3	689	L689I	Ctt	Att	311	311	All	0.000059
ORF1ab/nsp3	689	L689L	ctT	ctC	207	307	All	0.00004
ORF1ab/nsp3	689	L689L	ctT	ctA	56	307	All	0.000011
ORF1ab/nsp3	689	L689L	ctT	ctG	43	307	All	0.000008
ORF1ab/nsp3	689	L689L	CtT	TtA	1	307	All	0
ORF1ab/nsp3	689	L689F	Ctt	Ttt	226	226	B.1.177.21	0.017282
ORF1ab/nsp3	689	L689I	Ctt	Att	216	216	AY.39.1	0.008556
ORF1ab/nsp3	689	L689F	Ctt	Ttt	158	158	B.1.617.2	0.000595
ORF1ab/nsp3	689	L689F	Ctt	Ttt	142	142	AY.25	0.000854
ORF1ab/nsp3	689	L689F	Ctt	Ttt	141	141	AY.103	0.000875
ORF1ab/nsp3	689	L689F	Ctt	Ttt	115	115	AY.3	0.001144
ORF1ab/nsp3	689	L689L	ctT	ctC	100	108	B.1.1.7	0.00009
ORF1ab/nsp3	689	L689L	ctT	ctA	7	108	B.1.1.7	0.000006
ORF1ab/nsp3	689	L689L	ctT	ctG	1	108	B.1.1.7	0.000001
ORF1ab/nsp3	689	L689F	Ctt	Ttt	94	94	AY.43	0.000416
ORF1ab/nsp3	689	L689F	Ctt	Ttt	87	87	AY.29	0.001372
ORF1ab/nsp3	689	L689F	Ctt	Ttt	87	87	B.1.160	0.002713
ORF1ab/nsp3	689	L689del	CTT	---	83	83	All	0.000016
ORF1ab/nsp3	689	L689F	Ctt	Ttt	69	69	B.1.177	0.000909
ORF1ab/nsp3	689	L689F	Ctt	Ttt	66	66	B.1.2	0.000581
ORF1ab/nsp3	689	L689F	Ctt	Ttt	55	55	B.1.596	0.004793
ORF1ab/nsp3	689	L689F	Ctt	Ttt	53	53	AY.44	0.000323
ORF1ab/nsp3	689	L689F	Ctt	Ttt	42	42	B.1.561	0.016673
ORF1ab/nsp3	689	L689F	Ctt	Ttt	40	40	P.1	0.00063
ORF1ab/nsp3	689	L689L	ctT	ctG	34	38	B.1.177	0.000448
ORF1ab/nsp3	689	L689L	ctT	ctA	4	38	B.1.177	0.000053
ORF1ab/nsp3	689	L689F	Ctt	Ttt	32	32	B.1	0.000293
ORF1ab/nsp3	689	L689F	Ctt	Ttt	32	32	B.1.1	0.000581
ORF1ab/nsp3	689	L689F	Ctt	Ttt	32	32	B.1.351	0.000951
ORF1ab/nsp3	689	L689F	Ctt	Ttt	32	32	B.1.526	0.000752
ORF1ab/nsp3	689	L689F	Ctt	Ttt	32	32	C.36	0.029144
ORF1ab/nsp3	689	L689F	Ctt	Ttt	31	31	AY.102	0.000822
ORF1ab/nsp3	689	L689I	Ctt	Att	29	29	AY.100	0.001334
ORF1ab/nsp3	689	L689F	Ctt	Ttt	29	29	B.1.177.60	0.006335
ORF1ab/nsp3	689	L689F	Ctt	Ttt	27	27	AY.33	0.001803
ORF1ab/nsp3	689	L689F	Ctt	Ttt	27	27	B.1.177.86	0.004953
ORF1ab/nsp3	689	L689L	ctT	ctC	23	26	AY.4	0.000036
ORF1ab/nsp3	689	L689L	ctT	ctA	3	26	AY.4	0.000005
ORF1ab/nsp3	689	L689I	Ctt	Att	26	26	B.1.617.2	0.000098
ORF1ab/nsp3	689	L689F	Ctt	Ttt	24	24	AY.20	0.000933
ORF1ab/nsp3	689	L689F	Ctt	Ttt	21	21	AY.46.6	0.001516
ORF1ab/nsp3	689	L689F	Ctt	Ttt	21	21	AY.47	0.000653
ORF1ab/nsp3	689	L689del	CTT	---	21	21	B.1.1.7	0.000019
ORF1ab/nsp3	689	L689F	Ctt	Ttt	19	19	AY.26	0.000538
ORF1ab/nsp3	689	L689F	Ctt	Ttt	19	19	B.1.429	0.000447
ORF1ab/nsp3	689	L689F	Ctt	Ttt	18	18	AY.75	0.001008
ORF1ab/nsp3	689	L689F	Ctt	Ttt	18	18	AY.98.1	0.000872
ORF1ab/nsp3	689	L689F	Ctt	Ttt	17	17	AY.120	0.000632
ORF1ab/nsp3	689	L689F	Ctt	Ttt	17	17	C.37	0.001973
ORF1ab/nsp3	689	L689F	Ctt	Ttt	16	16	AY.100	0.000736
ORF1ab/nsp3	689	L689F	Ctt	Ttt	16	16	AY.39	0.000395
ORF1ab/nsp3	689	L689F	Ctt	Ttt	16	16	AY.99.2	0.001475
ORF1ab/nsp3	689	L689L	ctT	ctA	15	15	B.1.627	0.030303
ORF1ab/nsp3	689	L689F	Ctt	Ttt	14	14	AY.119	0.000494
ORF1ab/nsp3	689	L689F	Ctt	Ttt	14	14	AY.42	0.000563
ORF1ab/nsp3	689	L689F	Ctt	Ttt	14	14	B.1.234	0.001847
ORF1ab/nsp3	689	L689F	Ctt	Ttt	14	14	B.1.632	0.09396
ORF1ab/nsp3	689	L689F	Ctt	Ttt	14	14	B.4.8	1
ORF1ab/nsp3	689	L689F	Ctt	Ttt	13	13	AY.4.2	0.000282
ORF1ab/nsp3	689	L689F	Ctt	Ttt	13	13	B.1.243	0.000905
ORF1ab/nsp3	689	L689F	Ctt	Ttt	13	13	B.1.577	0.008935
ORF1ab/nsp3	689	L689F	Ctt	Ttt	12	12	AY.109	0.008876
ORF1ab/nsp3	689	L689L	ctT	ctC	12	12	AY.25	0.000072
ORF1ab/nsp3	689	L689F	Ctt	Ttt	12	12	R.1	0.00108
ORF1ab/nsp3	689	L689F	Ctt	Ttt	11	11	AY.39.1	0.000436
ORF1ab/nsp3	689	L689F	Ctt	Ttt	11	11	AY.98	0.000869
ORF1ab/nsp3	689	L689F	Ctt	Ttt	10	10	B.1.36	0.001459
ORF1ab/nsp3	689	L689V	Ctt	Gtt	9	9	All	0.000002
ORF1ab/nsp3	689	L689F	Ctt	Ttt	9	9	AY.6	0.00037
ORF1ab/nsp3	689	L689F	Ctt	Ttt	9	9	B.1.427	0.000454
ORF1ab/nsp3	689	L689F	Ctt	Ttt	8	8	AY.23	0.000558
ORF1ab/nsp3	689	L689F	Ctt	Ttt	8	8	AY.62	0.003486
ORF1ab/nsp3	689	L689F	Ctt	Ttt	8	8	B.1.1.50	0.005431
ORF1ab/nsp3	689	L689F	Ctt	Ttt	8	8	B.1.1.519	0.000318
ORF1ab/nsp3	689	L689L	ctT	ctC	5	8	B.1.160	0.000156
ORF1ab/nsp3	689	L689L	ctT	ctG	2	8	B.1.160	0.000062
ORF1ab/nsp3	689	L689L	ctT	ctA	1	8	B.1.160	0.000031
ORF1ab/nsp3	689	L689F	Ctt	Ttt	8	8	B.1.369	0.002282
ORF1ab/nsp3	689	L689P	cTt	cCt	7	7	All	0.000001
ORF1ab/nsp3	689	L689L	ctT	ctC	7	7	AY.117	0.000592
ORF1ab/nsp3	689	L689F	Ctt	Ttt	7	7	B.1.1.176	0.003076
ORF1ab/nsp3	689	L689F	Ctt	Ttt	7	7	B.1.177.81	0.001325
ORF1ab/nsp3	689	L689L	ctT	ctC	7	7	B.1.36	0.001021
ORF1ab/nsp3	689	L689F	Ctt	Ttt	7	7	P.1.14	0.000335
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	AY.116	0.001721
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	AY.37	0.001896
ORF1ab/nsp3	689	L689del	CTT	---	6	6	AY.4	0.000009
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	AY.5	0.000124
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	AY.9.2	0.00022
ORF1ab/nsp3	689	L689L	ctT	ctA	3	6	B.1	0.000027
ORF1ab/nsp3	689	L689L	ctT	ctC	2	6	B.1	0.000018
ORF1ab/nsp3	689	L689L	CtT	TtA	1	6	B.1	0.000009
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	B.1.1.214	0.000333
ORF1ab/nsp3	689	L689L	ctT	ctC	6	6	B.1.1.277	0.004552
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	B.1.609	0.002876
ORF1ab/nsp3	689	L689L	ctT	ctC	4	6	B.1.617.2	0.000015
ORF1ab/nsp3	689	L689L	ctT	ctA	1	6	B.1.617.2	0.000004
ORF1ab/nsp3	689	L689L	ctT	ctG	1	6	B.1.617.2	0.000004
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	B.1.637	0.000438
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	D.2	0.00045
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	Q.1	0.000758
ORF1ab/nsp3	689	L689F	Ctt	Ttt	6	6	Q.8	0.000989
ORF1ab/nsp3	689	L689H	cTt	cAt	5	5	All	0.000001
ORF1ab/nsp3	689	L689L	ctT	ctC	5	5	AY.24	0.002155
ORF1ab/nsp3	689	L689L	ctT	ctC	5	5	AY.47	0.000156
ORF1ab/nsp3	689	L689F	Ctt	Ttt	5	5	AY.9	0.000338
ORF1ab/nsp3	689	L689F	Ctt	Ttt	5	5	B.1.177.56	0.003338
ORF1ab/nsp3	689	L689F	Ctt	Ttt	5	5	B.1.177.7	0.000824
ORF1ab/nsp3	689	L689F	Ctt	Ttt	5	5	B.1.396	0.003529
ORF1ab/nsp3	689	L689I	Ctt	Att	5	5	B.1.400	0.002145
ORF1ab/nsp3	689	L689del	CTT	---	5	5	B.1.617.2	0.000019
ORF1ab/nsp3	689	L689del	CTT	---	4	4		0.222222
ORF1ab/nsp3	689	L689R	cTt	cGt	3	4	All	0.000001
ORF1ab/nsp3	689	L689R	cTT	cGA	1	4	All	0
ORF1ab/nsp3	689	L689I	Ctt	Att	4	4	AY.103	0.000025
ORF1ab/nsp3	689	L689F	Ctt	Ttt	4	4	AY.113	0.00057
ORF1ab/nsp3	689	L689F	Ctt	Ttt	4	4	AY.41	0.001176
ORF1ab/nsp3	689	L689F	Ctt	Ttt	4	4	AY.7	0.000784
ORF1ab/nsp3	689	L689I	Ctt	Att	4	4	B.1.1.7	0.000004
ORF1ab/nsp3	689	L689F	Ctt	Ttt	4	4	B.1.177.57	0.001124
ORF1ab/nsp3	689	L689F	Ctt	Ttt	4	4	B.1.258	0.000266
ORF1ab/nsp3	689	L689F	Ctt	Ttt	4	4	B.1.564	0.001704
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	A	0.001161
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.117	0.000254
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.118	0.000188
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.3.1	0.000256
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.34	0.000291
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.35	0.000699
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.36	0.000445
ORF1ab/nsp3	689	L689I	Ctt	Att	3	3	AY.39	0.000074
ORF1ab/nsp3	689	L689L	ctT	ctC	2	3	AY.39	0.000049
ORF1ab/nsp3	689	L689L	ctT	ctA	1	3	AY.39	0.000025
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.45	0.000365
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.46	0.000312
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.90	0.002053
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	AY.93	0.000819
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B	0.000383
ORF1ab/nsp3	689	L689del	CTT	---	3	3	B.1	0.000027
ORF1ab/nsp3	689	L689L	ctT	ctC	3	3	B.1.1.189	0.004539
ORF1ab/nsp3	689	L689L	ctT	ctC	3	3	B.1.1.519	0.000119
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.110.3	0.002155
ORF1ab/nsp3	689	L689V	Ctt	Gtt	3	3	B.1.160	0.000094
ORF1ab/nsp3	689	L689L	ctT	ctA	3	3	B.1.177.4	0.000633
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.177.4	0.000633
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.177.40	0.015464
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.177.79	0.007026
ORF1ab/nsp3	689	L689I	Ctt	Att	3	3	B.1.2	0.000026
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.221	0.000213
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.36.8	0.003
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.426	0.003027
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.470	0.004213
ORF1ab/nsp3	689	L689F	Ctt	Ttt	3	3	B.1.595	0.000783
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	A.2.5.2	0.003145
ORF1ab/nsp3	689	L689I	Ctt	Att	2	2	A.29	0.010638
ORF1ab/nsp3	689	L689del1	Ctt	-tt	1	2	All	0
ORF1ab/nsp3	689	L689del1	cTt	c-t	1	2	All	0
ORF1ab/nsp3	689	L689L	ctT	ctC	2	2	AY.103	0.000012
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.106	0.00067
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.110	0.000225
ORF1ab/nsp3	689	L689L	ctT	ctA	1	2	AY.120	0.000037
ORF1ab/nsp3	689	L689L	ctT	ctC	1	2	AY.120	0.000037
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.121	0.000271
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.14	0.000176
ORF1ab/nsp3	689	L689I	Ctt	Att	2	2	AY.25	0.000012
ORF1ab/nsp3	689	L689L	ctT	ctA	1	2	AY.26	0.000028
ORF1ab/nsp3	689	L689L	ctT	ctG	1	2	AY.26	0.000028
ORF1ab/nsp3	689	L689L	ctT	ctC	2	2	AY.3	0.00002
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.32	0.001065
ORF1ab/nsp3	689	L689I	Ctt	Att	2	2	AY.4	0.000003
ORF1ab/nsp3	689	L689del	CTT	---	2	2	AY.4.5	0.000215
ORF1ab/nsp3	689	L689I	Ctt	Att	2	2	AY.44	0.000012
ORF1ab/nsp3	689	L689del	CTT	---	2	2	AY.44	0.000012
ORF1ab/nsp3	689	L689L	ctT	ctG	1	2	AY.44	0.000006
ORF1ab/nsp3	689	L689L	ctT	ctA	1	2	AY.44	0.000006
ORF1ab/nsp3	689	L689I	Ctt	Att	2	2	AY.46	0.000208
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.46.5	0.000397
ORF1ab/nsp3	689	L689I	Ctt	Att	2	2	AY.47	0.000062
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.5.4	0.000553
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.63	0.000774
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	AY.91	0.001461
ORF1ab/nsp3	689	L689R	cTT	cGA	1	2	B.1	0.000009
ORF1ab/nsp3	689	L689R	cTt	cGt	1	2	B.1	0.000009
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.1.263	0.003115
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.1.318	0.000604
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.1.420	0.002012
ORF1ab/nsp3	689	L689P	cTt	cCt	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.177.10	0.001756
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.177.23	0.006472
ORF1ab/nsp3	689	L689del	CTT	---	2	2	B.1.177.4	0.000422
ORF1ab/nsp3	689	L689L	ctT	ctC	1	2	B.1.2	0.000009
ORF1ab/nsp3	689	L689L	ctT	ctA	1	2	B.1.2	0.000009
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.206	0.001631
ORF1ab/nsp3	689	L689del	CTT	---	2	2	B.1.36	0.000292
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.517	0.000854
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.525	0.000226
ORF1ab/nsp3	689	L689H	cTt	cAt	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	689	L689del	CTT	---	2	2	B.1.619	0.001742
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	B.1.619.1	0.001283
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	C.35	0.001548
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	C.36.3	0.001134
ORF1ab/nsp3	689	L689del	CTT	---	2	2	P.1	0.000032
ORF1ab/nsp3	689	L689I	Ctt	Att	2	2	P.1	0.000032
ORF1ab/nsp3	689	L689F	Ctt	Ttt	2	2	P.1.15	0.000465
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1		0.055556
ORF1ab/nsp3	689	L689H	cTt	cAt	1	1		0.055556
ORF1ab/nsp3	689	L689Y	CTt	TAt	1	1		0.055556
ORF1ab/nsp3	689	L689I	Ctt	Att	1	1	A	0.000387
ORF1ab/nsp3	689	L689del	CTT	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	A.2.2	0.001689
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	A.2.4	0.003367
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	A.3	0.002096
ORF1ab/nsp3	689	L689Y	CTt	TAt	1	1	All	0
ORF1ab/nsp3	689	L689S	CTt	TCt	1	1	All	0
ORF1ab/nsp3	689	L689A	CTt	GCt	1	1	All	0
ORF1ab/nsp3	689	L689C	CTt	TGt	1	1	All	0
ORF1ab/nsp3	689	L689G	CTt	GGt	1	1	All	0
ORF1ab/nsp3	689	L689X	CTT	TGA	1	1	All	0
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AM.4	0.003571
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AU.3	0.00211
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.1	0.000396
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.101	0.00049
ORF1ab/nsp3	689	L689H	cTt	cAt	1	1	AY.103	0.000006
ORF1ab/nsp3	689	L689P	cTt	cCt	1	1	AY.103	0.000006
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.104	0.001984
ORF1ab/nsp3	689	L689S	CTt	TCt	1	1	AY.113	0.000142
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.114	0.000231
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.12	0.000316
ORF1ab/nsp3	689	L689del	CTT	---	1	1	AY.120	0.000037
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.120.2	0.001285
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	AY.16.1	0.00047
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.19	0.00114
ORF1ab/nsp3	689	L689I	Ctt	Att	1	1	AY.23	0.00007
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.24	0.000431
ORF1ab/nsp3	689	L689del	CTT	---	1	1	AY.25	0.000006
ORF1ab/nsp3	689	L689V	Ctt	Gtt	1	1	AY.26	0.000028
ORF1ab/nsp3	689	L689L	ctT	ctG	1	1	AY.27	0.000065
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.27	0.000065
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.34.1	0.00051
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.38	0.000499
ORF1ab/nsp3	689	L689V	Ctt	Gtt	1	1	AY.4	0.000002
ORF1ab/nsp3	689	L689P	cTt	cCt	1	1	AY.4	0.000002
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	AY.4.2	0.000022
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	689	L689I	Ctt	Att	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.4.3	0.000842
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.4.4	0.000409
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.4.5	0.000107
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.40	0.000964
ORF1ab/nsp3	689	L689A	CTt	GCt	1	1	AY.43	0.000004
ORF1ab/nsp3	689	L689del	CTT	---	1	1	AY.43	0.000004
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	AY.43	0.000004
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	AY.46.4	0.000165
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	AY.46.5	0.000198
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.52	0.000814
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	AY.52	0.000814
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	AY.6	0.000041
ORF1ab/nsp3	689	L689del	CTT	---	1	1	AY.66	0.00107
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	AY.68	0.000274
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.68	0.000274
ORF1ab/nsp3	689	L689P	cTt	cCt	1	1	AY.69	0.000187
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.69	0.000187
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.70	0.000209
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	AY.75	0.000056
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.75.1	0.00018
ORF1ab/nsp3	689	L689del	CTT	---	1	1	AY.78	0.001541
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.79	0.001211
ORF1ab/nsp3	689	L689del	CTT	---	1	1	AY.81	0.001992
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	AY.82	0.001357
ORF1ab/nsp3	689	L689I	Ctt	Att	1	1	AY.92	0.000287
ORF1ab/nsp3	689	L689del	CTT	---	1	1	AY.99	0.001049
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	AZ.1	0.000867
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	B	0.000128
ORF1ab/nsp3	689	L689X	CTT	TGA	1	1	B.1	0.000009
ORF1ab/nsp3	689	L689C	CTt	TGt	1	1	B.1	0.000009
ORF1ab/nsp3	689	L689del1	cTt	c-t	1	1	B.1	0.000009
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	B.1.1	0.000018
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.1	0.000018
ORF1ab/nsp3	689	L689V	Ctt	Gtt	1	1	B.1.1	0.000018
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.15	0.013514
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.161	0.003534
ORF1ab/nsp3	689	L689P	cTt	cCt	1	1	B.1.1.189	0.001513
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.27	0.00565
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.277	0.000759
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.322	0.008772
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.369	0.000446
ORF1ab/nsp3	689	L689H	cTt	cAt	1	1	B.1.1.371	0.010417
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.377	0.001381
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.397	0.002252
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.1.419	0.007407
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.487	0.005587
ORF1ab/nsp3	689	L689G	CTt	GGt	1	1	B.1.1.526	0.003546
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.1.54	0.003021
ORF1ab/nsp3	689	L689R	cTt	cGt	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.149	0.003425
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.157	0.002985
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.157	0.002985
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.160.16	0.000929
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.160.7	0.002079
ORF1ab/nsp3	689	L689V	Ctt	Gtt	1	1	B.1.177	0.000013
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.177	0.000013
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.24	0.001295
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.31	0.011494
ORF1ab/nsp3	689	L689L	ctT	ctG	1	1	B.1.177.31	0.011494
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.45	0.000381
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.49	0.037037
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.5	0.001242
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.177.50	0.004695
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	689	L689I	Ctt	Att	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.58	0.001332
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.62	0.001192
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	689	L689I	Ctt	Att	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.75	0.001041
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.8	0.000752
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.177.9	0.001332
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.210	0.002132
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.214.2	0.0006
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.215	0.009615
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.221.4	0.004167
ORF1ab/nsp3	689	L689L	ctT	ctG	1	1	B.1.223	0.002778
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.232	0.000537
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.239	0.001221
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.239	0.001221
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.243	0.00007
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.258.22	0.002667
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.349	0.000715
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.36.22	0.001208
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	B.1.36.36	0.000602
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.36.37	0.002778
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.367	0.000792
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.375	0.00082
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.378	0.006849
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.409	0.000781
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.427	0.00005
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	B.1.429	0.000024
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.436	0.001029
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.456	0.003268
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	689	L689R	cTt	cGt	1	1	B.1.526	0.000024
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.534	0.0125
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.546	0.003704
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.565	0.00081
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.568	0.001111
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.575	0.000303
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.582	0.000491
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	B.1.595	0.000261
ORF1ab/nsp3	689	L689I	Ctt	Att	1	1	B.1.596	0.000087
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.596	0.000087
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.597	0.00463
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.612	0.002653
ORF1ab/nsp3	689	L689V	Ctt	Gtt	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	689	L689P	cTt	cCt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	689	L689V	Ctt	Gtt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.617.3	0.002985
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.1.629	0.013333
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.1.630	0.005236
ORF1ab/nsp3	689	L689del	CTT	---	1	1	B.15	0.017544
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.3.1	0.001658
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.4	0.002208
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	B.4.4	0.018868
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	B.40	0.000364
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	B.40	0.000364
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	C.16	0.00106
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	C.17	0.055556
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	C.23	0.005814
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	C.28	0.04
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	C.3	0.007634
ORF1ab/nsp3	689	L689L	ctT	ctC	1	1	P.1	0.000016
ORF1ab/nsp3	689	L689del1	Ctt	-tt	1	1	P.1.1	0.000318
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	P.1.17	0.000162
ORF1ab/nsp3	689	L689F	Ctt	Ttt	1	1	P.1.2	0.001156
ORF1ab/nsp3	689	L689L	ctT	ctA	1	1	P.1.7	0.000319
ORF1ab/nsp3	689	L689del	CTT	---	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.