CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp7 : CodonNum = 71

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/nsp7	71	L71F	L3930F	nonsyn	Ctt	Ttt	15431	15426	0.999676	12053-12055
ORF1ab/nsp7	71	L71F	L3930F	nonsyn	CtT	TtC	15431	5	0.000324023	12053-12055
ORF1ab/nsp7	71	L71L	L3930L	syn	ctT	ctC	889	855	0.961755	12053-12055
ORF1ab/nsp7	71	L71L	L3930L	syn	ctT	ctG	889	28	0.0314961	12053-12055
ORF1ab/nsp7	71	L71L	L3930L	syn	ctT	ctA	889	6	0.00674916	12053-12055
ORF1ab/nsp7	71	L71P	L3930P	nonsyn	cTt	cCt	28	27	0.964286	12053-12055
ORF1ab/nsp7	71	L71P	L3930P	nonsyn	cTT	cCC	28	1	0.0357143	12053-12055
ORF1ab/nsp7	71	L71I	L3930I	nonsyn	Ctt	Att	26	26	1	12053-12055
ORF1ab/nsp7	71	L71V	L3930V	nonsyn	Ctt	Gtt	14	14	1	12053-12055
ORF1ab/nsp7	71	L71del	L3930del	del	CTT	---	12	12	1	12053-12055
ORF1ab/nsp7	71	L71del1	L3930del1	del	cTt	c-t	7	7	1	12053-12055
ORF1ab/nsp7	71	L71del2	L3930del2	del	cTT	c--	2	2	1	12053-12055
ORF1ab/nsp7	71	L71R	L3930R	nonsyn	cTT	cGC	2	1	0.5	12053-12055
ORF1ab/nsp7	71	L71R	L3930R	nonsyn	cTt	cGt	2	1	0.5	12053-12055
ORF1ab/nsp7	71	L71H	L3930H	nonsyn	cTt	cAt	1	1	1	12053-12055
ORF1ab/nsp7	71	L71A	L3930A	nonsyn	CTt	GCt	1	1	1	12053-12055

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/nsp7	71	L71F	Ctt	Ttt	15426	15431	All	0.00295
ORF1ab/nsp7	71	L71F	CtT	TtC	5	15431	All	0.000001
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5327	5327	P.2	0.994214
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2158	2158	B.1.1.28	0.671646
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2007	2007	AY.4	0.003124
ORF1ab/nsp7	71	L71L	ctT	ctC	855	889	All	0.000164
ORF1ab/nsp7	71	L71L	ctT	ctG	28	889	All	0.000005
ORF1ab/nsp7	71	L71L	ctT	ctA	6	889	All	0.000001
ORF1ab/nsp7	71	L71L	ctT	ctC	677	683	B.1.1.7	0.000606
ORF1ab/nsp7	71	L71L	ctT	ctG	6	683	B.1.1.7	0.000005
ORF1ab/nsp7	71	L71F	Ctt	Ttt	621	621	P.3	0.990431
ORF1ab/nsp7	71	L71F	Ctt	Ttt	518	518	AY.39	0.012801
ORF1ab/nsp7	71	L71F	Ctt	Ttt	427	427	B.1.2	0.00376
ORF1ab/nsp7	71	L71F	Ctt	Ttt	318	318	P.6	1
ORF1ab/nsp7	71	L71F	Ctt	Ttt	314	314	B.1.617.2	0.001182
ORF1ab/nsp7	71	L71F	Ctt	Ttt	223	223	P.7	0.973799
ORF1ab/nsp7	71	L71F	Ctt	Ttt	222	222	B.1.1.7	0.000199
ORF1ab/nsp7	71	L71F	Ctt	Ttt	187	187	AY.46.4	0.030762
ORF1ab/nsp7	71	L71F	Ctt	Ttt	185	185	B.1	0.001695
ORF1ab/nsp7	71	L71F	Ctt	Ttt	177	177	B.1.576	0.160471
ORF1ab/nsp7	71	L71F	Ctt	Ttt	175	175	B.1.429	0.004118
ORF1ab/nsp7	71	L71F	Ctt	Ttt	153	153	B.1.617.1	0.019732
ORF1ab/nsp7	71	L71F	Ctt	Ttt	150	150	AY.42	0.006035
ORF1ab/nsp7	71	L71F	Ctt	Ttt	128	128	AY.25	0.00077
ORF1ab/nsp7	71	L71F	Ctt	Ttt	125	125	AY.3	0.001243
ORF1ab/nsp7	71	L71F	Ctt	Ttt	123	123	AY.4.2	0.002668
ORF1ab/nsp7	71	L71F	Ctt	Ttt	115	116	B.1.1	0.002086
ORF1ab/nsp7	71	L71F	CtT	TtC	1	116	B.1.1	0.000018
ORF1ab/nsp7	71	L71F	Ctt	Ttt	112	112	B.1.243	0.007793
ORF1ab/nsp7	71	L71F	Ctt	Ttt	105	105	AY.29	0.001656
ORF1ab/nsp7	71	L71F	Ctt	Ttt	98	98	AY.43	0.000434
ORF1ab/nsp7	71	L71F	Ctt	Ttt	83	83	B.1.177	0.001093
ORF1ab/nsp7	71	L71F	Ctt	Ttt	75	75	B.1.363	0.974026
ORF1ab/nsp7	71	L71F	Ctt	Ttt	66	66	B.1.1.12	0.492537
ORF1ab/nsp7	71	L71F	Ctt	Ttt	47	47	AY.103	0.000292
ORF1ab/nsp7	71	L71F	Ctt	Ttt	47	47	B.1.160	0.001466
ORF1ab/nsp7	71	L71L	ctT	ctC	42	42	AY.119	0.001483
ORF1ab/nsp7	71	L71F	Ctt	Ttt	41	41	AY.100	0.001886
ORF1ab/nsp7	71	L71L	ctT	ctC	39	39	B.1.617.2	0.000147
ORF1ab/nsp7	71	L71F	Ctt	Ttt	38	38	B.1.240	0.008191
ORF1ab/nsp7	71	L71F	Ctt	Ttt	35	35	AY.44	0.000213
ORF1ab/nsp7	71	L71F	Ctt	Ttt	32	32	B.1.1.222	0.006528
ORF1ab/nsp7	71	L71F	Ctt	Ttt	31	31	AY.61	0.003248
ORF1ab/nsp7	71	L71F	Ctt	Ttt	31	31	AY.7	0.006076
ORF1ab/nsp7	71	L71F	Ctt	Ttt	31	31	B.1.1.332	0.96875
ORF1ab/nsp7	71	L71P	cTt	cCt	27	28	All	0.000005
ORF1ab/nsp7	71	L71P	cTT	cCC	1	28	All	0
ORF1ab/nsp7	71	L71F	Ctt	Ttt	28	28	AY.119	0.000989
ORF1ab/nsp7	71	L71F	Ctt	Ttt	27	27	B.1.377	0.123288
ORF1ab/nsp7	71	L71I	Ctt	Att	26	26	All	0.000005
ORF1ab/nsp7	71	L71F	Ctt	Ttt	26	26	B.1.400	0.011154
ORF1ab/nsp7	71	L71F	Ctt	Ttt	25	25	AY.102	0.000663
ORF1ab/nsp7	71	L71F	Ctt	Ttt	24	24	AY.26	0.000679
ORF1ab/nsp7	71	L71F	Ctt	Ttt	23	23	AY.20	0.000894
ORF1ab/nsp7	71	L71F	Ctt	Ttt	23	23	B.1.221	0.001634
ORF1ab/nsp7	71	L71F	Ctt	Ttt	21	21	AY.33	0.001402
ORF1ab/nsp7	71	L71L	ctT	ctC	20	20	AY.43	0.000089
ORF1ab/nsp7	71	L71L	ctT	ctG	16	19	AY.103	0.000099
ORF1ab/nsp7	71	L71L	ctT	ctC	3	19	AY.103	0.000019
ORF1ab/nsp7	71	L71F	Ctt	Ttt	19	19	B.1.1.519	0.000755
ORF1ab/nsp7	71	L71F	Ctt	Ttt	18	18	B.1.241	0.01461
ORF1ab/nsp7	71	L71L	ctT	ctC	16	17	AY.4	0.000025
ORF1ab/nsp7	71	L71L	ctT	ctG	1	17	AY.4	0.000002
ORF1ab/nsp7	71	L71F	Ctt	Ttt	17	17	B.1.1.284	0.001826
ORF1ab/nsp7	71	L71F	Ctt	Ttt	17	17	B.1.406	0.10303
ORF1ab/nsp7	71	L71F	Ctt	Ttt	17	17	B.1.526	0.0004
ORF1ab/nsp7	71	L71F	Ctt	Ttt	17	17	B.1.575	0.005158
ORF1ab/nsp7	71	L71F	Ctt	Ttt	16	16	B.1.298	0.033827
ORF1ab/nsp7	71	L71F	Ctt	Ttt	15	15	AY.121	0.00203
ORF1ab/nsp7	71	L71L	ctT	ctC	9	15	AY.20	0.00035
ORF1ab/nsp7	71	L71L	ctT	ctA	6	15	AY.20	0.000233
ORF1ab/nsp7	71	L71F	Ctt	Ttt	15	15	AY.46.2	0.00953
ORF1ab/nsp7	71	L71F	Ctt	Ttt	15	15	AY.9	0.001014
ORF1ab/nsp7	71	L71F	Ctt	Ttt	15	15	P.1	0.000236
ORF1ab/nsp7	71	L71V	Ctt	Gtt	14	14	All	0.000003
ORF1ab/nsp7	71	L71F	Ctt	Ttt	14	14	AY.98.1	0.000678
ORF1ab/nsp7	71	L71F	Ctt	Ttt	13	13	B.1.1.413	0.089655
ORF1ab/nsp7	71	L71F	Ctt	Ttt	13	13	B.1.36	0.001897
ORF1ab/nsp7	71	L71F	Ctt	Ttt	13	13	B.1.471	0.035519
ORF1ab/nsp7	71	L71F	Ctt	Ttt	13	13	B.1.621	0.001151
ORF1ab/nsp7	71	L71del	CTT	---	12	12	All	0.000002
ORF1ab/nsp7	71	L71F	Ctt	Ttt	12	12	B.1.1.277	0.009105
ORF1ab/nsp7	71	L71F	Ctt	Ttt	12	12	B.1.1.432	0.01519
ORF1ab/nsp7	71	L71F	Ctt	Ttt	12	12	B.1.609	0.005753
ORF1ab/nsp7	71	L71L	ctT	ctC	11	11	AY.116	0.003155
ORF1ab/nsp7	71	L71F	Ctt	Ttt	10	10	B.10	0.082645
ORF1ab/nsp7	71	L71F	Ctt	Ttt	9	9	AY.13	0.001449
ORF1ab/nsp7	71	L71F	Ctt	Ttt	9	9	AY.5	0.000186
ORF1ab/nsp7	71	L71F	Ctt	Ttt	9	9	B.1.36.36	0.005418
ORF1ab/nsp7	71	L71F	Ctt	Ttt	9	9	B.1.427	0.000454
ORF1ab/nsp7	71	L71F	Ctt	Ttt	8	8	AY.23	0.000558
ORF1ab/nsp7	71	L71L	ctT	ctC	8	8	AY.39	0.000198
ORF1ab/nsp7	71	L71F	Ctt	Ttt	8	8	B.1.596	0.000697
ORF1ab/nsp7	71	L71del1	cTt	c-t	7	7	All	0.000001
ORF1ab/nsp7	71	L71I	Ctt	Att	7	7	AY.119	0.000247
ORF1ab/nsp7	71	L71I	Ctt	Att	7	7	AY.27	0.000453
ORF1ab/nsp7	71	L71F	Ctt	Ttt	7	7	AY.75	0.000392
ORF1ab/nsp7	71	L71F	Ctt	Ttt	7	7	B	0.000895
ORF1ab/nsp7	71	L71F	Ctt	Ttt	7	7	B.1.396	0.00494
ORF1ab/nsp7	71	L71F	Ctt	Ttt	7	7	C.37	0.000812
ORF1ab/nsp7	71	L71F	Ctt	Ttt	6	6	AY.104	0.011905
ORF1ab/nsp7	71	L71L	ctT	ctC	6	6	AY.44	0.000037
ORF1ab/nsp7	71	L71F	Ctt	Ttt	6	6	AY.54	0.000572
ORF1ab/nsp7	71	L71F	Ctt	Ttt	6	6	B.1.1.409	0.016997
ORF1ab/nsp7	71	L71F	Ctt	Ttt	6	6	B.1.258	0.000399
ORF1ab/nsp7	71	L71F	Ctt	Ttt	6	6	P.5	0.082192
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5	5	AY.120.1	0.001605
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5	5	AY.46	0.00052
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5	5	B.1.1.311	0.001791
ORF1ab/nsp7	71	L71P	cTt	cCt	4	5	B.1.1.7	0.000004
ORF1ab/nsp7	71	L71P	cTT	cCC	1	5	B.1.1.7	0.000001
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5	5	B.1.351	0.000149
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5	5	B.1.499	0.005252
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5	5	C.36	0.004554
ORF1ab/nsp7	71	L71F	Ctt	Ttt	5	5	P.1.1	0.001588
ORF1ab/nsp7	71	L71F	CtT	TtC	4	4		0.222222
ORF1ab/nsp7	71	L71del	CTT	---	4	4		0.222222
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	AY.118	0.000251
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	AY.3.1	0.000341
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	AY.39.1	0.000158
ORF1ab/nsp7	71	L71I	Ctt	Att	4	4	AY.4	0.000006
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	AY.71	0.0019
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	AY.92	0.001149
ORF1ab/nsp7	71	L71P	cTt	cCt	4	4	B.1	0.000037
ORF1ab/nsp7	71	L71L	ctT	ctC	4	4	B.1.1	0.000073
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	B.1.1.261	0.034483
ORF1ab/nsp7	71	L71L	ctT	ctG	4	4	B.1.2	0.000035
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	B.1.234	0.000528
ORF1ab/nsp7	71	L71F	Ctt	Ttt	4	4	R.1	0.00036
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	AU.2	0.007264
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	AY.113	0.000427
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	AY.117	0.000254
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	AY.30	0.001187
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	AY.47	0.000093
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	AY.6	0.000123
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	AY.62	0.001307
ORF1ab/nsp7	71	L71del	CTT	---	3	3	B.1	0.000027
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.1.33	0.001263
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.1.376	0.017857
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.110.3	0.002155
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.177.81	0.000568
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.36.10	0.014354
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.36.17	0.001482
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.36.29	0.001552
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.362	0.004622
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	B.1.525	0.000339
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	P.1.17	0.000485
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	Q.1	0.000379
ORF1ab/nsp7	71	L71F	Ctt	Ttt	3	3	Q.8	0.000495
ORF1ab/nsp7	71	L71V	Ctt	Gtt	2	2		0.111111
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	A.2.5	0.000998
ORF1ab/nsp7	71	L71del2	cTT	c--	2	2	All	0
ORF1ab/nsp7	71	L71R	cTt	cGt	1	2	All	0
ORF1ab/nsp7	71	L71R	cTT	cGC	1	2	All	0
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.1	0.000791
ORF1ab/nsp7	71	L71L	ctT	ctC	2	2	AY.102	0.000053
ORF1ab/nsp7	71	L71I	Ctt	Att	2	2	AY.103	0.000012
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.105	0.001286
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.120	0.000074
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.120.2	0.002571
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.16.1	0.00094
ORF1ab/nsp7	71	L71P	cTt	cCt	2	2	AY.25	0.000012
ORF1ab/nsp7	71	L71L	ctT	ctC	2	2	AY.3	0.00002
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.36	0.000296
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.5.3	0.000675
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.85	0.000854
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	AY.99.2	0.000184
ORF1ab/nsp7	71	L71del1	cTt	c-t	2	2	B.1	0.000018
ORF1ab/nsp7	71	L71P	cTt	cCt	2	2	B.1.1	0.000036
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.1.1	0.000653
ORF1ab/nsp7	71	L71L	ctT	ctC	2	2	B.1.1.10	0.00223
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.1.220	0.003717
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.1.263	0.003115
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.1.306	0.000877
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.1.318	0.000604
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.1.464	0.002946
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.1.528	0.009615
ORF1ab/nsp7	71	L71del	CTT	---	2	2	B.1.1.7	0.000002
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.157	0.00597
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.177.21	0.000153
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.177.60	0.000437
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.177.87	0.001456
ORF1ab/nsp7	71	L71del1	cTt	c-t	2	2	B.1.264	0.024691
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.311	0.000549
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.36.19	0.018519
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.369	0.00057
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.456	0.006536
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.551	0.002581
ORF1ab/nsp7	71	L71del1	cTt	c-t	2	2	B.1.596	0.000174
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.597	0.009259
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	B.1.602	0.013072
ORF1ab/nsp7	71	L71V	Ctt	Gtt	2	2	B.1.617.2	0.000008
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	C.32	0.046512
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	C.35	0.001548
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	D.2	0.00015
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	L.3	0.007092
ORF1ab/nsp7	71	L71F	Ctt	Ttt	2	2	P.1.9	0.009615
ORF1ab/nsp7	71	L71A	CTt	GCt	1	1		0.055556
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1		0.055556
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	A.2	0.000662
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	A.2.2	0.001689
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	AA.2	0.007692
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AD.1	0.004115
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AD.2	0.000219
ORF1ab/nsp7	71	L71A	CTt	GCt	1	1	All	0
ORF1ab/nsp7	71	L71H	cTt	cAt	1	1	All	0
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.101	0.00049
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	AY.102	0.000027
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	AY.103	0.000006
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.108	0.001103
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.109	0.00074
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.110	0.000113
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.114	0.000231
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	AY.119	0.000035
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	AY.12	0.000316
ORF1ab/nsp7	71	L71I	Ctt	Att	1	1	AY.120	0.000037
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.120.2.1	0.000498
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	AY.13	0.000161
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	AY.14	0.000088
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.16	0.00038
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.18	0.010101
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.19	0.00114
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.27	0.000065
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.29.1	0.000221
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	AY.3	0.00001
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	AY.3	0.00001
ORF1ab/nsp7	71	L71del	CTT	---	1	1	AY.3	0.00001
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.34	0.000097
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.34.1	0.00051
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	AY.39.1	0.00004
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	AY.4	0.000002
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.4.5	0.000107
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	AY.42	0.00004
ORF1ab/nsp7	71	L71del	CTT	---	1	1	AY.43	0.000004
ORF1ab/nsp7	71	L71del2	cTT	c--	1	1	AY.44	0.000006
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	AY.44	0.000006
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	AY.44	0.000006
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.45	0.000122
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	AY.45	0.000122
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	AY.46	0.000104
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.49	0.003195
ORF1ab/nsp7	71	L71I	Ctt	Att	1	1	AY.5	0.000021
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.5.4	0.000277
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.52	0.000814
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.56	0.001605
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	AY.62	0.000436
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.63	0.000387
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.67	0.000464
ORF1ab/nsp7	71	L71R	cTT	cGC	1	1	AY.67	0.000464
ORF1ab/nsp7	71	L71H	cTt	cAt	1	1	AY.69	0.000187
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.7.2	0.000559
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.75.1	0.00018
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.79	0.001211
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.9.1	0.000084
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.9.2	0.000037
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	AY.9.2	0.000037
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AY.94	0.000443
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	AY.98	0.000079
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	AZ.2	0.000821
ORF1ab/nsp7	71	L71I	Ctt	Att	1	1	B.1	0.000009
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	B.1	0.000009
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.122	0.045455
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.128	0.007092
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.161	0.003534
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.170	0.001247
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.198	0.001468
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.208	0.012195
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.216	0.00089
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	B.1.1.25	0.000569
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.269	0.001353
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	B.1.1.28	0.000311
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.299	0.012195
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.317	0.000412
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	B.1.1.33	0.000421
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.362	0.005618
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	B.1.1.369	0.000446
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	B.1.1.369	0.000446
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.37	0.000193
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.371	0.010417
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.434	0.000349
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.44	0.00241
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.448	0.002033
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.463	0.0625
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.523	0.001563
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.524	0.020833
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.63	0.000386
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.1.98	0.018519
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.111	0.001175
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.146	0.004237
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.151	0.011111
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.161	0.017241
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	B.1.177	0.000013
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	B.1.177	0.000013
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.177.19	0.001431
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.177.4	0.000211
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.177.52	0.001757
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.177.55	0.002331
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.177.57	0.000281
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.177.73	0.000566
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.192	0.009259
ORF1ab/nsp7	71	L71I	Ctt	Att	1	1	B.1.2	0.000009
ORF1ab/nsp7	71	L71del2	cTT	c--	1	1	B.1.2	0.000009
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.214	0.003663
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.214.2	0.0006
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.23	0.006061
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.232	0.000537
ORF1ab/nsp7	71	L71V	Ctt	Gtt	1	1	B.1.243	0.00007
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.258.11	0.000396
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.258.17	0.000104
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.265	0.001271
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	B.1.311	0.000275
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.320	0.001245
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.324	0.001605
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.341	0.022727
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.356	0.001727
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	B.1.36	0.000146
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	B.1.36.1	0.00114
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.36.18	0.00042
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.36.26	0.002857
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	B.1.36.29	0.000517
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.36.39	0.002217
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.36.8	0.001
ORF1ab/nsp7	71	L71I	Ctt	Att	1	1	B.1.371	0.001122
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.375	0.00082
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	B.1.396	0.000706
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.407	0.035714
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.416	0.001269
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.428	0.00102
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	B.1.429	0.000024
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.438.1	0.000107
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	B.1.438.1	0.000107
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.474	0.001901
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.499.1	0.111111
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.509	0.000866
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.540	0.009709
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.544	0.006024
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.545	0.014493
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.577	0.000687
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.582	0.000491
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	B.1.582	0.000491
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.595	0.000261
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.595.1	0.005848
ORF1ab/nsp7	71	L71P	cTt	cCt	1	1	B.1.617.1	0.000129
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.618	0.004032
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.620	0.000946
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.621.1	0.000506
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.623	0.000536
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.625	0.002353
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.627	0.00202
ORF1ab/nsp7	71	L71del1	cTt	c-t	1	1	B.1.637	0.000073
ORF1ab/nsp7	71	L71L	ctT	ctG	1	1	B.1.637	0.000073
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.637	0.000073
ORF1ab/nsp7	71	L71R	cTt	cGt	1	1	B.1.637	0.000073
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.78	0.008547
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.1.93	0.000934
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.31	0.003731
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	B.6	0.00091
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	C.1	0.002392
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	C.17	0.055556
ORF1ab/nsp7	71	L71I	Ctt	Att	1	1	C.36	0.000911
ORF1ab/nsp7	71	L71del	CTT	---	1	1	N.4	0.004255
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	N.9	0.005952
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	P.1.12	0.000484
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	P.1.15	0.000232
ORF1ab/nsp7	71	L71L	ctT	ctC	1	1	Q.1	0.000126
ORF1ab/nsp7	71	L71F	Ctt	Ttt	1	1	Q.2	0.000613

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.