CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp1 : CodonNum = 109

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/nsp1	109	P109P	P109P	syn	ccT	ccC	3536	2362	0.667986	590-592
ORF1ab/nsp1	109	P109P	P109P	syn	ccT	ccA	3536	1119	0.316459	590-592
ORF1ab/nsp1	109	P109P	P109P	syn	ccT	ccG	3536	55	0.0155543	590-592
ORF1ab/nsp1	109	P109S	P109S	nonsyn	Cct	Tct	422	422	1	590-592
ORF1ab/nsp1	109	P109H	P109H	nonsyn	cCt	cAt	212	212	1	590-592
ORF1ab/nsp1	109	P109L	P109L	nonsyn	cCt	cTt	65	64	0.984615	590-592
ORF1ab/nsp1	109	P109L	P109L	nonsyn	cCT	cTC	65	1	0.0153846	590-592
ORF1ab/nsp1	109	P109del	P109del	del	CCT	---	59	59	1	590-592
ORF1ab/nsp1	109	P109T	P109T	nonsyn	Cct	Act	19	19	1	590-592
ORF1ab/nsp1	109	P109R	P109R	nonsyn	cCt	cGt	4	4	1	590-592
ORF1ab/nsp1	109	P109del1	P109del1	del	ccT	cc-	3	3	1	590-592
ORF1ab/nsp1	109	P109V	P109V	nonsyn	CCt	GTt	3	3	1	590-592
ORF1ab/nsp1	109	P109C	P109C	nonsyn	CCt	TGt	3	2	0.666667	590-592
ORF1ab/nsp1	109	P109C	P109C	nonsyn	CCT	TGC	3	1	0.333333	590-592
ORF1ab/nsp1	109	P109A	P109A	nonsyn	Cct	Gct	2	2	1	590-592
ORF1ab/nsp1	109	P109del2	P109del2	del	CCt	--t	1	1	1	590-592

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/nsp1	109	P109P	ccT	ccC	2362	3536	All	0.000452
ORF1ab/nsp1	109	P109P	ccT	ccA	1119	3536	All	0.000214
ORF1ab/nsp1	109	P109P	ccT	ccG	55	3536	All	0.000011
ORF1ab/nsp1	109	P109P	ccT	ccC	1197	1197	P.1	0.018858
ORF1ab/nsp1	109	P109P	ccT	ccA	1032	1040	AY.3	0.010265
ORF1ab/nsp1	109	P109P	ccT	ccC	6	1040	AY.3	0.00006
ORF1ab/nsp1	109	P109P	ccT	ccG	2	1040	AY.3	0.00002
ORF1ab/nsp1	109	P109S	Cct	Tct	422	422	All	0.000081
ORF1ab/nsp1	109	P109H	cCt	cAt	212	212	All	0.000041
ORF1ab/nsp1	109	P109P	ccT	ccC	209	209	P.1.8	1
ORF1ab/nsp1	109	P109S	Cct	Tct	206	206	AY.4	0.000321
ORF1ab/nsp1	109	P109P	ccT	ccC	202	202	P.1.9	0.971154
ORF1ab/nsp1	109	P109H	cCt	cAt	180	180	AY.4	0.00028
ORF1ab/nsp1	109	P109P	ccT	ccC	152	160	B.1.1.7	0.000136
ORF1ab/nsp1	109	P109P	ccT	ccA	6	160	B.1.1.7	0.000005
ORF1ab/nsp1	109	P109P	ccT	ccG	2	160	B.1.1.7	0.000002
ORF1ab/nsp1	109	P109P	ccT	ccC	152	152	AY.101	0.074546
ORF1ab/nsp1	109	P109L	cCt	cTt	64	65	All	0.000012
ORF1ab/nsp1	109	P109L	cCT	cTC	1	65	All	0
ORF1ab/nsp1	109	P109del	CCT	---	59	59	All	0.000011
ORF1ab/nsp1	109	P109P	ccT	ccC	30	56	B.1.617.2	0.000113
ORF1ab/nsp1	109	P109P	ccT	ccA	25	56	B.1.617.2	0.000094
ORF1ab/nsp1	109	P109P	ccT	ccG	1	56	B.1.617.2	0.000004
ORF1ab/nsp1	109	P109P	ccT	ccC	39	53	AY.43	0.000173
ORF1ab/nsp1	109	P109P	ccT	ccA	14	53	AY.43	0.000062
ORF1ab/nsp1	109	P109P	ccT	ccC	48	51	AY.4	0.000075
ORF1ab/nsp1	109	P109P	ccT	ccG	3	51	AY.4	0.000005
ORF1ab/nsp1	109	P109P	ccT	ccG	26	39	AY.44	0.000158
ORF1ab/nsp1	109	P109P	ccT	ccC	9	39	AY.44	0.000055
ORF1ab/nsp1	109	P109P	ccT	ccA	4	39	AY.44	0.000024
ORF1ab/nsp1	109	P109P	ccT	ccC	32	32	B.1.280	0.228571
ORF1ab/nsp1	109	P109P	ccT	ccC	29	30	AY.25	0.000174
ORF1ab/nsp1	109	P109P	ccT	ccA	1	30	AY.25	0.000006
ORF1ab/nsp1	109	P109L	cCt	cTt	23	23	AY.4	0.000036
ORF1ab/nsp1	109	P109P	ccT	ccC	16	22	B.1.2	0.000141
ORF1ab/nsp1	109	P109P	ccT	ccA	4	22	B.1.2	0.000035
ORF1ab/nsp1	109	P109P	ccT	ccG	2	22	B.1.2	0.000018
ORF1ab/nsp1	109	P109T	Cct	Act	19	19	All	0.000004
ORF1ab/nsp1	109	P109P	ccT	ccC	12	19	AY.103	0.000075
ORF1ab/nsp1	109	P109P	ccT	ccG	5	19	AY.103	0.000031
ORF1ab/nsp1	109	P109P	ccT	ccA	2	19	AY.103	0.000012
ORF1ab/nsp1	109	P109S	Cct	Tct	18	18	B.1.1.7	0.000016
ORF1ab/nsp1	109	P109S	Cct	Tct	18	18	B.1.497	0.005666
ORF1ab/nsp1	109	P109P	ccT	ccC	18	18	P.1.12	0.008712
ORF1ab/nsp1	109	P109P	ccT	ccC	17	17	B.1.177.12	0.002579
ORF1ab/nsp1	109	P109S	Cct	Tct	16	16	AY.5	0.00033
ORF1ab/nsp1	109	P109S	Cct	Tct	15	15	B.1.621	0.001328
ORF1ab/nsp1	109	P109S	Cct	Tct	14	14	AY.44	0.000085
ORF1ab/nsp1	109	P109P	ccT	ccC	14	14	B.1.110.3	0.010057
ORF1ab/nsp1	109	P109S	Cct	Tct	12	12	AY.3	0.000119
ORF1ab/nsp1	109	P109P	ccT	ccC	10	11	B.1.1	0.000181
ORF1ab/nsp1	109	P109P	ccT	ccA	1	11	B.1.1	0.000018
ORF1ab/nsp1	109	P109S	Cct	Tct	10	10	AY.43	0.000044
ORF1ab/nsp1	109	P109P	ccT	ccC	8	9	B.1	0.000073
ORF1ab/nsp1	109	P109P	ccT	ccA	1	9	B.1	0.000009
ORF1ab/nsp1	109	P109P	ccT	ccC	9	9	B.1.429	0.000212
ORF1ab/nsp1	109	P109P	ccT	ccC	8	8	AY.100	0.000368
ORF1ab/nsp1	109	P109H	cCt	cAt	8	8	AY.47	0.000249
ORF1ab/nsp1	109	P109P	ccT	ccC	8	8	B.1.1.301	0.009434
ORF1ab/nsp1	109	P109P	ccT	ccC	5	8	B.1.177	0.000066
ORF1ab/nsp1	109	P109P	ccT	ccG	2	8	B.1.177	0.000026
ORF1ab/nsp1	109	P109P	ccT	ccA	1	8	B.1.177	0.000013
ORF1ab/nsp1	109	P109S	Cct	Tct	8	8	B.1.617.2	0.00003
ORF1ab/nsp1	109	P109P	ccT	ccC	8	8	B.3	0.006645
ORF1ab/nsp1	109	P109P	ccT	ccC	4	7	AY.118	0.000251
ORF1ab/nsp1	109	P109P	ccT	ccG	3	7	AY.118	0.000188
ORF1ab/nsp1	109	P109S	Cct	Tct	7	7	AY.25	0.000042
ORF1ab/nsp1	109	P109S	Cct	Tct	7	7	AY.4.5	0.000752
ORF1ab/nsp1	109	P109P	ccT	ccC	6	7	AY.5.3	0.002024
ORF1ab/nsp1	109	P109P	ccT	ccA	1	7	AY.5.3	0.000337
ORF1ab/nsp1	109	P109S	Cct	Tct	7	7	B.1.177.32	0.009447
ORF1ab/nsp1	109	P109P	ccT	ccA	4	7	B.1.637	0.000292
ORF1ab/nsp1	109	P109P	ccT	ccC	3	7	B.1.637	0.000219
ORF1ab/nsp1	109	P109S	Cct	Tct	6	6	AY.75	0.000336
ORF1ab/nsp1	109	P109P	ccT	ccC	6	6	B.1.1.303	0.016575
ORF1ab/nsp1	109	P109del	CCT	---	6	6	B.1.1.7	0.000005
ORF1ab/nsp1	109	P109S	Cct	Tct	6	6	B.1.177	0.000079
ORF1ab/nsp1	109	P109L	cCt	cTt	5	5	B.1.1.7	0.000004
ORF1ab/nsp1	109	P109P	ccT	ccC	5	5	P.1.14	0.000239
ORF1ab/nsp1	109	P109R	cCt	cGt	4	4	All	0.000001
ORF1ab/nsp1	109	P109P	ccT	ccC	3	4	AY.102	0.00008
ORF1ab/nsp1	109	P109P	ccT	ccA	1	4	AY.102	0.000027
ORF1ab/nsp1	109	P109P	ccT	ccC	4	4	AY.119	0.000141
ORF1ab/nsp1	109	P109P	ccT	ccC	4	4	AY.20	0.000155
ORF1ab/nsp1	109	P109P	ccT	ccC	4	4	AY.27	0.000259
ORF1ab/nsp1	109	P109S	Cct	Tct	4	4	AY.39	0.000099
ORF1ab/nsp1	109	P109P	ccT	ccA	3	4	AY.39	0.000074
ORF1ab/nsp1	109	P109P	ccT	ccC	1	4	AY.39	0.000025
ORF1ab/nsp1	109	P109del	CCT	---	4	4	AY.4	0.000006
ORF1ab/nsp1	109	P109L	cCt	cTt	4	4	AY.44	0.000024
ORF1ab/nsp1	109	P109P	ccT	ccA	3	4	AY.5	0.000062
ORF1ab/nsp1	109	P109P	ccT	ccC	1	4	AY.5	0.000021
ORF1ab/nsp1	109	P109S	Cct	Tct	4	4	B.1	0.000037
ORF1ab/nsp1	109	P109S	Cct	Tct	4	4	B.1.1	0.000073
ORF1ab/nsp1	109	P109del	CCT	---	4	4	B.1.1.33	0.001684
ORF1ab/nsp1	109	P109del	CCT	---	4	4	B.1.1.348	0.003185
ORF1ab/nsp1	109	P109H	cCt	cAt	4	4	B.1.177	0.000053
ORF1ab/nsp1	109	P109P	ccT	ccC	4	4	B.1.210	0.008529
ORF1ab/nsp1	109	P109L	cCt	cTt	4	4	B.1.617.2	0.000015
ORF1ab/nsp1	109	P109P	ccT	ccC	4	4	P.1.13	0.003594
ORF1ab/nsp1	109	P109del1	ccT	cc-	3	3	All	0.000001
ORF1ab/nsp1	109	P109V	CCt	GTt	3	3	All	0.000001
ORF1ab/nsp1	109	P109C	CCt	TGt	2	3	All	0
ORF1ab/nsp1	109	P109C	CCT	TGC	1	3	All	0
ORF1ab/nsp1	109	P109P	ccT	ccA	3	3	AY.114	0.000693
ORF1ab/nsp1	109	P109T	Cct	Act	3	3	AY.12	0.000948
ORF1ab/nsp1	109	P109P	ccT	ccA	2	3	AY.23	0.000139
ORF1ab/nsp1	109	P109P	ccT	ccC	1	3	AY.23	0.00007
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	AY.26	0.000085
ORF1ab/nsp1	109	P109del	CCT	---	3	3	AY.43	0.000013
ORF1ab/nsp1	109	P109P	ccT	ccC	2	3	AY.45	0.000243
ORF1ab/nsp1	109	P109P	ccT	ccA	1	3	AY.45	0.000122
ORF1ab/nsp1	109	P109S	Cct	Tct	3	3	AY.46	0.000312
ORF1ab/nsp1	109	P109P	ccT	ccC	2	3	AY.46	0.000208
ORF1ab/nsp1	109	P109P	ccT	ccA	1	3	AY.46	0.000104
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	AY.46.2	0.001906
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	AY.6	0.000123
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	AY.65	0.001599
ORF1ab/nsp1	109	P109L	cCt	cTt	2	3	B.1.1	0.000036
ORF1ab/nsp1	109	P109L	cCT	cTC	1	3	B.1.1	0.000018
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	B.1.160	0.000094
ORF1ab/nsp1	109	P109del	CCT	---	3	3	B.1.177.4	0.000633
ORF1ab/nsp1	109	P109S	Cct	Tct	3	3	B.1.177.52	0.005272
ORF1ab/nsp1	109	P109S	Cct	Tct	3	3	B.1.177.72	0.010169
ORF1ab/nsp1	109	P109del	CCT	---	3	3	B.1.2	0.000026
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	B.1.427	0.000151
ORF1ab/nsp1	109	P109S	Cct	Tct	3	3	B.1.443	0.014019
ORF1ab/nsp1	109	P109P	ccT	ccC	2	3	B.1.526	0.000047
ORF1ab/nsp1	109	P109P	ccT	ccG	1	3	B.1.526	0.000024
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	B.1.575	0.00091
ORF1ab/nsp1	109	P109P	ccT	ccG	2	3	B.1.621	0.000177
ORF1ab/nsp1	109	P109P	ccT	ccC	1	3	B.1.621	0.000089
ORF1ab/nsp1	109	P109P	ccT	ccC	3	3	P.1.16	0.001122
ORF1ab/nsp1	109	P109V	CCt	GTt	2	2		0.111111
ORF1ab/nsp1	109	P109L	cCt	cTt	2	2		0.111111
ORF1ab/nsp1	109	P109C	CCt	TGt	2	2		0.111111
ORF1ab/nsp1	109	P109A	Cct	Gct	2	2	All	0
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	AY.102	0.000053
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	AY.103	0.000012
ORF1ab/nsp1	109	P109P	ccT	ccC	2	2	AY.24	0.000862
ORF1ab/nsp1	109	P109del	CCT	---	2	2	AY.25	0.000012
ORF1ab/nsp1	109	P109L	cCt	cTt	2	2	AY.25	0.000012
ORF1ab/nsp1	109	P109T	Cct	Act	2	2	AY.3	0.00002
ORF1ab/nsp1	109	P109P	ccT	ccG	2	2	AY.30	0.000791
ORF1ab/nsp1	109	P109L	cCt	cTt	2	2	AY.39	0.000049
ORF1ab/nsp1	109	P109T	Cct	Act	2	2	AY.4	0.000003
ORF1ab/nsp1	109	P109P	ccT	ccC	2	2	AY.4.2	0.000043
ORF1ab/nsp1	109	P109L	cCt	cTt	2	2	AY.43	0.000009
ORF1ab/nsp1	109	P109H	cCt	cAt	2	2	AY.44	0.000012
ORF1ab/nsp1	109	P109P	ccT	ccC	2	2	AY.50	0.001599
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	AY.7.1	0.000225
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	AY.9.1	0.000167
ORF1ab/nsp1	109	P109P	ccT	ccC	2	2	AZ.3	0.00304
ORF1ab/nsp1	109	P109H	cCt	cAt	2	2	B.1	0.000018
ORF1ab/nsp1	109	P109A	Cct	Gct	2	2	B.1.1.7	0.000002
ORF1ab/nsp1	109	P109del	CCT	---	2	2	B.1.177.54	0.001213
ORF1ab/nsp1	109	P109P	ccT	ccC	2	2	B.1.177.7	0.00033
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	B.1.177.85	0.01087
ORF1ab/nsp1	109	P109H	cCt	cAt	2	2	B.1.2	0.000018
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	B.1.2	0.000018
ORF1ab/nsp1	109	P109P	ccT	ccC	2	2	B.1.258	0.000133
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	B.1.351	0.000059
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	B.1.367	0.001585
ORF1ab/nsp1	109	P109L	cCt	cTt	2	2	B.1.595	0.000522
ORF1ab/nsp1	109	P109P	ccT	ccC	1	2	B.1.596	0.000087
ORF1ab/nsp1	109	P109P	ccT	ccG	1	2	B.1.596	0.000087
ORF1ab/nsp1	109	P109T	Cct	Act	2	2	B.1.617.2	0.000008
ORF1ab/nsp1	109	P109P	ccT	ccC	1	2	C.37	0.000116
ORF1ab/nsp1	109	P109P	ccT	ccA	1	2	C.37	0.000116
ORF1ab/nsp1	109	P109L	cCt	cTt	2	2	D.2	0.00015
ORF1ab/nsp1	109	P109del	CCT	---	2	2	N.4	0.008511
ORF1ab/nsp1	109	P109del	CCT	---	2	2	N.6	0.014184
ORF1ab/nsp1	109	P109P	ccT	ccC	2	2	P.1.1	0.000635
ORF1ab/nsp1	109	P109S	Cct	Tct	2	2	P.1.17	0.000324
ORF1ab/nsp1	109	P109del	CCT	---	2	2	P.2	0.000373
ORF1ab/nsp1	109	P109P	ccT	ccG	1	1		0.055556
ORF1ab/nsp1	109	P109del	CCT	---	1	1	A	0.000387
ORF1ab/nsp1	109	P109del2	CCt	--t	1	1	All	0
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.100	0.000046
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.103	0.000006
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.105	0.000643
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.106	0.000335
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.106	0.000335
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.114	0.000231
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.116	0.000287
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	AY.117	0.000085
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.117	0.000085
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.119	0.000035
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.12	0.000316
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.120	0.000037
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	AY.13	0.000161
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.16	0.00038
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.20	0.000039
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.23	0.00007
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.24	0.000431
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.25	0.000006
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.26	0.000028
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.27	0.000065
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.29	0.000016
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.29	0.000016
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.3	0.00001
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.33	0.000067
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	AY.33	0.000067
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.34	0.000097
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.38	0.000499
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.39	0.000025
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.39.1	0.00004
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.39.1	0.00004
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	AY.39.2	0.001541
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.4.2	0.000022
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.4.3	0.000842
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.4.5	0.000107
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.4.5	0.000107
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.41	0.000294
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.42	0.00004
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	AY.42	0.00004
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.43	0.000004
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.43	0.000004
ORF1ab/nsp1	109	P109del1	ccT	cc-	1	1	AY.44	0.000006
ORF1ab/nsp1	109	P109R	cCt	cGt	1	1	AY.44	0.000006
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.46.5	0.000198
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.47	0.000031
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.47	0.000031
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.5	0.000021
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.5.3	0.000337
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.52	0.000814
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.54	0.000095
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.54	0.000095
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	AY.56	0.001605
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.64	0.000595
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.65	0.000533
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	AY.7	0.000196
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.7.1	0.000113
ORF1ab/nsp1	109	P109del1	ccT	cc-	1	1	AY.79	0.001211
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.9	0.000068
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.9	0.000068
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.9.1	0.000084
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.9.1	0.000084
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.9.2	0.000037
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	AY.90	0.000684
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.92	0.000287
ORF1ab/nsp1	109	P109del	CCT	---	1	1	AY.95	0.000761
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	AY.96	0.002075
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.98	0.000079
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	AY.98.1	0.000048
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	AY.99	0.001049
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1	0.000009
ORF1ab/nsp1	109	P109R	cCt	cGt	1	1	B.1	0.000009
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.1	0.000018
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.1.170	0.001247
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.1.198	0.001468
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.1.294	0.001266
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.1.298	0.000862
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	B.1.1.306	0.000438
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.1.409	0.002833
ORF1ab/nsp1	109	P109P	ccT	ccA	1	1	B.1.1.50	0.000679
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.1.50	0.000679
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.1.519	0.00004
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	B.1.1.519	0.00004
ORF1ab/nsp1	109	P109V	CCt	GTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp1	109	P109del2	CCt	--t	1	1	B.1.1.7	0.000001
ORF1ab/nsp1	109	P109R	cCt	cGt	1	1	B.1.1.7	0.000001
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	B.1.1.70	0.000341
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.160	0.000031
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.160.16	0.000929
ORF1ab/nsp1	109	P109R	cCt	cGt	1	1	B.1.177	0.000013
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.177.12	0.000152
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	B.1.177.12	0.000152
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.177.21	0.000076
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.177.33	0.001645
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.177.33	0.001645
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.177.44	0.000519
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.179	0.003759
ORF1ab/nsp1	109	P109del1	ccT	cc-	1	1	B.1.2	0.000009
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	B.1.2	0.000009
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	B.1.2	0.000009
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.206	0.000816
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.211	0.025
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.243	0.00007
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.258	0.000067
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.258	0.000067
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.311	0.000275
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.340	0.004292
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.351	0.00003
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.351	0.00003
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.36	0.000146
ORF1ab/nsp1	109	P109T	Cct	Act	1	1	B.1.36.29	0.000517
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.401	0.008197
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.411	0.003704
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.427	0.00005
ORF1ab/nsp1	109	P109del	CCT	---	1	1	B.1.429	0.000024
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.1.582	0.000491
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.582	0.000491
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	B.1.596	0.000087
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	B.1.596	0.000087
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.597	0.00463
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	B.1.617.1	0.000129
ORF1ab/nsp1	109	P109C	CCT	TGC	1	1	B.1.617.2	0.000004
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	B.60	0.015873
ORF1ab/nsp1	109	P109del	CCT	---	1	1	C.17	0.055556
ORF1ab/nsp1	109	P109del	CCT	---	1	1	C.35	0.000774
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	C.37.1	0.002618
ORF1ab/nsp1	109	P109P	ccT	ccG	1	1	D.2	0.000075
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	P.1	0.000016
ORF1ab/nsp1	109	P109L	cCt	cTt	1	1	P.1	0.000016
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	P.1.12	0.000484
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	P.1.15	0.000232
ORF1ab/nsp1	109	P109P	ccT	ccG	1	1	P.1.17	0.000162
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	P.1.7	0.000319
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	P.2	0.000187
ORF1ab/nsp1	109	P109H	cCt	cAt	1	1	Q.7	0.001111
ORF1ab/nsp1	109	P109P	ccT	ccC	1	1	Q.8	0.000165
ORF1ab/nsp1	109	P109S	Cct	Tct	1	1	R.1	0.00009

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.