CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp10 : CodonNum = 136

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/nsp10	136	P136P	P4389P	syn	ccC	ccT	3166	3071	0.969994	13430-13432
ORF1ab/nsp10	136	P136P	P4389P	syn	ccC	ccA	3166	92	0.0290587	13430-13432
ORF1ab/nsp10	136	P136P	P4389P	syn	ccC	ccG	3166	3	0.000947568	13430-13432
ORF1ab/nsp10	136	P136S	P4389S	nonsyn	Ccc	Tcc	949	949	1	13430-13432
ORF1ab/nsp10	136	P136L	P4389L	nonsyn	cCc	cTc	675	674	0.998519	13430-13432
ORF1ab/nsp10	136	P136L	P4389L	nonsyn	cCC	cTT	675	1	0.00148148	13430-13432
ORF1ab/nsp10	136	P136H	P4389H	nonsyn	cCc	cAc	418	418	1	13430-13432
ORF1ab/nsp10	136	P136T	P4389T	nonsyn	Ccc	Acc	280	280	1	13430-13432
ORF1ab/nsp10	136	P136del	P4389del	del	CCC	---	74	74	1	13430-13432
ORF1ab/nsp10	136	P136I	P4389I	nonsyn	CCc	ATc	3	2	0.666667	13430-13432
ORF1ab/nsp10	136	P136I	P4389I	nonsyn	CCC	ATT	3	1	0.333333	13430-13432
ORF1ab/nsp10	136	P136Q	P4389Q	nonsyn	cCC	cAA	2	2	1	13430-13432
ORF1ab/nsp10	136	P136del2	P4389del2	del	CCc	--c	2	2	1	13430-13432
ORF1ab/nsp10	136	P136A	P4389A	nonsyn	Ccc	Gcc	1	1	1	13430-13432
ORF1ab/nsp10	136	P136V	P4389V	nonsyn	CCc	GTc	1	1	1	13430-13432
ORF1ab/nsp10	136	P136R	P4389R	nonsyn	cCc	cGc	1	1	1	13430-13432

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/nsp10	136	P136P	ccC	ccT	3071	3166	All	0.000587
ORF1ab/nsp10	136	P136P	ccC	ccA	92	3166	All	0.000018
ORF1ab/nsp10	136	P136P	ccC	ccG	3	3166	All	0.000001
ORF1ab/nsp10	136	P136P	ccC	ccT	1754	1769	AY.4	0.00273
ORF1ab/nsp10	136	P136P	ccC	ccA	15	1769	AY.4	0.000023
ORF1ab/nsp10	136	P136S	Ccc	Tcc	949	949	All	0.000182
ORF1ab/nsp10	136	P136L	cCc	cTc	674	675	All	0.000129
ORF1ab/nsp10	136	P136L	cCC	cTT	1	675	All	0
ORF1ab/nsp10	136	P136P	ccC	ccT	448	454	B.1.1.7	0.000401
ORF1ab/nsp10	136	P136P	ccC	ccA	5	454	B.1.1.7	0.000004
ORF1ab/nsp10	136	P136P	ccC	ccG	1	454	B.1.1.7	0.000001
ORF1ab/nsp10	136	P136H	cCc	cAc	418	418	All	0.00008
ORF1ab/nsp10	136	P136T	Ccc	Acc	280	280	All	0.000054
ORF1ab/nsp10	136	P136T	Ccc	Acc	223	223	AY.4.2	0.004837
ORF1ab/nsp10	136	P136S	Ccc	Tcc	196	196	B.1.177	0.002581
ORF1ab/nsp10	136	P136H	cCc	cAc	181	181	B.1.617.2	0.000682
ORF1ab/nsp10	136	P136H	cCc	cAc	138	138	AY.100	0.006349
ORF1ab/nsp10	136	P136P	ccC	ccT	113	113	P.1.12	0.054695
ORF1ab/nsp10	136	P136L	cCc	cTc	104	104	AY.4	0.000162
ORF1ab/nsp10	136	P136P	ccC	ccT	89	97	B.1.617.2	0.000335
ORF1ab/nsp10	136	P136P	ccC	ccA	8	97	B.1.617.2	0.00003
ORF1ab/nsp10	136	P136L	cCc	cTc	92	92	AY.44	0.00056
ORF1ab/nsp10	136	P136P	ccC	ccT	77	88	B.1	0.000705
ORF1ab/nsp10	136	P136P	ccC	ccA	11	88	B.1	0.000101
ORF1ab/nsp10	136	P136S	Ccc	Tcc	78	78	B.1.1	0.001415
ORF1ab/nsp10	136	P136S	Ccc	Tcc	77	77	AY.4	0.00012
ORF1ab/nsp10	136	P136del	CCC	---	74	74	All	0.000014
ORF1ab/nsp10	136	P136S	Ccc	Tcc	71	71	B.1.617.2	0.000267
ORF1ab/nsp10	136	P136L	cCc	cTc	66	66	B.1.617.2	0.000249
ORF1ab/nsp10	136	P136S	Ccc	Tcc	47	47	B.1.1.7	0.000042
ORF1ab/nsp10	136	P136P	ccC	ccT	45	45	AY.3	0.000448
ORF1ab/nsp10	136	P136S	Ccc	Tcc	45	45	B.1.160	0.001403
ORF1ab/nsp10	136	P136P	ccC	ccT	44	44	B.1.1.442	0.814815
ORF1ab/nsp10	136	P136L	cCc	cTc	42	42	B.1.2	0.00037
ORF1ab/nsp10	136	P136P	ccC	ccT	39	39	B.1.526	0.000917
ORF1ab/nsp10	136	P136P	ccC	ccA	23	38	AY.44	0.00014
ORF1ab/nsp10	136	P136P	ccC	ccT	15	38	AY.44	0.000091
ORF1ab/nsp10	136	P136L	cCc	cTc	37	37	AY.25	0.000223
ORF1ab/nsp10	136	P136L	cCc	cTc	37	37	B.1.177	0.000487
ORF1ab/nsp10	136	P136S	Ccc	Tcc	31	31	AY.43	0.000137
ORF1ab/nsp10	136	P136S	Ccc	Tcc	29	29	AY.103	0.00018
ORF1ab/nsp10	136	P136L	cCc	cTc	29	29	AY.3	0.000288
ORF1ab/nsp10	136	P136L	cCc	cTc	28	28	B.1.1	0.000508
ORF1ab/nsp10	136	P136S	Ccc	Tcc	27	27	AY.44	0.000164
ORF1ab/nsp10	136	P136L	cCc	cTc	26	26	B.1	0.000238
ORF1ab/nsp10	136	P136del	CCC	---	25	25	B.1.1.7	0.000022
ORF1ab/nsp10	136	P136S	Ccc	Tcc	24	24	AY.25	0.000144
ORF1ab/nsp10	136	P136P	ccC	ccT	24	24	AY.45	0.00292
ORF1ab/nsp10	136	P136L	cCc	cTc	23	24	B.1.1.7	0.000021
ORF1ab/nsp10	136	P136L	cCC	cTT	1	24	B.1.1.7	0.000001
ORF1ab/nsp10	136	P136P	ccC	ccT	23	23	AY.25	0.000138
ORF1ab/nsp10	136	P136P	ccC	ccT	23	23	B.1.575	0.006978
ORF1ab/nsp10	136	P136T	Ccc	Acc	22	22	AY.4	0.000034
ORF1ab/nsp10	136	P136S	Ccc	Tcc	22	22	B.1.36.22	0.02657
ORF1ab/nsp10	136	P136S	Ccc	Tcc	21	21	B.1	0.000192
ORF1ab/nsp10	136	P136H	cCc	cAc	20	20	B.1.1.7	0.000018
ORF1ab/nsp10	136	P136S	Ccc	Tcc	20	20	B.1.2	0.000176
ORF1ab/nsp10	136	P136P	ccC	ccT	18	19	AY.102	0.000477
ORF1ab/nsp10	136	P136P	ccC	ccA	1	19	AY.102	0.000027
ORF1ab/nsp10	136	P136P	ccC	ccT	18	19	AY.103	0.000112
ORF1ab/nsp10	136	P136P	ccC	ccA	1	19	AY.103	0.000006
ORF1ab/nsp10	136	P136P	ccC	ccT	18	19	AY.43	0.00008
ORF1ab/nsp10	136	P136P	ccC	ccA	1	19	AY.43	0.000004
ORF1ab/nsp10	136	P136L	cCc	cTc	18	18	AY.43	0.00008
ORF1ab/nsp10	136	P136S	Ccc	Tcc	18	18	B.1.177.19	0.025751
ORF1ab/nsp10	136	P136H	cCc	cAc	17	17	AY.26	0.000481
ORF1ab/nsp10	136	P136P	ccC	ccT	17	17	B.1.1.33	0.007155
ORF1ab/nsp10	136	P136P	ccC	ccT	16	17	B.1.177	0.000211
ORF1ab/nsp10	136	P136P	ccC	ccA	1	17	B.1.177	0.000013
ORF1ab/nsp10	136	P136P	ccC	ccT	14	16	B.1.2	0.000123
ORF1ab/nsp10	136	P136P	ccC	ccA	2	16	B.1.2	0.000018
ORF1ab/nsp10	136	P136L	cCc	cTc	15	15	AY.29	0.000237
ORF1ab/nsp10	136	P136S	Ccc	Tcc	15	15	B.1.36	0.002189
ORF1ab/nsp10	136	P136P	ccC	ccT	14	14	B.1.1	0.000254
ORF1ab/nsp10	136	P136S	Ccc	Tcc	14	14	B.1.429	0.000329
ORF1ab/nsp10	136	P136P	ccC	ccT	13	13	AY.39	0.000321
ORF1ab/nsp10	136	P136S	Ccc	Tcc	13	13	P.1	0.000205
ORF1ab/nsp10	136	P136P	ccC	ccT	12	12	B.1.429	0.000282
ORF1ab/nsp10	136	P136L	cCc	cTc	11	11	AY.103	0.000068
ORF1ab/nsp10	136	P136S	Ccc	Tcc	11	11	B	0.001406
ORF1ab/nsp10	136	P136T	Ccc	Acc	11	11	B.1.617.2	0.000041
ORF1ab/nsp10	136	P136S	Ccc	Tcc	9	9	AY.100	0.000414
ORF1ab/nsp10	136	P136P	ccC	ccT	9	9	AY.4.1	0.006637
ORF1ab/nsp10	136	P136P	ccC	ccT	9	9	B.1.1.50	0.00611
ORF1ab/nsp10	136	P136P	ccC	ccT	4	8	AY.42	0.000161
ORF1ab/nsp10	136	P136P	ccC	ccA	4	8	AY.42	0.000161
ORF1ab/nsp10	136	P136L	cCc	cTc	8	8	B.1.1.155	0.571429
ORF1ab/nsp10	136	P136P	ccC	ccT	8	8	B.1.177.81	0.001515
ORF1ab/nsp10	136	P136P	ccC	ccT	8	8	P.2	0.001493
ORF1ab/nsp10	136	P136P	ccC	ccT	7	7	AY.117	0.000592
ORF1ab/nsp10	136	P136P	ccC	ccT	7	7	AY.51	0.006364
ORF1ab/nsp10	136	P136S	Ccc	Tcc	7	7	AY.71	0.003325
ORF1ab/nsp10	136	P136S	Ccc	Tcc	7	7	B.1.1.214	0.000388
ORF1ab/nsp10	136	P136P	ccC	ccT	7	7	B.1.177.51	0.031963
ORF1ab/nsp10	136	P136S	Ccc	Tcc	7	7	B.1.575	0.002124
ORF1ab/nsp10	136	P136S	Ccc	Tcc	6	6	AY.1	0.002374
ORF1ab/nsp10	136	P136L	cCc	cTc	6	6	AY.117	0.000507
ORF1ab/nsp10	136	P136S	Ccc	Tcc	6	6	AY.119	0.000212
ORF1ab/nsp10	136	P136P	ccC	ccT	5	6	AY.23	0.000349
ORF1ab/nsp10	136	P136P	ccC	ccA	1	6	AY.23	0.00007
ORF1ab/nsp10	136	P136L	cCc	cTc	6	6	AY.27	0.000388
ORF1ab/nsp10	136	P136L	cCc	cTc	6	6	AY.84	0.002625
ORF1ab/nsp10	136	P136S	Ccc	Tcc	6	6	AY.89	0.029412
ORF1ab/nsp10	136	P136del	CCC	---	6	6	B.1	0.000055
ORF1ab/nsp10	136	P136P	ccC	ccT	6	6	B.1.111	0.007051
ORF1ab/nsp10	136	P136P	ccC	ccT	6	6	B.1.36	0.000875
ORF1ab/nsp10	136	P136L	cCc	cTc	6	6	B.1.427	0.000303
ORF1ab/nsp10	136	P136H	cCc	cAc	5	5	AY.29	0.000079
ORF1ab/nsp10	136	P136S	Ccc	Tcc	5	5	AY.39	0.000124
ORF1ab/nsp10	136	P136H	cCc	cAc	5	5	AY.44	0.00003
ORF1ab/nsp10	136	P136S	Ccc	Tcc	5	5	AY.47	0.000156
ORF1ab/nsp10	136	P136P	ccC	ccT	5	5	AY.61	0.000524
ORF1ab/nsp10	136	P136H	cCc	cAc	5	5	AY.78	0.007704
ORF1ab/nsp10	136	P136H	cCc	cAc	5	5	B.1	0.000046
ORF1ab/nsp10	136	P136L	cCc	cTc	5	5	B.1.128	0.003177
ORF1ab/nsp10	136	P136P	ccC	ccT	5	5	B.1.139	0.003666
ORF1ab/nsp10	136	P136P	ccC	ccT	5	5	B.1.210	0.010661
ORF1ab/nsp10	136	P136S	Ccc	Tcc	5	5	B.1.391	0.005637
ORF1ab/nsp10	136	P136S	Ccc	Tcc	5	5	B.1.427	0.000252
ORF1ab/nsp10	136	P136P	ccC	ccT	5	5	P.1	0.000079
ORF1ab/nsp10	136	P136S	Ccc	Tcc	4	4	AY.102	0.000106
ORF1ab/nsp10	136	P136S	Ccc	Tcc	4	4	AY.107	0.001864
ORF1ab/nsp10	136	P136S	Ccc	Tcc	4	4	AY.117	0.000338
ORF1ab/nsp10	136	P136H	cCc	cAc	4	4	AY.25	0.000024
ORF1ab/nsp10	136	P136S	Ccc	Tcc	4	4	AY.32	0.00213
ORF1ab/nsp10	136	P136del	CCC	---	4	4	AY.4	0.000006
ORF1ab/nsp10	136	P136del	CCC	---	4	4	AY.43	0.000018
ORF1ab/nsp10	136	P136P	ccC	ccT	4	4	AY.46.5	0.000794
ORF1ab/nsp10	136	P136L	cCc	cTc	4	4	AY.5	0.000083
ORF1ab/nsp10	136	P136S	Ccc	Tcc	4	4	AY.54	0.000381
ORF1ab/nsp10	136	P136S	Ccc	Tcc	4	4	AY.61	0.000419
ORF1ab/nsp10	136	P136L	cCc	cTc	4	4	AY.9.2	0.000147
ORF1ab/nsp10	136	P136P	ccC	ccT	2	4	AY.98.1	0.000097
ORF1ab/nsp10	136	P136P	ccC	ccA	2	4	AY.98.1	0.000097
ORF1ab/nsp10	136	P136P	ccC	ccT	4	4	B.1.1.348	0.003185
ORF1ab/nsp10	136	P136H	cCc	cAc	4	4	B.1.240	0.000862
ORF1ab/nsp10	136	P136L	cCc	cTc	4	4	B.1.258.20	0.063492
ORF1ab/nsp10	136	P136L	cCc	cTc	4	4	B.1.429	0.000094
ORF1ab/nsp10	136	P136P	ccC	ccT	4	4	B.1.525	0.000453
ORF1ab/nsp10	136	P136S	Ccc	Tcc	4	4	B.1.621	0.000354
ORF1ab/nsp10	136	P136P	ccC	ccT	3	4	D.2	0.000225
ORF1ab/nsp10	136	P136P	ccC	ccA	1	4	D.2	0.000075
ORF1ab/nsp10	136	P136L	cCc	cTc	4	4	P.1	0.000063
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	A.28	0.007937
ORF1ab/nsp10	136	P136I	CCc	ATc	2	3	All	0
ORF1ab/nsp10	136	P136I	CCC	ATT	1	3	All	0
ORF1ab/nsp10	136	P136L	cCc	cTc	3	3	AY.102	0.00008
ORF1ab/nsp10	136	P136P	ccC	ccT	2	3	AY.113	0.000285
ORF1ab/nsp10	136	P136P	ccC	ccA	1	3	AY.113	0.000142
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	AY.14	0.000264
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	AY.20	0.000117
ORF1ab/nsp10	136	P136L	cCc	cTc	3	3	AY.26	0.000085
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	AY.3	0.00003
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	AY.36	0.000445
ORF1ab/nsp10	136	P136H	cCc	cAc	3	3	AY.4	0.000005
ORF1ab/nsp10	136	P136L	cCc	cTc	3	3	AY.4.2	0.000065
ORF1ab/nsp10	136	P136T	Ccc	Acc	3	3	AY.43	0.000013
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	AY.5	0.000062
ORF1ab/nsp10	136	P136L	cCc	cTc	3	3	AY.59	0.001589
ORF1ab/nsp10	136	P136L	cCc	cTc	3	3	AY.75	0.000168
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	AY.9.1	0.000251
ORF1ab/nsp10	136	P136T	Ccc	Acc	3	3	B.1	0.000027
ORF1ab/nsp10	136	P136del	CCC	---	3	3	B.1.1	0.000054
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	B.1.1.311	0.001074
ORF1ab/nsp10	136	P136T	Ccc	Acc	3	3	B.1.1.7	0.000003
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	B.1.1.70	0.001023
ORF1ab/nsp10	136	P136del	CCC	---	3	3	B.1.177	0.00004
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	B.1.177.43	0.004431
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	B.1.177.9	0.003995
ORF1ab/nsp10	136	P136del	CCC	---	3	3	B.1.2	0.000026
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	B.1.243	0.000209
ORF1ab/nsp10	136	P136L	cCc	cTc	3	3	B.1.258.17	0.000312
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	B.1.427	0.000151
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	B.1.433	0.009585
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	B.1.470	0.004213
ORF1ab/nsp10	136	P136P	ccC	ccT	3	3	B.1.565	0.002431
ORF1ab/nsp10	136	P136L	cCc	cTc	3	3	B.1.596	0.000261
ORF1ab/nsp10	136	P136S	Ccc	Tcc	3	3	C.16	0.003181
ORF1ab/nsp10	136	P136P	ccC	ccA	3	3	Q.1	0.000379
ORF1ab/nsp10	136	P136Q	cCC	cAA	2	2	All	0
ORF1ab/nsp10	136	P136del2	CCc	--c	2	2	All	0
ORF1ab/nsp10	136	P136H	cCc	cAc	2	2	AY.102	0.000053
ORF1ab/nsp10	136	P136H	cCc	cAc	2	2	AY.103	0.000012
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.119	0.000071
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	AY.119	0.000071
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	AY.120	0.000074
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	AY.2	0.000712
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.20	0.000078
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.23	0.000139
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	AY.26	0.000057
ORF1ab/nsp10	136	P136P	ccC	ccT	1	2	AY.26	0.000028
ORF1ab/nsp10	136	P136P	ccC	ccA	1	2	AY.26	0.000028
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	AY.29	0.000032
ORF1ab/nsp10	136	P136H	cCc	cAc	2	2	AY.3	0.00002
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.33	0.000134
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.34	0.000194
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	AY.34	0.000194
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	AY.38	0.000999
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.39	0.000049
ORF1ab/nsp10	136	P136T	Ccc	Acc	2	2	AY.39	0.000049
ORF1ab/nsp10	136	P136T	Ccc	Acc	2	2	AY.42	0.00008
ORF1ab/nsp10	136	P136H	cCc	cAc	2	2	AY.43	0.000009
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.46	0.000208
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.68	0.000547
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	AY.79	0.002421
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.9.1	0.000167
ORF1ab/nsp10	136	P136H	cCc	cAc	2	2	AY.98	0.000158
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	AY.98.1	0.000097
ORF1ab/nsp10	136	P136P	ccC	ccT	1	2	AY.99	0.001049
ORF1ab/nsp10	136	P136P	ccC	ccA	1	2	AY.99	0.001049
ORF1ab/nsp10	136	P136P	ccC	ccA	1	2	B	0.000128
ORF1ab/nsp10	136	P136P	ccC	ccT	1	2	B	0.000128
ORF1ab/nsp10	136	P136I	CCc	ATc	2	2	B.1	0.000018
ORF1ab/nsp10	136	P136H	cCc	cAc	2	2	B.1.1	0.000036
ORF1ab/nsp10	136	P136del	CCC	---	2	2	B.1.1.318	0.000604
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	B.1.1.318	0.000604
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	B.1.1.33	0.000842
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	B.1.1.519	0.000079
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	B.1.160	0.000062
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	B.1.177.10	0.001756
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	B.1.177.21	0.000153
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	B.1.177.21	0.000153
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	B.1.177.60	0.000437
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	B.1.177.69	0.002967
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	B.1.234	0.000264
ORF1ab/nsp10	136	P136P	ccC	ccA	1	2	B.1.351	0.00003
ORF1ab/nsp10	136	P136P	ccC	ccT	1	2	B.1.351	0.00003
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	B.1.36.18	0.00084
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	B.1.371	0.002245
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	B.1.595	0.000522
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	B.1.617.1	0.000258
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	B.1.617.1	0.000258
ORF1ab/nsp10	136	P136del	CCC	---	2	2	B.1.617.2	0.000008
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	B.1.637	0.000146
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	C.26	0.014706
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	C.35	0.001548
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	C.36.3.1	0.005435
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	C.37	0.000232
ORF1ab/nsp10	136	P136del	CCC	---	2	2	P.1	0.000032
ORF1ab/nsp10	136	P136L	cCc	cTc	2	2	P.1.14	0.000096
ORF1ab/nsp10	136	P136H	cCc	cAc	2	2	P.1.14	0.000096
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	P.1.7	0.000639
ORF1ab/nsp10	136	P136S	Ccc	Tcc	2	2	P.3	0.00319
ORF1ab/nsp10	136	P136P	ccC	ccT	2	2	Q.8	0.00033
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	A	0.000387
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	A.1	0.000282
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	A.2.5	0.000499
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AA.2	0.007692
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AD.2	0.000219
ORF1ab/nsp10	136	P136V	CCc	GTc	1	1	All	0
ORF1ab/nsp10	136	P136R	cCc	cGc	1	1	All	0
ORF1ab/nsp10	136	P136A	Ccc	Gcc	1	1	All	0
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.100	0.000046
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.101	0.00049
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.103	0.000006
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.108	0.001103
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.108	0.001103
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.110	0.000113
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.111	0.000183
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.113	0.000142
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	AY.116	0.000287
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.116	0.000287
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.118	0.000063
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.118	0.000063
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.119	0.000035
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.119	0.000035
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.12	0.000316
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	AY.12	0.000316
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.120	0.000037
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.120.2.1	0.000498
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.13	0.000161
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.14	0.000088
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.16	0.00038
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.16.1	0.00047
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	AY.20	0.000039
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.23	0.00007
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.23	0.00007
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	AY.24	0.000431
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.24	0.000431
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.24	0.000431
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.25	0.000006
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	AY.29	0.000016
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.3.1	0.000085
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.33	0.000067
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.33	0.000067
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.34	0.000097
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.34.1	0.00051
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.36	0.000148
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.36	0.000148
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.37	0.000316
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.39	0.000025
ORF1ab/nsp10	136	P136V	CCc	GTc	1	1	AY.39	0.000025
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.39.1.1	0.000725
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.39.2	0.001541
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.4.2	0.000022
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.4.2	0.000022
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.4.3	0.000842
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.4.4	0.000409
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.4.5	0.000107
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.4.5	0.000107
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.42	0.00004
ORF1ab/nsp10	136	P136R	cCc	cGc	1	1	AY.44	0.000006
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	AY.44	0.000006
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.46.5	0.000198
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.47	0.000031
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.5	0.000021
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.5	0.000021
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	AY.53	0.000288
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.54	0.000095
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	AY.55	0.000917
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.55	0.000917
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.56	0.001605
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.58	0.000907
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.6	0.000041
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.6	0.000041
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	AY.61	0.000105
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.69	0.000187
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.69	0.000187
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.70	0.000209
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.72	0.001361
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.73	0.000665
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.74	0.000116
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.74	0.000116
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.75	0.000056
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.75.1	0.00018
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.75.1	0.00018
ORF1ab/nsp10	136	P136del2	CCc	--c	1	1	AY.79	0.001211
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.79	0.001211
ORF1ab/nsp10	136	P136A	Ccc	Gcc	1	1	AY.82	0.001357
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	AY.85	0.000427
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.9	0.000068
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.9.1	0.000084
ORF1ab/nsp10	136	P136del	CCC	---	1	1	AY.9.2	0.000037
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.90	0.000684
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.94	0.000443
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	AY.94	0.000443
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.98	0.000079
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.98	0.000079
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	AY.98.1	0.000048
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	AY.99.2	0.000092
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	B	0.000128
ORF1ab/nsp10	136	P136Q	cCC	cAA	1	1	B	0.000128
ORF1ab/nsp10	136	P136Q	cCC	cAA	1	1	B.1	0.000009
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.1.1	0.000327
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.1	0.000327
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.1.123	0.017857
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.135	0.004695
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.214	0.000055
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.222	0.000204
ORF1ab/nsp10	136	P136P	ccC	ccG	1	1	B.1.1.25	0.000569
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.1.28	0.000311
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.1.306	0.000438
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.311	0.000358
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.1.311	0.000358
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.312	0.001912
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.317	0.000412
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.1.318	0.000302
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	B.1.1.318	0.000302
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	B.1.1.324	0.052632
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.333	0.001076
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	B.1.1.335	0.012987
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.359	0.027778
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.1.359	0.027778
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.1.372	0.000689
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.1.376	0.005952
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.402	0.011111
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	B.1.1.409	0.002833
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.412	0.007634
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.432	0.001266
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.1.434	0.000349
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.1.45	0.014085
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.485	0.016667
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.1.519	0.00004
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.1.528	0.004808
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.111	0.001175
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.126	0.001276
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.149	0.003425
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	B.1.160	0.000031
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.160	0.000031
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.10	0.000878
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.177.12	0.000152
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.15	0.000631
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.177.17	0.000821
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.177.21	0.000076
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.177.33	0.001645
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.35	0.000691
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.177.5	0.001242
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.177.54	0.000606
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.177.65	0.000665
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.177.73	0.000566
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.74	0.015152
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.75	0.001041
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.77	0.000726
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.177.81	0.000189
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.86	0.000183
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.177.87	0.000728
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	B.1.2	0.000009
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	B.1.2	0.000009
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.221	0.000071
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	B.1.232	0.000537
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.235	0.002519
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.240	0.000216
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.258	0.000067
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.258	0.000067
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.258.10	0.011364
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.305	0.002151
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.351	0.00003
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.351	0.00003
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.351.3	0.000876
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.36	0.000146
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.36.10	0.004785
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.36.16	0.001425
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.367	0.000792
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.377	0.004566
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.400	0.000429
ORF1ab/nsp10	136	P136P	ccC	ccG	1	1	B.1.422	0.000812
ORF1ab/nsp10	136	P136del2	CCc	--c	1	1	B.1.429	0.000024
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.438.1	0.000107
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.438.1	0.000107
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.456	0.003268
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.458	0.111111
ORF1ab/nsp10	136	P136P	ccC	ccA	1	1	B.1.466.2	0.000391
ORF1ab/nsp10	136	P136T	Ccc	Acc	1	1	B.1.487	0.019608
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.493	0.025641
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.506	0.02381
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.524	0.001406
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	B.1.526	0.000024
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.526	0.000024
ORF1ab/nsp10	136	P136del	CCC	---	1	1	B.1.533	0.009615
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	B.1.568	0.001111
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.571	0.009709
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.582	0.000491
ORF1ab/nsp10	136	P136I	CCC	ATT	1	1	B.1.617.2	0.000004
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.617.3	0.002985
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.621	0.000089
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	B.1.623	0.000536
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.1.628	0.000352
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	B.1.628	0.000352
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	B.3	0.000831
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	C.16	0.00106
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	P.1	0.000016
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	P.1.10	0.000269
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	P.1.10.1	0.00813
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	P.1.14	0.000048
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	P.1.14	0.000048
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	P.1.15	0.000232
ORF1ab/nsp10	136	P136del	CCC	---	1	1	P.1.15	0.000232
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	P.1.17	0.000162
ORF1ab/nsp10	136	P136H	cCc	cAc	1	1	P.1.2	0.001156
ORF1ab/nsp10	136	P136del	CCC	---	1	1	P.2	0.000187
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	P.2	0.000187
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	Q.2	0.000613
ORF1ab/nsp10	136	P136S	Ccc	Tcc	1	1	Q.3	0.000145
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	Q.4	0.000455
ORF1ab/nsp10	136	P136L	cCc	cTc	1	1	Q.7	0.001111
ORF1ab/nsp10	136	P136P	ccC	ccT	1	1	W.3	0.005263

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.