CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1265

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	1265	S1265del	S2083del	del	AGT	---	1164	1164	1	6512-6514
ORF1ab/nsp3	1265	S1265N	S2083N	nonsyn	aGt	aAt	803	803	1	6512-6514
ORF1ab/nsp3	1265	S1265I	S2083I	nonsyn	aGt	aTt	294	291	0.989796	6512-6514
ORF1ab/nsp3	1265	S1265I	S2083I	nonsyn	aGT	aTA	294	2	0.00680272	6512-6514
ORF1ab/nsp3	1265	S1265I	S2083I	nonsyn	aGT	aTC	294	1	0.00340136	6512-6514
ORF1ab/nsp3	1265	S1265R	S2083R	nonsyn	Agt	Cgt	243	196	0.806584	6512-6514
ORF1ab/nsp3	1265	S1265R	S2083R	nonsyn	agT	agG	243	41	0.168724	6512-6514
ORF1ab/nsp3	1265	S1265R	S2083R	nonsyn	agT	agA	243	6	0.0246914	6512-6514
ORF1ab/nsp3	1265	S1265G	S2083G	nonsyn	Agt	Ggt	40	39	0.975	6512-6514
ORF1ab/nsp3	1265	S1265G	S2083G	nonsyn	AgT	GgG	40	1	0.025	6512-6514
ORF1ab/nsp3	1265	S1265S	S2083S	syn	agT	agC	24	24	1	6512-6514
ORF1ab/nsp3	1265	S1265C	S2083C	nonsyn	Agt	Tgt	10	10	1	6512-6514
ORF1ab/nsp3	1265	S1265del2	S2083del2	del	aGT	a--	8	6	0.75	6512-6514
ORF1ab/nsp3	1265	S1265del2	S2083del2	del	AGt	--t	8	2	0.25	6512-6514
ORF1ab/nsp3	1265	S1265del1	S2083del1	del	AGt	-Tt	7	2	0.285714	6512-6514
ORF1ab/nsp3	1265	S1265del1	S2083del1	del	agT	ag-	7	2	0.285714	6512-6514
ORF1ab/nsp3	1265	S1265del1	S2083del1	del	aGT	a-N	7	1	0.142857	6512-6514
ORF1ab/nsp3	1265	S1265del1	S2083del1	del	Agt	-gt	7	1	0.142857	6512-6514
ORF1ab/nsp3	1265	S1265del1	S2083del1	del	aGT	aA-	7	1	0.142857	6512-6514
ORF1ab/nsp3	1265	S1265T	S2083T	nonsyn	aGt	aCt	5	5	1	6512-6514
ORF1ab/nsp3	1265	S1265D	S2083D	nonsyn	AGt	GAt	1	1	1	6512-6514
ORF1ab/nsp3	1265	S1265E	S2083E	nonsyn	AGT	GAG	1	1	1	6512-6514
ORF1ab/nsp3	1265	S1265K	S2083K	nonsyn	aGT	aAG	1	1	1	6512-6514
ORF1ab/nsp3	1265	S1265Q	S2083Q	nonsyn	AGT	CAA	1	1	1	6512-6514

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	1265	S1265del	AGT	---	1164	1164	All	0.000223
ORF1ab/nsp3	1265	S1265N	aGt	aAt	803	803	All	0.000154
ORF1ab/nsp3	1265	S1265N	aGt	aAt	420	420	B.1.160	0.013099
ORF1ab/nsp3	1265	S1265I	aGt	aTt	291	294	All	0.000056
ORF1ab/nsp3	1265	S1265I	aGT	aTA	2	294	All	0
ORF1ab/nsp3	1265	S1265I	aGT	aTC	1	294	All	0
ORF1ab/nsp3	1265	S1265R	Agt	Cgt	196	243	All	0.000037
ORF1ab/nsp3	1265	S1265R	agT	agG	41	243	All	0.000008
ORF1ab/nsp3	1265	S1265R	agT	agA	6	243	All	0.000001
ORF1ab/nsp3	1265	S1265R	Agt	Cgt	192	192	B.1.112	0.994819
ORF1ab/nsp3	1265	S1265del	AGT	---	160	160	B.1.617.2	0.000602
ORF1ab/nsp3	1265	S1265N	aGt	aAt	137	137	B.1.160.18	1
ORF1ab/nsp3	1265	S1265del	AGT	---	114	114	AY.4	0.000177
ORF1ab/nsp3	1265	S1265del	AGT	---	79	79	AY.39	0.001952
ORF1ab/nsp3	1265	S1265del	AGT	---	71	71	AY.46.5	0.014087
ORF1ab/nsp3	1265	S1265N	aGt	aAt	70	70	B.1.1.7	0.000063
ORF1ab/nsp3	1265	S1265del	AGT	---	63	63	P.1.7	0.020115
ORF1ab/nsp3	1265	S1265N	aGt	aAt	59	59	AY.4	0.000092
ORF1ab/nsp3	1265	S1265del	AGT	---	57	57	B.1.1.222	0.011628
ORF1ab/nsp3	1265	S1265del	AGT	---	57	57	B.1.1.7	0.000051
ORF1ab/nsp3	1265	S1265I	aGt	aTt	50	50	AY.4	0.000078
ORF1ab/nsp3	1265	S1265I	aGt	aTt	43	43	B.1.160	0.001341
ORF1ab/nsp3	1265	S1265N	aGt	aAt	42	42	B.1.1.333	0.04521
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	39	40	All	0.000007
ORF1ab/nsp3	1265	S1265G	AgT	GgG	1	40	All	0
ORF1ab/nsp3	1265	S1265del	AGT	---	37	37	B.1.177	0.000487
ORF1ab/nsp3	1265	S1265I	aGt	aTt	33	33	B.1.1.7	0.00003
ORF1ab/nsp3	1265	S1265del	AGT	---	32	32	AY.103	0.000199
ORF1ab/nsp3	1265	S1265del	AGT	---	30	30	AY.44	0.000183
ORF1ab/nsp3	1265	S1265del	AGT	---	25	25	B.1.351	0.000743
ORF1ab/nsp3	1265	S1265R	agT	agG	25	25	B.1.617.2	0.000094
ORF1ab/nsp3	1265	S1265S	agT	agC	24	24	All	0.000005
ORF1ab/nsp3	1265	S1265del	AGT	---	24	24	B.1	0.00022
ORF1ab/nsp3	1265	S1265del	AGT	---	23	23	AY.40	0.022179
ORF1ab/nsp3	1265	S1265del	AGT	---	21	21	AY.43	0.000093
ORF1ab/nsp3	1265	S1265del	AGT	---	18	18	AY.29	0.000284
ORF1ab/nsp3	1265	S1265del	AGT	---	16	16	B.1.160	0.000499
ORF1ab/nsp3	1265	S1265del	AGT	---	15	15	P.1	0.000236
ORF1ab/nsp3	1265	S1265del	AGT	---	14	14	AY.14	0.001232
ORF1ab/nsp3	1265	S1265I	aGt	aTt	14	14	B.1.1	0.000254
ORF1ab/nsp3	1265	S1265del	AGT	---	14	14	B.1.2	0.000123
ORF1ab/nsp3	1265	S1265del	AGT	---	13	13	AY.25	0.000078
ORF1ab/nsp3	1265	S1265del	AGT	---	13	13	AY.42	0.000523
ORF1ab/nsp3	1265	S1265N	aGt	aAt	13	13	B.1	0.000119
ORF1ab/nsp3	1265	S1265I	aGt	aTt	12	13	B.1	0.00011
ORF1ab/nsp3	1265	S1265I	aGT	aTC	1	13	B.1	0.000009
ORF1ab/nsp3	1265	S1265del	AGT	---	13	13	B.1.110.3	0.009339
ORF1ab/nsp3	1265	S1265I	aGt	aTt	11	12	AY.103	0.000068
ORF1ab/nsp3	1265	S1265I	aGT	aTA	1	12	AY.103	0.000006
ORF1ab/nsp3	1265	S1265N	aGt	aAt	12	12	AY.14	0.001056
ORF1ab/nsp3	1265	S1265C	Agt	Tgt	10	10	All	0.000002
ORF1ab/nsp3	1265	S1265del	AGT	---	10	10	AY.3	0.000099
ORF1ab/nsp3	1265	S1265I	aGt	aTt	10	10	B.1.1.294	0.012658
ORF1ab/nsp3	1265	S1265I	aGt	aTt	9	9	AY.43	0.00004
ORF1ab/nsp3	1265	S1265del	AGT	---	9	9	B.1.1	0.000163
ORF1ab/nsp3	1265	S1265del2	aGT	a--	6	8	All	0.000001
ORF1ab/nsp3	1265	S1265del2	AGt	--t	2	8	All	0
ORF1ab/nsp3	1265	S1265del	AGT	---	8	8	AY.46	0.000833
ORF1ab/nsp3	1265	S1265del	AGT	---	8	8	AY.9.2	0.000294
ORF1ab/nsp3	1265	S1265I	aGt	aTt	8	8	B.1.2	0.00007
ORF1ab/nsp3	1265	S1265I	aGt	aTt	8	8	B.1.617.2	0.00003
ORF1ab/nsp3	1265	S1265I	aGt	aTt	8	8	C.14	0.034632
ORF1ab/nsp3	1265	S1265del1	agT	ag-	2	7	All	0
ORF1ab/nsp3	1265	S1265del1	AGt	-Tt	2	7	All	0
ORF1ab/nsp3	1265	S1265del1	Agt	-gt	1	7	All	0
ORF1ab/nsp3	1265	S1265del1	aGT	aA-	1	7	All	0
ORF1ab/nsp3	1265	S1265del1	aGT	a-N	1	7	All	0
ORF1ab/nsp3	1265	S1265del	AGT	---	7	7	AY.111	0.001282
ORF1ab/nsp3	1265	S1265del	AGT	---	7	7	AY.26	0.000198
ORF1ab/nsp3	1265	S1265del	AGT	---	7	7	AY.33	0.000467
ORF1ab/nsp3	1265	S1265N	aGt	aAt	7	7	B.1.221	0.000497
ORF1ab/nsp3	1265	S1265del	AGT	---	6	6	A	0.002322
ORF1ab/nsp3	1265	S1265del	AGT	---	6	6	AY.119	0.000212
ORF1ab/nsp3	1265	S1265C	Agt	Tgt	6	6	AY.3	0.00006
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	6	6	AY.4	0.000009
ORF1ab/nsp3	1265	S1265del	AGT	---	6	6	AY.4.2	0.00013
ORF1ab/nsp3	1265	S1265I	aGt	aTt	6	6	B.1.1.216	0.005343
ORF1ab/nsp3	1265	S1265del	AGT	---	6	6	B.1.1.316	0.00555
ORF1ab/nsp3	1265	S1265del	AGT	---	6	6	B.1.214.2	0.003597
ORF1ab/nsp3	1265	S1265T	aGt	aCt	5	5	All	0.000001
ORF1ab/nsp3	1265	S1265del	AGT	---	5	5	AY.102	0.000133
ORF1ab/nsp3	1265	S1265del	AGT	---	5	5	AY.120	0.000186
ORF1ab/nsp3	1265	S1265del	AGT	---	5	5	AY.36	0.000741
ORF1ab/nsp3	1265	S1265I	aGt	aTt	4	5	AY.44	0.000024
ORF1ab/nsp3	1265	S1265I	aGT	aTA	1	5	AY.44	0.000006
ORF1ab/nsp3	1265	S1265del	AGT	---	5	5	AY.45	0.000608
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	5	5	B.1.1.7	0.000004
ORF1ab/nsp3	1265	S1265N	aGt	aAt	5	5	B.1.160.32	0.021459
ORF1ab/nsp3	1265	S1265R	agT	agG	4	5	B.1.429	0.000094
ORF1ab/nsp3	1265	S1265R	agT	agA	1	5	B.1.429	0.000024
ORF1ab/nsp3	1265	S1265del	AGT	---	4	4	A.2.2	0.006757
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	4	4	AY.103	0.000025
ORF1ab/nsp3	1265	S1265R	agT	agG	3	4	AY.103	0.000019
ORF1ab/nsp3	1265	S1265R	agT	agA	1	4	AY.103	0.000006
ORF1ab/nsp3	1265	S1265I	aGt	aTt	4	4	AY.3	0.00004
ORF1ab/nsp3	1265	S1265R	Agt	Cgt	3	4	B.1	0.000027
ORF1ab/nsp3	1265	S1265R	agT	agA	1	4	B.1	0.000009
ORF1ab/nsp3	1265	S1265del	AGT	---	4	4	B.1.1.25	0.002274
ORF1ab/nsp3	1265	S1265S	agT	agC	4	4	B.1.2	0.000035
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	4	4	B.1.36.7	0.016
ORF1ab/nsp3	1265	S1265I	aGt	aTt	4	4	B.1.429	0.000094
ORF1ab/nsp3	1265	S1265I	aGt	aTt	4	4	B.1.575	0.001214
ORF1ab/nsp3	1265	S1265del	AGT	---	4	4	B.1.637	0.000292
ORF1ab/nsp3	1265	S1265I	aGt	aTt	4	4	B.23	0.011696
ORF1ab/nsp3	1265	S1265del	AGT	---	4	4	P.1.14	0.000191
ORF1ab/nsp3	1265	S1265I	aGt	aTt	3	3	AY.102	0.00008
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	AY.106	0.001005
ORF1ab/nsp3	1265	S1265N	aGt	aAt	3	3	AY.109	0.002219
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	AY.20	0.000117
ORF1ab/nsp3	1265	S1265S	agT	agC	3	3	AY.25	0.000018
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	AY.27	0.000194
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	3	3	AY.3	0.00003
ORF1ab/nsp3	1265	S1265I	aGt	aTt	3	3	AY.39	0.000074
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	AY.47	0.000093
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	AY.5	0.000062
ORF1ab/nsp3	1265	S1265I	aGt	aTt	3	3	AY.61	0.000314
ORF1ab/nsp3	1265	S1265N	aGt	aAt	3	3	AY.9.2	0.00011
ORF1ab/nsp3	1265	S1265S	agT	agC	3	3	B.1	0.000027
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	B.1.1.50	0.002037
ORF1ab/nsp3	1265	S1265I	aGt	aTt	3	3	B.1.1.519	0.000119
ORF1ab/nsp3	1265	S1265I	aGt	aTt	3	3	B.1.221	0.000213
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	3	3	B.1.429	0.000071
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	B.1.429	0.000071
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	B.1.575	0.00091
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	C.1.2	0.012766
ORF1ab/nsp3	1265	S1265del	AGT	---	3	3	C.36.3	0.001702
ORF1ab/nsp3	1265	S1265I	aGt	aTt	2	2	A.2.5	0.000998
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.1	0.000791
ORF1ab/nsp3	1265	S1265T	aGt	aCt	2	2	AY.20	0.000078
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.23	0.000139
ORF1ab/nsp3	1265	S1265N	aGt	aAt	2	2	AY.23	0.000139
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	2	2	AY.25	0.000012
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.32	0.001065
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.38	0.000999
ORF1ab/nsp3	1265	S1265N	aGt	aAt	2	2	AY.39	0.000049
ORF1ab/nsp3	1265	S1265R	agT	agG	2	2	AY.4	0.000003
ORF1ab/nsp3	1265	S1265S	agT	agC	2	2	AY.4	0.000003
ORF1ab/nsp3	1265	S1265N	aGt	aAt	2	2	AY.4.5	0.000215
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.41	0.000588
ORF1ab/nsp3	1265	S1265R	agT	agG	2	2	AY.43	0.000009
ORF1ab/nsp3	1265	S1265del1	Agt	-gt	1	2	AY.44	0.000006
ORF1ab/nsp3	1265	S1265del1	aGT	a-N	1	2	AY.44	0.000006
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.46.4	0.000329
ORF1ab/nsp3	1265	S1265I	aGt	aTt	2	2	AY.5	0.000041
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.5.3	0.000675
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.6	0.000082
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.61	0.00021
ORF1ab/nsp3	1265	S1265I	aGt	aTt	2	2	AY.74	0.000231
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	AY.9.1	0.000167
ORF1ab/nsp3	1265	S1265I	aGt	aTt	2	2	B	0.000256
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	2	B.1.1	0.000018
ORF1ab/nsp3	1265	S1265G	AgT	GgG	1	2	B.1.1	0.000018
ORF1ab/nsp3	1265	S1265del2	aGT	a--	2	2	B.1.1.222	0.000408
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	B.1.1.39	0.001019
ORF1ab/nsp3	1265	S1265N	aGt	aAt	2	2	B.1.177	0.000026
ORF1ab/nsp3	1265	S1265I	aGt	aTt	2	2	B.1.177	0.000026
ORF1ab/nsp3	1265	S1265S	agT	agC	2	2	B.1.177.56	0.001335
ORF1ab/nsp3	1265	S1265T	aGt	aCt	2	2	B.1.2	0.000018
ORF1ab/nsp3	1265	S1265N	aGt	aAt	2	2	B.1.210	0.004264
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	B.1.240	0.000431
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	B.1.243	0.000139
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	B.1.36.8	0.002
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	B.1.411	0.007407
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	B.1.596	0.000174
ORF1ab/nsp3	1265	S1265del2	aGT	a--	1	2	B.1.617.2	0.000004
ORF1ab/nsp3	1265	S1265del2	AGt	--t	1	2	B.1.617.2	0.000004
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	C.37	0.000232
ORF1ab/nsp3	1265	S1265del	AGT	---	2	2	D.2	0.00015
ORF1ab/nsp3	1265	S1265I	aGt	aTt	2	2	P.1	0.000032
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	A.1	0.000282
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	A.2.4	0.003367
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	AL.1	0.012987
ORF1ab/nsp3	1265	S1265K	aGT	aAG	1	1	All	0
ORF1ab/nsp3	1265	S1265E	AGT	GAG	1	1	All	0
ORF1ab/nsp3	1265	S1265D	AGt	GAt	1	1	All	0
ORF1ab/nsp3	1265	S1265Q	AGT	CAA	1	1	All	0
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.100	0.000046
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.103	0.000006
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	AY.104	0.001984
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	AY.105	0.000643
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.106	0.000335
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.107	0.000466
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	AY.117	0.000085
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	AY.118	0.000063
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.121	0.000135
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.121	0.000135
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.121	0.000135
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.13	0.000161
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.13	0.000161
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.16	0.00038
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.16.1	0.00047
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.19	0.00114
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.20	0.000039
ORF1ab/nsp3	1265	S1265del2	aGT	a--	1	1	AY.25	0.000006
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.25	0.000006
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.26	0.000028
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.26	0.000028
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.29	0.000016
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.3.1	0.000085
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.30	0.000396
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.31	0.018519
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.34	0.000097
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.34	0.000097
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.39.1	0.00004
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1265	S1265R	agT	agG	1	1	AY.41	0.000294
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	AY.43	0.000004
ORF1ab/nsp3	1265	S1265del1	agT	ag-	1	1	AY.43	0.000004
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	AY.44	0.000006
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.44	0.000006
ORF1ab/nsp3	1265	S1265del2	aGT	a--	1	1	AY.45	0.000122
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.46	0.000104
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.46.4	0.000165
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.46.6	0.000072
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.47	0.000031
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.47	0.000031
ORF1ab/nsp3	1265	S1265del2	aGT	a--	1	1	AY.5.3	0.000337
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.51	0.000909
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.53	0.000288
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.54	0.000095
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.56	0.001605
ORF1ab/nsp3	1265	S1265R	agT	agG	1	1	AY.57	0.000656
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.58	0.000907
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.59	0.00053
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.6	0.000041
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.67	0.000464
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	AY.7.2	0.000559
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.72	0.001361
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.75	0.000056
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.75	0.000056
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	AY.78	0.001541
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	AY.89	0.004902
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AY.93	0.000273
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	AY.97	0.001701
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	AY.98.1	0.000048
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	AZ.2	0.000821
ORF1ab/nsp3	1265	S1265del1	aGT	aA-	1	1	B	0.000128
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B	0.000128
ORF1ab/nsp3	1265	S1265C	Agt	Tgt	1	1	B.1	0.000009
ORF1ab/nsp3	1265	S1265E	AGT	GAG	1	1	B.1.1	0.000018
ORF1ab/nsp3	1265	S1265K	aGT	aAG	1	1	B.1.1	0.000018
ORF1ab/nsp3	1265	S1265D	AGt	GAt	1	1	B.1.1	0.000018
ORF1ab/nsp3	1265	S1265R	agT	agG	1	1	B.1.1	0.000018
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.1	0.000018
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.128	0.007092
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.1.148	0.008772
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.1.176	0.000439
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.1.194	0.00495
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.255	0.00303
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	B.1.1.274	0.005051
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.1.284	0.000107
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.297	0.002237
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.309	0.005848
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.335	0.012987
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.337	0.003597
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.1.344	0.010753
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.375	0.011905
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.420	0.001006
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.1.434	0.000349
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.448	0.002033
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.486	0.001577
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.1.525	0.005464
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1265	S1265R	agT	agA	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.111	0.001175
ORF1ab/nsp3	1265	S1265R	agT	agA	1	1	B.1.177	0.000013
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	1265	S1265S	agT	agC	1	1	B.1.177.26	0.006993
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.177.77	0.000726
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp3	1265	S1265del2	AGt	--t	1	1	B.1.2	0.000009
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.221	0.000071
ORF1ab/nsp3	1265	S1265R	Agt	Cgt	1	1	B.1.221.1	0.002907
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.240	0.000216
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.258.11	0.000396
ORF1ab/nsp3	1265	S1265del1	AGt	-Tt	1	1	B.1.336	0.002439
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.346	0.001311
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.36.27	0.000763
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.36.31	0.001751
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.36.38	0.001642
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.369	0.000285
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.396	0.000706
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	B.1.408	0.00369
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.415	0.014286
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.427	0.00005
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.441	0.009615
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.453	0.003236
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.467	0.04
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.497	0.000315
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.499	0.00105
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.499	0.00105
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.503	0.002488
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.525	0.000113
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.526	0.000024
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.527	0.003704
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.536	0.02381
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.560	0.00463
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.561	0.000397
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.595	0.000261
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.596	0.000087
ORF1ab/nsp3	1265	S1265del1	AGt	-Tt	1	1	B.1.596	0.000087
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.596.1	0.009346
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1265	S1265C	Agt	Tgt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1265	S1265del1	agT	ag-	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1265	S1265T	aGt	aCt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.620	0.000946
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	B.1.621	0.000089
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1265	S1265R	agT	agG	1	1	B.1.621	0.000089
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	B.1.630	0.005236
ORF1ab/nsp3	1265	S1265R	agT	agA	1	1	B.1.637	0.000073
ORF1ab/nsp3	1265	S1265Q	AGT	CAA	1	1	C.35	0.000774
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	C.36	0.000911
ORF1ab/nsp3	1265	S1265N	aGt	aAt	1	1	C.37	0.000116
ORF1ab/nsp3	1265	S1265R	agT	agG	1	1	D.2	0.000075
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	D.2	0.000075
ORF1ab/nsp3	1265	S1265C	Agt	Tgt	1	1	D.2	0.000075
ORF1ab/nsp3	1265	S1265G	Agt	Ggt	1	1	P.1	0.000016
ORF1ab/nsp3	1265	S1265C	Agt	Tgt	1	1	P.1	0.000016
ORF1ab/nsp3	1265	S1265I	aGt	aTt	1	1	P.1.14	0.000048
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	P.2	0.000187
ORF1ab/nsp3	1265	S1265del	AGT	---	1	1	Q.1	0.000126

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.