CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp16 : CodonNum = 141

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/nsp16	141	K141R	K6939R	nonsyn	aAa	aGa	1007	1007	1	21079-21081
ORF1ab/nsp16	141	K141Q	K6939Q	nonsyn	Aaa	Caa	539	539	1	21079-21081
ORF1ab/nsp16	141	K141K	K6939K	syn	aaA	aaG	219	219	1	21079-21081
ORF1ab/nsp16	141	K141N	K6939N	nonsyn	aaA	aaC	81	52	0.641975	21079-21081
ORF1ab/nsp16	141	K141N	K6939N	nonsyn	aaA	aaT	81	29	0.358025	21079-21081
ORF1ab/nsp16	141	K141T	K6939T	nonsyn	aAa	aCa	61	61	1	21079-21081
ORF1ab/nsp16	141	K141E	K6939E	nonsyn	Aaa	Gaa	51	51	1	21079-21081
ORF1ab/nsp16	141	K141del	K6939del	del	AAA	---	50	50	1	21079-21081
ORF1ab/nsp16	141	K141I	K6939I	nonsyn	aAa	aTa	7	7	1	21079-21081
ORF1ab/nsp16	141	K141del1	K6939del1	del	Aaa	-aa	6	4	0.666667	21079-21081
ORF1ab/nsp16	141	K141del1	K6939del1	del	aaA	aa-	6	2	0.333333	21079-21081
ORF1ab/nsp16	141	K141X	K6939X	nonsyn	Aaa	Taa	3	3	1	21079-21081
ORF1ab/nsp16	141	K141G	K6939G	nonsyn	AAA	GGT	2	2	1	21079-21081

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/nsp16	141	K141R	aAa	aGa	1007	1007	All	0.000193
ORF1ab/nsp16	141	K141R	aAa	aGa	776	776	B.1.361	1
ORF1ab/nsp16	141	K141Q	Aaa	Caa	539	539	All	0.000103
ORF1ab/nsp16	141	K141Q	Aaa	Caa	525	525	B.1.1.7	0.00047
ORF1ab/nsp16	141	K141K	aaA	aaG	219	219	All	0.000042
ORF1ab/nsp16	141	K141N	aaA	aaC	52	81	All	0.00001
ORF1ab/nsp16	141	K141N	aaA	aaT	29	81	All	0.000006
ORF1ab/nsp16	141	K141T	aAa	aCa	61	61	All	0.000012
ORF1ab/nsp16	141	K141R	aAa	aGa	53	53	B.1	0.000485
ORF1ab/nsp16	141	K141E	Aaa	Gaa	51	51	All	0.00001
ORF1ab/nsp16	141	K141del	AAA	---	50	50	All	0.00001
ORF1ab/nsp16	141	K141K	aaA	aaG	49	49	B.1.1	0.000889
ORF1ab/nsp16	141	K141K	aaA	aaG	48	48	B.1.1.7	0.000043
ORF1ab/nsp16	141	K141R	aAa	aGa	44	44	B.1.2	0.000387
ORF1ab/nsp16	141	K141T	aAa	aCa	41	41	AY.4	0.000064
ORF1ab/nsp16	141	K141K	aaA	aaG	41	41	B.1.526	0.000964
ORF1ab/nsp16	141	K141R	aAa	aGa	21	21	B.1.1.7	0.000019
ORF1ab/nsp16	141	K141N	aaA	aaC	15	20	B.1.1.7	0.000013
ORF1ab/nsp16	141	K141N	aaA	aaT	5	20	B.1.1.7	0.000004
ORF1ab/nsp16	141	K141E	Aaa	Gaa	19	19	B.1.438.1	0.002038
ORF1ab/nsp16	141	K141K	aaA	aaG	17	17	B.1.551	0.021935
ORF1ab/nsp16	141	K141N	aaA	aaC	13	13	AY.43	0.000058
ORF1ab/nsp16	141	K141del	AAA	---	13	13	B.1.1.7	0.000012
ORF1ab/nsp16	141	K141E	Aaa	Gaa	12	12	B.1.617.2	0.000045
ORF1ab/nsp16	141	K141R	aAa	aGa	11	11	AY.33	0.000735
ORF1ab/nsp16	141	K141R	aAa	aGa	11	11	B.1.596	0.000959
ORF1ab/nsp16	141	K141R	aAa	aGa	10	10	B.1.214.3	0.071429
ORF1ab/nsp16	141	K141R	aAa	aGa	10	10	B.1.279	0.005136
ORF1ab/nsp16	141	K141N	aaA	aaT	9	9	B.1.517	0.003843
ORF1ab/nsp16	141	K141K	aaA	aaG	8	8	P.1	0.000126
ORF1ab/nsp16	141	K141I	aAa	aTa	7	7	All	0.000001
ORF1ab/nsp16	141	K141R	aAa	aGa	7	7	AY.100	0.000322
ORF1ab/nsp16	141	K141del1	Aaa	-aa	4	6	All	0.000001
ORF1ab/nsp16	141	K141del1	aaA	aa-	2	6	All	0
ORF1ab/nsp16	141	K141K	aaA	aaG	6	6	AY.14	0.000528
ORF1ab/nsp16	141	K141N	aaA	aaC	6	6	AY.99.2	0.000553
ORF1ab/nsp16	141	K141K	aaA	aaG	6	6	B.1	0.000055
ORF1ab/nsp16	141	K141N	aaA	aaT	4	6	B.1.617.2	0.000015
ORF1ab/nsp16	141	K141N	aaA	aaC	2	6	B.1.617.2	0.000008
ORF1ab/nsp16	141	K141del	AAA	---	5	5	AY.4	0.000008
ORF1ab/nsp16	141	K141R	aAa	aGa	5	5	B.1.595	0.001305
ORF1ab/nsp16	141	K141K	aaA	aaG	4	4	AY.116	0.001147
ORF1ab/nsp16	141	K141R	aAa	aGa	4	4	AY.4	0.000006
ORF1ab/nsp16	141	K141del	AAA	---	4	4	AY.4.5	0.00043
ORF1ab/nsp16	141	K141E	Aaa	Gaa	4	4	AY.44	0.000024
ORF1ab/nsp16	141	K141R	aAa	aGa	4	4	AY.46.6	0.000289
ORF1ab/nsp16	141	K141R	aAa	aGa	4	4	B.1.1	0.000073
ORF1ab/nsp16	141	K141T	aAa	aCa	4	4	B.1.513	0.055556
ORF1ab/nsp16	141	K141R	aAa	aGa	4	4	B.1.617.2	0.000015
ORF1ab/nsp16	141	K141X	Aaa	Taa	3	3	All	0.000001
ORF1ab/nsp16	141	K141Q	Aaa	Caa	3	3	AY.103	0.000019
ORF1ab/nsp16	141	K141R	aAa	aGa	3	3	AY.103	0.000019
ORF1ab/nsp16	141	K141K	aaA	aaG	3	3	AY.113	0.000427
ORF1ab/nsp16	141	K141R	aAa	aGa	3	3	AY.29	0.000047
ORF1ab/nsp16	141	K141N	aaA	aaC	3	3	AY.9.2	0.00011
ORF1ab/nsp16	141	K141del1	aaA	aa-	2	3	B.1	0.000018
ORF1ab/nsp16	141	K141del1	Aaa	-aa	1	3	B.1	0.000009
ORF1ab/nsp16	141	K141R	aAa	aGa	3	3	B.1.1.519	0.000119
ORF1ab/nsp16	141	K141T	aAa	aCa	3	3	B.1.1.7	0.000003
ORF1ab/nsp16	141	K141R	aAa	aGa	3	3	B.1.330	0.085714
ORF1ab/nsp16	141	K141T	aAa	aCa	3	3	B.1.525	0.000339
ORF1ab/nsp16	141	K141R	aAa	aGa	3	3	B.1.78	0.025641
ORF1ab/nsp16	141	K141del	AAA	---	3	3	P.1.15	0.000697
ORF1ab/nsp16	141	K141G	AAA	GGT	2	2		0.111111
ORF1ab/nsp16	141	K141del	AAA	---	2	2		0.111111
ORF1ab/nsp16	141	K141G	AAA	GGT	2	2	All	0
ORF1ab/nsp16	141	K141N	aaA	aaT	1	2	AY.102	0.000027
ORF1ab/nsp16	141	K141N	aaA	aaC	1	2	AY.102	0.000027
ORF1ab/nsp16	141	K141E	Aaa	Gaa	2	2	AY.25	0.000012
ORF1ab/nsp16	141	K141N	aaA	aaT	2	2	AY.25	0.000012
ORF1ab/nsp16	141	K141N	aaA	aaC	2	2	AY.26	0.000057
ORF1ab/nsp16	141	K141Q	Aaa	Caa	2	2	AY.33	0.000134
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	AY.4.2.1	0.000298
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	AY.44	0.000012
ORF1ab/nsp16	141	K141N	aaA	aaC	1	2	AY.46	0.000104
ORF1ab/nsp16	141	K141N	aaA	aaT	1	2	AY.46	0.000104
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	AY.9.2	0.000073
ORF1ab/nsp16	141	K141R	aAa	aGa	2	2	AY.92	0.000575
ORF1ab/nsp16	141	K141T	aAa	aCa	2	2	B.1.1	0.000036
ORF1ab/nsp16	141	K141N	aaA	aaT	2	2	B.1.1	0.000036
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	B.1.1.214	0.000111
ORF1ab/nsp16	141	K141E	Aaa	Gaa	2	2	B.1.1.7	0.000002
ORF1ab/nsp16	141	K141N	aaA	aaC	2	2	B.1.177.20	0.003035
ORF1ab/nsp16	141	K141R	aAa	aGa	2	2	B.1.369	0.00057
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	B.1.509	0.001732
ORF1ab/nsp16	141	K141del	AAA	---	2	2	B.1.617.2	0.000008
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	B.1.637	0.000146
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	B.40	0.000729
ORF1ab/nsp16	141	K141I	aAa	aTa	2	2	B.6	0.00182
ORF1ab/nsp16	141	K141K	aaA	aaG	2	2	C.37	0.000232
ORF1ab/nsp16	141	K141R	aAa	aGa	2	2	P.1	0.000032
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	A	0.000387
ORF1ab/nsp16	141	K141I	aAa	aTa	1	1	AY.103	0.000006
ORF1ab/nsp16	141	K141del	AAA	---	1	1	AY.103	0.000006
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	AY.111	0.000183
ORF1ab/nsp16	141	K141N	aaA	aaC	1	1	AY.116	0.000287
ORF1ab/nsp16	141	K141N	aaA	aaT	1	1	AY.118	0.000063
ORF1ab/nsp16	141	K141del	AAA	---	1	1	AY.120	0.000037
ORF1ab/nsp16	141	K141del	AAA	---	1	1	AY.120.1	0.000321
ORF1ab/nsp16	141	K141del1	Aaa	-aa	1	1	AY.120.1	0.000321
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	AY.23	0.00007
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	AY.25	0.000006
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	AY.27	0.000065
ORF1ab/nsp16	141	K141I	aAa	aTa	1	1	AY.3	0.00001
ORF1ab/nsp16	141	K141del	AAA	---	1	1	AY.33	0.000067
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	AY.39.1	0.00004
ORF1ab/nsp16	141	K141N	aaA	aaT	1	1	AY.4	0.000002
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	AY.4	0.000002
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	AY.4	0.000002
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	AY.42	0.00004
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	AY.42	0.00004
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	AY.43	0.000004
ORF1ab/nsp16	141	K141I	aAa	aTa	1	1	AY.43	0.000004
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	AY.43	0.000004
ORF1ab/nsp16	141	K141del	AAA	---	1	1	AY.43	0.000004
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	AY.44	0.000006
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	AY.44	0.000006
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	AY.46	0.000104
ORF1ab/nsp16	141	K141N	aaA	aaT	1	1	AY.5	0.000021
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	AY.53	0.000288
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	AY.65	0.000533
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	AY.67	0.000464
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	AY.68	0.000274
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	AY.69	0.000187
ORF1ab/nsp16	141	K141I	aAa	aTa	1	1	AY.74	0.000116
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	AY.9	0.000068
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	AY.9	0.000068
ORF1ab/nsp16	141	K141del	AAA	---	1	1	AY.9.2	0.000037
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	AY.9.2	0.000037
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	AY.94	0.000443
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	AY.98	0.000079
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B	0.000128
ORF1ab/nsp16	141	K141N	aaA	aaC	1	1	B.1	0.000009
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	B.1	0.000009
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	B.1	0.000009
ORF1ab/nsp16	141	K141I	aAa	aTa	1	1	B.1	0.000009
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	B.1.1	0.000018
ORF1ab/nsp16	141	K141X	Aaa	Taa	1	1	B.1.1.28	0.000311
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.1.30	0.076923
ORF1ab/nsp16	141	K141N	aaA	aaT	1	1	B.1.1.306	0.000438
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.1.343	0.020833
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.1.370	0.012658
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.1.409	0.002833
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.1.487	0.005587
ORF1ab/nsp16	141	K141del1	Aaa	-aa	1	1	B.1.1.519	0.00004
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.1.519	0.00004
ORF1ab/nsp16	141	K141X	Aaa	Taa	1	1	B.1.1.7	0.000001
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	B.1.160	0.000031
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	B.1.160	0.000031
ORF1ab/nsp16	141	K141N	aaA	aaC	1	1	B.1.162	0.005025
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.170	0.00431
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.177	0.000013
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.177	0.000013
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.177	0.000013
ORF1ab/nsp16	141	K141N	aaA	aaC	1	1	B.1.177.17	0.000821
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	B.1.177.17	0.000821
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.177.20	0.001517
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp16	141	K141N	aaA	aaC	1	1	B.1.177.60	0.000218
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	B.1.177.60	0.000218
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.177.60	0.000218
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.177.62	0.001192
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.177.73	0.000566
ORF1ab/nsp16	141	K141E	Aaa	Gaa	1	1	B.1.177.9	0.001332
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp16	141	K141N	aaA	aaT	1	1	B.1.2	0.000009
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.206	0.000816
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.243	0.00007
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.258	0.000067
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.258	0.000067
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	B.1.356	0.001727
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.36	0.000146
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.36	0.000146
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	B.1.36.1	0.00114
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.36.29	0.000517
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.36.35	0.002604
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.427	0.00005
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	B.1.429	0.000024
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.524	0.001406
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	B.1.524	0.001406
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.525	0.000113
ORF1ab/nsp16	141	K141X	Aaa	Taa	1	1	B.1.546	0.003704
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.580	0.004065
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.612	0.002653
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	B.1.617.2	0.000004
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	B.1.617.2	0.000004
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	B.1.617.2	0.000004
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.620	0.000946
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.1.621	0.000089
ORF1ab/nsp16	141	K141del1	Aaa	-aa	1	1	B.1.636	0.006711
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	B.1.88.1	0.004808
ORF1ab/nsp16	141	K141T	aAa	aCa	1	1	B.1.91	0.002075
ORF1ab/nsp16	141	K141del	AAA	---	1	1	B.34	0.013699
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	C.11	0.010638
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	C.37.1	0.002618
ORF1ab/nsp16	141	K141N	aaA	aaC	1	1	D.2	0.000075
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	D.3	0.005917
ORF1ab/nsp16	141	K141N	aaA	aaC	1	1	P.1	0.000016
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	P.1.10	0.000269
ORF1ab/nsp16	141	K141K	aaA	aaG	1	1	P.1.4	0.000977
ORF1ab/nsp16	141	K141Q	Aaa	Caa	1	1	Q.1	0.000126
ORF1ab/nsp16	141	K141R	aAa	aGa	1	1	Q.2	0.000613
ORF1ab/nsp16	141	K141del	AAA	---	1	1	U.3	0.003861

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.