CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1249

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	1249	K1249del	K2067del	del	AAA	---	581	581	1	6464-6466
ORF1ab/nsp3	1249	K1249K	K2067K	syn	aaA	aaG	417	417	1	6464-6466
ORF1ab/nsp3	1249	K1249E	K2067E	nonsyn	Aaa	Gaa	164	164	1	6464-6466
ORF1ab/nsp3	1249	K1249R	K2067R	nonsyn	aAa	aGa	73	73	1	6464-6466
ORF1ab/nsp3	1249	K1249N	K2067N	nonsyn	aaA	aaT	60	46	0.766667	6464-6466
ORF1ab/nsp3	1249	K1249N	K2067N	nonsyn	aaA	aaC	60	14	0.233333	6464-6466
ORF1ab/nsp3	1249	K1249Q	K2067Q	nonsyn	Aaa	Caa	58	58	1	6464-6466
ORF1ab/nsp3	1249	K1249T	K2067T	nonsyn	aAa	aCa	22	22	1	6464-6466
ORF1ab/nsp3	1249	K1249del1	K2067del1	del	Aaa	-aa	13	13	1	6464-6466
ORF1ab/nsp3	1249	K1249I	K2067I	nonsyn	aAa	aTa	10	10	1	6464-6466
ORF1ab/nsp3	1249	K1249del2	K2067del2	del	AAa	--a	1	1	1	6464-6466

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	1249	K1249del	AAA	---	581	581	All	0.000111
ORF1ab/nsp3	1249	K1249del	AAA	---	525	525	L.1	1
ORF1ab/nsp3	1249	K1249K	aaA	aaG	417	417	All	0.00008
ORF1ab/nsp3	1249	K1249K	aaA	aaG	191	191	B.1.195	0.959799
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	164	164	All	0.000031
ORF1ab/nsp3	1249	K1249K	aaA	aaG	103	103	B.1.2	0.000907
ORF1ab/nsp3	1249	K1249R	aAa	aGa	73	73	All	0.000014
ORF1ab/nsp3	1249	K1249N	aaA	aaT	46	60	All	0.000009
ORF1ab/nsp3	1249	K1249N	aaA	aaC	14	60	All	0.000003
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	58	58	All	0.000011
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	55	55	B.1.36.24	0.339506
ORF1ab/nsp3	1249	K1249R	aAa	aGa	37	37	AY.25	0.000223
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	33	33	AY.3	0.000328
ORF1ab/nsp3	1249	K1249N	aaA	aaT	33	33	B.1.351	0.000981
ORF1ab/nsp3	1249	K1249K	aaA	aaG	30	30	B.1	0.000275
ORF1ab/nsp3	1249	K1249T	aAa	aCa	22	22	All	0.000004
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	18	18	AY.25	0.000108
ORF1ab/nsp3	1249	K1249K	aaA	aaG	16	16	B.1.1.7	0.000014
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	14	14	B.1.1.7	0.000013
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	13	13	All	0.000002
ORF1ab/nsp3	1249	K1249del	AAA	---	13	13	B.1	0.000119
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	13	13	B.1.1.7	0.000012
ORF1ab/nsp3	1249	K1249K	aaA	aaG	12	12	C.37	0.001393
ORF1ab/nsp3	1249	K1249I	aAa	aTa	10	10	All	0.000002
ORF1ab/nsp3	1249	K1249K	aaA	aaG	9	9	B.1.160	0.000281
ORF1ab/nsp3	1249	K1249K	aaA	aaG	9	9	P.1	0.000142
ORF1ab/nsp3	1249	K1249K	aaA	aaG	8	8	B.1.1.519	0.000318
ORF1ab/nsp3	1249	K1249T	aAa	aCa	7	7	AY.25	0.000042
ORF1ab/nsp3	1249	K1249T	aAa	aCa	7	7	AY.44	0.000043
ORF1ab/nsp3	1249	K1249del	AAA	---	7	7	B.1.1.7	0.000006
ORF1ab/nsp3	1249	K1249del	AAA	---	7	7	B.1.525	0.000792
ORF1ab/nsp3	1249	K1249K	aaA	aaG	7	7	B.1.617.2	0.000026
ORF1ab/nsp3	1249	K1249del	AAA	---	6	6	B.1.1.10	0.006689
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	6	6	B.1.1.214	0.000333
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	6	6	B.1.617.2	0.000023
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	5	5	AY.4	0.000008
ORF1ab/nsp3	1249	K1249K	aaA	aaG	4	4	AY.102	0.000106
ORF1ab/nsp3	1249	K1249K	aaA	aaG	4	4	AY.4	0.000006
ORF1ab/nsp3	1249	K1249N	aaA	aaC	3	4	AY.4	0.000005
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	4	AY.4	0.000002
ORF1ab/nsp3	1249	K1249del	AAA	---	4	4	B.1.1.519	0.000159
ORF1ab/nsp3	1249	K1249I	aAa	aTa	4	4	B.1.177	0.000053
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	4	4	B.1.2	0.000035
ORF1ab/nsp3	1249	K1249N	aaA	aaC	3	3	AY.103	0.000019
ORF1ab/nsp3	1249	K1249K	aaA	aaG	3	3	AY.3	0.00003
ORF1ab/nsp3	1249	K1249R	aAa	aGa	3	3	AY.4	0.000005
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	3	3	AY.75	0.000168
ORF1ab/nsp3	1249	K1249R	aAa	aGa	3	3	B.1	0.000027
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	3	3	B.1.1.63	0.001157
ORF1ab/nsp3	1249	K1249R	aAa	aGa	3	3	B.1.1.7	0.000003
ORF1ab/nsp3	1249	K1249N	aaA	aaT	2	3	B.1.1.7	0.000002
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	3	B.1.1.7	0.000001
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	3	3	B.1.234	0.000396
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	3	3	B.1.617.2	0.000011
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	2	2	AY.103	0.000012
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	2	2	AY.105	0.001286
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	2	2	AY.121	0.000271
ORF1ab/nsp3	1249	K1249R	aAa	aGa	2	2	AY.26	0.000057
ORF1ab/nsp3	1249	K1249R	aAa	aGa	2	2	AY.39	0.000049
ORF1ab/nsp3	1249	K1249T	aAa	aCa	2	2	AY.4	0.000003
ORF1ab/nsp3	1249	K1249I	aAa	aTa	2	2	AY.4	0.000003
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	2	2	AY.4	0.000003
ORF1ab/nsp3	1249	K1249del	AAA	---	2	2	AY.4	0.000003
ORF1ab/nsp3	1249	K1249K	aaA	aaG	2	2	AY.43	0.000009
ORF1ab/nsp3	1249	K1249K	aaA	aaG	2	2	AY.44	0.000012
ORF1ab/nsp3	1249	K1249R	aAa	aGa	2	2	AY.46	0.000208
ORF1ab/nsp3	1249	K1249del	AAA	---	2	2	AY.47	0.000062
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	2	2	AY.6	0.000082
ORF1ab/nsp3	1249	K1249K	aaA	aaG	2	2	B	0.000256
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	2	2	B.1	0.000018
ORF1ab/nsp3	1249	K1249del	AAA	---	2	2	B.1.1	0.000036
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	2	2	B.1.1	0.000036
ORF1ab/nsp3	1249	K1249K	aaA	aaG	2	2	B.1.1	0.000036
ORF1ab/nsp3	1249	K1249R	aAa	aGa	2	2	B.1.1.216	0.001781
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	2	2	B.1.1.519	0.000079
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	2	2	B.1.160	0.000062
ORF1ab/nsp3	1249	K1249N	aaA	aaT	2	2	B.1.160	0.000062
ORF1ab/nsp3	1249	K1249T	aAa	aCa	2	2	B.1.177	0.000026
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	2	2	B.1.36.8	0.002
ORF1ab/nsp3	1249	K1249R	aAa	aGa	2	2	B.1.429	0.000047
ORF1ab/nsp3	1249	K1249T	aAa	aCa	2	2	B.1.561	0.000794
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	2	2	D.2	0.00015
ORF1ab/nsp3	1249	K1249R	aAa	aGa	2	2	P.1	0.000032
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	A.27	0.001656
ORF1ab/nsp3	1249	K1249del2	AAa	--a	1	1	All	0
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.100	0.000046
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	AY.103	0.000006
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.103	0.000006
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.103	0.000006
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	AY.103	0.000006
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	AY.107	0.000466
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.111	0.000183
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	AY.113	0.000142
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.117	0.000085
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	1	AY.117	0.000085
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.120.2	0.001285
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.20	0.000039
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	AY.20	0.000039
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.23	0.00007
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	1	AY.25	0.000006
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.25	0.000006
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	AY.25	0.000006
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	AY.25	0.000006
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	AY.25	0.000006
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.29	0.000016
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.33	0.000067
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	AY.39	0.000025
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	AY.39	0.000025
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	AY.39.1	0.00004
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	AY.43	0.000004
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.43	0.000004
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	1	AY.43	0.000004
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.44	0.000006
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.44	0.000006
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	AY.44	0.000006
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	AY.44	0.000006
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.45	0.000122
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	AY.47	0.000031
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	AY.48	0.000465
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	AY.59	0.00053
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	AY.79	0.001211
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	AY.9	0.000068
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	AY.98.1	0.000048
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	1	B	0.000128
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	B	0.000128
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	B.1	0.000009
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	1	B.1	0.000009
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1	0.000009
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	B.1.1	0.000018
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	B.1.1	0.000018
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	1	B.1.1	0.000018
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.1.133	0.008475
ORF1ab/nsp3	1249	K1249T	aAa	aCa	1	1	B.1.1.189	0.001513
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	B.1.1.284	0.000107
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1249	K1249I	aAa	aTa	1	1	B.1.1.362	0.005618
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	B.1.1.397	0.002252
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	1	B.1.1.47	0.005348
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1249	K1249I	aAa	aTa	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1249	K1249T	aAa	aCa	1	1	B.1.139	0.000733
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	B.1.157	0.002985
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.177	0.000013
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	B.1.177	0.000013
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.177	0.000013
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.177.62	0.001192
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	1	B.1.177.75	0.001041
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp3	1249	K1249I	aAa	aTa	1	1	B.1.2	0.000009
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	B.1.2	0.000009
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.2	0.000009
ORF1ab/nsp3	1249	K1249del2	AAa	--a	1	1	B.1.2	0.000009
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	B.1.2	0.000009
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	1	B.1.243	0.00007
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.258	0.000067
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	B.1.319	0.003049
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.351	0.00003
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.36	0.000146
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.36.10	0.004785
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	1	B.1.427	0.00005
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	B.1.427	0.00005
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	B.1.427	0.00005
ORF1ab/nsp3	1249	K1249N	aaA	aaC	1	1	B.1.429	0.000024
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.429	0.000024
ORF1ab/nsp3	1249	K1249N	aaA	aaT	1	1	B.1.473	0.019231
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.560	0.00463
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.564	0.000426
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	B.1.565	0.00081
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	B.1.598	0.016949
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	B.1.609	0.000479
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	B.1.609	0.000479
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1249	K1249R	aAa	aGa	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1249	K1249del	AAA	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.1.637	0.000073
ORF1ab/nsp3	1249	K1249K	aaA	aaG	1	1	B.4	0.002208
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	B.40	0.000364
ORF1ab/nsp3	1249	K1249I	aAa	aTa	1	1	D.2	0.000075
ORF1ab/nsp3	1249	K1249E	Aaa	Gaa	1	1	P.1.10	0.000269
ORF1ab/nsp3	1249	K1249del1	Aaa	-aa	1	1	Q.3	0.000145
ORF1ab/nsp3	1249	K1249Q	Aaa	Caa	1	1	R.1	0.00009
ORF1ab/nsp3	1249	K1249N	aaA	aaT	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.