CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 787

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
S	787	Q787K		nonsyn	Caa	Aaa	596	596	1	23921-23923
S	787	Q787Q		syn	caA	caG	124	124	1	23921-23923
S	787	Q787H		nonsyn	caA	caC	112	58	0.517857	23921-23923
S	787	Q787H		nonsyn	caA	caT	112	54	0.482143	23921-23923
S	787	Q787R		nonsyn	cAa	cGa	100	100	1	23921-23923
S	787	Q787del		del	CAA	---	93	93	1	23921-23923
S	787	Q787L		nonsyn	cAa	cTa	59	58	0.983051	23921-23923
S	787	Q787L		nonsyn	cAA	cTC	59	1	0.0169492	23921-23923
S	787	Q787X		nonsyn	Caa	Taa	25	25	1	23921-23923
S	787	Q787P		nonsyn	cAa	cCa	8	8	1	23921-23923
S	787	Q787del1		del	cAa	c-a	7	4	0.571429	23921-23923
S	787	Q787del1		del	caA	ca-	7	1	0.142857	23921-23923
S	787	Q787del1		del	CaA	-aG	7	1	0.142857	23921-23923
S	787	Q787del1		del	CAA	-NN	7	1	0.142857	23921-23923
S	787	Q787E		nonsyn	Caa	Gaa	5	5	1	23921-23923
S	787	Q787T		nonsyn	CAa	ACa	4	4	1	23921-23923
S	787	Q787A		nonsyn	CAa	GCa	2	2	1	23921-23923
S	787	Q787del2		del	CAA	--N	2	1	0.5	23921-23923
S	787	Q787del2		del	CAA	--T	2	1	0.5	23921-23923
S	787	Q787S		nonsyn	CAa	TCa	1	1	1	23921-23923
S	787	Q787V		nonsyn	CAA	GTG	1	1	1	23921-23923

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
S	787	Q787K	Caa	Aaa	596	596	All	0.000114
S	787	Q787K	Caa	Aaa	318	318	B.1.1.7	0.000285
S	787	Q787Q	caA	caG	124	124	All	0.000024
S	787	Q787H	caA	caC	58	112	All	0.000011
S	787	Q787H	caA	caT	54	112	All	0.00001
S	787	Q787R	cAa	cGa	100	100	All	0.000019
S	787	Q787del	CAA	---	93	93	All	0.000018
S	787	Q787L	cAa	cTa	58	59	All	0.000011
S	787	Q787L	cAA	cTC	1	59	All	0
S	787	Q787R	cAa	cGa	45	45	B.1.579	0.505618
S	787	Q787K	Caa	Aaa	33	33	B.1.1.37	0.006365
S	787	Q787K	Caa	Aaa	33	33	B.1.617.2	0.000124
S	787	Q787Q	caA	caG	30	30	B.1.1.7	0.000027
S	787	Q787Q	caA	caG	29	29	B.1.466.2	0.011346
S	787	Q787K	Caa	Aaa	27	27	B.1.2	0.000238
S	787	Q787X	Caa	Taa	25	25	All	0.000005
S	787	Q787K	Caa	Aaa	25	25	AY.102	0.000663
S	787	Q787K	Caa	Aaa	22	22	AY.4	0.000034
S	787	Q787H	caA	caC	19	21	B.1.1	0.000345
S	787	Q787H	caA	caT	2	21	B.1.1	0.000036
S	787	Q787H	caA	caC	20	20	C.37	0.002321
S	787	Q787R	cAa	cGa	17	17	B.1.1.7	0.000015
S	787	Q787K	Caa	Aaa	17	17	B.1.177	0.000224
S	787	Q787L	cAa	cTa	15	15	B.1.243	0.001044
S	787	Q787Q	caA	caG	14	14	AY.44	0.000085
S	787	Q787K	Caa	Aaa	13	13	AY.43	0.000058
S	787	Q787del	CAA	---	13	13	B.1.1.7	0.000012
S	787	Q787H	caA	caT	11	11	B.1.2	0.000097
S	787	Q787del	CAA	---	10	10	B.1.621	0.000885
S	787	Q787K	Caa	Aaa	9	9	B.1	0.000082
S	787	Q787P	cAa	cCa	8	8	All	0.000002
S	787	Q787Q	caA	caG	8	8	B.1.36	0.001167
S	787	Q787H	caA	caT	8	8	B.1.429	0.000188
S	787	Q787del1	cAa	c-a	4	7	All	0.000001
S	787	Q787del1	caA	ca-	1	7	All	0
S	787	Q787del1	CAA	-NN	1	7	All	0
S	787	Q787del1	CaA	-aG	1	7	All	0
S	787	Q787L	cAa	cTa	7	7	AY.103	0.000043
S	787	Q787del	CAA	---	7	7	AY.25	0.000042
S	787	Q787R	cAa	cGa	7	7	AY.29	0.00011
S	787	Q787Q	caA	caG	7	7	AY.4	0.000011
S	787	Q787K	Caa	Aaa	7	7	AY.44	0.000043
S	787	Q787H	caA	caT	5	6	AY.103	0.000031
S	787	Q787H	caA	caC	1	6	AY.103	0.000006
S	787	Q787Q	caA	caG	6	6	AY.39.1	0.000238
S	787	Q787K	Caa	Aaa	6	6	AY.46.6	0.000433
S	787	Q787K	Caa	Aaa	6	6	AY.67	0.002786
S	787	Q787K	Caa	Aaa	6	6	B.1.1	0.000109
S	787	Q787del	CAA	---	6	6	P.1.15	0.001394
S	787	Q787E	Caa	Gaa	5	5	All	0.000001
S	787	Q787H	caA	caC	3	5	AY.25	0.000018
S	787	Q787H	caA	caT	2	5	AY.25	0.000012
S	787	Q787K	Caa	Aaa	5	5	AY.4.5	0.000537
S	787	Q787del	CAA	---	5	5	B.1	0.000046
S	787	Q787K	Caa	Aaa	5	5	B.1.1.207	0.00591
S	787	Q787H	caA	caT	4	5	B.1.1.420	0.004024
S	787	Q787H	caA	caC	1	5	B.1.1.420	0.001006
S	787	Q787R	cAa	cGa	5	5	B.1.429	0.000118
S	787	Q787H	caA	caC	3	5	B.1.617.2	0.000011
S	787	Q787H	caA	caT	2	5	B.1.617.2	0.000008
S	787	Q787del	CAA	---	5	5	P.1	0.000079
S	787	Q787T	CAa	ACa	4	4	All	0.000001
S	787	Q787K	Caa	Aaa	4	4	AY.117	0.000338
S	787	Q787K	Caa	Aaa	4	4	AY.12	0.001264
S	787	Q787Q	caA	caG	4	4	AY.25	0.000024
S	787	Q787K	Caa	Aaa	4	4	AY.34.1	0.00204
S	787	Q787R	cAa	cGa	4	4	AY.4	0.000006
S	787	Q787H	caA	caC	3	4	AY.4	0.000005
S	787	Q787H	caA	caT	1	4	AY.4	0.000002
S	787	Q787del	CAA	---	4	4	AY.43	0.000018
S	787	Q787H	caA	caT	4	4	AY.44	0.000024
S	787	Q787R	cAa	cGa	4	4	B.1	0.000037
S	787	Q787X	Caa	Taa	4	4	B.1.1	0.000073
S	787	Q787L	cAa	cTa	4	4	B.1.1.25	0.002274
S	787	Q787H	caA	caT	4	4	B.1.1.7	0.000004
S	787	Q787Q	caA	caG	4	4	B.1.177	0.000053
S	787	Q787R	cAa	cGa	4	4	B.1.2	0.000035
S	787	Q787P	cAa	cCa	3	3		0.166667
S	787	Q787K	Caa	Aaa	3	3	AY.103	0.000019
S	787	Q787K	Caa	Aaa	3	3	AY.120	0.000112
S	787	Q787X	Caa	Taa	3	3	B.1	0.000027
S	787	Q787H	caA	caT	3	3	B.1	0.000027
S	787	Q787L	cAa	cTa	3	3	B.1.1.7	0.000003
S	787	Q787del1	cAa	c-a	3	3	B.1.1.7	0.000003
S	787	Q787X	Caa	Taa	3	3	B.1.2	0.000026
S	787	Q787K	Caa	Aaa	3	3	B.1.36.9	0.009646
S	787	Q787Q	caA	caG	3	3	B.1.617.2	0.000011
S	787	Q787L	cAa	cTa	3	3	C.37	0.000348
S	787	Q787L	cAa	cTa	3	3	P.1	0.000047
S	787	Q787E	Caa	Gaa	2	2		0.111111
S	787	Q787A	CAa	GCa	2	2		0.111111
S	787	Q787A	CAa	GCa	2	2	All	0
S	787	Q787del2	CAA	--N	1	2	All	0
S	787	Q787del2	CAA	--T	1	2	All	0
S	787	Q787K	Caa	Aaa	2	2	AY.107	0.000932
S	787	Q787K	Caa	Aaa	2	2	AY.119	0.000071
S	787	Q787H	caA	caT	2	2	AY.120	0.000074
S	787	Q787K	Caa	Aaa	2	2	AY.25	0.000012
S	787	Q787K	Caa	Aaa	2	2	AY.3	0.00002
S	787	Q787del	CAA	---	2	2	AY.34.1	0.00102
S	787	Q787del	CAA	---	2	2	AY.4	0.000003
S	787	Q787L	cAa	cTa	2	2	AY.4	0.000003
S	787	Q787H	caA	caC	2	2	AY.43	0.000009
S	787	Q787L	cAa	cTa	2	2	AY.47	0.000062
S	787	Q787X	Caa	Taa	2	2	AY.55	0.001835
S	787	Q787Q	caA	caG	2	2	B.1.1	0.000036
S	787	Q787del	CAA	---	2	2	B.1.1	0.000036
S	787	Q787Q	caA	caG	2	2	B.1.1.10	0.00223
S	787	Q787del	CAA	---	2	2	B.1.1.291	0.001485
S	787	Q787X	Caa	Taa	2	2	B.1.1.7	0.000002
S	787	Q787L	cAa	cTa	2	2	B.1.160	0.000062
S	787	Q787H	caA	caC	2	2	B.1.160	0.000062
S	787	Q787R	cAa	cGa	2	2	B.1.258	0.000133
S	787	Q787R	cAa	cGa	2	2	B.1.351	0.000059
S	787	Q787Q	caA	caG	2	2	B.1.438.1	0.000215
S	787	Q787L	cAa	cTa	2	2	B.1.525	0.000226
S	787	Q787K	Caa	Aaa	2	2	B.1.600	0.011696
S	787	Q787K	Caa	Aaa	2	2	B.1.617.1	0.000258
S	787	Q787del	CAA	---	2	2	B.1.617.2	0.000008
S	787	Q787H	caA	caT	2	2	P.1	0.000032
S	787	Q787del	CAA	---	2	2	P.1.7	0.000639
S	787	Q787Q	caA	caG	2	2	R.1	0.00018
S	787	Q787K	Caa	Aaa	1	1		0.055556
S	787	Q787T	CAa	ACa	1	1		0.055556
S	787	Q787del	CAA	---	1	1	A	0.000387
S	787	Q787X	Caa	Taa	1	1	A.2.4	0.003367
S	787	Q787K	Caa	Aaa	1	1	AE.3	0.032258
S	787	Q787S	CAa	TCa	1	1	All	0
S	787	Q787V	CAA	GTG	1	1	All	0
S	787	Q787del	CAA	---	1	1	AY.10	0.00053
S	787	Q787del	CAA	---	1	1	AY.100	0.000046
S	787	Q787R	cAa	cGa	1	1	AY.100	0.000046
S	787	Q787del	CAA	---	1	1	AY.103	0.000006
S	787	Q787R	cAa	cGa	1	1	AY.103	0.000006
S	787	Q787K	Caa	Aaa	1	1	AY.110	0.000113
S	787	Q787H	caA	caC	1	1	AY.111	0.000183
S	787	Q787L	cAa	cTa	1	1	AY.116	0.000287
S	787	Q787X	Caa	Taa	1	1	AY.117	0.000085
S	787	Q787del	CAA	---	1	1	AY.120	0.000037
S	787	Q787L	cAa	cTa	1	1	AY.16.1	0.00047
S	787	Q787R	cAa	cGa	1	1	AY.19	0.00114
S	787	Q787Q	caA	caG	1	1	AY.20	0.000039
S	787	Q787del	CAA	---	1	1	AY.24	0.000431
S	787	Q787E	Caa	Gaa	1	1	AY.26	0.000028
S	787	Q787L	cAa	cTa	1	1	AY.26	0.000028
S	787	Q787X	Caa	Taa	1	1	AY.26	0.000028
S	787	Q787K	Caa	Aaa	1	1	AY.29	0.000016
S	787	Q787del	CAA	---	1	1	AY.29	0.000016
S	787	Q787L	cAa	cTa	1	1	AY.3	0.00001
S	787	Q787del	CAA	---	1	1	AY.3	0.00001
S	787	Q787H	caA	caT	1	1	AY.32	0.000532
S	787	Q787K	Caa	Aaa	1	1	AY.33	0.000067
S	787	Q787P	cAa	cCa	1	1	AY.38	0.000499
S	787	Q787X	Caa	Taa	1	1	AY.39.1	0.00004
S	787	Q787P	cAa	cCa	1	1	AY.4	0.000002
S	787	Q787X	Caa	Taa	1	1	AY.4	0.000002
S	787	Q787X	Caa	Taa	1	1	AY.43	0.000004
S	787	Q787R	cAa	cGa	1	1	AY.43	0.000004
S	787	Q787E	Caa	Gaa	1	1	AY.43	0.000004
S	787	Q787T	CAa	ACa	1	1	AY.43	0.000004
S	787	Q787E	Caa	Gaa	1	1	AY.44	0.000006
S	787	Q787del2	CAA	--N	1	1	AY.45	0.000122
S	787	Q787L	cAa	cTa	1	1	AY.45	0.000122
S	787	Q787K	Caa	Aaa	1	1	AY.46	0.000104
S	787	Q787K	Caa	Aaa	1	1	AY.46.3	0.000934
S	787	Q787del2	CAA	--T	1	1	AY.5.3	0.000337
S	787	Q787K	Caa	Aaa	1	1	AY.5.4	0.000277
S	787	Q787del1	CAA	-NN	1	1	AY.54	0.000095
S	787	Q787del	CAA	---	1	1	AY.68	0.000274
S	787	Q787Q	caA	caG	1	1	AY.69	0.000187
S	787	Q787del	CAA	---	1	1	AY.75	0.000056
S	787	Q787L	cAa	cTa	1	1	AY.75	0.000056
S	787	Q787K	Caa	Aaa	1	1	AY.84	0.000437
S	787	Q787H	caA	caT	1	1	AY.86	0.00083
S	787	Q787K	Caa	Aaa	1	1	AY.9	0.000068
S	787	Q787H	caA	caT	1	1	AY.9.2	0.000037
S	787	Q787L	cAa	cTa	1	1	B.1	0.000009
S	787	Q787Q	caA	caG	1	1	B.1	0.000009
S	787	Q787P	cAa	cCa	1	1	B.1.1	0.000018
S	787	Q787S	CAa	TCa	1	1	B.1.1	0.000018
S	787	Q787R	cAa	cGa	1	1	B.1.1	0.000018
S	787	Q787T	CAa	ACa	1	1	B.1.1	0.000018
S	787	Q787L	cAa	cTa	1	1	B.1.1	0.000018
S	787	Q787del1	CaA	-aG	1	1	B.1.1	0.000018
S	787	Q787del	CAA	---	1	1	B.1.1.139	0.022727
S	787	Q787R	cAa	cGa	1	1	B.1.1.142	0.017544
S	787	Q787del	CAA	---	1	1	B.1.1.236	0.006897
S	787	Q787H	caA	caC	1	1	B.1.1.306	0.000438
S	787	Q787del	CAA	---	1	1	B.1.1.315	0.008475
S	787	Q787K	Caa	Aaa	1	1	B.1.1.317	0.000412
S	787	Q787K	Caa	Aaa	1	1	B.1.1.362	0.005618
S	787	Q787del	CAA	---	1	1	B.1.1.372	0.000689
S	787	Q787K	Caa	Aaa	1	1	B.1.1.374	0.002375
S	787	Q787L	cAa	cTa	1	1	B.1.1.409	0.002833
S	787	Q787del	CAA	---	1	1	B.1.1.409	0.002833
S	787	Q787del1	cAa	c-a	1	1	B.1.1.426	0.035714
S	787	Q787K	Caa	Aaa	1	1	B.1.1.525	0.005464
S	787	Q787V	CAA	GTG	1	1	B.1.1.7	0.000001
S	787	Q787L	cAa	cTa	1	1	B.1.112	0.005181
S	787	Q787L	cAa	cTa	1	1	B.1.126	0.001276
S	787	Q787del	CAA	---	1	1	B.1.140	0.018868
S	787	Q787del1	caA	ca-	1	1	B.1.160	0.000031
S	787	Q787K	Caa	Aaa	1	1	B.1.160	0.000031
S	787	Q787del	CAA	---	1	1	B.1.160	0.000031
S	787	Q787X	Caa	Taa	1	1	B.1.177	0.000013
S	787	Q787R	cAa	cGa	1	1	B.1.177	0.000013
S	787	Q787Q	caA	caG	1	1	B.1.177.32	0.00135
S	787	Q787K	Caa	Aaa	1	1	B.1.177.42	0.000894
S	787	Q787L	cAa	cTa	1	1	B.1.177.75	0.001041
S	787	Q787X	Caa	Taa	1	1	B.1.182	0.007246
S	787	Q787P	cAa	cCa	1	1	B.1.2	0.000009
S	787	Q787del	CAA	---	1	1	B.1.2	0.000009
S	787	Q787T	CAa	ACa	1	1	B.1.2	0.000009
S	787	Q787X	Caa	Taa	1	1	B.1.221	0.000071
S	787	Q787Q	caA	caG	1	1	B.1.236	0.002053
S	787	Q787K	Caa	Aaa	1	1	B.1.243	0.00007
S	787	Q787del	CAA	---	1	1	B.1.258	0.000067
S	787	Q787del	CAA	---	1	1	B.1.258.17	0.000104
S	787	Q787K	Caa	Aaa	1	1	B.1.340	0.004292
S	787	Q787K	Caa	Aaa	1	1	B.1.349	0.000715
S	787	Q787K	Caa	Aaa	1	1	B.1.351	0.00003
S	787	Q787L	cAa	cTa	1	1	B.1.351	0.00003
S	787	Q787H	caA	caC	1	1	B.1.351	0.00003
S	787	Q787K	Caa	Aaa	1	1	B.1.36	0.000146
S	787	Q787K	Caa	Aaa	1	1	B.1.36.18	0.00042
S	787	Q787del	CAA	---	1	1	B.1.36.18	0.00042
S	787	Q787K	Caa	Aaa	1	1	B.1.367	0.000792
S	787	Q787K	Caa	Aaa	1	1	B.1.438.1	0.000107
S	787	Q787Q	caA	caG	1	1	B.1.456	0.003268
S	787	Q787K	Caa	Aaa	1	1	B.1.459	0.004082
S	787	Q787Q	caA	caG	1	1	B.1.460	0.017857
S	787	Q787L	cAA	cTC	1	1	B.1.466.2	0.000391
S	787	Q787Q	caA	caG	1	1	B.1.471	0.002732
S	787	Q787del	CAA	---	1	1	B.1.525	0.000113
S	787	Q787K	Caa	Aaa	1	1	B.1.526	0.000024
S	787	Q787Q	caA	caG	1	1	B.1.526	0.000024
S	787	Q787del	CAA	---	1	1	B.1.561	0.000397
S	787	Q787R	cAa	cGa	1	1	B.1.577	0.000687
S	787	Q787K	Caa	Aaa	1	1	B.1.596	0.000087
S	787	Q787K	Caa	Aaa	1	1	B.1.599	0.00365
S	787	Q787R	cAa	cGa	1	1	B.1.599	0.00365
S	787	Q787P	cAa	cCa	1	1	B.1.617.2	0.000004
S	787	Q787L	cAa	cTa	1	1	B.1.617.2	0.000004
S	787	Q787X	Caa	Taa	1	1	B.1.617.2	0.000004
S	787	Q787del	CAA	---	1	1	B.1.620	0.000946
S	787	Q787del	CAA	---	1	1	B.1.638	0.052632
S	787	Q787K	Caa	Aaa	1	1	B.1.9	0.006173
S	787	Q787del	CAA	---	1	1	B.34	0.013699
S	787	Q787H	caA	caC	1	1	B.6.6	0.000889
S	787	Q787del	CAA	---	1	1	C.37	0.000116
S	787	Q787R	cAa	cGa	1	1	D.2	0.000075
S	787	Q787K	Caa	Aaa	1	1	P.1	0.000016
S	787	Q787Q	caA	caG	1	1	P.1.1	0.000318
S	787	Q787del	CAA	---	1	1	P.1.1	0.000318
S	787	Q787X	Caa	Taa	1	1	P.1.1	0.000318
S	787	Q787del	CAA	---	1	1	P.1.13	0.000898
S	787	Q787H	caA	caT	1	1	P.1.6	0.001946
S	787	Q787K	Caa	Aaa	1	1	P.1.9	0.004808
S	787	Q787L	cAa	cTa	1	1	P.2	0.000187
S	787	Q787Q	caA	caG	1	1	Q.1	0.000126
S	787	Q787del	CAA	---	1	1	Q.2	0.000613
S	787	Q787del	CAA	---	1	1	Q.8	0.000165

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.