CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = E : Mut = L65L

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
E	65	L65L		syn	ctG	ctT	3225	2592	0.803721	26437-26439
E	65	L65L		syn	Ctg	Ttg	3225	394	0.122171	26437-26439
E	65	L65L		syn	ctG	ctA	3225	206	0.063876	26437-26439
E	65	L65L		syn	ctG	ctC	3225	32	0.00992248	26437-26439
E	65	L65L		syn	CtG	TtA	3225	1	0.000310078	26437-26439

Details of the mutation L65L 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
E	65	L65L	ctG	ctT	2592	3225	All	0.000496
E	65	L65L	Ctg	Ttg	394	3225	All	0.000075
E	65	L65L	ctG	ctA	206	3225	All	0.000039
E	65	L65L	ctG	ctC	32	3225	All	0.000006
E	65	L65L	CtG	TtA	1	3225	All	0
E	65	L65L	ctG	ctT	344	404	AY.4	0.000535
E	65	L65L	Ctg	Ttg	53	404	AY.4	0.000082
E	65	L65L	ctG	ctA	5	404	AY.4	0.000008
E	65	L65L	ctG	ctC	2	404	AY.4	0.000003
E	65	L65L	ctG	ctA	136	392	B.1.1.7	0.000122
E	65	L65L	ctG	ctT	135	392	B.1.1.7	0.000121
E	65	L65L	Ctg	Ttg	120	392	B.1.1.7	0.000107
E	65	L65L	ctG	ctC	1	392	B.1.1.7	0.000001
E	65	L65L	ctG	ctT	312	313	AY.3	0.003103
E	65	L65L	ctG	ctC	1	313	AY.3	0.00001
E	65	L65L	ctG	ctT	296	310	B.1.617.2	0.001115
E	65	L65L	Ctg	Ttg	8	310	B.1.617.2	0.00003
E	65	L65L	ctG	ctA	3	310	B.1.617.2	0.000011
E	65	L65L	ctG	ctC	3	310	B.1.617.2	0.000011
E	65	L65L	ctG	ctT	285	285	AY.94	0.126162
E	65	L65L	ctG	ctT	189	201	AY.44	0.00115
E	65	L65L	Ctg	Ttg	6	201	AY.44	0.000037
E	65	L65L	ctG	ctA	3	201	AY.44	0.000018
E	65	L65L	ctG	ctC	3	201	AY.44	0.000018
E	65	L65L	ctG	ctT	128	133	AY.43	0.000567
E	65	L65L	Ctg	Ttg	4	133	AY.43	0.000018
E	65	L65L	ctG	ctA	1	133	AY.43	0.000004
E	65	L65L	ctG	ctT	76	92	AY.103	0.000472
E	65	L65L	Ctg	Ttg	15	92	AY.103	0.000093
E	65	L65L	ctG	ctA	1	92	AY.103	0.000006
E	65	L65L	ctG	ctT	38	81	B.1	0.000348
E	65	L65L	Ctg	Ttg	23	81	B.1	0.000211
E	65	L65L	ctG	ctA	20	81	B.1	0.000183
E	65	L65L	ctG	ctT	40	54	B.1.177	0.000527
E	65	L65L	Ctg	Ttg	14	54	B.1.177	0.000184
E	65	L65L	ctG	ctT	38	42	AY.39	0.000939
E	65	L65L	Ctg	Ttg	3	42	AY.39	0.000074
E	65	L65L	ctG	ctC	1	42	AY.39	0.000025
E	65	L65L	ctG	ctT	27	39	AY.25	0.000162
E	65	L65L	ctG	ctA	9	39	AY.25	0.000054
E	65	L65L	ctG	ctC	2	39	AY.25	0.000012
E	65	L65L	Ctg	Ttg	1	39	AY.25	0.000006
E	65	L65L	ctG	ctT	39	39	C.36.3	0.022121
E	65	L65L	ctG	ctT	36	36	AY.101	0.017656
E	65	L65L	ctG	ctT	31	36	AY.54	0.002956
E	65	L65L	Ctg	Ttg	5	36	AY.54	0.000477
E	65	L65L	ctG	ctT	18	31	B.1.2	0.000158
E	65	L65L	Ctg	Ttg	9	31	B.1.2	0.000079
E	65	L65L	ctG	ctC	3	31	B.1.2	0.000026
E	65	L65L	ctG	ctA	1	31	B.1.2	0.000009
E	65	L65L	ctG	ctT	30	31	B.1.351	0.000892
E	65	L65L	Ctg	Ttg	1	31	B.1.351	0.00003
E	65	L65L	ctG	ctT	14	29	AY.120	0.000521
E	65	L65L	Ctg	Ttg	13	29	AY.120	0.000483
E	65	L65L	ctG	ctA	2	29	AY.120	0.000074
E	65	L65L	ctG	ctT	24	29	B.1.526	0.000564
E	65	L65L	Ctg	Ttg	3	29	B.1.526	0.000071
E	65	L65L	ctG	ctA	2	29	B.1.526	0.000047
E	65	L65L	ctG	ctT	21	25	AY.102	0.000557
E	65	L65L	Ctg	Ttg	3	25	AY.102	0.00008
E	65	L65L	ctG	ctA	1	25	AY.102	0.000027
E	65	L65L	ctG	ctT	23	23	B.1.240	0.004958
E	65	L65L	ctG	ctT	15	21	B.1.1.519	0.000596
E	65	L65L	Ctg	Ttg	5	21	B.1.1.519	0.000199
E	65	L65L	ctG	ctA	1	21	B.1.1.519	0.00004
E	65	L65L	ctG	ctT	12	19	P.1	0.000189
E	65	L65L	Ctg	Ttg	4	19	P.1	0.000063
E	65	L65L	ctG	ctA	2	19	P.1	0.000032
E	65	L65L	ctG	ctC	1	19	P.1	0.000016
E	65	L65L	ctG	ctT	15	17	AY.118	0.00094
E	65	L65L	ctG	ctA	2	17	AY.118	0.000125
E	65	L65L	ctG	ctT	15	17	AY.33	0.001002
E	65	L65L	Ctg	Ttg	2	17	AY.33	0.000134
E	65	L65L	ctG	ctT	17	17	AY.4.2	0.000369
E	65	L65L	ctG	ctT	11	17	AY.5	0.000227
E	65	L65L	Ctg	Ttg	6	17	AY.5	0.000124
E	65	L65L	ctG	ctT	13	16	AY.26	0.000368
E	65	L65L	Ctg	Ttg	3	16	AY.26	0.000085
E	65	L65L	ctG	ctT	13	16	AY.42	0.000523
E	65	L65L	ctG	ctC	3	16	AY.42	0.000121
E	65	L65L	ctG	ctT	14	16	B.1.1	0.000254
E	65	L65L	Ctg	Ttg	2	16	B.1.1	0.000036
E	65	L65L	ctG	ctT	11	14	AY.29	0.000174
E	65	L65L	Ctg	Ttg	3	14	AY.29	0.000047
E	65	L65L	ctG	ctT	13	13	B.1.1.369	0.005801
E	65	L65L	ctG	ctT	11	11	B.1.1.37	0.002122
E	65	L65L	Ctg	Ttg	10	10	AY.69	0.001867
E	65	L65L	ctG	ctT	10	10	B.1.1.28	0.003112
E	65	L65L	ctG	ctT	8	10	B.1.596	0.000697
E	65	L65L	Ctg	Ttg	1	10	B.1.596	0.000087
E	65	L65L	ctG	ctA	1	10	B.1.596	0.000087
E	65	L65L	ctG	ctT	9	9	AY.119	0.000318
E	65	L65L	Ctg	Ttg	9	9	B.1.1.232	0.016334
E	65	L65L	ctG	ctT	8	8	B.1.177.7	0.001319
E	65	L65L	ctG	ctT	6	8	P.1.7	0.001916
E	65	L65L	Ctg	Ttg	2	8	P.1.7	0.000639
E	65	L65L	ctG	ctT	4	7		0.222222
E	65	L65L	ctG	ctA	1	7		0.055556
E	65	L65L	Ctg	Ttg	1	7		0.055556
E	65	L65L	CtG	TtA	1	7		0.055556
E	65	L65L	ctG	ctT	6	7	AY.46	0.000624
E	65	L65L	Ctg	Ttg	1	7	AY.46	0.000104
E	65	L65L	ctG	ctT	7	7	AY.46.6	0.000505
E	65	L65L	ctG	ctT	7	7	B.1.617.1	0.000903
E	65	L65L	ctG	ctT	4	7	C.37	0.000464
E	65	L65L	Ctg	Ttg	3	7	C.37	0.000348
E	65	L65L	ctG	ctT	6	7	P.1.14	0.000287
E	65	L65L	Ctg	Ttg	1	7	P.1.14	0.000048
E	65	L65L	ctG	ctT	6	6	AY.5.4	0.00166
E	65	L65L	ctG	ctT	6	6	AY.78	0.009245
E	65	L65L	ctG	ctT	6	6	AY.98.1	0.000291
E	65	L65L	Ctg	Ttg	5	5	AY.111	0.000916
E	65	L65L	ctG	ctT	4	5	AY.121	0.000541
E	65	L65L	Ctg	Ttg	1	5	AY.121	0.000135
E	65	L65L	ctG	ctT	3	5	AY.20	0.000117
E	65	L65L	Ctg	Ttg	2	5	AY.20	0.000078
E	65	L65L	ctG	ctT	4	5	AY.23	0.000279
E	65	L65L	ctG	ctA	1	5	AY.23	0.00007
E	65	L65L	ctG	ctT	4	5	B.1.1.70	0.001364
E	65	L65L	Ctg	Ttg	1	5	B.1.1.70	0.000341
E	65	L65L	ctG	ctT	5	5	B.1.480	0.012438
E	65	L65L	Ctg	Ttg	5	5	B.1.577	0.003436
E	65	L65L	Ctg	Ttg	5	5	P.1.15	0.001162
E	65	L65L	ctG	ctT	3	4	AY.3.1	0.000256
E	65	L65L	ctG	ctC	1	4	AY.3.1	0.000085
E	65	L65L	ctG	ctT	4	4	AY.45	0.000487
E	65	L65L	ctG	ctT	3	4	AY.47	0.000093
E	65	L65L	Ctg	Ttg	1	4	AY.47	0.000031
E	65	L65L	ctG	ctT	4	4	AY.6	0.000165
E	65	L65L	ctG	ctT	4	4	AY.61	0.000419
E	65	L65L	ctG	ctT	4	4	AY.75	0.000224
E	65	L65L	ctG	ctT	4	4	AY.9.2	0.000147
E	65	L65L	ctG	ctC	4	4	B.1.575	0.001214
E	65	L65L	Ctg	Ttg	2	4	B.1.621	0.000177
E	65	L65L	ctG	ctC	1	4	B.1.621	0.000089
E	65	L65L	ctG	ctT	1	4	B.1.621	0.000089
E	65	L65L	Ctg	Ttg	3	4	Q.3	0.000435
E	65	L65L	ctG	ctT	1	4	Q.3	0.000145
E	65	L65L	ctG	ctT	3	4	R.1	0.00027
E	65	L65L	ctG	ctA	1	4	R.1	0.00009
E	65	L65L	Ctg	Ttg	3	3	A.27	0.004967
E	65	L65L	ctG	ctT	3	3	AM.4	0.010714
E	65	L65L	ctG	ctT	3	3	AY.106	0.001005
E	65	L65L	Ctg	Ttg	2	3	AY.109	0.001479
E	65	L65L	ctG	ctT	1	3	AY.109	0.00074
E	65	L65L	ctG	ctT	3	3	AY.16.1	0.00141
E	65	L65L	ctG	ctT	3	3	AY.34	0.000291
E	65	L65L	ctG	ctT	2	3	AY.34.1	0.00102
E	65	L65L	ctG	ctA	1	3	AY.34.1	0.00051
E	65	L65L	ctG	ctT	2	3	AY.39.1	0.000079
E	65	L65L	Ctg	Ttg	1	3	AY.39.1	0.00004
E	65	L65L	ctG	ctT	3	3	AY.9	0.000203
E	65	L65L	ctG	ctT	3	3	B.1.1.306	0.001315
E	65	L65L	ctG	ctC	3	3	B.1.1.434	0.001046
E	65	L65L	ctG	ctT	3	3	B.1.110.3	0.002155
E	65	L65L	Ctg	Ttg	3	3	B.1.258	0.0002
E	65	L65L	Ctg	Ttg	2	3	B.1.609	0.000959
E	65	L65L	ctG	ctT	1	3	B.1.609	0.000479
E	65	L65L	ctG	ctT	3	3	B.1.637	0.000219
E	65	L65L	ctG	ctT	3	3	C.39	0.056604
E	65	L65L	Ctg	Ttg	1	3	D.2	0.000075
E	65	L65L	ctG	ctT	1	3	D.2	0.000075
E	65	L65L	ctG	ctA	1	3	D.2	0.000075
E	65	L65L	ctG	ctT	3	3	Q.2	0.00184
E	65	L65L	ctG	ctT	1	2	A.2	0.000662
E	65	L65L	ctG	ctA	1	2	A.2	0.000662
E	65	L65L	ctG	ctT	1	2	AY.100	0.000046
E	65	L65L	Ctg	Ttg	1	2	AY.100	0.000046
E	65	L65L	ctG	ctT	2	2	AY.105	0.001286
E	65	L65L	ctG	ctT	2	2	AY.116.1	0.000623
E	65	L65L	ctG	ctT	2	2	AY.12	0.000632
E	65	L65L	ctG	ctT	2	2	AY.4.4	0.000818
E	65	L65L	ctG	ctT	1	2	AY.46.4	0.000165
E	65	L65L	ctG	ctC	1	2	AY.46.4	0.000165
E	65	L65L	ctG	ctT	2	2	AY.67	0.000929
E	65	L65L	ctG	ctT	2	2	AY.68	0.000547
E	65	L65L	Ctg	Ttg	2	2	AY.7	0.000392
E	65	L65L	ctG	ctT	2	2	AY.84	0.000875
E	65	L65L	ctG	ctT	2	2	AY.92	0.000575
E	65	L65L	ctG	ctT	2	2	AY.99.2	0.000184
E	65	L65L	ctG	ctT	2	2	B	0.000256
E	65	L65L	ctG	ctT	2	2	B.1.1.214	0.000111
E	65	L65L	ctG	ctT	2	2	B.1.1.229	0.011494
E	65	L65L	ctG	ctT	2	2	B.1.1.403	0.051282
E	65	L65L	ctG	ctT	2	2	B.1.177.79	0.004684
E	65	L65L	ctG	ctT	2	2	B.1.351.2	0.000605
E	65	L65L	ctG	ctT	2	2	B.1.456	0.006536
E	65	L65L	ctG	ctT	1	2	B.1.595	0.000261
E	65	L65L	ctG	ctA	1	2	B.1.595	0.000261
E	65	L65L	ctG	ctA	2	2	B.1.618	0.008065
E	65	L65L	Ctg	Ttg	1	2	P.2	0.000187
E	65	L65L	ctG	ctT	1	2	P.2	0.000187
E	65	L65L	ctG	ctT	1	1	A	0.000387
E	65	L65L	ctG	ctA	1	1	A.23.1	0.000704
E	65	L65L	ctG	ctT	1	1	AD.2	0.000219
E	65	L65L	Ctg	Ttg	1	1	AY.107	0.000466
E	65	L65L	ctG	ctA	1	1	AY.113	0.000142
E	65	L65L	ctG	ctT	1	1	AY.116	0.000287
E	65	L65L	ctG	ctT	1	1	AY.120.1	0.000321
E	65	L65L	ctG	ctT	1	1	AY.120.2.1	0.000498
E	65	L65L	ctG	ctT	1	1	AY.13	0.000161
E	65	L65L	Ctg	Ttg	1	1	AY.14	0.000088
E	65	L65L	ctG	ctT	1	1	AY.17	0.008197
E	65	L65L	ctG	ctT	1	1	AY.32	0.000532
E	65	L65L	ctG	ctT	1	1	AY.35	0.000233
E	65	L65L	ctG	ctT	1	1	AY.36	0.000148
E	65	L65L	ctG	ctT	1	1	AY.37	0.000316
E	65	L65L	Ctg	Ttg	1	1	AY.4.2.1	0.000149
E	65	L65L	ctG	ctT	1	1	AY.4.5	0.000107
E	65	L65L	ctG	ctT	1	1	AY.41	0.000294
E	65	L65L	ctG	ctT	1	1	AY.46.2	0.000635
E	65	L65L	ctG	ctT	1	1	AY.46.3	0.000934
E	65	L65L	ctG	ctT	1	1	AY.52	0.000814
E	65	L65L	Ctg	Ttg	1	1	AY.55	0.000917
E	65	L65L	ctG	ctT	1	1	AY.56	0.001605
E	65	L65L	ctG	ctT	1	1	AY.57	0.000656
E	65	L65L	ctG	ctT	1	1	AY.58	0.000907
E	65	L65L	Ctg	Ttg	1	1	AY.62	0.000436
E	65	L65L	ctG	ctA	1	1	AY.63	0.000387
E	65	L65L	ctG	ctT	1	1	AY.7.1	0.000113
E	65	L65L	ctG	ctT	1	1	AY.73	0.000665
E	65	L65L	ctG	ctT	1	1	AY.82	0.001357
E	65	L65L	ctG	ctA	1	1	AY.85	0.000427
E	65	L65L	ctG	ctT	1	1	AY.86	0.00083
E	65	L65L	ctG	ctT	1	1	AY.87	0.000833
E	65	L65L	ctG	ctT	1	1	AY.88	0.000884
E	65	L65L	ctG	ctT	1	1	AY.90	0.000684
E	65	L65L	ctG	ctT	1	1	AY.98	0.000079
E	65	L65L	ctG	ctA	1	1	B.1.1.1	0.000327
E	65	L65L	ctG	ctT	1	1	B.1.1.101	0.01
E	65	L65L	ctG	ctT	1	1	B.1.1.161	0.003534
E	65	L65L	ctG	ctT	1	1	B.1.1.176	0.000439
E	65	L65L	ctG	ctT	1	1	B.1.1.216	0.00089
E	65	L65L	ctG	ctA	1	1	B.1.1.222	0.000204
E	65	L65L	ctG	ctT	1	1	B.1.1.280	0.003086
E	65	L65L	ctG	ctT	1	1	B.1.1.284	0.000107
E	65	L65L	ctG	ctT	1	1	B.1.1.33	0.000421
E	65	L65L	ctG	ctT	1	1	B.1.1.348	0.000796
E	65	L65L	Ctg	Ttg	1	1	B.1.1.359	0.027778
E	65	L65L	ctG	ctT	1	1	B.1.1.367	0.055556
E	65	L65L	ctG	ctT	1	1	B.1.1.370	0.012658
E	65	L65L	ctG	ctT	1	1	B.1.1.389	0.006061
E	65	L65L	ctG	ctT	1	1	B.1.1.4	0.002976
E	65	L65L	Ctg	Ttg	1	1	B.1.1.442	0.018519
E	65	L65L	ctG	ctC	1	1	B.1.1.526	0.003546
E	65	L65L	Ctg	Ttg	1	1	B.1.1.99	0.02381
E	65	L65L	ctG	ctT	1	1	B.1.103	0.019231
E	65	L65L	Ctg	Ttg	1	1	B.1.137	0.5
E	65	L65L	ctG	ctT	1	1	B.1.147	0.000756
E	65	L65L	ctG	ctT	1	1	B.1.177.32	0.00135
E	65	L65L	Ctg	Ttg	1	1	B.1.177.46	0.000918
E	65	L65L	ctG	ctT	1	1	B.1.177.54	0.000606
E	65	L65L	ctG	ctT	1	1	B.1.177.85	0.005435
E	65	L65L	Ctg	Ttg	1	1	B.1.189	0.004292
E	65	L65L	ctG	ctT	1	1	B.1.214.2	0.0006
E	65	L65L	ctG	ctT	1	1	B.1.22	0.001318
E	65	L65L	ctG	ctT	1	1	B.1.221	0.000071
E	65	L65L	ctG	ctT	1	1	B.1.232	0.000537
E	65	L65L	Ctg	Ttg	1	1	B.1.243	0.00007
E	65	L65L	ctG	ctT	1	1	B.1.265	0.001271
E	65	L65L	ctG	ctT	1	1	B.1.301	0.005917
E	65	L65L	ctG	ctT	1	1	B.1.311	0.000275
E	65	L65L	Ctg	Ttg	1	1	B.1.320	0.001245
E	65	L65L	ctG	ctT	1	1	B.1.325	0.006897
E	65	L65L	ctG	ctT	1	1	B.1.348	0.018182
E	65	L65L	ctG	ctC	1	1	B.1.36.29	0.000517
E	65	L65L	ctG	ctT	1	1	B.1.362	0.001541
E	65	L65L	ctG	ctT	1	1	B.1.369	0.000285
E	65	L65L	Ctg	Ttg	1	1	B.1.398	0.002976
E	65	L65L	ctG	ctT	1	1	B.1.400	0.000429
E	65	L65L	Ctg	Ttg	1	1	B.1.413	0.004255
E	65	L65L	ctG	ctT	1	1	B.1.428	0.00102
E	65	L65L	ctG	ctT	1	1	B.1.470	0.001404
E	65	L65L	ctG	ctT	1	1	B.1.492	0.007042
E	65	L65L	Ctg	Ttg	1	1	B.1.517	0.000427
E	65	L65L	ctG	ctT	1	1	B.1.520	0.021739
E	65	L65L	ctG	ctT	1	1	B.1.521	0.004975
E	65	L65L	ctG	ctT	1	1	B.1.525	0.000113
E	65	L65L	Ctg	Ttg	1	1	B.1.598	0.016949
E	65	L65L	Ctg	Ttg	1	1	B.1.612	0.002653
E	65	L65L	ctG	ctT	1	1	B.1.623	0.000536
E	65	L65L	ctG	ctT	1	1	B.55	0.00295
E	65	L65L	ctG	ctT	1	1	C.1.2	0.004255
E	65	L65L	Ctg	Ttg	1	1	C.2.1	0.006667
E	65	L65L	ctG	ctT	1	1	C.26	0.007353
E	65	L65L	ctG	ctT	1	1	C.37.1	0.002618
E	65	L65L	ctG	ctT	1	1	N.5	0.001767
E	65	L65L	ctG	ctA	1	1	P.1.10	0.000269
E	65	L65L	ctG	ctT	1	1	P.1.13	0.000898
E	65	L65L	ctG	ctT	1	1	P.1.17	0.000162

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.