CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = R21I

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	21	R21I		nonsyn	aGa	aTa	6627	6624	0.999547	21623-21625
S	21	R21I		nonsyn	aGA	aTT	6627	3	0.000452694	21623-21625

Details of the mutation R21I 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	21	R21I	aGa	aTa	6624	6627	All	0.001267
S	21	R21I	aGA	aTT	3	6627	All	0.000001
S	21	R21I	aGa	aTa	1474	1474	AY.4	0.002294
S	21	R21I	aGa	aTa	890	890	B.1.1.279	0.997758
S	21	R21I	aGa	aTa	852	852	B.1.1.7	0.000763
S	21	R21I	aGa	aTa	384	384	AY.43	0.001701
S	21	R21I	aGa	aTa	314	314	B.1.617.2	0.001182
S	21	R21I	aGa	aTa	217	217	AY.44	0.001321
S	21	R21I	aGa	aTa	204	204	B.1.1	0.003701
S	21	R21I	aGa	aTa	172	172	B.1.1.365	0.960894
S	21	R21I	aGa	aTa	171	171	B.1.1.237	0.924324
S	21	R21I	aGa	aTa	160	160	B.1.1.363	0.958084
S	21	R21I	aGa	aTa	145	145	C.37.1	0.379581
S	21	R21I	aGa	aTa	102	102	B.1.2	0.000898
S	21	R21I	aGa	aTa	98	98	AY.103	0.000608
S	21	R21I	aGa	aTa	90	90	AY.3	0.000895
S	21	R21I	aGa	aTa	68	68	AY.98.1	0.003293
S	21	R21I	aGa	aTa	60	60	B.1.1.149	0.983607
S	21	R21I	aGa	aTa	57	57	P.1.14	0.002725
S	21	R21I	aGa	aTa	56	56	AY.39	0.001384
S	21	R21I	aGa	aTa	53	53	B.1	0.000485
S	21	R21I	aGa	aTa	49	49	P.1	0.000772
S	21	R21I	aGa	aTa	43	43	B.1.177	0.000566
S	21	R21I	aGa	aTa	40	40	AY.117	0.003381
S	21	R21I	aGa	aTa	39	39	P.1.10	0.010509
S	21	R21I	aGa	aTa	32	32	AY.120	0.00119
S	21	R21I	aGa	aTa	32	32	B.1.1.360	1
S	21	R21I	aGa	aTa	29	29	R.1	0.00261
S	21	R21I	aGa	aTa	28	28	B.1.1.379	0.875
S	21	R21I	aGa	aTa	27	27	AY.12	0.008534
S	21	R21I	aGa	aTa	26	26	AY.25	0.000156
S	21	R21I	aGa	aTa	22	22	AY.5	0.000454
S	21	R21I	aGa	aTa	22	22	B.1.429	0.000518
S	21	R21I	aGa	aTa	21	21	AY.102	0.000557
S	21	R21I	aGa	aTa	20	20	B.1.351	0.000595
S	21	R21I	aGa	aTa	19	19	AY.29	0.0003
S	21	R21I	aGa	aTa	18	18	AY.46.6	0.0013
S	21	R21I	aGa	aTa	17	17	AY.26	0.000481
S	21	R21I	aGa	aTa	15	15	AY.86	0.012448
S	21	R21I	aGa	aTa	14	14	B.1.526	0.000329
S	21	R21I	aGa	aTa	13	13	AY.45	0.001582
S	21	R21I	aGa	aTa	13	13	AY.83	0.022414
S	21	R21I	aGa	aTa	13	13	B.1.1.30	1
S	21	R21I	aGa	aTa	12	12	AY.61	0.001257
S	21	R21I	aGa	aTa	12	12	C.37	0.001393
S	21	R21I	aGa	aTa	11	11	AY.104	0.021825
S	21	R21I	aGa	aTa	11	11	AY.6	0.000452
S	21	R21I	aGa	aTa	10	10	AY.100	0.00046
S	21	R21I	aGa	aTa	10	10	B.1.160	0.000312
S	21	R21I	aGa	aTa	10	10	B.1.177.73	0.005663
S	21	R21I	aGa	aTa	10	10	B.1.195	0.050251
S	21	R21I	aGa	aTa	10	10	B.1.311	0.002746
S	21	R21I	aGa	aTa	9	9	AY.121	0.001218
S	21	R21I	aGa	aTa	9	9	AY.33	0.000601
S	21	R21I	aGa	aTa	9	9	B.1.1.519	0.000357
S	21	R21I	aGa	aTa	9	9	B.1.177.21	0.000688
S	21	R21I	aGa	aTa	8	8	AY.47	0.000249
S	21	R21I	aGa	aTa	7	7	AY.119	0.000247
S	21	R21I	aGa	aTa	7	7	AY.14	0.000616
S	21	R21I	aGa	aTa	7	7	AY.4.2	0.000152
S	21	R21I	aGa	aTa	7	7	AY.42	0.000282
S	21	R21I	aGa	aTa	7	7	AY.46	0.000729
S	21	R21I	aGa	aTa	7	7	B.1.258	0.000466
S	21	R21I	aGa	aTa	6	6	AY.118	0.000376
S	21	R21I	aGa	aTa	6	6	AY.20	0.000233
S	21	R21I	aGa	aTa	6	6	AY.9.2	0.00022
S	21	R21I	aGa	aTa	6	6	B.1.1.222	0.001224
S	21	R21I	aGa	aTa	6	6	B.1.617.1	0.000774
S	21	R21I	aGa	aTa	5	5	AY.113	0.000712
S	21	R21I	aGa	aTa	5	5	AY.9.1	0.000419
S	21	R21I	aGa	aTa	5	5	B.1.232	0.002687
S	21	R21I	aGa	aTa	5	5	B.1.252	0.033113
S	21	R21I	aGa	aTa	5	5	B.1.427	0.000252
S	21	R21I	aGa	aTa	5	5	C.36.3	0.002836
S	21	R21I	aGa	aTa	4	4	AY.101	0.001962
S	21	R21I	aGa	aTa	4	4	AY.116.1	0.001246
S	21	R21I	aGa	aTa	4	4	AY.23	0.000279
S	21	R21I	aGa	aTa	4	4	AY.36	0.000593
S	21	R21I	aGa	aTa	4	4	AY.39.1	0.000158
S	21	R21I	aGA	aTT	3	4	AY.52	0.002443
S	21	R21I	aGa	aTa	1	4	AY.52	0.000814
S	21	R21I	aGa	aTa	4	4	AY.84	0.00175
S	21	R21I	aGa	aTa	4	4	AY.98	0.000316
S	21	R21I	aGa	aTa	4	4	B	0.000511
S	21	R21I	aGa	aTa	4	4	B.1.177.12	0.000607
S	21	R21I	aGa	aTa	4	4	B.1.177.60	0.000874
S	21	R21I	aGa	aTa	4	4	B.1.206	0.003263
S	21	R21I	aGa	aTa	4	4	B.1.351.2	0.00121
S	21	R21I	aGa	aTa	4	4	B.1.36	0.000584
S	21	R21I	aGa	aTa	4	4	C.36	0.003643
S	21	R21I	aGa	aTa	4	4	P.2	0.000747
S	21	R21I	aGa	aTa	4	4	Q.1	0.000505
S	21	R21I	aGa	aTa	3	3	A.23.1	0.002113
S	21	R21I	aGa	aTa	3	3	AY.106	0.001005
S	21	R21I	aGa	aTa	3	3	AY.7	0.000588
S	21	R21I	aGa	aTa	3	3	AY.7.1	0.000338
S	21	R21I	aGa	aTa	3	3	AY.7.2	0.001678
S	21	R21I	aGa	aTa	3	3	AY.74	0.000347
S	21	R21I	aGa	aTa	3	3	B.1.1.28	0.000934
S	21	R21I	aGa	aTa	3	3	B.1.1.284	0.000322
S	21	R21I	aGa	aTa	3	3	B.1.1.355	0.046154
S	21	R21I	aGa	aTa	3	3	B.1.1.369	0.001339
S	21	R21I	aGa	aTa	3	3	B.1.1.70	0.001023
S	21	R21I	aGa	aTa	3	3	B.1.243	0.000209
S	21	R21I	aGa	aTa	3	3	B.1.39	0.011719
S	21	R21I	aGa	aTa	3	3	B.1.576	0.00272
S	21	R21I	aGa	aTa	3	3	N.5	0.0053
S	21	R21I	aGa	aTa	3	3	P.1.12	0.001452
S	21	R21I	aGa	aTa	3	3	P.1.15	0.000697
S	21	R21I	aGa	aTa	3	3	P.1.2	0.003468
S	21	R21I	aGa	aTa	2	2	A	0.000774
S	21	R21I	aGa	aTa	2	2	A.2.5	0.000998
S	21	R21I	aGa	aTa	2	2	AY.109	0.001479
S	21	R21I	aGa	aTa	2	2	AY.27	0.000129
S	21	R21I	aGa	aTa	2	2	AY.34	0.000194
S	21	R21I	aGa	aTa	2	2	AY.35	0.000466
S	21	R21I	aGa	aTa	2	2	AY.4.2.1	0.000298
S	21	R21I	aGa	aTa	2	2	AY.54	0.000191
S	21	R21I	aGa	aTa	2	2	AY.68	0.000547
S	21	R21I	aGa	aTa	2	2	AY.75	0.000112
S	21	R21I	aGa	aTa	2	2	AY.9	0.000135
S	21	R21I	aGa	aTa	2	2	AY.93	0.000546
S	21	R21I	aGa	aTa	2	2	AY.94	0.000885
S	21	R21I	aGa	aTa	2	2	B.1.1.371	0.020833
S	21	R21I	aGa	aTa	2	2	B.1.111	0.00235
S	21	R21I	aGa	aTa	2	2	B.1.13	0.004751
S	21	R21I	aGa	aTa	2	2	B.1.210	0.004264
S	21	R21I	aGa	aTa	2	2	B.1.258.17	0.000208
S	21	R21I	aGa	aTa	2	2	B.1.313	0.013158
S	21	R21I	aGa	aTa	2	2	B.1.351.3	0.001753
S	21	R21I	aGa	aTa	2	2	B.1.36.31	0.003503
S	21	R21I	aGa	aTa	2	2	B.1.398	0.005952
S	21	R21I	aGa	aTa	2	2	B.1.617.3	0.00597
S	21	R21I	aGa	aTa	2	2	B.1.621	0.000177
S	21	R21I	aGa	aTa	2	2	B.1.637	0.000146
S	21	R21I	aGa	aTa	2	2	B.6.5	0.153846
S	21	R21I	aGa	aTa	2	2	P.1.7	0.000639
S	21	R21I	aGa	aTa	2	2	Q.3	0.00029
S	21	R21I	aGa	aTa	2	2	V.1	0.045455
S	21	R21I	aGa	aTa	1	1		0.055556
S	21	R21I	aGa	aTa	1	1	AE.8	0.000489
S	21	R21I	aGa	aTa	1	1	AY.1	0.000396
S	21	R21I	aGa	aTa	1	1	AY.116	0.000287
S	21	R21I	aGa	aTa	1	1	AY.13	0.000161
S	21	R21I	aGa	aTa	1	1	AY.16	0.00038
S	21	R21I	aGa	aTa	1	1	AY.16.1	0.00047
S	21	R21I	aGa	aTa	1	1	AY.2	0.000356
S	21	R21I	aGa	aTa	1	1	AY.28	0.00189
S	21	R21I	aGa	aTa	1	1	AY.32	0.000532
S	21	R21I	aGa	aTa	1	1	AY.4.4	0.000409
S	21	R21I	aGa	aTa	1	1	AY.4.5	0.000107
S	21	R21I	aGa	aTa	1	1	AY.46.2	0.000635
S	21	R21I	aGa	aTa	1	1	AY.5.2	0.002463
S	21	R21I	aGa	aTa	1	1	AY.5.3	0.000337
S	21	R21I	aGa	aTa	1	1	AY.5.4	0.000277
S	21	R21I	aGa	aTa	1	1	AY.55	0.000917
S	21	R21I	aGa	aTa	1	1	AY.58	0.000907
S	21	R21I	aGa	aTa	1	1	AY.59	0.00053
S	21	R21I	aGa	aTa	1	1	AY.63	0.000387
S	21	R21I	aGa	aTa	1	1	AY.69	0.000187
S	21	R21I	aGa	aTa	1	1	AY.70	0.000209
S	21	R21I	aGa	aTa	1	1	AY.78	0.001541
S	21	R21I	aGa	aTa	1	1	AY.82	0.001357
S	21	R21I	aGa	aTa	1	1	AY.88	0.000884
S	21	R21I	aGa	aTa	1	1	AY.90	0.000684
S	21	R21I	aGa	aTa	1	1	AY.92	0.000287
S	21	R21I	aGa	aTa	1	1	AY.96	0.002075
S	21	R21I	aGa	aTa	1	1	AY.99	0.001049
S	21	R21I	aGa	aTa	1	1	B.1.1.101	0.01
S	21	R21I	aGa	aTa	1	1	B.1.1.111	0.014706
S	21	R21I	aGa	aTa	1	1	B.1.1.176	0.000439
S	21	R21I	aGa	aTa	1	1	B.1.1.226	0.005814
S	21	R21I	aGa	aTa	1	1	B.1.1.277	0.000759
S	21	R21I	aGa	aTa	1	1	B.1.1.29	0.010309
S	21	R21I	aGa	aTa	1	1	B.1.1.294	0.001266
S	21	R21I	aGa	aTa	1	1	B.1.1.306	0.000438
S	21	R21I	aGa	aTa	1	1	B.1.1.307	0.002532
S	21	R21I	aGa	aTa	1	1	B.1.1.318	0.000302
S	21	R21I	aGa	aTa	1	1	B.1.1.326	0.001761
S	21	R21I	aGa	aTa	1	1	B.1.1.33	0.000421
S	21	R21I	aGa	aTa	1	1	B.1.1.37	0.000193
S	21	R21I	aGa	aTa	1	1	B.1.1.378	0.007299
S	21	R21I	aGa	aTa	1	1	B.1.1.406	0.006494
S	21	R21I	aGa	aTa	1	1	B.1.1.416	0.000905
S	21	R21I	aGa	aTa	1	1	B.1.1.51	0.001718
S	21	R21I	aGa	aTa	1	1	B.1.142	0.002899
S	21	R21I	aGa	aTa	1	1	B.1.147	0.000756
S	21	R21I	aGa	aTa	1	1	B.1.177.17	0.000821
S	21	R21I	aGa	aTa	1	1	B.1.177.56	0.000668
S	21	R21I	aGa	aTa	1	1	B.1.177.8	0.000752
S	21	R21I	aGa	aTa	1	1	B.1.177.82	0.000477
S	21	R21I	aGa	aTa	1	1	B.1.177.9	0.001332
S	21	R21I	aGa	aTa	1	1	B.1.221	0.000071
S	21	R21I	aGa	aTa	1	1	B.1.221.2	0.004016
S	21	R21I	aGa	aTa	1	1	B.1.258.7	0.001912
S	21	R21I	aGa	aTa	1	1	B.1.279	0.000514
S	21	R21I	aGa	aTa	1	1	B.1.298	0.002114
S	21	R21I	aGa	aTa	1	1	B.1.301	0.005917
S	21	R21I	aGa	aTa	1	1	B.1.315	0.006061
S	21	R21I	aGa	aTa	1	1	B.1.336	0.002439
S	21	R21I	aGa	aTa	1	1	B.1.349	0.000715
S	21	R21I	aGa	aTa	1	1	B.1.36.16	0.001425
S	21	R21I	aGa	aTa	1	1	B.1.36.17	0.000494
S	21	R21I	aGa	aTa	1	1	B.1.36.22	0.001208
S	21	R21I	aGa	aTa	1	1	B.1.361	0.001289
S	21	R21I	aGa	aTa	1	1	B.1.369	0.000285
S	21	R21I	aGa	aTa	1	1	B.1.391	0.001127
S	21	R21I	aGa	aTa	1	1	B.1.396	0.000706
S	21	R21I	aGa	aTa	1	1	B.1.413	0.004255
S	21	R21I	aGa	aTa	1	1	B.1.438.1	0.000107
S	21	R21I	aGa	aTa	1	1	B.1.497	0.000315
S	21	R21I	aGa	aTa	1	1	B.1.517	0.000427
S	21	R21I	aGa	aTa	1	1	B.1.524	0.001406
S	21	R21I	aGa	aTa	1	1	B.1.533	0.009615
S	21	R21I	aGa	aTa	1	1	B.1.564	0.000426
S	21	R21I	aGa	aTa	1	1	B.1.565	0.00081
S	21	R21I	aGa	aTa	1	1	B.1.596	0.000087
S	21	R21I	aGa	aTa	1	1	B.1.619	0.000871
S	21	R21I	aGa	aTa	1	1	B.1.620	0.000946
S	21	R21I	aGa	aTa	1	1	B.1.623	0.000536
S	21	R21I	aGa	aTa	1	1	B.3.1	0.001658
S	21	R21I	aGa	aTa	1	1	P.1.10.2	0.041667
S	21	R21I	aGa	aTa	1	1	P.1.16	0.000374
S	21	R21I	aGa	aTa	1	1	P.1.17	0.000162
S	21	R21I	aGa	aTa	1	1	Q.7	0.001111

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.