CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1238 & Codon = acT

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	1238	T1238T		syn	acC	acT	15737	7974	0.506704	25274-25276

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	1238	T1238T	acC	acT	7974	15737	All	0.001525
S	1238	T1238T	acC	acT	2678	2763	B.1.1.7	0.002397
S	1238	T1238T	acC	acT	1343	1400	AY.4	0.00209
S	1238	T1238T	acC	acT	396	396	R.1	0.035644
S	1238	T1238T	acC	acT	331	332	B.1.617.1	0.042688
S	1238	T1238T	acC	acT	288	295	AY.119	0.010169
S	1238	T1238T	acC	acT	199	222	AY.103	0.001236
S	1238	T1238T	acC	acT	201	201	B.1.1.214	0.011147
S	1238	T1238T	acC	acT	154	185	B.1.617.2	0.00058
S	1238	T1238T	acC	acT	154	171	B.1.2	0.001356
S	1238	T1238T	acC	acT	88	161	AY.3	0.000875
S	1238	T1238T	acC	acT	72	95	AY.25	0.000433
S	1238	T1238T	acC	acT	92	95	P.1	0.001449
S	1238	T1238T	acC	acT	76	94	B.1	0.000696
S	1238	T1238T	acC	acT	90	93	B.1.429	0.002118
S	1238	T1238T	acC	acT	88	88	AY.18	0.888889
S	1238	T1238T	acC	acT	72	85	B.1.1	0.001306
S	1238	T1238T	acC	acT	63	75	AY.43	0.000279
S	1238	T1238T	acC	acT	66	71	AY.44	0.000402
S	1238	T1238T	acC	acT	61	61	B.1.627	0.123232
S	1238	T1238T	acC	acT	58	59	AY.74	0.006708
S	1238	T1238T	acC	acT	37	59	B.1.177	0.000487
S	1238	T1238T	acC	acT	59	59	B.1.177.86	0.010824
S	1238	T1238T	acC	acT	5	53	AY.47	0.000156
S	1238	T1238T	acC	acT	47	47	B.1.160.21	0.959184
S	1238	T1238T	acC	acT	46	46	B.1.311	0.01263
S	1238	T1238T	acC	acT	41	41	AY.98.1	0.001986
S	1238	T1238T	acC	acT	13	39	B.1.427	0.000656
S	1238	T1238T	acC	acT	36	36	B.1.609	0.017258
S	1238	T1238T	acC	acT	33	35	AY.75	0.001849
S	1238	T1238T	acC	acT	35	35	B.1.1.519	0.00139
S	1238	T1238T	acC	acT	34	35	B.1.526	0.000799
S	1238	T1238T	acC	acT	35	35	C.36.3	0.019853
S	1238	T1238T	acC	acT	33	33	B.1.619.1	0.021167
S	1238	T1238T	acC	acT	9	32	AY.14	0.000792
S	1238	T1238T	acC	acT	27	27	B.1.160	0.000842
S	1238	T1238T	acC	acT	26	26	B.1.177.32	0.035088
S	1238	T1238T	acC	acT	24	24	B.1.139	0.017595
S	1238	T1238T	acC	acT	24	24	Q.3	0.003481
S	1238	T1238T	acC	acT	22	23	AY.42	0.000885
S	1238	T1238T	acC	acT	19	23	B.1.36	0.002772
S	1238	T1238T	acC	acT	1	22	AY.27	0.000065
S	1238	T1238T	acC	acT	21	21	AY.120.1	0.006742
S	1238	T1238T	acC	acT	21	21	B.1.177.81	0.003976
S	1238	T1238T	acC	acT	19	19	AY.20	0.000738
S	1238	T1238T	acC	acT	16	19	B.1.351	0.000476
S	1238	T1238T	acC	acT	11	18	AY.4.2	0.000239
S	1238	T1238T	acC	acT	17	17	AY.117	0.001437
S	1238	T1238T	acC	acT	16	17	AY.39	0.000395
S	1238	T1238T	acC	acT	16	17	AY.5	0.00033
S	1238	T1238T	acC	acT	17	17	AY.6	0.000699
S	1238	T1238T	acC	acT	16	16	AY.70	0.003336
S	1238	T1238T	acC	acT	16	16	AY.85	0.006835
S	1238	T1238T	acC	acT	16	16	B.1.596	0.001394
S	1238	T1238T	acC	acT	16	16	C.37	0.001857
S	1238	T1238T	acC	acT	15	15	B.1.1.434	0.005228
S	1238	T1238T	acC	acT	11	15	B.1.243	0.000765
S	1238	T1238T	acC	acT	15	15	B.1.517	0.006405
S	1238	T1238T	acC	acT	15	15	P.1.15	0.003485
S	1238	T1238T	acC	acT	12	14	AY.102	0.000318
S	1238	T1238T	acC	acT	14	14	P.1.14	0.000669
S	1238	T1238T	acC	acT	12	13	AY.100	0.000552
S	1238	T1238T	acC	acT	13	13	AY.16	0.004935
S	1238	T1238T	acC	acT	13	13	AY.4.2.1	0.001937
S	1238	T1238T	acC	acT	11	12	AY.118	0.000689
S	1238	T1238T	acC	acT	10	12	AY.29	0.000158
S	1238	T1238T	acC	acT	12	12	AY.9	0.000811
S	1238	T1238T	acC	acT	11	12	B.1.466.2	0.004304
S	1238	T1238T	acC	acT	11	12	B.1.470	0.015449
S	1238	T1238T	acC	acT	9	11	AY.99.2	0.000829
S	1238	T1238T	acC	acT	3	10	B.1.1.222	0.000612
S	1238	T1238T	acC	acT	10	10	B.1.1.512	0.285714
S	1238	T1238T	acC	acT	9	10	B.1.599	0.032847
S	1238	T1238T	acC	acT	9	10	B.1.621	0.000797
S	1238	T1238T	acC	acT	7	9	AY.98	0.000553
S	1238	T1238T	acC	acT	9	9	B.1.575	0.002731
S	1238	T1238T	acC	acT	8	8	AY.5.4	0.002214
S	1238	T1238T	acC	acT	8	8	B.1.438.1	0.000858
S	1238	T1238T	acC	acT	7	8	B.1.623	0.003755
S	1238	T1238T	acC	acT	8	8	Q.1	0.001011
S	1238	T1238T	acC	acT	7	7	B.1.36.29	0.003621
S	1238	T1238T	acC	acT	7	7	B.1.577	0.004811
S	1238	T1238T	acC	acT	6	6	AY.33	0.000401
S	1238	T1238T	acC	acT	6	6	AY.34	0.000582
S	1238	T1238T	acC	acT	6	6	AY.5.3	0.002024
S	1238	T1238T	acC	acT	6	6	B.1.1.28	0.001867
S	1238	T1238T	acC	acT	6	6	B.1.240	0.001293
S	1238	T1238T	acC	acT	6	6	B.1.258	0.000399
S	1238	T1238T	acC	acT	6	6	B.1.403	0.019608
S	1238	T1238T	acC	acT	5	6	B.1.637	0.000365
S	1238	T1238T	acC	acT	5	5	AY.120	0.000186
S	1238	T1238T	acC	acT	3	5	AY.3.1	0.000256
S	1238	T1238T	acC	acT	3	5	AY.9.2	0.00011
S	1238	T1238T	acC	acT	5	5	B.1.1.39	0.002548
S	1238	T1238T	acC	acT	5	5	B.1.1.50	0.003394
S	1238	T1238T	acC	acT	5	5	B.1.177.18	0.0058
S	1238	T1238T	acC	acT	3	5	B.1.525	0.000339
S	1238	T1238T	acC	acT	4	4	AY.51	0.003636
S	1238	T1238T	acC	acT	4	4	AY.88	0.003537
S	1238	T1238T	acC	acT	3	4	B	0.000383
S	1238	T1238T	acC	acT	4	4	B.1.1.303	0.01105
S	1238	T1238T	acC	acT	4	4	B.1.177.43	0.005908
S	1238	T1238T	acC	acT	4	4	B.1.177.60	0.000874
S	1238	T1238T	acC	acT	4	4	B.1.595	0.001044
S	1238	T1238T	acC	acT	4	4	B.1.78	0.034188
S	1238	T1238T	acC	acT	4	4	D.2	0.0003
S	1238	T1238T	acC	acT	4	4	P.1.10	0.001078
S	1238	T1238T	acC	acT	2	3	AD.2	0.000438
S	1238	T1238T	acC	acT	1	3	AY.23	0.00007
S	1238	T1238T	acC	acT	3	3	AY.26	0.000085
S	1238	T1238T	acC	acT	3	3	AY.4.1	0.002212
S	1238	T1238T	acC	acT	2	3	AY.61	0.00021
S	1238	T1238T	acC	acT	3	3	AY.86	0.00249
S	1238	T1238T	acC	acT	3	3	AY.9.1	0.000251
S	1238	T1238T	acC	acT	3	3	AY.97	0.005102
S	1238	T1238T	acC	acT	3	3	B.1.1.1	0.00098
S	1238	T1238T	acC	acT	3	3	B.1.1.220	0.005576
S	1238	T1238T	acC	acT	3	3	B.1.1.280	0.009259
S	1238	T1238T	acC	acT	3	3	B.1.1.33	0.001263
S	1238	T1238T	acC	acT	3	3	B.1.1.70	0.001023
S	1238	T1238T	acC	acT	3	3	B.1.416	0.003807
S	1238	T1238T	acC	acT	1	3	B.1.551	0.00129
S	1238	T1238T	acC	acT	3	3	B.30	0.044118
S	1238	T1238T	acC	acT	3	3	C.1	0.007177
S	1238	T1238T	acC	acT	3	3	Q.8	0.000495
S	1238	T1238T	acC	acT	1	2		0.055556
S	1238	T1238T	acC	acT	2	2	AJ.1	0.090909
S	1238	T1238T	acC	acT	2	2	AY.111	0.000366
S	1238	T1238T	acC	acT	2	2	AY.12	0.000632
S	1238	T1238T	acC	acT	1	2	AY.30	0.000396
S	1238	T1238T	acC	acT	2	2	AY.32	0.001065
S	1238	T1238T	acC	acT	1	2	AY.46	0.000104
S	1238	T1238T	acC	acT	2	2	AY.46.6	0.000144
S	1238	T1238T	acC	acT	1	2	AY.55	0.000917
S	1238	T1238T	acC	acT	2	2	AY.56	0.00321
S	1238	T1238T	acC	acT	2	2	AY.58	0.001815
S	1238	T1238T	acC	acT	2	2	AY.64	0.00119
S	1238	T1238T	acC	acT	2	2	AY.77	0.002255
S	1238	T1238T	acC	acT	2	2	AY.92	0.000575
S	1238	T1238T	acC	acT	2	2	B.1.1.174	0.006757
S	1238	T1238T	acC	acT	2	2	B.1.1.326	0.003521
S	1238	T1238T	acC	acT	2	2	B.1.1.37	0.000386
S	1238	T1238T	acC	acT	1	2	B.1.1.389	0.006061
S	1238	T1238T	acC	acT	2	2	B.1.1.63	0.000772
S	1238	T1238T	acC	acT	2	2	B.1.111	0.00235
S	1238	T1238T	acC	acT	2	2	B.1.161	0.034483
S	1238	T1238T	acC	acT	2	2	B.1.177.17	0.001642
S	1238	T1238T	acC	acT	2	2	B.1.177.7	0.00033
S	1238	T1238T	acC	acT	2	2	B.1.214	0.007326
S	1238	T1238T	acC	acT	1	2	B.1.221	0.000071
S	1238	T1238T	acC	acT	2	2	B.1.234	0.000264
S	1238	T1238T	acC	acT	2	2	B.1.36.18	0.00084
S	1238	T1238T	acC	acT	2	2	B.1.367	0.001585
S	1238	T1238T	acC	acT	1	2	B.1.565	0.00081
S	1238	T1238T	acC	acT	2	2	B.1.589	0.015152
S	1238	T1238T	acC	acT	2	2	B.6	0.00182
S	1238	T1238T	acC	acT	1	2	C.36	0.000911
S	1238	T1238T	acC	acT	2	2	N.3	0.011628
S	1238	T1238T	acC	acT	2	2	P.1.12	0.000968
S	1238	T1238T	acC	acT	2	2	P.1.2	0.002312
S	1238	T1238T	acC	acT	1	2	P.2	0.000187
S	1238	T1238T	acC	acT	1	1	A.23.1	0.000704
S	1238	T1238T	acC	acT	1	1	A.5	0.001923
S	1238	T1238T	acC	acT	1	1	AE.8	0.000489
S	1238	T1238T	acC	acT	1	1	AU.2	0.002421
S	1238	T1238T	acC	acT	1	1	AY.106	0.000335
S	1238	T1238T	acC	acT	1	1	AY.11	0.001339
S	1238	T1238T	acC	acT	1	1	AY.113	0.000142
S	1238	T1238T	acC	acT	1	1	AY.115	0.005208
S	1238	T1238T	acC	acT	1	1	AY.116	0.000287
S	1238	T1238T	acC	acT	1	1	AY.121	0.000135
S	1238	T1238T	acC	acT	1	1	AY.13	0.000161
S	1238	T1238T	acC	acT	1	1	AY.2	0.000356
S	1238	T1238T	acC	acT	1	1	AY.21	0.001898
S	1238	T1238T	acC	acT	1	1	AY.28	0.00189
S	1238	T1238T	acC	acT	1	1	AY.29.1	0.000221
S	1238	T1238T	acC	acT	1	1	AY.36	0.000148
S	1238	T1238T	acC	acT	1	1	AY.4.5	0.000107
S	1238	T1238T	acC	acT	1	1	AY.46.1	0.001027
S	1238	T1238T	acC	acT	1	1	AY.46.2	0.000635
S	1238	T1238T	acC	acT	1	1	AY.48	0.000465
S	1238	T1238T	acC	acT	1	1	AY.49	0.003195
S	1238	T1238T	acC	acT	1	1	AY.53	0.000288
S	1238	T1238T	acC	acT	1	1	AY.54	0.000095
S	1238	T1238T	acC	acT	1	1	AY.65	0.000533
S	1238	T1238T	acC	acT	1	1	AY.67	0.000464
S	1238	T1238T	acC	acT	1	1	AY.7	0.000196
S	1238	T1238T	acC	acT	1	1	AY.71	0.000475
S	1238	T1238T	acC	acT	1	1	AY.79	0.001211
S	1238	T1238T	acC	acT	1	1	AY.91	0.00073
S	1238	T1238T	acC	acT	1	1	AY.93	0.000273
S	1238	T1238T	acC	acT	1	1	B.1.1.153	0.001095
S	1238	T1238T	acC	acT	1	1	B.1.1.163	0.007634
S	1238	T1238T	acC	acT	1	1	B.1.1.216	0.00089
S	1238	T1238T	acC	acT	1	1	B.1.1.231	0.003096
S	1238	T1238T	acC	acT	1	1	B.1.1.240	0.004695
S	1238	T1238T	acC	acT	1	1	B.1.1.241	0.00207
S	1238	T1238T	acC	acT	1	1	B.1.1.243	0.004082
S	1238	T1238T	acC	acT	1	1	B.1.1.284	0.000107
S	1238	T1238T	acC	acT	1	1	B.1.1.301	0.001179
S	1238	T1238T	acC	acT	1	1	B.1.1.312	0.001912
S	1238	T1238T	acC	acT	1	1	B.1.1.368	0.003086
S	1238	T1238T	acC	acT	1	1	B.1.1.370	0.012658
S	1238	T1238T	acC	acT	1	1	B.1.1.397	0.002252
S	1238	T1238T	acC	acT	1	1	B.1.1.486	0.001577
S	1238	T1238T	acC	acT	1	1	B.1.1.52	0.012195
S	1238	T1238T	acC	acT	1	1	B.1.1.98	0.018519
S	1238	T1238T	acC	acT	1	1	B.1.110	0.004525
S	1238	T1238T	acC	acT	1	1	B.1.120	0.007692
S	1238	T1238T	acC	acT	1	1	B.1.128	0.000635
S	1238	T1238T	acC	acT	1	1	B.1.158	0.02381
S	1238	T1238T	acC	acT	1	1	B.1.160.20	0.008929
S	1238	T1238T	acC	acT	1	1	B.1.177.24	0.001295
S	1238	T1238T	acC	acT	1	1	B.1.177.4	0.000211
S	1238	T1238T	acC	acT	1	1	B.1.177.52	0.001757
S	1238	T1238T	acC	acT	1	1	B.1.177.54	0.000606
S	1238	T1238T	acC	acT	1	1	B.1.177.61	0.043478
S	1238	T1238T	acC	acT	1	1	B.1.232	0.000537
S	1238	T1238T	acC	acT	1	1	B.1.236	0.002053
S	1238	T1238T	acC	acT	1	1	B.1.237	0.004975
S	1238	T1238T	acC	acT	1	1	B.1.239	0.001221
S	1238	T1238T	acC	acT	1	1	B.1.241	0.000812
S	1238	T1238T	acC	acT	1	1	B.1.251	0.021739
S	1238	T1238T	acC	acT	1	1	B.1.258.11	0.000396
S	1238	T1238T	acC	acT	1	1	B.1.258.17	0.000104
S	1238	T1238T	acC	acT	1	1	B.1.265	0.001271
S	1238	T1238T	acC	acT	1	1	B.1.281	0.021739
S	1238	T1238T	acC	acT	1	1	B.1.332	0.003497
S	1238	T1238T	acC	acT	1	1	B.1.341	0.022727
S	1238	T1238T	acC	acT	1	1	B.1.349	0.000715
S	1238	T1238T	acC	acT	1	1	B.1.369	0.000285
S	1238	T1238T	acC	acT	1	1	B.1.499	0.00105
S	1238	T1238T	acC	acT	1	1	B.1.503	0.002488
S	1238	T1238T	acC	acT	1	1	B.1.540	0.009709
S	1238	T1238T	acC	acT	1	1	B.31	0.003731
S	1238	T1238T	acC	acT	1	1	B.61	0.005747
S	1238	T1238T	acC	acT	1	1	P.1.7	0.000319
S	1238	T1238T	acC	acT	1	1	Q.7	0.001111
S	1238	T1238T	acC	acT	1	1	W.4	0.001351

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.