CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = T54T

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
N	54	T54T		syn	acC	acT	3254	3087	0.948679	28433-28435
N	54	T54T		syn	acC	acA	3254	145	0.0445605	28433-28435
N	54	T54T		syn	acC	acG	3254	22	0.00676091	28433-28435

Details of the mutation T54T 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
N	54	T54T	acC	acT	3087	3254	All	0.00059
N	54	T54T	acC	acA	145	3254	All	0.000028
N	54	T54T	acC	acG	22	3254	All	0.000004
N	54	T54T	acC	acT	550	567	B.1.1.7	0.000492
N	54	T54T	acC	acA	15	567	B.1.1.7	0.000013
N	54	T54T	acC	acG	2	567	B.1.1.7	0.000002
N	54	T54T	acC	acT	446	447	C.37	0.051764
N	54	T54T	acC	acA	1	447	C.37	0.000116
N	54	T54T	acC	acT	321	323	AY.44	0.001954
N	54	T54T	acC	acA	2	323	AY.44	0.000012
N	54	T54T	acC	acT	227	240	B.1.617.2	0.000855
N	54	T54T	acC	acA	11	240	B.1.617.2	0.000041
N	54	T54T	acC	acG	2	240	B.1.617.2	0.000008
N	54	T54T	acC	acT	178	178	B.1.429	0.004188
N	54	T54T	acC	acT	140	145	P.1	0.002206
N	54	T54T	acC	acA	3	145	P.1	0.000047
N	54	T54T	acC	acG	2	145	P.1	0.000032
N	54	T54T	acC	acT	103	130	AY.4	0.00016
N	54	T54T	acC	acA	27	130	AY.4	0.000042
N	54	T54T	acC	acT	123	123	B.1.526	0.002891
N	54	T54T	acC	acT	86	86	B.1.593	0.934783
N	54	T54T	acC	acT	66	66	R.1	0.005941
N	54	T54T	acC	acT	50	50	B.1.2	0.00044
N	54	T54T	acC	acT	36	44	B.1	0.00033
N	54	T54T	acC	acA	7	44	B.1	0.000064
N	54	T54T	acC	acG	1	44	B.1	0.000009
N	54	T54T	acC	acT	33	41	AY.43	0.000146
N	54	T54T	acC	acA	7	41	AY.43	0.000031
N	54	T54T	acC	acG	1	41	AY.43	0.000004
N	54	T54T	acC	acT	37	40	AY.25	0.000223
N	54	T54T	acC	acA	3	40	AY.25	0.000018
N	54	T54T	acC	acT	39	39	AY.4.2	0.000846
N	54	T54T	acC	acT	27	35	B.1.177	0.000356
N	54	T54T	acC	acA	8	35	B.1.177	0.000105
N	54	T54T	acC	acT	20	34	AY.3	0.000199
N	54	T54T	acC	acA	14	34	AY.3	0.000139
N	54	T54T	acC	acT	26	26	AY.46.6	0.001877
N	54	T54T	acC	acT	24	26	B.1.160	0.000749
N	54	T54T	acC	acA	2	26	B.1.160	0.000062
N	54	T54T	acC	acT	25	25	AY.102	0.000663
N	54	T54T	acC	acT	23	23	B.1.617.1	0.002966
N	54	T54T	acC	acT	18	21	AY.103	0.000112
N	54	T54T	acC	acA	3	21	AY.103	0.000019
N	54	T54T	acC	acT	18	18	B.1.351	0.000535
N	54	T54T	acC	acT	16	16	AY.29	0.000252
N	54	T54T	acC	acT	12	12	B.1.1.309	0.070175
N	54	T54T	acC	acT	12	12	B.1.110.3	0.008621
N	54	T54T	acC	acT	11	11	AY.118	0.000689
N	54	T54T	acC	acT	8	11	AY.20	0.000311
N	54	T54T	acC	acA	3	11	AY.20	0.000117
N	54	T54T	acC	acA	10	11	AY.34	0.00097
N	54	T54T	acC	acT	1	11	AY.34	0.000097
N	54	T54T	acC	acT	11	11	AY.7	0.002156
N	54	T54T	acC	acT	11	11	B.1.177.60	0.002403
N	54	T54T	acC	acT	11	11	B.1.637	0.000804
N	54	T54T	acC	acT	10	10	AY.100	0.00046
N	54	T54T	acC	acT	8	10	AY.33	0.000534
N	54	T54T	acC	acA	2	10	AY.33	0.000134
N	54	T54T	acC	acT	10	10	AY.5	0.000206
N	54	T54T	acC	acT	10	10	B.1.1	0.000181
N	54	T54T	acC	acT	8	9	AY.98.1	0.000387
N	54	T54T	acC	acG	1	9	AY.98.1	0.000048
N	54	T54T	acC	acT	9	9	B.1.1.298	0.007759
N	54	T54T	acC	acT	7	8	AY.26	0.000198
N	54	T54T	acC	acA	1	8	AY.26	0.000028
N	54	T54T	acC	acT	8	8	B.1.1.519	0.000318
N	54	T54T	acC	acT	8	8	B.1.1.70	0.002729
N	54	T54T	acC	acT	8	8	B.1.177.65	0.005323
N	54	T54T	acC	acT	7	8	B.1.621	0.00062
N	54	T54T	acC	acA	1	8	B.1.621	0.000089
N	54	T54T	acC	acT	7	7	Q.8	0.001154
N	54	T54T	acC	acT	6	6	AY.109	0.004438
N	54	T54T	acC	acT	4	6	AY.117	0.000338
N	54	T54T	acC	acA	2	6	AY.117	0.000169
N	54	T54T	acC	acT	4	6	AY.39	0.000099
N	54	T54T	acC	acA	2	6	AY.39	0.000049
N	54	T54T	acC	acT	6	6	B.1.1.214	0.000333
N	54	T54T	acC	acT	6	6	B.1.311	0.001647
N	54	T54T	acC	acT	6	6	C.36.3	0.003403
N	54	T54T	acC	acT	5	5	AY.1	0.001979
N	54	T54T	acC	acT	5	5	AY.113	0.000712
N	54	T54T	acC	acT	4	5	AY.119	0.000141
N	54	T54T	acC	acG	1	5	AY.119	0.000035
N	54	T54T	acC	acT	5	5	AY.36	0.000741
N	54	T54T	acC	acT	5	5	B.1.13	0.011876
N	54	T54T	acC	acT	5	5	B.1.177.4	0.001055
N	54	T54T	acC	acT	5	5	B.1.221	0.000355
N	54	T54T	acC	acT	5	5	B.1.575	0.001517
N	54	T54T	acC	acT	4	5	P.1.14	0.000191
N	54	T54T	acC	acA	1	5	P.1.14	0.000048
N	54	T54T	acC	acT	5	5	P.3	0.007974
N	54	T54T	acC	acT	4	4	AY.39.1	0.000158
N	54	T54T	acC	acT	4	4	AY.98	0.000316
N	54	T54T	acC	acT	4	4	B.1.232	0.002149
N	54	T54T	acC	acT	4	4	B.1.243	0.000278
N	54	T54T	acC	acT	4	4	B.1.258.17	0.000416
N	54	T54T	acC	acG	4	4	B.1.409	0.003125
N	54	T54T	acC	acT	4	4	B.1.427	0.000202
N	54	T54T	acC	acT	4	4	P.1.12	0.001936
N	54	T54T	acC	acT	2	3	A.23.1	0.001408
N	54	T54T	acC	acA	1	3	A.23.1	0.000704
N	54	T54T	acC	acG	2	3	AY.23	0.000139
N	54	T54T	acC	acT	1	3	AY.23	0.00007
N	54	T54T	acC	acT	3	3	AY.32	0.001597
N	54	T54T	acC	acT	3	3	AY.47	0.000093
N	54	T54T	acC	acT	3	3	AY.5.2	0.007389
N	54	T54T	acC	acT	3	3	AY.58	0.002722
N	54	T54T	acC	acA	2	3	AY.6	0.000082
N	54	T54T	acC	acT	1	3	AY.6	0.000041
N	54	T54T	acC	acT	3	3	AY.75	0.000168
N	54	T54T	acC	acT	3	3	B	0.000383
N	54	T54T	acC	acT	3	3	B.1.165	0.035714
N	54	T54T	acC	acA	3	3	B.1.422	0.002437
N	54	T54T	acC	acT	3	3	B.1.617.3	0.008955
N	54	T54T	acC	acT	3	3	C.36	0.002732
N	54	T54T	acC	acT	3	3	D.2	0.000225
N	54	T54T	acC	acT	3	3	Q.1	0.000379
N	54	T54T	acC	acT	2	2	A.1	0.000564
N	54	T54T	acC	acT	2	2	AY.108	0.002205
N	54	T54T	acC	acT	1	2	AY.111	0.000183
N	54	T54T	acC	acG	1	2	AY.111	0.000183
N	54	T54T	acC	acT	2	2	AY.116	0.000574
N	54	T54T	acC	acT	2	2	AY.116.1	0.000623
N	54	T54T	acC	acT	2	2	AY.120	0.000074
N	54	T54T	acC	acT	2	2	AY.42	0.00008
N	54	T54T	acC	acT	2	2	AY.46.4	0.000329
N	54	T54T	acC	acT	2	2	AY.5.3	0.000675
N	54	T54T	acC	acT	2	2	AY.75.1	0.000361
N	54	T54T	acC	acT	2	2	AY.85	0.000854
N	54	T54T	acC	acT	2	2	AY.94	0.000885
N	54	T54T	acC	acT	2	2	AY.99.2	0.000184
N	54	T54T	acC	acT	2	2	B.1.1.121	0.004854
N	54	T54T	acC	acT	2	2	B.1.1.171	0.007353
N	54	T54T	acC	acT	2	2	B.1.1.222	0.000408
N	54	T54T	acC	acT	2	2	B.1.1.25	0.001137
N	54	T54T	acC	acA	2	2	B.1.1.265	0.006309
N	54	T54T	acC	acT	2	2	B.1.1.277	0.001517
N	54	T54T	acC	acT	2	2	B.1.1.284	0.000215
N	54	T54T	acC	acT	2	2	B.1.1.434	0.000697
N	54	T54T	acC	acT	2	2	B.1.1.47	0.010695
N	54	T54T	acC	acT	2	2	B.1.160.20	0.017857
N	54	T54T	acC	acT	2	2	B.1.177.12	0.000303
N	54	T54T	acC	acT	2	2	B.1.177.21	0.000153
N	54	T54T	acC	acT	2	2	B.1.177.35	0.001382
N	54	T54T	acC	acT	2	2	B.1.177.81	0.000379
N	54	T54T	acC	acT	1	2	B.1.189	0.004292
N	54	T54T	acC	acA	1	2	B.1.189	0.004292
N	54	T54T	acC	acT	2	2	B.1.258	0.000133
N	54	T54T	acC	acA	2	2	B.1.351.2	0.000605
N	54	T54T	acC	acT	2	2	B.1.36.39	0.004435
N	54	T54T	acC	acT	2	2	B.1.396	0.001411
N	54	T54T	acC	acT	2	2	B.1.555	0.044444
N	54	T54T	acC	acT	2	2	B.1.595	0.000522
N	54	T54T	acC	acA	1	2	B.1.596	0.000087
N	54	T54T	acC	acT	1	2	B.1.596	0.000087
N	54	T54T	acC	acT	2	2	B.1.628	0.000705
N	54	T54T	acC	acT	2	2	C.37.1	0.005236
N	54	T54T	acC	acT	2	2	P.1.15	0.000465
N	54	T54T	acC	acG	1	1		0.055556
N	54	T54T	acC	acT	1	1	A.2	0.000662
N	54	T54T	acC	acG	1	1	A.2.5.2	0.001572
N	54	T54T	acC	acT	1	1	A.5	0.001923
N	54	T54T	acC	acT	1	1	AD.2	0.000219
N	54	T54T	acC	acT	1	1	AY.106	0.000335
N	54	T54T	acC	acT	1	1	AY.107	0.000466
N	54	T54T	acC	acT	1	1	AY.110	0.000113
N	54	T54T	acC	acT	1	1	AY.121	0.000135
N	54	T54T	acC	acT	1	1	AY.28	0.00189
N	54	T54T	acC	acT	1	1	AY.29.1	0.000221
N	54	T54T	acC	acA	1	1	AY.34.1	0.00051
N	54	T54T	acC	acT	1	1	AY.61	0.000105
N	54	T54T	acC	acT	1	1	AY.62	0.000436
N	54	T54T	acC	acT	1	1	AY.74	0.000116
N	54	T54T	acC	acA	1	1	AY.77	0.001127
N	54	T54T	acC	acT	1	1	AY.80	0.001129
N	54	T54T	acC	acT	1	1	AY.87	0.000833
N	54	T54T	acC	acT	1	1	AY.9.1	0.000084
N	54	T54T	acC	acT	1	1	AY.9.2	0.000037
N	54	T54T	acC	acG	1	1	AY.92	0.000287
N	54	T54T	acC	acT	1	1	B.1.1.1	0.000327
N	54	T54T	acC	acT	1	1	B.1.1.135	0.004695
N	54	T54T	acC	acT	1	1	B.1.1.141	0.002012
N	54	T54T	acC	acT	1	1	B.1.1.174	0.003378
N	54	T54T	acC	acT	1	1	B.1.1.207	0.001182
N	54	T54T	acC	acT	1	1	B.1.1.210	0.005714
N	54	T54T	acC	acT	1	1	B.1.1.28	0.000311
N	54	T54T	acC	acT	1	1	B.1.1.316	0.000925
N	54	T54T	acC	acT	1	1	B.1.1.372	0.000689
N	54	T54T	acC	acA	1	1	B.1.1.380	0.009804
N	54	T54T	acC	acT	1	1	B.1.1.389	0.006061
N	54	T54T	acC	acT	1	1	B.1.1.39	0.00051
N	54	T54T	acC	acT	1	1	B.1.1.402	0.011111
N	54	T54T	acC	acT	1	1	B.1.160.14	0.002119
N	54	T54T	acC	acT	1	1	B.1.160.8	0.001289
N	54	T54T	acC	acG	1	1	B.1.160.9	0.007194
N	54	T54T	acC	acT	1	1	B.1.177.63	0.002703
N	54	T54T	acC	acT	1	1	B.1.177.7	0.000165
N	54	T54T	acC	acT	1	1	B.1.177.73	0.000566
N	54	T54T	acC	acT	1	1	B.1.177.77	0.000726
N	54	T54T	acC	acT	1	1	B.1.177.83	0.001481
N	54	T54T	acC	acA	1	1	B.1.177.86	0.000183
N	54	T54T	acC	acT	1	1	B.1.195	0.005025
N	54	T54T	acC	acA	1	1	B.1.22	0.001318
N	54	T54T	acC	acT	1	1	B.1.234	0.000132
N	54	T54T	acC	acT	1	1	B.1.323	0.020833
N	54	T54T	acC	acT	1	1	B.1.343	0.020833
N	54	T54T	acC	acT	1	1	B.1.351.3	0.000876
N	54	T54T	acC	acT	1	1	B.1.36.17	0.000494
N	54	T54T	acC	acT	1	1	B.1.36.26	0.002857
N	54	T54T	acC	acA	1	1	B.1.36.29	0.000517
N	54	T54T	acC	acT	1	1	B.1.369	0.000285
N	54	T54T	acC	acT	1	1	B.1.389	0.001002
N	54	T54T	acC	acT	1	1	B.1.413	0.004255
N	54	T54T	acC	acT	1	1	B.1.429.1	0.012048
N	54	T54T	acC	acT	1	1	B.1.453	0.003236
N	54	T54T	acC	acT	1	1	B.1.466.2	0.000391
N	54	T54T	acC	acT	1	1	B.1.471	0.002732
N	54	T54T	acC	acA	1	1	B.1.488	0.2
N	54	T54T	acC	acT	1	1	B.1.499	0.00105
N	54	T54T	acC	acT	1	1	B.1.503	0.002488
N	54	T54T	acC	acT	1	1	B.1.524	0.001406
N	54	T54T	acC	acT	1	1	B.1.581	0.009434
N	54	T54T	acC	acA	1	1	B.1.582	0.000491
N	54	T54T	acC	acG	1	1	B.1.623	0.000536
N	54	T54T	acC	acT	1	1	B.11	0.005128
N	54	T54T	acC	acT	1	1	B.6	0.00091
N	54	T54T	acC	acT	1	1	B.61	0.005747
N	54	T54T	acC	acT	1	1	C.1	0.002392
N	54	T54T	acC	acT	1	1	P.1.1	0.000318
N	54	T54T	acC	acT	1	1	P.1.10	0.000269
N	54	T54T	acC	acT	1	1	P.1.10.1	0.00813
N	54	T54T	acC	acT	1	1	P.1.17	0.000162
N	54	T54T	acC	acT	1	1	P.1.2	0.001156
N	54	T54T	acC	acT	1	1	P.2	0.000187
N	54	T54T	acC	acT	1	1	Q.3	0.000145

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.