CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = E : Mut = T9I

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	9	T9I		nonsyn	aCa	aTa	5362	5362	1	26269-26271

Details of the mutation T9I 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	9	T9I	aCa	aTa	5362	5362	All	0.001026
E	9	T9I	aCa	aTa	2151	2151	B.1.1.7	0.001926
E	9	T9I	aCa	aTa	437	437	AY.3	0.004347
E	9	T9I	aCa	aTa	358	358	AY.4	0.000557
E	9	T9I	aCa	aTa	232	232	AY.9.2.1	0.458498
E	9	T9I	aCa	aTa	219	219	B.1.505	0.960526
E	9	T9I	aCa	aTa	131	131	B.1.617.2	0.000493
E	9	T9I	aCa	aTa	103	103	B.1.2	0.000907
E	9	T9I	aCa	aTa	102	102	B.1.1	0.00185
E	9	T9I	aCa	aTa	81	81	B.1	0.000742
E	9	T9I	aCa	aTa	73	73	P.1	0.00115
E	9	T9I	aCa	aTa	68	68	AY.44	0.000414
E	9	T9I	aCa	aTa	67	67	AY.103	0.000416
E	9	T9I	aCa	aTa	63	63	AY.25	0.000379
E	9	T9I	aCa	aTa	57	57	B.1.427	0.002878
E	9	T9I	aCa	aTa	50	50	B.1.628	0.017618
E	9	T9I	aCa	aTa	48	48	AY.43	0.000213
E	9	T9I	aCa	aTa	46	46	B.1.160	0.001435
E	9	T9I	aCa	aTa	42	42	B.1.177	0.000553
E	9	T9I	aCa	aTa	42	42	B.1.258	0.002795
E	9	T9I	aCa	aTa	40	40	AY.110	0.004508
E	9	T9I	aCa	aTa	35	35	B.1.1.519	0.00139
E	9	T9I	aCa	aTa	35	35	B.1.429	0.000824
E	9	T9I	aCa	aTa	32	32	AY.4.2	0.000694
E	9	T9I	aCa	aTa	29	29	B.1.526	0.000682
E	9	T9I	aCa	aTa	27	27	AY.3.1	0.002302
E	9	T9I	aCa	aTa	23	23	AY.5	0.000475
E	9	T9I	aCa	aTa	20	20	AY.102	0.00053
E	9	T9I	aCa	aTa	19	19	AY.39	0.00047
E	9	T9I	aCa	aTa	19	19	B.1.637	0.001388
E	9	T9I	aCa	aTa	18	18	B.1.361	0.023196
E	9	T9I	aCa	aTa	17	17	AY.47	0.000529
E	9	T9I	aCa	aTa	15	15	AY.119	0.00053
E	9	T9I	aCa	aTa	15	15	B.1.1.318	0.004526
E	9	T9I	aCa	aTa	14	14	AY.29	0.000221
E	9	T9I	aCa	aTa	14	14	C.37	0.001625
E	9	T9I	aCa	aTa	13	13	B.1.240	0.002802
E	9	T9I	aCa	aTa	13	13	B.1.243	0.000905
E	9	T9I	aCa	aTa	13	13	B.1.596	0.001133
E	9	T9I	aCa	aTa	12	12	B.1.369	0.003423
E	9	T9I	aCa	aTa	11	11	AY.20	0.000428
E	9	T9I	aCa	aTa	11	11	AY.42	0.000443
E	9	T9I	aCa	aTa	11	11	B.1.311	0.00302
E	9	T9I	aCa	aTa	10	10	AY.14	0.00088
E	9	T9I	aCa	aTa	10	10	B.1.36.36	0.00602
E	9	T9I	aCa	aTa	10	10	P.1.14	0.000478
E	9	T9I	aCa	aTa	9	9	AY.120	0.000335
E	9	T9I	aCa	aTa	9	9	B.1.428	0.009184
E	9	T9I	aCa	aTa	9	9	B.1.617.1	0.001161
E	9	T9I	aCa	aTa	8	8	AY.26	0.000226
E	9	T9I	aCa	aTa	8	8	AY.46.4	0.001316
E	9	T9I	aCa	aTa	8	8	B.1.1.222	0.001632
E	9	T9I	aCa	aTa	8	8	B.1.438.1	0.000858
E	9	T9I	aCa	aTa	8	8	B.1.525	0.000905
E	9	T9I	aCa	aTa	7	7	AY.117	0.000592
E	9	T9I	aCa	aTa	7	7	AY.118	0.000439
E	9	T9I	aCa	aTa	7	7	AY.75	0.000392
E	9	T9I	aCa	aTa	7	7	B.1.1.365	0.039106
E	9	T9I	aCa	aTa	7	7	B.1.223	0.019444
E	9	T9I	aCa	aTa	7	7	P.1.1	0.002224
E	9	T9I	aCa	aTa	7	7	R.1	0.00063
E	9	T9I	aCa	aTa	6	6	AY.54	0.000572
E	9	T9I	aCa	aTa	6	6	AY.9	0.000406
E	9	T9I	aCa	aTa	6	6	B.1.1.288	0.011494
E	9	T9I	aCa	aTa	6	6	B.1.1.304	0.016854
E	9	T9I	aCa	aTa	6	6	B.1.1.335	0.077922
E	9	T9I	aCa	aTa	6	6	B.1.351	0.000178
E	9	T9I	aCa	aTa	5	5	AY.113	0.000712
E	9	T9I	aCa	aTa	5	5	AY.33	0.000334
E	9	T9I	aCa	aTa	5	5	AY.45	0.000608
E	9	T9I	aCa	aTa	5	5	AY.46.6	0.000361
E	9	T9I	aCa	aTa	5	5	AY.61	0.000524
E	9	T9I	aCa	aTa	5	5	B.1.1.297	0.011186
E	9	T9I	aCa	aTa	5	5	B.1.1.33	0.002104
E	9	T9I	aCa	aTa	5	5	B.1.1.372	0.003444
E	9	T9I	aCa	aTa	5	5	B.1.177.81	0.000947
E	9	T9I	aCa	aTa	5	5	B.1.36	0.00073
E	9	T9I	aCa	aTa	5	5	B.1.470	0.007022
E	9	T9I	aCa	aTa	5	5	B.1.517	0.002135
E	9	T9I	aCa	aTa	5	5	Q.8	0.000825
E	9	T9I	aCa	aTa	4	4	AY.34	0.000388
E	9	T9I	aCa	aTa	4	4	AY.39.1	0.000158
E	9	T9I	aCa	aTa	4	4	AY.5.3	0.00135
E	9	T9I	aCa	aTa	4	4	AY.7.2	0.002237
E	9	T9I	aCa	aTa	4	4	AY.74	0.000463
E	9	T9I	aCa	aTa	4	4	AY.9.1	0.000335
E	9	T9I	aCa	aTa	4	4	AY.9.2	0.000147
E	9	T9I	aCa	aTa	4	4	B.1.1.28	0.001245
E	9	T9I	aCa	aTa	4	4	B.1.1.416	0.00362
E	9	T9I	aCa	aTa	4	4	B.1.108	0.023256
E	9	T9I	aCa	aTa	4	4	B.1.177.4	0.000844
E	9	T9I	aCa	aTa	4	4	B.1.177.7	0.000659
E	9	T9I	aCa	aTa	4	4	B.1.258.17	0.000416
E	9	T9I	aCa	aTa	4	4	C.35	0.003096
E	9	T9I	aCa	aTa	4	4	P.1.15	0.000929
E	9	T9I	aCa	aTa	4	4	P.2	0.000747
E	9	T9I	aCa	aTa	3	3	A.23.1	0.002113
E	9	T9I	aCa	aTa	3	3	AP.1	0.004505
E	9	T9I	aCa	aTa	3	3	AY.114	0.000693
E	9	T9I	aCa	aTa	3	3	AY.121	0.000406
E	9	T9I	aCa	aTa	3	3	AY.99.2	0.000276
E	9	T9I	aCa	aTa	3	3	B.1.1.371	0.03125
E	9	T9I	aCa	aTa	3	3	B.1.1.434	0.001046
E	9	T9I	aCa	aTa	3	3	B.1.1.70	0.001023
E	9	T9I	aCa	aTa	3	3	B.1.177.86	0.00055
E	9	T9I	aCa	aTa	3	3	B.1.214.3	0.021429
E	9	T9I	aCa	aTa	3	3	B.1.221	0.000213
E	9	T9I	aCa	aTa	3	3	B.1.232	0.001612
E	9	T9I	aCa	aTa	3	3	B.1.234	0.000396
E	9	T9I	aCa	aTa	3	3	B.1.527	0.011111
E	9	T9I	aCa	aTa	3	3	B.1.561	0.001191
E	9	T9I	aCa	aTa	3	3	B.1.582	0.001472
E	9	T9I	aCa	aTa	3	3	B.1.621.1	0.001517
E	9	T9I	aCa	aTa	3	3	Q.3	0.000435
E	9	T9I	aCa	aTa	2	2	AD.2	0.000438
E	9	T9I	aCa	aTa	2	2	AY.108	0.002205
E	9	T9I	aCa	aTa	2	2	AY.23	0.000139
E	9	T9I	aCa	aTa	2	2	AY.30	0.000791
E	9	T9I	aCa	aTa	2	2	AY.32	0.001065
E	9	T9I	aCa	aTa	2	2	AY.34.1	0.00102
E	9	T9I	aCa	aTa	2	2	AY.36	0.000296
E	9	T9I	aCa	aTa	2	2	AY.4.2.1	0.000298
E	9	T9I	aCa	aTa	2	2	AY.4.5	0.000215
E	9	T9I	aCa	aTa	2	2	AY.48	0.00093
E	9	T9I	aCa	aTa	2	2	AY.65	0.001066
E	9	T9I	aCa	aTa	2	2	AY.69	0.000373
E	9	T9I	aCa	aTa	2	2	AY.7	0.000392
E	9	T9I	aCa	aTa	2	2	AY.70	0.000417
E	9	T9I	aCa	aTa	2	2	AY.75.1	0.000361
E	9	T9I	aCa	aTa	2	2	AY.92	0.000575
E	9	T9I	aCa	aTa	2	2	B	0.000256
E	9	T9I	aCa	aTa	2	2	B.1.1.243	0.008163
E	9	T9I	aCa	aTa	2	2	B.1.1.277	0.001517
E	9	T9I	aCa	aTa	2	2	B.1.1.316	0.00185
E	9	T9I	aCa	aTa	2	2	B.1.1.348	0.001592
E	9	T9I	aCa	aTa	2	2	B.1.1.380	0.019608
E	9	T9I	aCa	aTa	2	2	B.1.1.398	0.006452
E	9	T9I	aCa	aTa	2	2	B.1.1.409	0.005666
E	9	T9I	aCa	aTa	2	2	B.1.1.526	0.007092
E	9	T9I	aCa	aTa	2	2	B.1.166	0.016949
E	9	T9I	aCa	aTa	2	2	B.1.349	0.00143
E	9	T9I	aCa	aTa	2	2	B.1.36.29	0.001035
E	9	T9I	aCa	aTa	2	2	B.1.36.9	0.006431
E	9	T9I	aCa	aTa	2	2	B.1.396	0.001411
E	9	T9I	aCa	aTa	2	2	B.1.499	0.002101
E	9	T9I	aCa	aTa	2	2	B.1.530	0.014286
E	9	T9I	aCa	aTa	2	2	B.1.577	0.001375
E	9	T9I	aCa	aTa	2	2	B.1.621	0.000177
E	9	T9I	aCa	aTa	2	2	B.58	0.020408
E	9	T9I	aCa	aTa	2	2	D.2	0.00015
E	9	T9I	aCa	aTa	2	2	Q.1	0.000253
E	9	T9I	aCa	aTa	1	1		0.055556
E	9	T9I	aCa	aTa	1	1	A.2	0.000662
E	9	T9I	aCa	aTa	1	1	AH.3	0.003802
E	9	T9I	aCa	aTa	1	1	AY.100	0.000046
E	9	T9I	aCa	aTa	1	1	AY.101	0.00049
E	9	T9I	aCa	aTa	1	1	AY.105	0.000643
E	9	T9I	aCa	aTa	1	1	AY.111	0.000183
E	9	T9I	aCa	aTa	1	1	AY.116	0.000287
E	9	T9I	aCa	aTa	1	1	AY.12	0.000316
E	9	T9I	aCa	aTa	1	1	AY.13	0.000161
E	9	T9I	aCa	aTa	1	1	AY.40	0.000964
E	9	T9I	aCa	aTa	1	1	AY.46	0.000104
E	9	T9I	aCa	aTa	1	1	AY.55	0.000917
E	9	T9I	aCa	aTa	1	1	AY.6	0.000041
E	9	T9I	aCa	aTa	1	1	AY.62	0.000436
E	9	T9I	aCa	aTa	1	1	AY.64	0.000595
E	9	T9I	aCa	aTa	1	1	AY.7.1	0.000113
E	9	T9I	aCa	aTa	1	1	AY.8	0.000606
E	9	T9I	aCa	aTa	1	1	AY.82	0.001357
E	9	T9I	aCa	aTa	1	1	AY.83	0.001724
E	9	T9I	aCa	aTa	1	1	AY.84	0.000437
E	9	T9I	aCa	aTa	1	1	AY.90	0.000684
E	9	T9I	aCa	aTa	1	1	AY.91	0.00073
E	9	T9I	aCa	aTa	1	1	AY.98.1	0.000048
E	9	T9I	aCa	aTa	1	1	AY.99	0.001049
E	9	T9I	aCa	aTa	1	1	B.1.1.10	0.001115
E	9	T9I	aCa	aTa	1	1	B.1.1.170	0.001247
E	9	T9I	aCa	aTa	1	1	B.1.1.171	0.003676
E	9	T9I	aCa	aTa	1	1	B.1.1.176	0.000439
E	9	T9I	aCa	aTa	1	1	B.1.1.198	0.001468
E	9	T9I	aCa	aTa	1	1	B.1.1.214	0.000055
E	9	T9I	aCa	aTa	1	1	B.1.1.216	0.00089
E	9	T9I	aCa	aTa	1	1	B.1.1.263	0.001558
E	9	T9I	aCa	aTa	1	1	B.1.1.284	0.000107
E	9	T9I	aCa	aTa	1	1	B.1.1.306	0.000438
E	9	T9I	aCa	aTa	1	1	B.1.1.311	0.000358
E	9	T9I	aCa	aTa	1	1	B.1.1.317	0.000412
E	9	T9I	aCa	aTa	1	1	B.1.1.326	0.001761
E	9	T9I	aCa	aTa	1	1	B.1.1.329	0.003846
E	9	T9I	aCa	aTa	1	1	B.1.1.39	0.00051
E	9	T9I	aCa	aTa	1	1	B.1.1.397	0.002252
E	9	T9I	aCa	aTa	1	1	B.1.1.413	0.006897
E	9	T9I	aCa	aTa	1	1	B.1.1.447	0.035714
E	9	T9I	aCa	aTa	1	1	B.1.1.466	0.008696
E	9	T9I	aCa	aTa	1	1	B.1.1.486	0.001577
E	9	T9I	aCa	aTa	1	1	B.1.1.50	0.000679
E	9	T9I	aCa	aTa	1	1	B.1.1.51	0.001718
E	9	T9I	aCa	aTa	1	1	B.1.1.52	0.012195
E	9	T9I	aCa	aTa	1	1	B.1.1.71	0.006061
E	9	T9I	aCa	aTa	1	1	B.1.1.83	0.00271
E	9	T9I	aCa	aTa	1	1	B.1.110.3	0.000718
E	9	T9I	aCa	aTa	1	1	B.1.146	0.004237
E	9	T9I	aCa	aTa	1	1	B.1.160.15	0.00495
E	9	T9I	aCa	aTa	1	1	B.1.160.28	0.002924
E	9	T9I	aCa	aTa	1	1	B.1.177.10	0.000878
E	9	T9I	aCa	aTa	1	1	B.1.177.11	0.001698
E	9	T9I	aCa	aTa	1	1	B.1.177.45	0.000381
E	9	T9I	aCa	aTa	1	1	B.1.177.54	0.000606
E	9	T9I	aCa	aTa	1	1	B.1.177.57	0.000281
E	9	T9I	aCa	aTa	1	1	B.1.212	0.016667
E	9	T9I	aCa	aTa	1	1	B.1.235	0.002519
E	9	T9I	aCa	aTa	1	1	B.1.258.21	0.007752
E	9	T9I	aCa	aTa	1	1	B.1.265	0.001271
E	9	T9I	aCa	aTa	1	1	B.1.270	0.005618
E	9	T9I	aCa	aTa	1	1	B.1.36.18	0.00042
E	9	T9I	aCa	aTa	1	1	B.1.36.27	0.000763
E	9	T9I	aCa	aTa	1	1	B.1.36.31	0.001751
E	9	T9I	aCa	aTa	1	1	B.1.36.35	0.002604
E	9	T9I	aCa	aTa	1	1	B.1.367	0.000792
E	9	T9I	aCa	aTa	1	1	B.1.371	0.001122
E	9	T9I	aCa	aTa	1	1	B.1.378	0.006849
E	9	T9I	aCa	aTa	1	1	B.1.382	0.008929
E	9	T9I	aCa	aTa	1	1	B.1.390	0.010638
E	9	T9I	aCa	aTa	1	1	B.1.391	0.001127
E	9	T9I	aCa	aTa	1	1	B.1.478	0.011765
E	9	T9I	aCa	aTa	1	1	B.1.497	0.000315
E	9	T9I	aCa	aTa	1	1	B.1.509	0.000866
E	9	T9I	aCa	aTa	1	1	B.1.529	0.055556
E	9	T9I	aCa	aTa	1	1	B.1.550	0.013699
E	9	T9I	aCa	aTa	1	1	B.1.568	0.001111
E	9	T9I	aCa	aTa	1	1	B.1.576	0.000907
E	9	T9I	aCa	aTa	1	1	B.1.580	0.004065
E	9	T9I	aCa	aTa	1	1	B.1.595	0.000261
E	9	T9I	aCa	aTa	1	1	B.1.619.1	0.000641
E	9	T9I	aCa	aTa	1	1	B.1.623	0.000536
E	9	T9I	aCa	aTa	1	1	B.38	0.02381
E	9	T9I	aCa	aTa	1	1	B.4	0.002208
E	9	T9I	aCa	aTa	1	1	B.40	0.000364
E	9	T9I	aCa	aTa	1	1	C.14	0.004329
E	9	T9I	aCa	aTa	1	1	C.36	0.000911
E	9	T9I	aCa	aTa	1	1	C.37.1	0.002618
E	9	T9I	aCa	aTa	1	1	P.1.13	0.000898
E	9	T9I	aCa	aTa	1	1	P.1.17	0.000162
E	9	T9I	aCa	aTa	1	1	P.1.2	0.001156
E	9	T9I	aCa	aTa	1	1	P.1.7	0.000319
E	9	T9I	aCa	aTa	1	1	P.7	0.004367
E	9	T9I	aCa	aTa	1	1	Q.4	0.000455

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.