CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : Mut = Y179Y

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
M	179	Y179Y		syn	taC	taT	10978	10978	1	27057-27059

Details of the mutation Y179Y 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
M	179	Y179Y	taC	taT	10978	10978	All	0.0021
M	179	Y179Y	taC	taT	2696	2696	B.1.1.7	0.002414
M	179	Y179Y	taC	taT	1448	1448	B.1.351	0.043044
M	179	Y179Y	taC	taT	791	791	D.2	0.059358
M	179	Y179Y	taC	taT	679	679	AY.4	0.001057
M	179	Y179Y	taC	taT	507	507	B.1.617.2	0.001909
M	179	Y179Y	taC	taT	387	387	AY.43	0.001715
M	179	Y179Y	taC	taT	379	379	AY.54	0.036137
M	179	Y179Y	taC	taT	318	318	B.1.2	0.0028
M	179	Y179Y	taC	taT	288	288	AY.39	0.007117
M	179	Y179Y	taC	taT	260	260	B.1.160	0.008109
M	179	Y179Y	taC	taT	214	214	AY.25	0.001287
M	179	Y179Y	taC	taT	168	168	AY.44	0.001023
M	179	Y179Y	taC	taT	139	139	P.1	0.00219
M	179	Y179Y	taC	taT	132	132	AY.103	0.00082
M	179	Y179Y	taC	taT	127	127	B.1.596	0.011067
M	179	Y179Y	taC	taT	121	121	B.1	0.001108
M	179	Y179Y	taC	taT	116	116	AY.3	0.001154
M	179	Y179Y	taC	taT	106	106	AY.118	0.006641
M	179	Y179Y	taC	taT	103	103	AY.119	0.003637
M	179	Y179Y	taC	taT	102	102	B.1.36.12	0.980769
M	179	Y179Y	taC	taT	87	87	B.1.429	0.002047
M	179	Y179Y	taC	taT	72	72	B.1.1	0.001306
M	179	Y179Y	taC	taT	71	71	AY.47	0.002208
M	179	Y179Y	taC	taT	71	71	B.1.177	0.000935
M	179	Y179Y	taC	taT	67	67	B.1.177.21	0.005123
M	179	Y179Y	taC	taT	57	57	AY.36	0.008448
M	179	Y179Y	taC	taT	49	49	B.1.1.1	0.016008
M	179	Y179Y	taC	taT	48	48	AY.42	0.001931
M	179	Y179Y	taC	taT	46	46	AY.5	0.00095
M	179	Y179Y	taC	taT	40	40	B.1.311	0.010983
M	179	Y179Y	taC	taT	38	38	B.1.1.325	0.974359
M	179	Y179Y	taC	taT	38	38	B.1.1.519	0.001509
M	179	Y179Y	taC	taT	37	37	AY.2	0.013177
M	179	Y179Y	taC	taT	37	37	B.1.526	0.00087
M	179	Y179Y	taC	taT	32	32	B.1.617.1	0.004127
M	179	Y179Y	taC	taT	30	30	AY.7	0.00588
M	179	Y179Y	taC	taT	30	30	B.1.234	0.003958
M	179	Y179Y	taC	taT	27	27	AY.102	0.000716
M	179	Y179Y	taC	taT	27	27	B.1.1.214	0.001497
M	179	Y179Y	taC	taT	26	26	B.1.177.81	0.004922
M	179	Y179Y	taC	taT	25	25	B.1.637	0.001827
M	179	Y179Y	taC	taT	25	25	C.37	0.002902
M	179	Y179Y	taC	taT	24	24	AY.27	0.001553
M	179	Y179Y	taC	taT	22	22	AY.4.2	0.000477
M	179	Y179Y	taC	taT	22	22	AY.98	0.001738
M	179	Y179Y	taC	taT	21	21	AY.20	0.000816
M	179	Y179Y	taC	taT	19	19	AY.98.1	0.00092
M	179	Y179Y	taC	taT	19	19	B.1.1.517	0.129252
M	179	Y179Y	taC	taT	16	16	AY.116.1	0.004983
M	179	Y179Y	taC	taT	14	14	AU.2	0.033898
M	179	Y179Y	taC	taT	14	14	AY.34	0.001358
M	179	Y179Y	taC	taT	14	14	AY.46.6	0.001011
M	179	Y179Y	taC	taT	14	14	B.1.1.174	0.047297
M	179	Y179Y	taC	taT	14	14	B.1.1.25	0.007959
M	179	Y179Y	taC	taT	14	14	B.1.177.86	0.002568
M	179	Y179Y	taC	taT	14	14	B.1.597	0.064815
M	179	Y179Y	taC	taT	13	13	AY.121	0.001759
M	179	Y179Y	taC	taT	12	12	AY.14	0.001056
M	179	Y179Y	taC	taT	12	12	B.1.1.63	0.00463
M	179	Y179Y	taC	taT	11	11	P.1.14	0.000526
M	179	Y179Y	taC	taT	11	11	Q.3	0.001595
M	179	Y179Y	taC	taT	10	10	AY.100	0.00046
M	179	Y179Y	taC	taT	10	10	AY.106	0.003349
M	179	Y179Y	taC	taT	10	10	AY.120	0.000372
M	179	Y179Y	taC	taT	10	10	B.1.177.60	0.002184
M	179	Y179Y	taC	taT	10	10	B.1.243	0.000696
M	179	Y179Y	taC	taT	10	10	B.1.427	0.000505
M	179	Y179Y	taC	taT	9	9	AY.29	0.000142
M	179	Y179Y	taC	taT	9	9	AY.46	0.000937
M	179	Y179Y	taC	taT	9	9	AY.46.3	0.008403
M	179	Y179Y	taC	taT	9	9	AY.9	0.000608
M	179	Y179Y	taC	taT	9	9	B.1.36	0.001313
M	179	Y179Y	taC	taT	9	9	B.1.438.1	0.000965
M	179	Y179Y	taC	taT	9	9	P.3	0.014354
M	179	Y179Y	taC	taT	8	8	B.1.1.33	0.003367
M	179	Y179Y	taC	taT	8	8	B.1.258	0.000532
M	179	Y179Y	taC	taT	8	8	B.1.466.2	0.00313
M	179	Y179Y	taC	taT	8	8	B.1.621	0.000708
M	179	Y179Y	taC	taT	7	7	AY.75	0.000392
M	179	Y179Y	taC	taT	7	7	B.1.1.153	0.007667
M	179	Y179Y	taC	taT	7	7	B.1.1.26	0.036649
M	179	Y179Y	taC	taT	7	7	B.1.1.28	0.002179
M	179	Y179Y	taC	taT	7	7	B.1.409	0.005469
M	179	Y179Y	taC	taT	7	7	B.1.582	0.003435
M	179	Y179Y	taC	taT	6	6	AE.1	0.068182
M	179	Y179Y	taC	taT	6	6	AY.110	0.000676
M	179	Y179Y	taC	taT	6	6	AY.116	0.001721
M	179	Y179Y	taC	taT	6	6	AY.33	0.000401
M	179	Y179Y	taC	taT	6	6	AY.4.5	0.000645
M	179	Y179Y	taC	taT	6	6	AY.45	0.00073
M	179	Y179Y	taC	taT	6	6	AY.9.2	0.00022
M	179	Y179Y	taC	taT	6	6	B.1.324	0.009631
M	179	Y179Y	taC	taT	6	6	B.1.369	0.001711
M	179	Y179Y	taC	taT	5	5	AY.23	0.000349
M	179	Y179Y	taC	taT	5	5	AY.3.1	0.000426
M	179	Y179Y	taC	taT	5	5	AY.38	0.002496
M	179	Y179Y	taC	taT	5	5	AY.39.1.1	0.003623
M	179	Y179Y	taC	taT	5	5	AY.6	0.000206
M	179	Y179Y	taC	taT	5	5	AY.99.2	0.000461
M	179	Y179Y	taC	taT	5	5	B.1.1.222	0.00102
M	179	Y179Y	taC	taT	5	5	B.1.1.371	0.052083
M	179	Y179Y	taC	taT	5	5	B.1.1.372	0.003444
M	179	Y179Y	taC	taT	5	5	B.1.36.31	0.008757
M	179	Y179Y	taC	taT	5	5	B.1.381	0.039062
M	179	Y179Y	taC	taT	5	5	B.1.525	0.000566
M	179	Y179Y	taC	taT	5	5	B.1.623	0.002682
M	179	Y179Y	taC	taT	5	5	P.1.3	0.172414
M	179	Y179Y	taC	taT	5	5	P.1.7	0.001596
M	179	Y179Y	taC	taT	4	4	AY.117	0.000338
M	179	Y179Y	taC	taT	4	4	AY.16	0.001519
M	179	Y179Y	taC	taT	4	4	AY.72	0.005442
M	179	Y179Y	taC	taT	4	4	AY.75.1	0.000721
M	179	Y179Y	taC	taT	4	4	AY.79	0.004843
M	179	Y179Y	taC	taT	4	4	AY.92	0.001149
M	179	Y179Y	taC	taT	4	4	B	0.000511
M	179	Y179Y	taC	taT	4	4	B.1.160.30	0.011905
M	179	Y179Y	taC	taT	4	4	B.1.221	0.000284
M	179	Y179Y	taC	taT	4	4	B.1.36.29	0.002069
M	179	Y179Y	taC	taT	4	4	B.1.499	0.004202
M	179	Y179Y	taC	taT	4	4	P.1.15	0.000929
M	179	Y179Y	taC	taT	4	4	P.2	0.000747
M	179	Y179Y	taC	taT	4	4	Q.1	0.000505
M	179	Y179Y	taC	taT	4	4	Q.8	0.00066
M	179	Y179Y	taC	taT	4	4	R.1	0.00036
M	179	Y179Y	taC	taT	4	4	W.4	0.005405
M	179	Y179Y	taC	taT	3	3	AY.1	0.001187
M	179	Y179Y	taC	taT	3	3	AY.13	0.000483
M	179	Y179Y	taC	taT	3	3	AY.46.2	0.001906
M	179	Y179Y	taC	taT	3	3	AY.5.4	0.00083
M	179	Y179Y	taC	taT	3	3	AY.57	0.001969
M	179	Y179Y	taC	taT	3	3	AY.62	0.001307
M	179	Y179Y	taC	taT	3	3	AY.65	0.001599
M	179	Y179Y	taC	taT	3	3	AY.84	0.001312
M	179	Y179Y	taC	taT	3	3	AY.9.1	0.000251
M	179	Y179Y	taC	taT	3	3	B.1.1.348	0.002389
M	179	Y179Y	taC	taT	3	3	B.1.177.59	0.048387
M	179	Y179Y	taC	taT	3	3	B.1.177.7	0.000495
M	179	Y179Y	taC	taT	3	3	B.1.177.73	0.001699
M	179	Y179Y	taC	taT	3	3	B.1.240	0.000647
M	179	Y179Y	taC	taT	3	3	B.1.258.21	0.023256
M	179	Y179Y	taC	taT	3	3	B.1.375	0.002459
M	179	Y179Y	taC	taT	3	3	B.1.400	0.001287
M	179	Y179Y	taC	taT	3	3	B.1.471	0.008197
M	179	Y179Y	taC	taT	3	3	B.1.551	0.003871
M	179	Y179Y	taC	taT	3	3	B.1.575	0.00091
M	179	Y179Y	taC	taT	3	3	B.1.628	0.001057
M	179	Y179Y	taC	taT	2	2	AY.108	0.002205
M	179	Y179Y	taC	taT	2	2	AY.113	0.000285
M	179	Y179Y	taC	taT	2	2	AY.15	0.004444
M	179	Y179Y	taC	taT	2	2	AY.32	0.001065
M	179	Y179Y	taC	taT	2	2	AY.35	0.000466
M	179	Y179Y	taC	taT	2	2	AY.41	0.000588
M	179	Y179Y	taC	taT	2	2	AY.46.1	0.002053
M	179	Y179Y	taC	taT	2	2	AY.46.5	0.000397
M	179	Y179Y	taC	taT	2	2	AY.49	0.00639
M	179	Y179Y	taC	taT	2	2	AY.55	0.001835
M	179	Y179Y	taC	taT	2	2	AY.61	0.00021
M	179	Y179Y	taC	taT	2	2	AY.89	0.009804
M	179	Y179Y	taC	taT	2	2	AZ.2	0.001642
M	179	Y179Y	taC	taT	2	2	B.1.1.205	0.007435
M	179	Y179Y	taC	taT	2	2	B.1.1.216	0.001781
M	179	Y179Y	taC	taT	2	2	B.1.1.316	0.00185
M	179	Y179Y	taC	taT	2	2	B.1.1.354	0.008772
M	179	Y179Y	taC	taT	2	2	B.1.1.434	0.000697
M	179	Y179Y	taC	taT	2	2	B.1.1.518	0.012658
M	179	Y179Y	taC	taT	2	2	B.1.147	0.001512
M	179	Y179Y	taC	taT	2	2	B.1.177.11	0.003396
M	179	Y179Y	taC	taT	2	2	B.1.177.12	0.000303
M	179	Y179Y	taC	taT	2	2	B.1.177.16	0.001329
M	179	Y179Y	taC	taT	2	2	B.1.177.54	0.001213
M	179	Y179Y	taC	taT	2	2	B.1.177.75	0.002081
M	179	Y179Y	taC	taT	2	2	B.1.36.27	0.001527
M	179	Y179Y	taC	taT	2	2	B.1.367	0.001585
M	179	Y179Y	taC	taT	2	2	B.1.465	0.007605
M	179	Y179Y	taC	taT	2	2	B.1.473	0.038462
M	179	Y179Y	taC	taT	2	2	B.1.595	0.000522
M	179	Y179Y	taC	taT	2	2	B.29	0.007018
M	179	Y179Y	taC	taT	2	2	B.40	0.000729
M	179	Y179Y	taC	taT	2	2	C.35	0.001548
M	179	Y179Y	taC	taT	2	2	P.1.16	0.000748
M	179	Y179Y	taC	taT	2	2	Q.2	0.001227
M	179	Y179Y	taC	taT	1	1	A	0.000387
M	179	Y179Y	taC	taT	1	1	A.2.2	0.001689
M	179	Y179Y	taC	taT	1	1	A.2.3	0.004739
M	179	Y179Y	taC	taT	1	1	A.23.1	0.000704
M	179	Y179Y	taC	taT	1	1	AY.10	0.00053
M	179	Y179Y	taC	taT	1	1	AY.101	0.00049
M	179	Y179Y	taC	taT	1	1	AY.120.2.1	0.000498
M	179	Y179Y	taC	taT	1	1	AY.26	0.000028
M	179	Y179Y	taC	taT	1	1	AY.30	0.000396
M	179	Y179Y	taC	taT	1	1	AY.39.1	0.00004
M	179	Y179Y	taC	taT	1	1	AY.4.2.1	0.000149
M	179	Y179Y	taC	taT	1	1	AY.4.3	0.000842
M	179	Y179Y	taC	taT	1	1	AY.46.4	0.000165
M	179	Y179Y	taC	taT	1	1	AY.48	0.000465
M	179	Y179Y	taC	taT	1	1	AY.5.3	0.000337
M	179	Y179Y	taC	taT	1	1	AY.59	0.00053
M	179	Y179Y	taC	taT	1	1	AY.64	0.000595
M	179	Y179Y	taC	taT	1	1	AY.71	0.000475
M	179	Y179Y	taC	taT	1	1	AY.74	0.000116
M	179	Y179Y	taC	taT	1	1	AY.78	0.001541
M	179	Y179Y	taC	taT	1	1	AY.8	0.000606
M	179	Y179Y	taC	taT	1	1	AY.99	0.001049
M	179	Y179Y	taC	taT	1	1	B.1.1.111	0.014706
M	179	Y179Y	taC	taT	1	1	B.1.1.141	0.002012
M	179	Y179Y	taC	taT	1	1	B.1.1.161	0.003534
M	179	Y179Y	taC	taT	1	1	B.1.1.189	0.001513
M	179	Y179Y	taC	taT	1	1	B.1.1.198	0.001468
M	179	Y179Y	taC	taT	1	1	B.1.1.231	0.003096
M	179	Y179Y	taC	taT	1	1	B.1.1.244	0.015385
M	179	Y179Y	taC	taT	1	1	B.1.1.284	0.000107
M	179	Y179Y	taC	taT	1	1	B.1.1.306	0.000438
M	179	Y179Y	taC	taT	1	1	B.1.1.351	0.002793
M	179	Y179Y	taC	taT	1	1	B.1.1.373	0.02381
M	179	Y179Y	taC	taT	1	1	B.1.1.378	0.007299
M	179	Y179Y	taC	taT	1	1	B.1.1.39	0.00051
M	179	Y179Y	taC	taT	1	1	B.1.1.397	0.002252
M	179	Y179Y	taC	taT	1	1	B.1.1.404	0.015873
M	179	Y179Y	taC	taT	1	1	B.1.1.409	0.002833
M	179	Y179Y	taC	taT	1	1	B.1.1.413	0.006897
M	179	Y179Y	taC	taT	1	1	B.1.1.419	0.007407
M	179	Y179Y	taC	taT	1	1	B.1.1.507	0.008696
M	179	Y179Y	taC	taT	1	1	B.1.111	0.001175
M	179	Y179Y	taC	taT	1	1	B.1.149	0.003425
M	179	Y179Y	taC	taT	1	1	B.1.160.25	0.011111
M	179	Y179Y	taC	taT	1	1	B.1.177.19	0.001431
M	179	Y179Y	taC	taT	1	1	B.1.177.20	0.001517
M	179	Y179Y	taC	taT	1	1	B.1.177.28	0.007407
M	179	Y179Y	taC	taT	1	1	B.1.177.33	0.001645
M	179	Y179Y	taC	taT	1	1	B.1.177.38	0.010417
M	179	Y179Y	taC	taT	1	1	B.1.177.4	0.000211
M	179	Y179Y	taC	taT	1	1	B.1.177.42	0.000894
M	179	Y179Y	taC	taT	1	1	B.1.177.43	0.001477
M	179	Y179Y	taC	taT	1	1	B.1.177.50	0.004695
M	179	Y179Y	taC	taT	1	1	B.1.177.65	0.000665
M	179	Y179Y	taC	taT	1	1	B.1.177.87	0.000728
M	179	Y179Y	taC	taT	1	1	B.1.214.2	0.0006
M	179	Y179Y	taC	taT	1	1	B.1.243.1	0.022222
M	179	Y179Y	taC	taT	1	1	B.1.250	0.014493
M	179	Y179Y	taC	taT	1	1	B.1.258.16	0.001637
M	179	Y179Y	taC	taT	1	1	B.1.265	0.001271
M	179	Y179Y	taC	taT	1	1	B.1.279	0.000514
M	179	Y179Y	taC	taT	1	1	B.1.280	0.007143
M	179	Y179Y	taC	taT	1	1	B.1.343	0.020833
M	179	Y179Y	taC	taT	1	1	B.1.351.3	0.000876
M	179	Y179Y	taC	taT	1	1	B.1.36.10	0.004785
M	179	Y179Y	taC	taT	1	1	B.1.398	0.002976
M	179	Y179Y	taC	taT	1	1	B.1.415.1	0.007576
M	179	Y179Y	taC	taT	1	1	B.1.436	0.001029
M	179	Y179Y	taC	taT	1	1	B.1.456	0.003268
M	179	Y179Y	taC	taT	1	1	B.1.459	0.004082
M	179	Y179Y	taC	taT	1	1	B.1.509	0.000866
M	179	Y179Y	taC	taT	1	1	B.1.527	0.003704
M	179	Y179Y	taC	taT	1	1	B.1.538	0.008065
M	179	Y179Y	taC	taT	1	1	B.1.549	0.007194
M	179	Y179Y	taC	taT	1	1	B.1.561	0.000397
M	179	Y179Y	taC	taT	1	1	B.1.576	0.000907
M	179	Y179Y	taC	taT	1	1	B.1.577	0.000687
M	179	Y179Y	taC	taT	1	1	B.1.587	0.001898
M	179	Y179Y	taC	taT	1	1	B.1.609	0.000479
M	179	Y179Y	taC	taT	1	1	B.1.619	0.000871
M	179	Y179Y	taC	taT	1	1	B.3.1	0.001658
M	179	Y179Y	taC	taT	1	1	B.4.1	0.018868
M	179	Y179Y	taC	taT	1	1	C.22	0.071429
M	179	Y179Y	taC	taT	1	1	C.36	0.000911
M	179	Y179Y	taC	taT	1	1	N.5	0.001767
M	179	Y179Y	taC	taT	1	1	N.9	0.005952
M	179	Y179Y	taC	taT	1	1	P.1.1	0.000318
M	179	Y179Y	taC	taT	1	1	P.1.12	0.000484
M	179	Y179Y	taC	taT	1	1	P.6	0.003145
M	179	Y179Y	taC	taT	1	1	Z.1	0.00289

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.