CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 229 & Codon = aTc

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
ORF3a	229	T229I		nonsyn	aCc	aTc	3955	3955	1	26077-26079

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
ORF3a	229	T229I	aCc	aTc	3955	3955	All	0.000756
ORF3a	229	T229I	aCc	aTc	953	953	B.1.1.7	0.000853
ORF3a	229	T229I	aCc	aTc	479	479	AY.4	0.000746
ORF3a	229	T229I	aCc	aTc	205	205	AY.103	0.001273
ORF3a	229	T229I	aCc	aTc	176	176	AY.25	0.001059
ORF3a	229	T229I	aCc	aTc	163	163	AY.44	0.000992
ORF3a	229	T229I	aCc	aTc	113	113	B.1	0.001035
ORF3a	229	T229I	aCc	aTc	111	111	B.1.160	0.003462
ORF3a	229	T229I	aCc	aTc	92	92	AY.26	0.002605
ORF3a	229	T229I	aCc	aTc	86	86	B.1.617.2	0.000324
ORF3a	229	T229I	aCc	aTc	73	73	B.1.177.54	0.044269
ORF3a	229	T229I	aCc	aTc	68	68	AY.39	0.00168
ORF3a	229	T229I	aCc	aTc	64	64	B.1.177.82	0.030549
ORF3a	229	T229I	aCc	aTc	62	62	B.1.2	0.000546
ORF3a	229	T229I	aCc	aTc	60	60	P.1	0.000945
ORF3a	229	T229I	aCc	aTc	58	58	B.1.258.9	0.29
ORF3a	229	T229I	aCc	aTc	44	44	AY.47	0.001369
ORF3a	229	T229I	aCc	aTc	43	43	AY.120	0.001599
ORF3a	229	T229I	aCc	aTc	42	42	AY.39.1	0.001664
ORF3a	229	T229I	aCc	aTc	42	42	AY.43	0.000186
ORF3a	229	T229I	aCc	aTc	42	42	B.1.536	1
ORF3a	229	T229I	aCc	aTc	38	38	AY.4.2	0.000824
ORF3a	229	T229I	aCc	aTc	36	36	B.1.177	0.000474
ORF3a	229	T229I	aCc	aTc	31	31	AY.5	0.00064
ORF3a	229	T229I	aCc	aTc	30	30	R.1	0.0027
ORF3a	229	T229I	aCc	aTc	29	29	AY.102	0.000769
ORF3a	229	T229I	aCc	aTc	28	28	B.1.1	0.000508
ORF3a	229	T229I	aCc	aTc	26	26	B.1.1.519	0.001032
ORF3a	229	T229I	aCc	aTc	26	26	C.37	0.003018
ORF3a	229	T229I	aCc	aTc	24	24	B.1.311	0.00659
ORF3a	229	T229I	aCc	aTc	23	23	B.1.258	0.001531
ORF3a	229	T229I	aCc	aTc	22	22	AY.3	0.000219
ORF3a	229	T229I	aCc	aTc	22	22	B.1.596	0.001917
ORF3a	229	T229I	aCc	aTc	20	20	AY.20	0.000777
ORF3a	229	T229I	aCc	aTc	20	20	B.1.1.219	0.1
ORF3a	229	T229I	aCc	aTc	18	18	B.1.429	0.000424
ORF3a	229	T229I	aCc	aTc	17	17	AY.29	0.000268
ORF3a	229	T229I	aCc	aTc	14	14	B.1.258.14	0.013725
ORF3a	229	T229I	aCc	aTc	13	13	AY.119	0.000459
ORF3a	229	T229I	aCc	aTc	12	12	B.1.1.214	0.000665
ORF3a	229	T229I	aCc	aTc	12	12	B.1.36	0.001751
ORF3a	229	T229I	aCc	aTc	12	12	B.1.427	0.000606
ORF3a	229	T229I	aCc	aTc	12	12	B.1.526	0.000282
ORF3a	229	T229I	aCc	aTc	12	12	D.2	0.0009
ORF3a	229	T229I	aCc	aTc	12	12	P.1.10	0.003234
ORF3a	229	T229I	aCc	aTc	12	12	P.1.14	0.000574
ORF3a	229	T229I	aCc	aTc	11	11	AY.42	0.000443
ORF3a	229	T229I	aCc	aTc	10	10	Q.1	0.001263
ORF3a	229	T229I	aCc	aTc	9	9	B.1.1.217	0.032727
ORF3a	229	T229I	aCc	aTc	9	9	B.1.221.1	0.026163
ORF3a	229	T229I	aCc	aTc	9	9	B.1.588	0.008189
ORF3a	229	T229I	aCc	aTc	8	8	AY.99.2	0.000737
ORF3a	229	T229I	aCc	aTc	8	8	B.1.621	0.000708
ORF3a	229	T229I	aCc	aTc	7	7	AY.46	0.000729
ORF3a	229	T229I	aCc	aTc	7	7	B.1.1.220	0.013011
ORF3a	229	T229I	aCc	aTc	7	7	B.1.1.371	0.072917
ORF3a	229	T229I	aCc	aTc	7	7	B.1.108	0.040698
ORF3a	229	T229I	aCc	aTc	7	7	B.1.221	0.000497
ORF3a	229	T229I	aCc	aTc	7	7	B.1.243	0.000487
ORF3a	229	T229I	aCc	aTc	7	7	B.1.595	0.001827
ORF3a	229	T229I	aCc	aTc	6	6	AY.100	0.000276
ORF3a	229	T229I	aCc	aTc	6	6	AY.23	0.000418
ORF3a	229	T229I	aCc	aTc	6	6	AY.36	0.000889
ORF3a	229	T229I	aCc	aTc	6	6	AY.45	0.00073
ORF3a	229	T229I	aCc	aTc	6	6	B.1.1.10	0.006689
ORF3a	229	T229I	aCc	aTc	6	6	B.1.177.60	0.001311
ORF3a	229	T229I	aCc	aTc	6	6	B.1.351	0.000178
ORF3a	229	T229I	aCc	aTc	6	6	B.1.438.1	0.000644
ORF3a	229	T229I	aCc	aTc	6	6	B.1.517	0.002562
ORF3a	229	T229I	aCc	aTc	6	6	B.11	0.030769
ORF3a	229	T229I	aCc	aTc	5	5	AY.111	0.000916
ORF3a	229	T229I	aCc	aTc	5	5	AY.121	0.000677
ORF3a	229	T229I	aCc	aTc	5	5	AY.33	0.000334
ORF3a	229	T229I	aCc	aTc	5	5	AY.6	0.000206
ORF3a	229	T229I	aCc	aTc	5	5	B.1.1.277	0.003794
ORF3a	229	T229I	aCc	aTc	5	5	B.1.177.4	0.001055
ORF3a	229	T229I	aCc	aTc	5	5	B.1.258.17	0.00052
ORF3a	229	T229I	aCc	aTc	5	5	Q.8	0.000825
ORF3a	229	T229I	aCc	aTc	4	4	AY.113	0.00057
ORF3a	229	T229I	aCc	aTc	4	4	AY.120.1	0.001284
ORF3a	229	T229I	aCc	aTc	4	4	AY.32	0.00213
ORF3a	229	T229I	aCc	aTc	4	4	AY.61	0.000419
ORF3a	229	T229I	aCc	aTc	4	4	B.1.1.222	0.000816
ORF3a	229	T229I	aCc	aTc	4	4	B.1.1.311	0.001433
ORF3a	229	T229I	aCc	aTc	4	4	B.1.177.86	0.000734
ORF3a	229	T229I	aCc	aTc	4	4	B.1.478	0.047059
ORF3a	229	T229I	aCc	aTc	4	4	B.1.637	0.000292
ORF3a	229	T229I	aCc	aTc	4	4	Q.4	0.001819
ORF3a	229	T229I	aCc	aTc	3	3	AY.117	0.000254
ORF3a	229	T229I	aCc	aTc	3	3	AY.3.1	0.000256
ORF3a	229	T229I	aCc	aTc	3	3	AY.75	0.000168
ORF3a	229	T229I	aCc	aTc	3	3	AY.75.1	0.000541
ORF3a	229	T229I	aCc	aTc	3	3	AY.86	0.00249
ORF3a	229	T229I	aCc	aTc	3	3	AY.9.1	0.000251
ORF3a	229	T229I	aCc	aTc	3	3	AY.98	0.000237
ORF3a	229	T229I	aCc	aTc	3	3	B.1.1.25	0.001706
ORF3a	229	T229I	aCc	aTc	3	3	B.1.110	0.013575
ORF3a	229	T229I	aCc	aTc	3	3	B.1.177.21	0.000229
ORF3a	229	T229I	aCc	aTc	3	3	B.1.258.3	0.005025
ORF3a	229	T229I	aCc	aTc	3	3	B.1.318	0.115385
ORF3a	229	T229I	aCc	aTc	3	3	B.1.400	0.001287
ORF3a	229	T229I	aCc	aTc	3	3	B.1.509	0.002597
ORF3a	229	T229I	aCc	aTc	3	3	B.1.564	0.001278
ORF3a	229	T229I	aCc	aTc	3	3	B.1.619.1	0.001924
ORF3a	229	T229I	aCc	aTc	3	3	Q.3	0.000435
ORF3a	229	T229I	aCc	aTc	2	2	AY.16.1	0.00094
ORF3a	229	T229I	aCc	aTc	2	2	AY.29.1	0.000441
ORF3a	229	T229I	aCc	aTc	2	2	AY.46.2	0.001271
ORF3a	229	T229I	aCc	aTc	2	2	AY.59	0.001059
ORF3a	229	T229I	aCc	aTc	2	2	AY.71	0.00095
ORF3a	229	T229I	aCc	aTc	2	2	AY.77	0.002255
ORF3a	229	T229I	aCc	aTc	2	2	AY.8	0.001212
ORF3a	229	T229I	aCc	aTc	2	2	AY.95	0.001522
ORF3a	229	T229I	aCc	aTc	2	2	AY.97	0.003401
ORF3a	229	T229I	aCc	aTc	2	2	AY.98.1	0.000097
ORF3a	229	T229I	aCc	aTc	2	2	B.1.1.382	0.071429
ORF3a	229	T229I	aCc	aTc	2	2	B.1.1.39	0.001019
ORF3a	229	T229I	aCc	aTc	2	2	B.1.1.63	0.000772
ORF3a	229	T229I	aCc	aTc	2	2	B.1.127	0.004396
ORF3a	229	T229I	aCc	aTc	2	2	B.1.36.39	0.004435
ORF3a	229	T229I	aCc	aTc	2	2	B.1.369	0.00057
ORF3a	229	T229I	aCc	aTc	2	2	B.1.525	0.000226
ORF3a	229	T229I	aCc	aTc	2	2	B.1.564.1	0.003155
ORF3a	229	T229I	aCc	aTc	2	2	B.1.565	0.001621
ORF3a	229	T229I	aCc	aTc	2	2	B.1.575	0.000607
ORF3a	229	T229I	aCc	aTc	2	2	B.1.576	0.001813
ORF3a	229	T229I	aCc	aTc	2	2	B.1.597	0.009259
ORF3a	229	T229I	aCc	aTc	2	2	B.1.617.1	0.000258
ORF3a	229	T229I	aCc	aTc	2	2	B.40	0.000729
ORF3a	229	T229I	aCc	aTc	2	2	C.36.2	0.068966
ORF3a	229	T229I	aCc	aTc	2	2	C.37.1	0.005236
ORF3a	229	T229I	aCc	aTc	2	2	P.1.2	0.002312
ORF3a	229	T229I	aCc	aTc	2	2	P.1.7	0.000639
ORF3a	229	T229I	aCc	aTc	1	1	A.1	0.000282
ORF3a	229	T229I	aCc	aTc	1	1	A.23.1	0.000704
ORF3a	229	T229I	aCc	aTc	1	1	AY.101	0.00049
ORF3a	229	T229I	aCc	aTc	1	1	AY.104	0.001984
ORF3a	229	T229I	aCc	aTc	1	1	AY.106	0.000335
ORF3a	229	T229I	aCc	aTc	1	1	AY.109	0.00074
ORF3a	229	T229I	aCc	aTc	1	1	AY.116	0.000287
ORF3a	229	T229I	aCc	aTc	1	1	AY.16	0.00038
ORF3a	229	T229I	aCc	aTc	1	1	AY.21	0.001898
ORF3a	229	T229I	aCc	aTc	1	1	AY.23.1	0.000417
ORF3a	229	T229I	aCc	aTc	1	1	AY.27	0.000065
ORF3a	229	T229I	aCc	aTc	1	1	AY.30	0.000396
ORF3a	229	T229I	aCc	aTc	1	1	AY.34	0.000097
ORF3a	229	T229I	aCc	aTc	1	1	AY.38	0.000499
ORF3a	229	T229I	aCc	aTc	1	1	AY.4.5	0.000107
ORF3a	229	T229I	aCc	aTc	1	1	AY.41	0.000294
ORF3a	229	T229I	aCc	aTc	1	1	AY.46.3	0.000934
ORF3a	229	T229I	aCc	aTc	1	1	AY.46.6	0.000072
ORF3a	229	T229I	aCc	aTc	1	1	AY.5.4	0.000277
ORF3a	229	T229I	aCc	aTc	1	1	AY.56	0.001605
ORF3a	229	T229I	aCc	aTc	1	1	AY.58	0.000907
ORF3a	229	T229I	aCc	aTc	1	1	AY.62	0.000436
ORF3a	229	T229I	aCc	aTc	1	1	AY.64	0.000595
ORF3a	229	T229I	aCc	aTc	1	1	AY.69	0.000187
ORF3a	229	T229I	aCc	aTc	1	1	AY.70	0.000209
ORF3a	229	T229I	aCc	aTc	1	1	AY.72	0.001361
ORF3a	229	T229I	aCc	aTc	1	1	AY.84	0.000437
ORF3a	229	T229I	aCc	aTc	1	1	AY.85	0.000427
ORF3a	229	T229I	aCc	aTc	1	1	AY.9	0.000068
ORF3a	229	T229I	aCc	aTc	1	1	AY.9.2	0.000037
ORF3a	229	T229I	aCc	aTc	1	1	AY.91	0.00073
ORF3a	229	T229I	aCc	aTc	1	1	AY.92	0.000287
ORF3a	229	T229I	aCc	aTc	1	1	AY.99	0.001049
ORF3a	229	T229I	aCc	aTc	1	1	AZ.3	0.00152
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.121	0.002427
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.144	0.028571
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.153	0.001095
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.225	0.007194
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.229	0.005747
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.265	0.003155
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.275	0.011236
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.28	0.000311
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.298	0.000862
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.306	0.000438
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.318	0.000302
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.33	0.000421
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.348	0.000796
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.369	0.000446
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.37	0.000193
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.386	0.066667
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.398	0.003226
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.413	0.006897
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.434	0.000349
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.467	0.019231
ORF3a	229	T229I	aCc	aTc	1	1	B.1.1.70	0.000341
ORF3a	229	T229I	aCc	aTc	1	1	B.1.111	0.001175
ORF3a	229	T229I	aCc	aTc	1	1	B.1.160.16	0.000929
ORF3a	229	T229I	aCc	aTc	1	1	B.1.160.29	0.004219
ORF3a	229	T229I	aCc	aTc	1	1	B.1.167	0.007812
ORF3a	229	T229I	aCc	aTc	1	1	B.1.177.58	0.001332
ORF3a	229	T229I	aCc	aTc	1	1	B.1.177.6	0.000977
ORF3a	229	T229I	aCc	aTc	1	1	B.1.177.8	0.000752
ORF3a	229	T229I	aCc	aTc	1	1	B.1.177.83	0.001481
ORF3a	229	T229I	aCc	aTc	1	1	B.1.177.85	0.005435
ORF3a	229	T229I	aCc	aTc	1	1	B.1.177.87	0.000728
ORF3a	229	T229I	aCc	aTc	1	1	B.1.188	0.016667
ORF3a	229	T229I	aCc	aTc	1	1	B.1.232	0.000537
ORF3a	229	T229I	aCc	aTc	1	1	B.1.234	0.000132
ORF3a	229	T229I	aCc	aTc	1	1	B.1.239	0.001221
ORF3a	229	T229I	aCc	aTc	1	1	B.1.281	0.021739
ORF3a	229	T229I	aCc	aTc	1	1	B.1.349	0.000715
ORF3a	229	T229I	aCc	aTc	1	1	B.1.36.1	0.00114
ORF3a	229	T229I	aCc	aTc	1	1	B.1.36.17	0.000494
ORF3a	229	T229I	aCc	aTc	1	1	B.1.36.29	0.000517
ORF3a	229	T229I	aCc	aTc	1	1	B.1.36.36	0.000602
ORF3a	229	T229I	aCc	aTc	1	1	B.1.36.38	0.001642
ORF3a	229	T229I	aCc	aTc	1	1	B.1.363	0.012987
ORF3a	229	T229I	aCc	aTc	1	1	B.1.375	0.00082
ORF3a	229	T229I	aCc	aTc	1	1	B.1.404	0.001302
ORF3a	229	T229I	aCc	aTc	1	1	B.1.422	0.000812
ORF3a	229	T229I	aCc	aTc	1	1	B.1.465	0.003802
ORF3a	229	T229I	aCc	aTc	1	1	B.1.497	0.000315
ORF3a	229	T229I	aCc	aTc	1	1	B.1.499	0.00105
ORF3a	229	T229I	aCc	aTc	1	1	B.1.524	0.001406
ORF3a	229	T229I	aCc	aTc	1	1	B.1.532	0.006211
ORF3a	229	T229I	aCc	aTc	1	1	B.1.545	0.014493
ORF3a	229	T229I	aCc	aTc	1	1	B.1.590	0.004545
ORF3a	229	T229I	aCc	aTc	1	1	B.1.617.3	0.002985
ORF3a	229	T229I	aCc	aTc	1	1	B.1.628	0.000352
ORF3a	229	T229I	aCc	aTc	1	1	B.1.634	0.003425
ORF3a	229	T229I	aCc	aTc	1	1	B.39	0.002331
ORF3a	229	T229I	aCc	aTc	1	1	C.36.3	0.000567
ORF3a	229	T229I	aCc	aTc	1	1	P.1.10.1	0.00813
ORF3a	229	T229I	aCc	aTc	1	1	P.1.12	0.000484
ORF3a	229	T229I	aCc	aTc	1	1	P.1.15	0.000232
ORF3a	229	T229I	aCc	aTc	1	1	P.1.17	0.000162
ORF3a	229	T229I	aCc	aTc	1	1	P.1.4	0.000977
ORF3a	229	T229I	aCc	aTc	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.