CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 60 & Codon = tcT

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	60	S60S		syn	tcC	tcT	7811	7002	0.896428	25570-25572

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	60	S60S	tcC	tcT	7002	7811	All	0.001339
ORF3a	60	S60S	tcC	tcT	2575	2677	B.1.1.7	0.002305
ORF3a	60	S60S	tcC	tcT	648	712	B.1.617.2	0.00244
ORF3a	60	S60S	tcC	tcT	385	399	AY.43	0.001706
ORF3a	60	S60S	tcC	tcT	392	392	AY.5.2	0.965517
ORF3a	60	S60S	tcC	tcT	376	376	AY.48	0.174884
ORF3a	60	S60S	tcC	tcT	274	314	B.1.429	0.006447
ORF3a	60	S60S	tcC	tcT	2	294	AY.61	0.00021
ORF3a	60	S60S	tcC	tcT	192	220	AY.4	0.000299
ORF3a	60	S60S	tcC	tcT	172	173	B.1.160	0.005364
ORF3a	60	S60S	tcC	tcT	143	144	B.1.177	0.001883
ORF3a	60	S60S	tcC	tcT	36	137	AY.103	0.000224
ORF3a	60	S60S	tcC	tcT	125	125	B.35	0.976562
ORF3a	60	S60S	tcC	tcT	116	116	B.1.338	1
ORF3a	60	S60S	tcC	tcT	90	92	AY.39.1	0.003565
ORF3a	60	S60S	tcC	tcT	84	84	AH.3	0.319392
ORF3a	60	S60S	tcC	tcT	70	79	AY.44	0.000426
ORF3a	60	S60S	tcC	tcT	61	77	B.1.2	0.000537
ORF3a	60	S60S	tcC	tcT	61	61	B.1.243	0.004245
ORF3a	60	S60S	tcC	tcT	46	54	B.1	0.000421
ORF3a	60	S60S	tcC	tcT	49	52	P.1	0.000772
ORF3a	60	S60S	tcC	tcT	50	50	B.1.177.86	0.009173
ORF3a	60	S60S	tcC	tcT	42	46	AY.25	0.000253
ORF3a	60	S60S	tcC	tcT	43	43	B.1.36.29	0.022245
ORF3a	60	S60S	tcC	tcT	37	40	B.1.1	0.000671
ORF3a	60	S60S	tcC	tcT	35	38	AY.102	0.000928
ORF3a	60	S60S	tcC	tcT	38	38	B.1.1.311	0.01361
ORF3a	60	S60S	tcC	tcT	34	36	B.1.221	0.002415
ORF3a	60	S60S	tcC	tcT	35	35	B.1.564.1	0.055205
ORF3a	60	S60S	tcC	tcT	31	32	AY.32	0.016507
ORF3a	60	S60S	tcC	tcT	27	29	AY.39	0.000667
ORF3a	60	S60S	tcC	tcT	24	26	B.1.351	0.000713
ORF3a	60	S60S	tcC	tcT	25	25	B.1.438.1	0.002682
ORF3a	60	S60S	tcC	tcT	20	23	AY.20	0.000777
ORF3a	60	S60S	tcC	tcT	20	21	B.1.258	0.001331
ORF3a	60	S60S	tcC	tcT	20	20	B.1.1.487	0.111732
ORF3a	60	S60S	tcC	tcT	15	19	B.1.526	0.000353
ORF3a	60	S60S	tcC	tcT	17	17	B.1.240	0.003665
ORF3a	60	S60S	tcC	tcT	16	17	B.1.621	0.001416
ORF3a	60	S60S	tcC	tcT	12	16	AY.3	0.000119
ORF3a	60	S60S	tcC	tcT	12	16	AY.47	0.000373
ORF3a	60	S60S	tcC	tcT	10	16	AY.63	0.003868
ORF3a	60	S60S	tcC	tcT	15	15	C.36	0.013661
ORF3a	60	S60S	tcC	tcT	12	14	AY.26	0.00034
ORF3a	60	S60S	tcC	tcT	14	14	B.1.561	0.005558
ORF3a	60	S60S	tcC	tcT	12	13	B.1.637	0.000877
ORF3a	60	S60S	tcC	tcT	11	13	C.37	0.001277
ORF3a	60	S60S	tcC	tcT	11	12	B.1.427	0.000555
ORF3a	60	S60S	tcC	tcT	8	11	B.1.36	0.001167
ORF3a	60	S60S	tcC	tcT	4	10	AY.35	0.000932
ORF3a	60	S60S	tcC	tcT	9	10	D.2	0.000675
ORF3a	60	S60S	tcC	tcT	1	10	N.5	0.001767
ORF3a	60	S60S	tcC	tcT	9	9	AY.23	0.000628
ORF3a	60	S60S	tcC	tcT	7	9	AY.29	0.00011
ORF3a	60	S60S	tcC	tcT	9	9	AY.57	0.005906
ORF3a	60	S60S	tcC	tcT	9	9	B.1.36.21	0.019438
ORF3a	60	S60S	tcC	tcT	8	9	B.1.525	0.000905
ORF3a	60	S60S	tcC	tcT	8	8	AY.46	0.000833
ORF3a	60	S60S	tcC	tcT	8	8	AY.46.6	0.000578
ORF3a	60	S60S	tcC	tcT	8	8	AY.62	0.003486
ORF3a	60	S60S	tcC	tcT	8	8	AY.75	0.000448
ORF3a	60	S60S	tcC	tcT	8	8	B.1.1.519	0.000318
ORF3a	60	S60S	tcC	tcT	8	8	B.1.351.2	0.002421
ORF3a	60	S60S	tcC	tcT	8	8	B.1.568	0.008889
ORF3a	60	S60S	tcC	tcT	8	8	B.1.595	0.002088
ORF3a	60	S60S	tcC	tcT	8	8	B.1.628	0.002819
ORF3a	60	S60S	tcC	tcT	7	7	B.1.588	0.006369
ORF3a	60	S60S	tcC	tcT	7	7	Q.8	0.001154
ORF3a	60	S60S	tcC	tcT	5	6	AY.4.2	0.000108
ORF3a	60	S60S	tcC	tcT	6	6	B.1.44	0.05
ORF3a	60	S60S	tcC	tcT	5	5	AY.100	0.00023
ORF3a	60	S60S	tcC	tcT	5	5	AY.117	0.000423
ORF3a	60	S60S	tcC	tcT	4	5	AY.120	0.000149
ORF3a	60	S60S	tcC	tcT	4	5	AY.33	0.000267
ORF3a	60	S60S	tcC	tcT	5	5	AY.58	0.004537
ORF3a	60	S60S	tcC	tcT	2	5	AY.98.1	0.000097
ORF3a	60	S60S	tcC	tcT	5	5	B.1.1.158	0.060976
ORF3a	60	S60S	tcC	tcT	5	5	B.1.1.285	0.03268
ORF3a	60	S60S	tcC	tcT	5	5	B.6	0.00455
ORF3a	60	S60S	tcC	tcT	4	4	AY.34.1	0.00204
ORF3a	60	S60S	tcC	tcT	4	4	AY.5.4	0.001107
ORF3a	60	S60S	tcC	tcT	4	4	AY.9.1	0.000335
ORF3a	60	S60S	tcC	tcT	4	4	AY.99.2	0.000369
ORF3a	60	S60S	tcC	tcT	4	4	B.1.1.170	0.004988
ORF3a	60	S60S	tcC	tcT	4	4	B.1.1.214	0.000222
ORF3a	60	S60S	tcC	tcT	4	4	B.1.1.222	0.000816
ORF3a	60	S60S	tcC	tcT	4	4	B.1.1.28	0.001245
ORF3a	60	S60S	tcC	tcT	4	4	B.1.1.70	0.001364
ORF3a	60	S60S	tcC	tcT	4	4	B.1.177.54	0.002426
ORF3a	60	S60S	tcC	tcT	4	4	B.1.214.2	0.002398
ORF3a	60	S60S	tcC	tcT	4	4	B.1.258.17	0.000416
ORF3a	60	S60S	tcC	tcT	3	4	B.1.36.18	0.001261
ORF3a	60	S60S	tcC	tcT	4	4	B.1.462	0.028986
ORF3a	60	S60S	tcC	tcT	4	4	B.1.498	0.081633
ORF3a	60	S60S	tcC	tcT	3	4	B.1.596	0.000261
ORF3a	60	S60S	tcC	tcT	2	4	B.1.617.1	0.000258
ORF3a	60	S60S	tcC	tcT	4	4	C.14	0.017316
ORF3a	60	S60S	tcC	tcT	4	4	P.1.7	0.001277
ORF3a	60	S60S	tcC	tcT	4	4	W.4	0.005405
ORF3a	60	S60S	tcC	tcT	3	3	A.29	0.015957
ORF3a	60	S60S	tcC	tcT	3	3	AL.1	0.038961
ORF3a	60	S60S	tcC	tcT	1	3	AY.105	0.000643
ORF3a	60	S60S	tcC	tcT	1	3	AY.14	0.000088
ORF3a	60	S60S	tcC	tcT	2	3	AY.5	0.000041
ORF3a	60	S60S	tcC	tcT	3	3	AY.84	0.001312
ORF3a	60	S60S	tcC	tcT	3	3	B.1.1.1	0.00098
ORF3a	60	S60S	tcC	tcT	3	3	B.1.1.216	0.002671
ORF3a	60	S60S	tcC	tcT	3	3	B.1.1.33	0.001263
ORF3a	60	S60S	tcC	tcT	2	3	B.1.177.81	0.000379
ORF3a	60	S60S	tcC	tcT	3	3	B.1.367	0.002377
ORF3a	60	S60S	tcC	tcT	3	3	B.1.620	0.002838
ORF3a	60	S60S	tcC	tcT	2	3	P.1.12	0.000968
ORF3a	60	S60S	tcC	tcT	3	3	Q.3	0.000435
ORF3a	60	S60S	tcC	tcT	2	2	AY.110	0.000225
ORF3a	60	S60S	tcC	tcT	2	2	AY.113	0.000285
ORF3a	60	S60S	tcC	tcT	2	2	AY.116	0.000574
ORF3a	60	S60S	tcC	tcT	2	2	AY.16	0.000759
ORF3a	60	S60S	tcC	tcT	2	2	AY.24	0.000862
ORF3a	60	S60S	tcC	tcT	1	2	AY.38	0.000499
ORF3a	60	S60S	tcC	tcT	2	2	AY.45	0.000243
ORF3a	60	S60S	tcC	tcT	2	2	AY.46.5	0.000397
ORF3a	60	S60S	tcC	tcT	2	2	AY.5.3	0.000675
ORF3a	60	S60S	tcC	tcT	2	2	AY.54	0.000191
ORF3a	60	S60S	tcC	tcT	2	2	AY.65	0.001066
ORF3a	60	S60S	tcC	tcT	1	2	AY.74	0.000116
ORF3a	60	S60S	tcC	tcT	2	2	AY.75.1	0.000361
ORF3a	60	S60S	tcC	tcT	2	2	AY.91	0.001461
ORF3a	60	S60S	tcC	tcT	2	2	AY.93	0.000546
ORF3a	60	S60S	tcC	tcT	2	2	AY.98	0.000158
ORF3a	60	S60S	tcC	tcT	1	2	AY.99	0.001049
ORF3a	60	S60S	tcC	tcT	2	2	AZ.5	0.007018
ORF3a	60	S60S	tcC	tcT	2	2	B	0.000256
ORF3a	60	S60S	tcC	tcT	2	2	B.1.1.434	0.000697
ORF3a	60	S60S	tcC	tcT	2	2	B.1.1.50	0.001358
ORF3a	60	S60S	tcC	tcT	2	2	B.1.1.89	0.012121
ORF3a	60	S60S	tcC	tcT	2	2	B.1.177.4	0.000422
ORF3a	60	S60S	tcC	tcT	2	2	B.1.199	0.008264
ORF3a	60	S60S	tcC	tcT	2	2	B.1.232	0.001075
ORF3a	60	S60S	tcC	tcT	2	2	B.1.305	0.004301
ORF3a	60	S60S	tcC	tcT	2	2	B.1.311	0.000549
ORF3a	60	S60S	tcC	tcT	2	2	B.1.416	0.002538
ORF3a	60	S60S	tcC	tcT	2	2	B.1.497	0.00063
ORF3a	60	S60S	tcC	tcT	2	2	B.1.499	0.002101
ORF3a	60	S60S	tcC	tcT	2	2	B.1.575	0.000607
ORF3a	60	S60S	tcC	tcT	1	2	C.36.1	0.004149
ORF3a	60	S60S	tcC	tcT	1	2	P.1.14	0.000048
ORF3a	60	S60S	tcC	tcT	2	2	P.1.4	0.001953
ORF3a	60	S60S	tcC	tcT	2	2	P.2	0.000373
ORF3a	60	S60S	tcC	tcT	1	1	A	0.000387
ORF3a	60	S60S	tcC	tcT	1	1	A.2	0.000662
ORF3a	60	S60S	tcC	tcT	1	1	A.2.2	0.001689
ORF3a	60	S60S	tcC	tcT	1	1	A.2.5.2	0.001572
ORF3a	60	S60S	tcC	tcT	1	1	AY.109	0.00074
ORF3a	60	S60S	tcC	tcT	1	1	AY.111	0.000183
ORF3a	60	S60S	tcC	tcT	1	1	AY.118	0.000063
ORF3a	60	S60S	tcC	tcT	1	1	AY.119	0.000035
ORF3a	60	S60S	tcC	tcT	1	1	AY.120.1	0.000321
ORF3a	60	S60S	tcC	tcT	1	1	AY.13	0.000161
ORF3a	60	S60S	tcC	tcT	1	1	AY.27	0.000065
ORF3a	60	S60S	tcC	tcT	1	1	AY.34	0.000097
ORF3a	60	S60S	tcC	tcT	1	1	AY.37	0.000316
ORF3a	60	S60S	tcC	tcT	1	1	AY.39.2	0.001541
ORF3a	60	S60S	tcC	tcT	1	1	AY.4.2.1	0.000149
ORF3a	60	S60S	tcC	tcT	1	1	AY.4.5	0.000107
ORF3a	60	S60S	tcC	tcT	1	1	AY.40	0.000964
ORF3a	60	S60S	tcC	tcT	1	1	AY.41	0.000294
ORF3a	60	S60S	tcC	tcT	1	1	AY.42	0.00004
ORF3a	60	S60S	tcC	tcT	1	1	AY.51	0.000909
ORF3a	60	S60S	tcC	tcT	1	1	AY.53	0.000288
ORF3a	60	S60S	tcC	tcT	1	1	AY.67	0.000464
ORF3a	60	S60S	tcC	tcT	1	1	AY.69	0.000187
ORF3a	60	S60S	tcC	tcT	1	1	AY.80	0.001129
ORF3a	60	S60S	tcC	tcT	1	1	AY.9.2	0.000037
ORF3a	60	S60S	tcC	tcT	1	1	AY.95	0.000761
ORF3a	60	S60S	tcC	tcT	1	1	AY.99.1	0.001553
ORF3a	60	S60S	tcC	tcT	1	1	AZ.1	0.000867
ORF3a	60	S60S	tcC	tcT	1	1	AZ.2	0.000821
ORF3a	60	S60S	tcC	tcT	1	1	AZ.3	0.00152
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.10	0.001115
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.133	0.008475
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.136	0.021277
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.148	0.008772
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.152	0.04
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.189	0.001513
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.204	0.00304
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.207	0.001182
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.220	0.001859
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.241	0.00207
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.25	0.000569
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.277	0.000759
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.294	0.001266
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.298	0.000862
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.306	0.000438
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.318	0.000302
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.328	0.016949
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.332	0.03125
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.372	0.000689
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.373	0.02381
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.39	0.00051
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.435	0.034483
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.448	0.002033
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.47	0.005348
ORF3a	60	S60S	tcC	tcT	1	1	B.1.1.63	0.000386
ORF3a	60	S60S	tcC	tcT	1	1	B.1.162	0.005025
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.10	0.000878
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.12	0.000152
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.42	0.000894
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.5	0.001242
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.55	0.002331
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.57	0.000281
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.7	0.000165
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.72	0.00339
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.77	0.000726
ORF3a	60	S60S	tcC	tcT	1	1	B.1.177.79	0.002342
ORF3a	60	S60S	tcC	tcT	1	1	B.1.241	0.000812
ORF3a	60	S60S	tcC	tcT	1	1	B.1.258.11	0.000396
ORF3a	60	S60S	tcC	tcT	1	1	B.1.346	0.001311
ORF3a	60	S60S	tcC	tcT	1	1	B.1.349	0.000715
ORF3a	60	S60S	tcC	tcT	1	1	B.1.351.3	0.000876
ORF3a	60	S60S	tcC	tcT	1	1	B.1.36.12	0.009615
ORF3a	60	S60S	tcC	tcT	1	1	B.1.36.31	0.001751
ORF3a	60	S60S	tcC	tcT	1	1	B.1.361	0.001289
ORF3a	60	S60S	tcC	tcT	1	1	B.1.369	0.000285
ORF3a	60	S60S	tcC	tcT	1	1	B.1.396	0.000706
ORF3a	60	S60S	tcC	tcT	1	1	B.1.399	0.001934
ORF3a	60	S60S	tcC	tcT	1	1	B.1.432	0.011236
ORF3a	60	S60S	tcC	tcT	1	1	B.1.459	0.004082
ORF3a	60	S60S	tcC	tcT	1	1	B.1.466.2	0.000391
ORF3a	60	S60S	tcC	tcT	1	1	B.1.564	0.000426
ORF3a	60	S60S	tcC	tcT	1	1	B.1.593	0.01087
ORF3a	60	S60S	tcC	tcT	1	1	B.1.609	0.000479
ORF3a	60	S60S	tcC	tcT	1	1	B.1.9	0.006173
ORF3a	60	S60S	tcC	tcT	1	1	B.40	0.000364
ORF3a	60	S60S	tcC	tcT	1	1	C.16	0.00106
ORF3a	60	S60S	tcC	tcT	1	1	C.30.1	0.006711
ORF3a	60	S60S	tcC	tcT	1	1	P.1.10	0.000269
ORF3a	60	S60S	tcC	tcT	1	1	Q.1	0.000126
ORF3a	60	S60S	tcC	tcT	1	1	R.1	0.00009

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.