CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = T778T

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
S	778	T778T		syn	acC	acT	8031	7893	0.982817	23894-23896
S	778	T778T		syn	acC	acA	8031	78	0.00971236	23894-23896
S	778	T778T		syn	acC	acG	8031	60	0.00747105	23894-23896

Details of the mutation T778T 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
S	778	T778T	acC	acT	7893	8031	All	0.00151
S	778	T778T	acC	acA	78	8031	All	0.000015
S	778	T778T	acC	acG	60	8031	All	0.000011
S	778	T778T	acC	acT	2191	2192	AY.24	0.944397
S	778	T778T	acC	acA	1	2192	AY.24	0.000431
S	778	T778T	acC	acT	1105	1109	B.1.1.7	0.000989
S	778	T778T	acC	acG	3	1109	B.1.1.7	0.000003
S	778	T778T	acC	acA	1	1109	B.1.1.7	0.000001
S	778	T778T	acC	acT	312	312	AY.103	0.001937
S	778	T778T	acC	acT	303	303	AY.25	0.001822
S	778	T778T	acC	acT	292	298	AY.4	0.000454
S	778	T778T	acC	acG	4	298	AY.4	0.000006
S	778	T778T	acC	acA	2	298	AY.4	0.000003
S	778	T778T	acC	acT	275	285	B.1.617.2	0.001035
S	778	T778T	acC	acA	7	285	B.1.617.2	0.000026
S	778	T778T	acC	acG	3	285	B.1.617.2	0.000011
S	778	T778T	acC	acT	237	239	B.1.2	0.002087
S	778	T778T	acC	acA	2	239	B.1.2	0.000018
S	778	T778T	acC	acT	229	235	AY.44	0.001394
S	778	T778T	acC	acA	5	235	AY.44	0.00003
S	778	T778T	acC	acG	1	235	AY.44	0.000006
S	778	T778T	acC	acT	213	219	AY.26	0.00603
S	778	T778T	acC	acA	6	219	AY.26	0.00017
S	778	T778T	acC	acT	212	212	AY.74	0.024517
S	778	T778T	acC	acT	134	143	P.1	0.002111
S	778	T778T	acC	acA	6	143	P.1	0.000095
S	778	T778T	acC	acG	3	143	P.1	0.000047
S	778	T778T	acC	acT	130	132	B.1.177	0.001712
S	778	T778T	acC	acA	2	132	B.1.177	0.000026
S	778	T778T	acC	acT	106	106	B.1.1.317	0.043639
S	778	T778T	acC	acT	104	105	B.1.621	0.009206
S	778	T778T	acC	acG	1	105	B.1.621	0.000089
S	778	T778T	acC	acT	93	93	AY.43	0.000412
S	778	T778T	acC	acT	76	79	AY.29	0.001199
S	778	T778T	acC	acA	3	79	AY.29	0.000047
S	778	T778T	acC	acT	79	79	B.1.523	0.193627
S	778	T778T	acC	acT	68	72	B.1	0.000623
S	778	T778T	acC	acA	4	72	B.1	0.000037
S	778	T778T	acC	acT	42	63	B.1.1	0.000762
S	778	T778T	acC	acG	19	63	B.1.1	0.000345
S	778	T778T	acC	acA	2	63	B.1.1	0.000036
S	778	T778T	acC	acT	59	59	A.15	0.936508
S	778	T778T	acC	acT	56	56	B.1.36.21	0.12095
S	778	T778T	acC	acT	46	55	AY.120	0.00171
S	778	T778T	acC	acG	9	55	AY.120	0.000335
S	778	T778T	acC	acT	52	52	AY.98	0.004108
S	778	T778T	acC	acT	49	52	B.1.221	0.003481
S	778	T778T	acC	acG	3	52	B.1.221	0.000213
S	778	T778T	acC	acT	52	52	B.1.258.11	0.02061
S	778	T778T	acC	acT	52	52	P.1.7	0.016603
S	778	T778T	acC	acT	43	45	AY.3	0.000428
S	778	T778T	acC	acA	1	45	AY.3	0.00001
S	778	T778T	acC	acG	1	45	AY.3	0.00001
S	778	T778T	acC	acT	45	45	AY.4.2	0.000976
S	778	T778T	acC	acT	44	44	B.1.177.60	0.009611
S	778	T778T	acC	acT	41	41	AY.20	0.001593
S	778	T778T	acC	acT	41	41	B.1.1.519	0.001628
S	778	T778T	acC	acT	39	39	B.1.1.222	0.007956
S	778	T778T	acC	acT	39	39	B.1.243	0.002714
S	778	T778T	acC	acT	24	29	AY.39	0.000593
S	778	T778T	acC	acA	4	29	AY.39	0.000099
S	778	T778T	acC	acG	1	29	AY.39	0.000025
S	778	T778T	acC	acT	28	28	AY.3.1	0.002387
S	778	T778T	acC	acT	24	27	AY.102	0.000636
S	778	T778T	acC	acA	2	27	AY.102	0.000053
S	778	T778T	acC	acG	1	27	AY.102	0.000027
S	778	T778T	acC	acT	26	27	AY.13	0.004185
S	778	T778T	acC	acA	1	27	AY.13	0.000161
S	778	T778T	acC	acT	27	27	P.1.14	0.001291
S	778	T778T	acC	acT	26	26	A.2.5	0.012974
S	778	T778T	acC	acT	25	25	R.1	0.00225
S	778	T778T	acC	acT	24	24	B.1.177.82	0.011456
S	778	T778T	acC	acT	23	23	AY.23	0.001604
S	778	T778T	acC	acT	21	21	C.37	0.002437
S	778	T778T	acC	acT	19	20	AY.46.6	0.001372
S	778	T778T	acC	acG	1	20	AY.46.6	0.000072
S	778	T778T	acC	acT	20	20	B.1.324	0.032103
S	778	T778T	acC	acT	19	20	B.1.526	0.000447
S	778	T778T	acC	acA	1	20	B.1.526	0.000024
S	778	T778T	acC	acT	18	19	AY.121	0.002436
S	778	T778T	acC	acG	1	19	AY.121	0.000135
S	778	T778T	acC	acT	19	19	B.1.160	0.000593
S	778	T778T	acC	acT	19	19	B.1.177.73	0.010759
S	778	T778T	acC	acT	17	17	AY.9.1	0.001423
S	778	T778T	acC	acT	17	17	B.1.1.214	0.000943
S	778	T778T	acC	acT	17	17	B.1.258	0.001131
S	778	T778T	acC	acT	15	17	B.1.351	0.000446
S	778	T778T	acC	acG	1	17	B.1.351	0.00003
S	778	T778T	acC	acA	1	17	B.1.351	0.00003
S	778	T778T	acC	acT	17	17	B.1.429	0.0004
S	778	T778T	acC	acT	15	15	AY.71	0.007126
S	778	T778T	acC	acT	14	14	AY.119	0.000494
S	778	T778T	acC	acT	14	14	B.1.258.22	0.037333
S	778	T778T	acC	acT	13	13	B.1.1.70	0.004434
S	778	T778T	acC	acT	13	13	B.1.236	0.026694
S	778	T778T	acC	acT	7	12	AY.33	0.000467
S	778	T778T	acC	acA	5	12	AY.33	0.000334
S	778	T778T	acC	acT	12	12	B.1.596	0.001046
S	778	T778T	acC	acT	11	11	B.1.1.165	0.169231
S	778	T778T	acC	acT	9	10	AY.36	0.001334
S	778	T778T	acC	acG	1	10	AY.36	0.000148
S	778	T778T	acC	acT	9	10	AY.42	0.000362
S	778	T778T	acC	acG	1	10	AY.42	0.00004
S	778	T778T	acC	acT	10	10	AY.62	0.004357
S	778	T778T	acC	acT	9	10	AY.75	0.000504
S	778	T778T	acC	acA	1	10	AY.75	0.000056
S	778	T778T	acC	acT	10	10	AY.9.2	0.000367
S	778	T778T	acC	acT	9	9	B.1.214.3	0.064286
S	778	T778T	acC	acT	8	8	AY.46	0.000833
S	778	T778T	acC	acT	8	8	AY.46.2	0.005083
S	778	T778T	acC	acT	8	8	AY.54	0.000763
S	778	T778T	acC	acT	8	8	AY.6	0.000329
S	778	T778T	acC	acT	8	8	AY.72	0.010884
S	778	T778T	acC	acT	8	8	B.1.177.4	0.001688
S	778	T778T	acC	acT	8	8	B.1.177.8	0.00602
S	778	T778T	acC	acT	8	8	B.1.438.1	0.000858
S	778	T778T	acC	acT	8	8	B.1.561	0.003176
S	778	T778T	acC	acT	8	8	P.1.17	0.001294
S	778	T778T	acC	acT	7	7	AY.16	0.002658
S	778	T778T	acC	acA	5	7	AY.4.5	0.000537
S	778	T778T	acC	acT	2	7	AY.4.5	0.000215
S	778	T778T	acC	acA	4	7	AY.67	0.001857
S	778	T778T	acC	acT	3	7	AY.67	0.001393
S	778	T778T	acC	acT	6	6	AY.113	0.000854
S	778	T778T	acC	acT	6	6	AY.39.1	0.000238
S	778	T778T	acC	acT	4	6	AY.45	0.000487
S	778	T778T	acC	acG	2	6	AY.45	0.000243
S	778	T778T	acC	acT	6	6	AY.47	0.000187
S	778	T778T	acC	acT	4	6	AY.5	0.000083
S	778	T778T	acC	acA	2	6	AY.5	0.000041
S	778	T778T	acC	acT	6	6	AY.99.2	0.000553
S	778	T778T	acC	acT	6	6	B.1.177.43	0.008863
S	778	T778T	acC	acT	5	5	AY.100	0.00023
S	778	T778T	acC	acT	5	5	AY.116.1	0.001557
S	778	T778T	acC	acT	5	5	AY.117	0.000423
S	778	T778T	acC	acT	5	5	AY.98.1	0.000242
S	778	T778T	acC	acA	3	5	B.1.1.318	0.000905
S	778	T778T	acC	acT	2	5	B.1.1.318	0.000604
S	778	T778T	acC	acT	4	5	B.1.1.464	0.005891
S	778	T778T	acC	acA	1	5	B.1.1.464	0.001473
S	778	T778T	acC	acT	5	5	B.1.427	0.000252
S	778	T778T	acC	acT	5	5	P.1.1	0.001588
S	778	T778T	acC	acT	4	4	AY.23.1	0.001669
S	778	T778T	acC	acT	4	4	AY.4.2.1	0.000596
S	778	T778T	acC	acT	4	4	AY.60	0.003752
S	778	T778T	acC	acT	4	4	AY.64	0.002381
S	778	T778T	acC	acT	4	4	B.1.1.28	0.001245
S	778	T778T	acC	acT	4	4	B.1.1.372	0.002755
S	778	T778T	acC	acT	4	4	B.1.177.7	0.000659
S	778	T778T	acC	acT	4	4	B.1.199	0.016529
S	778	T778T	acC	acT	4	4	B.1.36	0.000584
S	778	T778T	acC	acT	4	4	B.1.426	0.004036
S	778	T778T	acC	acT	4	4	B.1.551	0.005161
S	778	T778T	acC	acT	4	4	B.40	0.001457
S	778	T778T	acC	acT	4	4	P.1.15	0.000929
S	778	T778T	acC	acT	4	4	Q.1	0.000505
S	778	T778T	acC	acT	3	3	AY.110	0.000338
S	778	T778T	acC	acT	3	3	AY.116	0.00086
S	778	T778T	acC	acT	3	3	AY.34	0.000291
S	778	T778T	acC	acT	3	3	AY.57	0.001969
S	778	T778T	acC	acT	3	3	AY.9	0.000203
S	778	T778T	acC	acT	3	3	B.1.1.119	0.103448
S	778	T778T	acC	acT	3	3	B.1.1.434	0.001046
S	778	T778T	acC	acT	3	3	B.1.232	0.001612
S	778	T778T	acC	acT	3	3	B.1.258.17	0.000312
S	778	T778T	acC	acG	2	3	B.1.36.29	0.001035
S	778	T778T	acC	acT	1	3	B.1.36.29	0.000517
S	778	T778T	acC	acT	3	3	B.1.617.1	0.000387
S	778	T778T	acC	acT	3	3	C.35	0.002322
S	778	T778T	acC	acT	3	3	N.6	0.021277
S	778	T778T	acC	acT	3	3	P.1.16	0.001122
S	778	T778T	acC	acT	3	3	P.1.17.1	0.002625
S	778	T778T	acC	acT	3	3	P.2	0.00056
S	778	T778T	acC	acT	2	2	AY.108	0.002205
S	778	T778T	acC	acT	2	2	AY.111	0.000366
S	778	T778T	acC	acT	2	2	AY.120.2	0.002571
S	778	T778T	acC	acT	2	2	AY.27	0.000129
S	778	T778T	acC	acT	2	2	AY.37	0.000632
S	778	T778T	acC	acT	2	2	AY.4.4	0.000818
S	778	T778T	acC	acT	1	2	AY.5.4	0.000277
S	778	T778T	acC	acA	1	2	AY.5.4	0.000277
S	778	T778T	acC	acA	1	2	AY.55	0.000917
S	778	T778T	acC	acT	1	2	AY.55	0.000917
S	778	T778T	acC	acT	2	2	AY.58	0.001815
S	778	T778T	acC	acT	2	2	AY.61	0.00021
S	778	T778T	acC	acT	2	2	AY.77	0.002255
S	778	T778T	acC	acT	2	2	AY.95	0.001522
S	778	T778T	acC	acT	2	2	B.1.1.101	0.02
S	778	T778T	acC	acT	2	2	B.1.1.163	0.015267
S	778	T778T	acC	acT	2	2	B.1.1.200	0.014925
S	778	T778T	acC	acT	2	2	B.1.1.306	0.000877
S	778	T778T	acC	acT	1	2	B.1.1.311	0.000358
S	778	T778T	acC	acA	1	2	B.1.1.311	0.000358
S	778	T778T	acC	acT	2	2	B.1.1.391	0.017094
S	778	T778T	acC	acT	2	2	B.1.1.433	0.002849
S	778	T778T	acC	acT	2	2	B.1.160.14	0.004237
S	778	T778T	acC	acT	2	2	B.1.177.18	0.00232
S	778	T778T	acC	acT	2	2	B.1.177.58	0.002663
S	778	T778T	acC	acT	2	2	B.1.177.86	0.000367
S	778	T778T	acC	acT	2	2	B.1.240	0.000431
S	778	T778T	acC	acT	2	2	B.1.241	0.001623
S	778	T778T	acC	acT	2	2	B.1.311	0.000549
S	778	T778T	acC	acT	2	2	B.1.351.5	0.001199
S	778	T778T	acC	acT	2	2	B.1.391	0.002255
S	778	T778T	acC	acT	2	2	B.1.399	0.003868
S	778	T778T	acC	acT	2	2	B.1.400	0.000858
S	778	T778T	acC	acT	2	2	B.1.453	0.006472
S	778	T778T	acC	acT	2	2	B.1.468	0.011429
S	778	T778T	acC	acT	2	2	B.1.538	0.016129
S	778	T778T	acC	acT	2	2	B.1.567	0.006667
S	778	T778T	acC	acT	2	2	B.1.595	0.000522
S	778	T778T	acC	acT	2	2	B.1.625	0.004706
S	778	T778T	acC	acT	2	2	B.1.637	0.000146
S	778	T778T	acC	acT	2	2	C.1	0.004785
S	778	T778T	acC	acT	2	2	P.1.12	0.000968
S	778	T778T	acC	acT	2	2	P.1.13	0.001797
S	778	T778T	acC	acT	1	1	A	0.000387
S	778	T778T	acC	acT	1	1	A.11	0.058824
S	778	T778T	acC	acT	1	1	AA.8	0.022222
S	778	T778T	acC	acT	1	1	AE.7	0.083333
S	778	T778T	acC	acT	1	1	AL.1	0.012987
S	778	T778T	acC	acT	1	1	AY.101	0.00049
S	778	T778T	acC	acT	1	1	AY.114	0.000231
S	778	T778T	acC	acT	1	1	AY.118	0.000063
S	778	T778T	acC	acT	1	1	AY.12	0.000316
S	778	T778T	acC	acT	1	1	AY.120.2.1	0.000498
S	778	T778T	acC	acT	1	1	AY.14	0.000088
S	778	T778T	acC	acT	1	1	AY.16.1	0.00047
S	778	T778T	acC	acT	1	1	AY.21	0.001898
S	778	T778T	acC	acT	1	1	AY.28	0.00189
S	778	T778T	acC	acT	1	1	AY.30	0.000396
S	778	T778T	acC	acT	1	1	AY.41	0.000294
S	778	T778T	acC	acT	1	1	AY.46.4	0.000165
S	778	T778T	acC	acA	1	1	AY.5.3	0.000337
S	778	T778T	acC	acT	1	1	AY.53	0.000288
S	778	T778T	acC	acT	1	1	AY.56	0.001605
S	778	T778T	acC	acT	1	1	AY.65	0.000533
S	778	T778T	acC	acT	1	1	AY.68	0.000274
S	778	T778T	acC	acT	1	1	AY.82	0.001357
S	778	T778T	acC	acT	1	1	AY.84	0.000437
S	778	T778T	acC	acT	1	1	AY.88	0.000884
S	778	T778T	acC	acT	1	1	AY.92	0.000287
S	778	T778T	acC	acT	1	1	AY.93	0.000273
S	778	T778T	acC	acT	1	1	AZ.2	0.000821
S	778	T778T	acC	acT	1	1	B	0.000128
S	778	T778T	acC	acT	1	1	B.1.1.139	0.022727
S	778	T778T	acC	acT	1	1	B.1.1.141	0.002012
S	778	T778T	acC	acT	1	1	B.1.1.216	0.00089
S	778	T778T	acC	acT	1	1	B.1.1.220	0.001859
S	778	T778T	acC	acT	1	1	B.1.1.226	0.005814
S	778	T778T	acC	acT	1	1	B.1.1.258	0.003257
S	778	T778T	acC	acT	1	1	B.1.1.277	0.000759
S	778	T778T	acC	acT	1	1	B.1.1.289	0.002083
S	778	T778T	acC	acT	1	1	B.1.1.312	0.001912
S	778	T778T	acC	acT	1	1	B.1.1.316	0.000925
S	778	T778T	acC	acT	1	1	B.1.1.319	0.017544
S	778	T778T	acC	acT	1	1	B.1.1.326	0.001761
S	778	T778T	acC	acT	1	1	B.1.1.333	0.001076
S	778	T778T	acC	acT	1	1	B.1.1.368	0.003086
S	778	T778T	acC	acT	1	1	B.1.1.371	0.010417
S	778	T778T	acC	acT	1	1	B.1.1.39	0.00051
S	778	T778T	acC	acT	1	1	B.1.1.397	0.002252
S	778	T778T	acC	acT	1	1	B.1.1.523	0.001563
S	778	T778T	acC	acT	1	1	B.1.143	0.021277
S	778	T778T	acC	acT	1	1	B.1.157	0.002985
S	778	T778T	acC	acT	1	1	B.1.177.12	0.000152
S	778	T778T	acC	acT	1	1	B.1.177.65	0.000665
S	778	T778T	acC	acT	1	1	B.1.177.83	0.001481
S	778	T778T	acC	acT	1	1	B.1.214	0.003663
S	778	T778T	acC	acT	1	1	B.1.214.1	0.02
S	778	T778T	acC	acT	1	1	B.1.214.2	0.0006
S	778	T778T	acC	acT	1	1	B.1.221.2	0.004016
S	778	T778T	acC	acT	1	1	B.1.234	0.000132
S	778	T778T	acC	acT	1	1	B.1.239	0.001221
S	778	T778T	acC	acT	1	1	B.1.279	0.000514
S	778	T778T	acC	acA	1	1	B.1.3	0.002618
S	778	T778T	acC	acT	1	1	B.1.337	0.005587
S	778	T778T	acC	acT	1	1	B.1.35	0.008475
S	778	T778T	acC	acT	1	1	B.1.36.1	0.00114
S	778	T778T	acC	acA	1	1	B.1.36.18	0.00042
S	778	T778T	acC	acT	1	1	B.1.36.31	0.001751
S	778	T778T	acC	acT	1	1	B.1.36.36	0.000602
S	778	T778T	acC	acT	1	1	B.1.362	0.001541
S	778	T778T	acC	acT	1	1	B.1.366	0.004878
S	778	T778T	acC	acT	1	1	B.1.369	0.000285
S	778	T778T	acC	acT	1	1	B.1.371	0.001122
S	778	T778T	acC	acT	1	1	B.1.409	0.000781
S	778	T778T	acC	acG	1	1	B.1.416	0.001269
S	778	T778T	acC	acT	1	1	B.1.416.1	0.001563
S	778	T778T	acC	acT	1	1	B.1.433	0.003195
S	778	T778T	acC	acT	1	1	B.1.456	0.003268
S	778	T778T	acC	acT	1	1	B.1.462	0.007246
S	778	T778T	acC	acT	1	1	B.1.466.2	0.000391
S	778	T778T	acC	acT	1	1	B.1.471	0.002732
S	778	T778T	acC	acT	1	1	B.1.474	0.001901
S	778	T778T	acC	acT	1	1	B.1.497	0.000315
S	778	T778T	acC	acT	1	1	B.1.499	0.00105
S	778	T778T	acC	acT	1	1	B.1.525	0.000113
S	778	T778T	acC	acT	1	1	B.1.580	0.004065
S	778	T778T	acC	acT	1	1	B.1.582	0.000491
S	778	T778T	acC	acT	1	1	B.1.618	0.004032
S	778	T778T	acC	acT	1	1	B.1.619.1	0.000641
S	778	T778T	acC	acT	1	1	B.1.9.4	0.006135
S	778	T778T	acC	acT	1	1	B.3	0.000831
S	778	T778T	acC	acG	1	1	D.2	0.000075
S	778	T778T	acC	acT	1	1	N.4	0.004255
S	778	T778T	acC	acT	1	1	P.1.4	0.000977
S	778	T778T	acC	acT	1	1	P.3	0.001595
S	778	T778T	acC	acT	1	1	S.1	0.00495
S	778	T778T	acC	acT	1	1	W.1	0.008696

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.