CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp5A-B : Mut = T45T

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
ORF1ab/nsp5A-B	45	T45T	T3308T	syn	acC	acT	2757	2224	0.806674	10187-10189
ORF1ab/nsp5A-B	45	T45T	T3308T	syn	acC	acA	2757	504	0.182807	10187-10189
ORF1ab/nsp5A-B	45	T45T	T3308T	syn	acC	acG	2757	29	0.0105187	10187-10189

Details of the mutation T45T 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
ORF1ab/nsp5A-B	45	T45T	acC	acT	2224	2757	All	0.000425
ORF1ab/nsp5A-B	45	T45T	acC	acA	504	2757	All	0.000096
ORF1ab/nsp5A-B	45	T45T	acC	acG	29	2757	All	0.000006
ORF1ab/nsp5A-B	45	T45T	acC	acT	497	619	B.1.1.7	0.000445
ORF1ab/nsp5A-B	45	T45T	acC	acA	118	619	B.1.1.7	0.000106
ORF1ab/nsp5A-B	45	T45T	acC	acG	4	619	B.1.1.7	0.000004
ORF1ab/nsp5A-B	45	T45T	acC	acT	270	276	B.1.2	0.002377
ORF1ab/nsp5A-B	45	T45T	acC	acA	6	276	B.1.2	0.000053
ORF1ab/nsp5A-B	45	T45T	acC	acA	172	245	AY.4	0.000268
ORF1ab/nsp5A-B	45	T45T	acC	acT	73	245	AY.4	0.000114
ORF1ab/nsp5A-B	45	T45T	acC	acT	241	241	AY.29	0.003801
ORF1ab/nsp5A-B	45	T45T	acC	acT	94	101	AY.3	0.000935
ORF1ab/nsp5A-B	45	T45T	acC	acA	7	101	AY.3	0.00007
ORF1ab/nsp5A-B	45	T45T	acC	acT	92	93	AY.44	0.00056
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	93	AY.44	0.000006
ORF1ab/nsp5A-B	45	T45T	acC	acT	76	86	P.1	0.001197
ORF1ab/nsp5A-B	45	T45T	acC	acA	10	86	P.1	0.000158
ORF1ab/nsp5A-B	45	T45T	acC	acT	43	61	AY.25	0.000259
ORF1ab/nsp5A-B	45	T45T	acC	acA	18	61	AY.25	0.000108
ORF1ab/nsp5A-B	45	T45T	acC	acT	52	60	B.1.617.2	0.000196
ORF1ab/nsp5A-B	45	T45T	acC	acA	7	60	B.1.617.2	0.000026
ORF1ab/nsp5A-B	45	T45T	acC	acG	1	60	B.1.617.2	0.000004
ORF1ab/nsp5A-B	45	T45T	acC	acT	50	50	B.1.258.11	0.019818
ORF1ab/nsp5A-B	45	T45T	acC	acA	44	45	AY.9.2	0.001616
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	45	AY.9.2	0.000037
ORF1ab/nsp5A-B	45	T45T	acC	acT	39	43	AY.43	0.000173
ORF1ab/nsp5A-B	45	T45T	acC	acA	3	43	AY.43	0.000013
ORF1ab/nsp5A-B	45	T45T	acC	acG	1	43	AY.43	0.000004
ORF1ab/nsp5A-B	45	T45T	acC	acT	36	40	B.1	0.00033
ORF1ab/nsp5A-B	45	T45T	acC	acA	2	40	B.1	0.000018
ORF1ab/nsp5A-B	45	T45T	acC	acG	2	40	B.1	0.000018
ORF1ab/nsp5A-B	45	T45T	acC	acT	34	38	AY.103	0.000211
ORF1ab/nsp5A-B	45	T45T	acC	acA	4	38	AY.103	0.000025
ORF1ab/nsp5A-B	45	T45T	acC	acT	36	38	AY.39	0.00089
ORF1ab/nsp5A-B	45	T45T	acC	acA	2	38	AY.39	0.000049
ORF1ab/nsp5A-B	45	T45T	acC	acT	37	37	B.1.429	0.000871
ORF1ab/nsp5A-B	45	T45T	acC	acA	30	31	AY.70	0.006255
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	31	AY.70	0.000209
ORF1ab/nsp5A-B	45	T45T	acC	acT	29	29	AY.5	0.000599
ORF1ab/nsp5A-B	45	T45T	acC	acT	20	25	AY.20	0.000777
ORF1ab/nsp5A-B	45	T45T	acC	acA	5	25	AY.20	0.000194
ORF1ab/nsp5A-B	45	T45T	acC	acT	25	25	B.1.240	0.005389
ORF1ab/nsp5A-B	45	T45T	acC	acA	18	21	AY.47	0.00056
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	21	AY.47	0.000093
ORF1ab/nsp5A-B	45	T45T	acC	acT	11	19	B.1.1	0.0002
ORF1ab/nsp5A-B	45	T45T	acC	acA	4	19	B.1.1	0.000073
ORF1ab/nsp5A-B	45	T45T	acC	acG	4	19	B.1.1	0.000073
ORF1ab/nsp5A-B	45	T45T	acC	acT	18	18	B.1.470	0.025281
ORF1ab/nsp5A-B	45	T45T	acC	acT	15	15	AY.102	0.000398
ORF1ab/nsp5A-B	45	T45T	acC	acT	12	14	B.1.351	0.000357
ORF1ab/nsp5A-B	45	T45T	acC	acA	2	14	B.1.351	0.000059
ORF1ab/nsp5A-B	45	T45T	acC	acT	13	13	AY.4.5	0.001397
ORF1ab/nsp5A-B	45	T45T	acC	acT	13	13	B.1.1.265	0.041009
ORF1ab/nsp5A-B	45	T45T	acC	acT	11	13	B.1.177	0.000145
ORF1ab/nsp5A-B	45	T45T	acC	acA	2	13	B.1.177	0.000026
ORF1ab/nsp5A-B	45	T45T	acC	acT	12	12	B.1.177.21	0.000918
ORF1ab/nsp5A-B	45	T45T	acC	acT	12	12	Q.3	0.00174
ORF1ab/nsp5A-B	45	T45T	acC	acG	10	11	AY.4.2	0.000217
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	11	AY.4.2	0.000022
ORF1ab/nsp5A-B	45	T45T	acC	acT	11	11	B.1.617.1	0.001419
ORF1ab/nsp5A-B	45	T45T	acC	acA	10	10	AY.54	0.000953
ORF1ab/nsp5A-B	45	T45T	acC	acT	10	10	B.1.1.291	0.007424
ORF1ab/nsp5A-B	45	T45T	acC	acA	7	10	B.1.221	0.000497
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	10	B.1.221	0.000213
ORF1ab/nsp5A-B	45	T45T	acC	acT	10	10	B.1.438.1	0.001073
ORF1ab/nsp5A-B	45	T45T	acC	acA	8	10	B.1.525	0.000905
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	10	B.1.525	0.000226
ORF1ab/nsp5A-B	45	T45T	acC	acT	10	10	P.1.14	0.000478
ORF1ab/nsp5A-B	45	T45T	acC	acT	9	9	B.1.36	0.001313
ORF1ab/nsp5A-B	45	T45T	acC	acT	8	8	AY.26	0.000226
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	8	B.1.1.519	0.000278
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	8	B.1.1.519	0.00004
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	8	B.1.160	0.000218
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	8	B.1.160	0.000031
ORF1ab/nsp5A-B	45	T45T	acC	acA	4	8	B.1.177.86	0.000734
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	8	B.1.177.86	0.000734
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	8	B.1.243	0.000487
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	8	B.1.243	0.00007
ORF1ab/nsp5A-B	45	T45T	acC	acT	8	8	B.1.466.2	0.00313
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	8	B.1.596	0.00061
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	8	B.1.596	0.000087
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	7	B.1.1.284	0.000752
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	7	B.1.177.77	0.005084
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	7	B.1.258	0.000466
ORF1ab/nsp5A-B	45	T45T	acC	acT	7	7	B.1.258.17	0.000728
ORF1ab/nsp5A-B	45	T45T	acC	acT	6	6	B.1.36.1	0.006842
ORF1ab/nsp5A-B	45	T45T	acC	acT	6	6	B.1.409	0.004687
ORF1ab/nsp5A-B	45	T45T	acC	acT	6	6	C.37	0.000696
ORF1ab/nsp5A-B	45	T45T	acC	acT	5	5	AY.113	0.000712
ORF1ab/nsp5A-B	45	T45T	acC	acT	5	5	AY.39.1	0.000198
ORF1ab/nsp5A-B	45	T45T	acC	acT	5	5	B.1.1.28	0.001556
ORF1ab/nsp5A-B	45	T45T	acC	acT	5	5	B.1.1.311	0.001791
ORF1ab/nsp5A-B	45	T45T	acC	acT	5	5	B.1.1.369	0.002231
ORF1ab/nsp5A-B	45	T45T	acC	acT	5	5	B.1.400	0.002145
ORF1ab/nsp5A-B	45	T45T	acC	acT	5	5	Q.1	0.000632
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	AY.119	0.000141
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	AY.29.1	0.000882
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	AY.46.6	0.000289
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	AY.73	0.002661
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	AY.89	0.019608
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	B.1.1.326	0.007042
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	B.1.1.467	0.076923
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	B.1.160.30	0.011905
ORF1ab/nsp5A-B	45	T45T	acC	acT	4	4	B.1.177.75	0.004162
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	A	0.001161
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	3	AY.100	0.000092
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	3	AY.100	0.000046
ORF1ab/nsp5A-B	45	T45T	acC	acG	2	3	AY.14	0.000176
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	3	AY.14	0.000088
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	AY.23	0.000209
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	AY.6	0.000123
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	AY.74	0.000347
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	AY.75.1	0.000541
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	3	AY.91	0.001461
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	3	AY.91	0.00073
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	3	B	0.000256
ORF1ab/nsp5A-B	45	T45T	acC	acG	1	3	B	0.000128
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	B.1.1.322	0.026316
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	B.1.1.70	0.001023
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	3	B.1.427	0.000101
ORF1ab/nsp5A-B	45	T45T	acC	acG	1	3	B.1.427	0.00005
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	B.1.526	0.000071
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	B.1.595	0.000783
ORF1ab/nsp5A-B	45	T45T	acC	acT	3	3	P.1.12	0.001452
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	3	P.2	0.000373
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	3	P.2	0.000187
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.117	0.000169
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.118	0.000125
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	2	AY.121	0.000135
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	2	AY.121	0.000135
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.2	0.000712
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.3.1	0.000171
ORF1ab/nsp5A-B	45	T45T	acC	acA	2	2	AY.34.1	0.00102
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.5.4	0.000553
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.57	0.001312
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.84	0.000875
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	AY.9.1	0.000167
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.1.289	0.004167
ORF1ab/nsp5A-B	45	T45T	acC	acG	2	2	B.1.1.409	0.005666
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.177.44	0.001038
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.214.2	0.001199
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.239	0.002442
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.36.18	0.00084
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.36.36	0.001204
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.36.8	0.002
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.575	0.000607
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.1.588	0.00182
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	B.4	0.004415
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	N.4	0.008511
ORF1ab/nsp5A-B	45	T45T	acC	acT	2	2	P.1.15	0.000465
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1		0.055556
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	A.2.2	0.001689
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	A.2.5	0.000499
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.10	0.00053
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.101	0.00049
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.109	0.00074
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	AY.110	0.000113
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.114	0.000231
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.28	0.00189
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.34	0.000097
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.35	0.000233
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.36	0.000148
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.37	0.000316
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.42	0.00004
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.45	0.000122
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.46	0.000104
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.46.1	0.001027
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	AY.46.2	0.000635
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.5.3	0.000337
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.59	0.00053
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.61	0.000105
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	AY.62	0.000436
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.7	0.000196
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.75	0.000056
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.79	0.001211
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.8	0.000606
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	AY.81	0.001992
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.88	0.000884
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.9	0.000068
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.98	0.000079
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	AY.99.2	0.000092
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.157	0.000913
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.176	0.000439
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.198	0.001468
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.222	0.000204
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.306	0.000438
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.318	0.000302
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.33	0.000421
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.388	0.045455
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.39	0.00051
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	B.1.1.398	0.003226
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.429	0.004608
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.1.466	0.008696
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.177.17	0.000821
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	B.1.177.4	0.000211
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.206	0.000816
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.232	0.000537
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.235	0.002519
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.338	0.008621
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.36.16	0.001425
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.36.17	0.000494
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.36.29	0.000517
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.367	0.000792
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.499	0.00105
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.544	0.006024
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.568	0.001111
ORF1ab/nsp5A-B	45	T45T	acC	acG	1	1	B.1.577	0.000687
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.620	0.000946
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.621	0.000089
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.623	0.000536
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.629	0.013333
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.634	0.003425
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	B.1.637	0.000073
ORF1ab/nsp5A-B	45	T45T	acC	acA	1	1	C.16	0.00106
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	D.2	0.000075
ORF1ab/nsp5A-B	45	T45T	acC	acT	1	1	Q.8	0.000165

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.