CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 29

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	29	T29A		nonsyn	Act	Gct	14470	14466	0.999724	21647-21649
S	29	T29A		nonsyn	AcT	GcC	14470	4	0.000276434	21647-21649
S	29	T29I		nonsyn	aCt	aTt	5905	5903	0.999661	21647-21649
S	29	T29I		nonsyn	aCT	aTC	5905	2	0.000338696	21647-21649
S	29	T29T		syn	acT	acC	1775	1721	0.969577	21647-21649
S	29	T29T		syn	acT	acA	1775	50	0.028169	21647-21649
S	29	T29T		syn	acT	acG	1775	4	0.00225352	21647-21649
S	29	T29S		nonsyn	Act	Tct	196	153	0.780612	21647-21649
S	29	T29S		nonsyn	aCt	aGt	196	42	0.214286	21647-21649
S	29	T29S		nonsyn	AcT	TcG	196	1	0.00510204	21647-21649
S	29	T29del		del	ACT	---	98	98	1	21647-21649
S	29	T29del1		del	acT	ac-	82	80	0.97561	21647-21649
S	29	T29del1		del	Act	-ct	82	2	0.0243902	21647-21649
S	29	T29V		nonsyn	ACt	GTt	13	13	1	21647-21649
S	29	T29P		nonsyn	Act	Cct	8	8	1	21647-21649
S	29	T29N		nonsyn	aCt	aAt	7	6	0.857143	21647-21649
S	29	T29N		nonsyn	aCT	aAC	7	1	0.142857	21647-21649
S	29	T29G		nonsyn	ACT	GGA	2	2	1	21647-21649
S	29	T29L		nonsyn	ACT	CTC	1	1	1	21647-21649

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
S	29	T29A	Act	Gct	14466	14470	All	0.002767
S	29	T29A	AcT	GcC	4	14470	All	0.000001
S	29	T29A	Act	Gct	13898	13902	AY.33	0.92808
S	29	T29A	AcT	GcC	4	13902	AY.33	0.000267
S	29	T29I	aCt	aTt	5903	5905	All	0.001129
S	29	T29I	aCT	aTC	2	5905	All	0
S	29	T29T	acT	acC	1721	1775	All	0.000329
S	29	T29T	acT	acA	50	1775	All	0.00001
S	29	T29T	acT	acG	4	1775	All	0.000001
S	29	T29I	aCt	aTt	822	822	B.1.1.7	0.000736
S	29	T29I	aCt	aTt	673	673	AY.4	0.001047
S	29	T29I	aCt	aTt	614	614	AY.103	0.003812
S	29	T29I	aCt	aTt	606	606	AY.121	0.082003
S	29	T29I	aCt	aTt	598	598	B.1.1.486	0.943218
S	29	T29T	acT	acC	555	555	AY.43	0.002459
S	29	T29T	acT	acC	549	550	B.1.617.2	0.002067
S	29	T29T	acT	acA	1	550	B.1.617.2	0.000004
S	29	T29A	Act	Gct	375	375	AY.4	0.000584
S	29	T29I	aCt	aTt	205	205	B.1.1.67	0.936073
S	29	T29S	Act	Tct	153	196	All	0.000029
S	29	T29S	aCt	aGt	42	196	All	0.000008
S	29	T29S	AcT	TcG	1	196	All	0
S	29	T29I	aCt	aTt	176	176	B.1	0.001612
S	29	T29I	aCt	aTt	171	171	B.1.617.2	0.000644
S	29	T29I	aCt	aTt	131	131	B.1.632	0.879195
S	29	T29I	aCt	aTt	114	114	B.1.2	0.001004
S	29	T29I	aCt	aTt	113	113	AY.43	0.000501
S	29	T29I	aCt	aTt	109	109	AY.44	0.000663
S	29	T29del	ACT	---	98	98	All	0.000019
S	29	T29del1	acT	ac-	80	82	All	0.000015
S	29	T29del1	Act	-ct	2	82	All	0
S	29	T29T	acT	acC	67	76	B.1.1.7	0.00006
S	29	T29T	acT	acA	9	76	B.1.1.7	0.000008
S	29	T29I	aCt	aTt	72	72	AY.25	0.000433
S	29	T29T	acT	acC	71	71	AY.44	0.000432
S	29	T29del1	acT	ac-	66	67	B.1.1.7	0.000059
S	29	T29del1	Act	-ct	1	67	B.1.1.7	0.000001
S	29	T29S	Act	Tct	60	60	AY.29	0.000946
S	29	T29T	acT	acC	51	53	AY.4	0.000079
S	29	T29T	acT	acG	1	53	AY.4	0.000002
S	29	T29T	acT	acA	1	53	AY.4	0.000002
S	29	T29I	aCt	aTt	52	53	B.1.1	0.000943
S	29	T29I	aCT	aTC	1	53	B.1.1	0.000018
S	29	T29I	aCt	aTt	51	51	AY.4.2	0.001106
S	29	T29I	aCt	aTt	50	50	B.1.1.519	0.001986
S	29	T29I	aCt	aTt	50	50	B.1.201	0.284091
S	29	T29I	aCt	aTt	50	50	B.1.243	0.003479
S	29	T29I	aCt	aTt	50	50	P.1	0.000788
S	29	T29A	Act	Gct	49	49	AY.103	0.000304
S	29	T29I	aCt	aTt	49	49	B.1.177	0.000645
S	29	T29S	Act	Tct	39	48	B.1.1.7	0.000035
S	29	T29S	aCt	aGt	9	48	B.1.1.7	0.000008
S	29	T29I	aCt	aTt	42	42	AY.3	0.000418
S	29	T29I	aCt	aTt	37	37	B.1.160	0.001154
S	29	T29T	acT	acC	36	36	AY.39	0.00089
S	29	T29I	aCt	aTt	36	36	AY.99.2	0.003318
S	29	T29I	aCt	aTt	36	36	C.35	0.027864
S	29	T29S	Act	Tct	34	34	AY.33	0.00227
S	29	T29T	acT	acC	34	34	AY.7	0.006664
S	29	T29T	acT	acA	27	29	AY.26	0.000764
S	29	T29T	acT	acC	2	29	AY.26	0.000057
S	29	T29A	Act	Gct	29	29	AY.34	0.002812
S	29	T29A	Act	Gct	26	26	B.1.617.2	0.000098
S	29	T29T	acT	acC	24	25	AY.25	0.000144
S	29	T29T	acT	acA	1	25	AY.25	0.000006
S	29	T29I	aCt	aTt	24	24	A	0.009288
S	29	T29T	acT	acC	24	24	B.1.1.207	0.028369
S	29	T29I	aCt	aTt	24	24	C.37	0.002786
S	29	T29I	aCt	aTt	23	23	AY.100	0.001058
S	29	T29I	aCt	aTt	23	23	AY.120	0.000855
S	29	T29T	acT	acC	23	23	AY.6	0.000946
S	29	T29I	aCt	aTt	22	22	B.1.177.81	0.004165
S	29	T29I	aCt	aTt	22	22	B.1.596	0.001917
S	29	T29I	aCt	aTt	20	20	AY.26	0.000566
S	29	T29del	ACT	---	20	20	B.1.1.7	0.000018
S	29	T29I	aCt	aTt	19	19	B.1.111	0.022327
S	29	T29I	aCt	aTt	18	18	B.1.1.372	0.012397
S	29	T29I	aCt	aTt	18	18	B.1.526	0.000423
S	29	T29I	aCt	aTt	17	17	AY.102	0.000451
S	29	T29I	aCt	aTt	17	17	AY.36	0.00252
S	29	T29I	aCt	aTt	17	17	B.1.1.306	0.007453
S	29	T29I	aCt	aTt	16	16	B.1.177.44	0.008303
S	29	T29I	aCt	aTt	16	16	B.1.234	0.002111
S	29	T29T	acT	acC	14	15	B.1.243	0.000974
S	29	T29T	acT	acA	1	15	B.1.243	0.00007
S	29	T29I	aCt	aTt	15	15	B.1.36.29	0.00776
S	29	T29I	aCt	aTt	15	15	Q.8	0.002474
S	29	T29I	aCt	aTt	14	14	AL.1	0.181818
S	29	T29T	acT	acC	14	14	AY.103	0.000087
S	29	T29T	acT	acC	14	14	AY.118	0.000877
S	29	T29I	aCt	aTt	14	14	AY.5	0.000289
S	29	T29I	aCt	aTt	14	14	B.1.1.284	0.001504
S	29	T29I	aCt	aTt	14	14	B.1.369	0.003993
S	29	T29V	ACt	GTt	13	13	All	0.000002
S	29	T29T	acT	acC	13	13	AY.119	0.000459
S	29	T29V	ACt	GTt	13	13	AY.33	0.000868
S	29	T29del	ACT	---	13	13	AY.33	0.000868
S	29	T29I	aCt	aTt	13	13	AY.39	0.000321
S	29	T29I	aCt	aTt	13	13	N.4	0.055319
S	29	T29I	aCt	aTt	12	12	AY.119	0.000424
S	29	T29T	acT	acC	10	12	AY.120.1	0.00321
S	29	T29T	acT	acG	2	12	AY.120.1	0.000642
S	29	T29A	Act	Gct	12	12	AY.4.5	0.00129
S	29	T29I	aCt	aTt	12	12	B.1.36	0.001751
S	29	T29I	aCt	aTt	12	12	P.2	0.00224
S	29	T29I	aCt	aTt	11	11	A.1	0.0031
S	29	T29T	acT	acC	11	11	AY.102	0.000292
S	29	T29I	aCt	aTt	11	11	AY.4.4	0.004501
S	29	T29A	Act	Gct	11	11	B.1.1.261	0.094828
S	29	T29I	aCt	aTt	11	11	B.1.409	0.008594
S	29	T29I	aCt	aTt	11	11	P.1.15	0.002556
S	29	T29I	aCt	aTt	10	10	AY.3.1	0.000853
S	29	T29I	aCt	aTt	10	10	AY.39.1	0.000396
S	29	T29A	Act	Gct	10	10	AY.43	0.000044
S	29	T29T	acT	acC	10	10	AY.61	0.001048
S	29	T29A	Act	Gct	10	10	AY.98.1	0.000484
S	29	T29I	aCt	aTt	10	10	B.1.1.39	0.005097
S	29	T29I	aCt	aTt	10	10	B.1.400	0.00429
S	29	T29T	acT	acC	9	9	A.2.5	0.004491
S	29	T29I	aCt	aTt	9	9	AY.111	0.001648
S	29	T29T	acT	acC	9	9	AY.23	0.000628
S	29	T29I	aCt	aTt	9	9	AY.27	0.000582
S	29	T29T	acT	acC	4	9	B.1	0.000037
S	29	T29T	acT	acA	4	9	B.1	0.000037
S	29	T29T	acT	acG	1	9	B.1	0.000009
S	29	T29I	aCt	aTt	9	9	B.1.1.303	0.024862
S	29	T29I	aCt	aTt	9	9	B.1.1.63	0.003472
S	29	T29del	ACT	---	9	9	B.1.177	0.000119
S	29	T29P	Act	Cct	8	8	All	0.000002
S	29	T29T	acT	acC	8	8	AY.111	0.001465
S	29	T29I	aCt	aTt	8	8	AY.23	0.000558
S	29	T29del	ACT	---	8	8	AY.4	0.000012
S	29	T29T	acT	acC	8	8	AY.46	0.000833
S	29	T29I	aCt	aTt	8	8	AY.47	0.000249
S	29	T29T	acT	acC	8	8	B.1.1.33	0.003367
S	29	T29A	Act	Gct	8	8	B.1.1.7	0.000007
S	29	T29T	acT	acC	8	8	P.1	0.000126
S	29	T29N	aCt	aAt	6	7	All	0.000001
S	29	T29N	aCT	aAC	1	7	All	0
S	29	T29T	acT	acC	7	7	AY.117	0.000592
S	29	T29I	aCt	aTt	7	7	AY.29	0.00011
S	29	T29I	aCt	aTt	7	7	AY.35	0.001631
S	29	T29S	Act	Tct	4	7	AY.4.2	0.000087
S	29	T29S	aCt	aGt	3	7	AY.4.2	0.000065
S	29	T29A	Act	Gct	7	7	AY.44	0.000043
S	29	T29I	aCt	aTt	7	7	AY.62	0.00305
S	29	T29I	aCt	aTt	7	7	B.1.1.222	0.001428
S	29	T29I	aCt	aTt	7	7	B.1.1.232	0.012704
S	29	T29I	aCt	aTt	7	7	B.1.1.265	0.022082
S	29	T29I	aCt	aTt	7	7	B.1.1.50	0.004752
S	29	T29T	acT	acC	7	7	B.1.617.1	0.000903
S	29	T29I	aCt	aTt	7	7	B.1.637	0.000512
S	29	T29I	aCt	aTt	6	6	AY.110	0.000676
S	29	T29I	aCt	aTt	6	6	AY.118	0.000376
S	29	T29I	aCt	aTt	6	6	AY.20	0.000233
S	29	T29S	Act	Tct	3	6	AY.4	0.000005
S	29	T29S	aCt	aGt	3	6	AY.4	0.000005
S	29	T29I	aCt	aTt	6	6	AY.93	0.001638
S	29	T29del	ACT	---	6	6	B.1.1	0.000109
S	29	T29T	acT	acC	5	6	B.1.177	0.000066
S	29	T29T	acT	acA	1	6	B.1.177	0.000013
S	29	T29T	acT	acC	6	6	B.1.177.82	0.002864
S	29	T29I	aCt	aTt	6	6	B.1.240	0.001293
S	29	T29I	aCt	aTt	6	6	B.1.429	0.000141
S	29	T29T	acT	acC	6	6	B.1.474	0.011407
S	29	T29del	ACT	---	5	5	AY.103	0.000031
S	29	T29I	aCt	aTt	5	5	AY.45	0.000608
S	29	T29T	acT	acC	5	5	AY.47	0.000156
S	29	T29T	acT	acC	5	5	AY.5	0.000103
S	29	T29T	acT	acC	5	5	AY.53	0.001438
S	29	T29T	acT	acC	4	5	B.1.2	0.000035
S	29	T29T	acT	acA	1	5	B.1.2	0.000009
S	29	T29I	aCt	aTt	5	5	B.1.258.17	0.00052
S	29	T29T	acT	acC	5	5	B.1.367	0.003962
S	29	T29S	aCt	aGt	5	5	B.1.429	0.000118
S	29	T29I	aCt	aTt	5	5	B.1.575	0.001517
S	29	T29I	aCt	aTt	5	5	B.1.617.1	0.000645
S	29	T29I	aCt	aTt	5	5	P.1.14	0.000239
S	29	T29I	aCt	aTt	5	5	P.1.7	0.001596
S	29	T29I	aCt	aTt	4	4	AY.108	0.00441
S	29	T29I	aCt	aTt	4	4	AY.117	0.000338
S	29	T29I	aCt	aTt	4	4	AY.42	0.000161
S	29	T29T	acT	acC	3	4	AY.42	0.000121
S	29	T29T	acT	acA	1	4	AY.42	0.00004
S	29	T29del	ACT	---	4	4	AY.43	0.000018
S	29	T29T	acT	acC	4	4	AY.45	0.000487
S	29	T29I	aCt	aTt	4	4	AY.46.4	0.000658
S	29	T29I	aCt	aTt	4	4	AY.9.1	0.000335
S	29	T29T	acT	acC	4	4	B.1.1	0.000073
S	29	T29I	aCt	aTt	4	4	B.1.1.214	0.000222
S	29	T29I	aCt	aTt	4	4	B.1.1.216	0.003562
S	29	T29T	acT	acC	4	4	B.1.177.69	0.005935
S	29	T29T	acT	acC	4	4	B.1.351	0.000119
S	29	T29I	aCt	aTt	4	4	B.1.432	0.044944
S	29	T29I	aCt	aTt	4	4	B.1.517	0.001708
S	29	T29I	aCt	aTt	4	4	B.1.621	0.000354
S	29	T29I	aCt	aTt	4	4	C.30	0.006908
S	29	T29I	aCt	aTt	4	4	C.36	0.003643
S	29	T29I	aCt	aTt	3	3	A.5	0.005769
S	29	T29I	aCt	aTt	3	3	AD.2	0.000657
S	29	T29S	Act	Tct	2	3	AY.103	0.000012
S	29	T29S	aCt	aGt	1	3	AY.103	0.000006
S	29	T29T	acT	acC	3	3	AY.34.1	0.00153
S	29	T29T	acT	acC	3	3	AY.4.5	0.000322
S	29	T29S	Act	Tct	2	3	AY.43	0.000009
S	29	T29S	aCt	aGt	1	3	AY.43	0.000004
S	29	T29T	acT	acC	3	3	AY.46.6	0.000217
S	29	T29I	aCt	aTt	3	3	AY.54	0.000286
S	29	T29I	aCt	aTt	3	3	AY.6	0.000123
S	29	T29I	aCt	aTt	3	3	AY.75	0.000168
S	29	T29I	aCt	aTt	3	3	AY.98	0.000237
S	29	T29del	ACT	---	3	3	B.1	0.000027
S	29	T29I	aCt	aTt	3	3	B.1.1.170	0.003741
S	29	T29I	aCt	aTt	3	3	B.1.1.25	0.001706
S	29	T29I	aCt	aTt	3	3	B.1.1.28	0.000934
S	29	T29I	aCt	aTt	3	3	B.1.1.397	0.006757
S	29	T29T	acT	acC	3	3	B.1.1.526	0.010638
S	29	T29I	aCt	aTt	3	3	B.1.177.12	0.000455
S	29	T29I	aCt	aTt	3	3	B.1.177.35	0.002073
S	29	T29I	aCt	aTt	3	3	B.1.177.73	0.001699
S	29	T29del1	acT	ac-	3	3	B.1.177.82	0.001432
S	29	T29I	aCt	aTt	3	3	B.1.177.82	0.001432
S	29	T29I	aCt	aTt	3	3	B.1.221	0.000213
S	29	T29S	aCt	aGt	3	3	B.1.243	0.000209
S	29	T29I	aCt	aTt	3	3	B.1.258	0.0002
S	29	T29I	aCt	aTt	3	3	B.1.311	0.000824
S	29	T29I	aCt	aTt	3	3	B.1.337	0.01676
S	29	T29I	aCt	aTt	3	3	B.1.346	0.003932
S	29	T29del1	acT	ac-	3	3	B.1.351	0.000089
S	29	T29I	aCt	aTt	3	3	B.1.351	0.000089
S	29	T29I	aCt	aTt	3	3	B.1.403	0.009804
S	29	T29I	aCt	aTt	3	3	B.1.427	0.000151
S	29	T29I	aCt	aTt	3	3	B.1.566	0.057692
S	29	T29I	aCt	aTt	3	3	B.1.623	0.001609
S	29	T29del	ACT	---	3	3	P.1	0.000047
S	29	T29I	aCt	aTt	3	3	Q.1	0.000379
S	29	T29P	Act	Cct	2	2	A.2	0.001324
S	29	T29I	aCt	aTt	2	2	A.23.1	0.001408
S	29	T29G	ACT	GGA	2	2	All	0
S	29	T29T	acT	acC	2	2	AY.105	0.001286
S	29	T29T	acT	acC	2	2	AY.106	0.00067
S	29	T29I	aCt	aTt	2	2	AY.113	0.000285
S	29	T29A	Act	Gct	2	2	AY.116	0.000574
S	29	T29T	acT	acC	2	2	AY.120	0.000074
S	29	T29S	Act	Tct	2	2	AY.120	0.000074
S	29	T29I	aCT	aTC	1	2	AY.120.1	0.000321
S	29	T29I	aCt	aTt	1	2	AY.120.1	0.000321
S	29	T29I	aCt	aTt	2	2	AY.15	0.004444
S	29	T29T	acT	acC	2	2	AY.20	0.000078
S	29	T29S	aCt	aGt	2	2	AY.23	0.000139
S	29	T29T	acT	acC	2	2	AY.3.1	0.000171
S	29	T29T	acT	acC	2	2	AY.33	0.000134
S	29	T29del	ACT	---	2	2	AY.34.1	0.00102
S	29	T29I	aCt	aTt	2	2	AY.37	0.000632
S	29	T29I	aCt	aTt	2	2	AY.4.2.1	0.000298
S	29	T29N	aCt	aAt	2	2	AY.43	0.000009
S	29	T29I	aCt	aTt	2	2	AY.46	0.000208
S	29	T29A	Act	Gct	2	2	AY.5	0.000041
S	29	T29I	aCt	aTt	2	2	AY.5.3	0.000675
S	29	T29T	acT	acC	2	2	AY.5.3	0.000675
S	29	T29del1	acT	ac-	2	2	AY.52	0.001629
S	29	T29A	Act	Gct	2	2	AY.58	0.001815
S	29	T29I	aCt	aTt	2	2	AY.61	0.00021
S	29	T29I	aCt	aTt	2	2	AY.63	0.000774
S	29	T29T	acT	acC	2	2	AY.75	0.000112
S	29	T29I	aCt	aTt	2	2	AY.75.1	0.000361
S	29	T29I	aCt	aTt	2	2	AY.84	0.000875
S	29	T29I	aCt	aTt	2	2	AY.85	0.000854
S	29	T29T	acT	acC	2	2	AY.89	0.009804
S	29	T29I	aCt	aTt	2	2	AY.9.2	0.000073
S	29	T29T	acT	acC	2	2	AY.9.2	0.000073
S	29	T29T	acT	acC	2	2	AY.92	0.000575
S	29	T29T	acT	acC	2	2	AY.98	0.000158
S	29	T29I	aCt	aTt	2	2	AY.98.1	0.000097
S	29	T29I	aCt	aTt	2	2	B	0.000256
S	29	T29A	Act	Gct	2	2	B.1	0.000018
S	29	T29I	aCt	aTt	2	2	B.1.1.10	0.00223
S	29	T29I	aCt	aTt	2	2	B.1.1.312	0.003824
S	29	T29I	aCt	aTt	2	2	B.1.1.326	0.003521
S	29	T29I	aCt	aTt	2	2	B.1.1.379	0.0625
S	29	T29I	aCt	aTt	2	2	B.1.1.416	0.00181
S	29	T29S	aCt	aGt	2	2	B.1.1.416	0.00181
S	29	T29I	aCt	aTt	2	2	B.1.1.432	0.002532
S	29	T29G	ACT	GGA	2	2	B.1.1.46	0.008734
S	29	T29I	aCt	aTt	2	2	B.1.1.523	0.003125
S	29	T29P	Act	Cct	2	2	B.1.1.7	0.000002
S	29	T29T	acT	acC	2	2	B.1.110.3	0.001437
S	29	T29I	aCt	aTt	2	2	B.1.110.3	0.001437
S	29	T29del1	acT	ac-	2	2	B.1.160	0.000062
S	29	T29I	aCt	aTt	2	2	B.1.177.21	0.000153
S	29	T29I	aCt	aTt	2	2	B.1.177.42	0.001789
S	29	T29I	aCt	aTt	2	2	B.1.177.75	0.002081
S	29	T29S	Act	Tct	2	2	B.1.2	0.000018
S	29	T29I	aCt	aTt	2	2	B.1.241	0.001623
S	29	T29I	aCt	aTt	2	2	B.1.258.14	0.001961
S	29	T29I	aCt	aTt	2	2	B.1.36.27	0.001527
S	29	T29I	aCt	aTt	2	2	B.1.36.38	0.003284
S	29	T29I	aCt	aTt	2	2	B.1.466.2	0.000782
S	29	T29I	aCt	aTt	2	2	B.1.467	0.08
S	29	T29I	aCt	aTt	2	2	B.1.499	0.002101
S	29	T29del	ACT	---	2	2	B.1.525	0.000226
S	29	T29I	aCt	aTt	2	2	B.1.540	0.019417
S	29	T29I	aCt	aTt	2	2	B.1.547	0.04878
S	29	T29I	aCt	aTt	2	2	B.1.562	0.037037
S	29	T29I	aCt	aTt	2	2	B.1.582	0.000981
S	29	T29I	aCt	aTt	2	2	B.1.631	0.006734
S	29	T29I	aCt	aTt	2	2	P.1.12	0.000968
S	29	T29S	aCt	aGt	1	1		0.055556
S	29	T29N	aCt	aAt	1	1		0.055556
S	29	T29I	aCt	aTt	1	1	A.2	0.000662
S	29	T29N	aCt	aAt	1	1	A.2.2	0.001689
S	29	T29del	ACT	---	1	1	A.2.4	0.003367
S	29	T29T	acT	acA	1	1	A.2.4	0.003367
S	29	T29L	ACT	CTC	1	1	All	0
S	29	T29T	acT	acC	1	1	AY.100	0.000046
S	29	T29del	ACT	---	1	1	AY.100	0.000046
S	29	T29del	ACT	---	1	1	AY.101	0.00049
S	29	T29S	aCt	aGt	1	1	AY.102	0.000027
S	29	T29del	ACT	---	1	1	AY.102	0.000027
S	29	T29A	Act	Gct	1	1	AY.102	0.000027
S	29	T29L	ACT	CTC	1	1	AY.103	0.000006
S	29	T29del1	acT	ac-	1	1	AY.103	0.000006
S	29	T29I	aCt	aTt	1	1	AY.106	0.000335
S	29	T29T	acT	acC	1	1	AY.110	0.000113
S	29	T29A	Act	Gct	1	1	AY.118	0.000063
S	29	T29T	acT	acC	1	1	AY.14	0.000088
S	29	T29I	aCt	aTt	1	1	AY.16	0.00038
S	29	T29I	aCt	aTt	1	1	AY.16.1	0.00047
S	29	T29I	aCt	aTt	1	1	AY.2	0.000356
S	29	T29S	aCt	aGt	1	1	AY.20	0.000039
S	29	T29T	acT	acC	1	1	AY.23.1	0.000417
S	29	T29N	aCt	aAt	1	1	AY.25	0.000006
S	29	T29del	ACT	---	1	1	AY.25	0.000006
S	29	T29S	aCt	aGt	1	1	AY.25	0.000006
S	29	T29A	Act	Gct	1	1	AY.29	0.000016
S	29	T29A	Act	Gct	1	1	AY.3	0.00001
S	29	T29del	ACT	---	1	1	AY.3	0.00001
S	29	T29I	aCt	aTt	1	1	AY.30	0.000396
S	29	T29I	aCt	aTt	1	1	AY.32	0.000532
S	29	T29P	Act	Cct	1	1	AY.33	0.000067
S	29	T29I	aCt	aTt	1	1	AY.34	0.000097
S	29	T29S	aCt	aGt	1	1	AY.39	0.000025
S	29	T29A	Act	Gct	1	1	AY.39	0.000025
S	29	T29P	Act	Cct	1	1	AY.4	0.000002
S	29	T29T	acT	acC	1	1	AY.4.2	0.000022
S	29	T29del	ACT	---	1	1	AY.4.5	0.000107
S	29	T29I	aCt	aTt	1	1	AY.41	0.000294
S	29	T29del	ACT	---	1	1	AY.42	0.00004
S	29	T29A	Act	Gct	1	1	AY.42	0.00004
S	29	T29S	aCt	aGt	1	1	AY.44	0.000006
S	29	T29I	aCt	aTt	1	1	AY.46.1	0.001027
S	29	T29T	acT	acC	1	1	AY.46.2	0.000635
S	29	T29S	aCt	aGt	1	1	AY.46.6	0.000072
S	29	T29I	aCt	aTt	1	1	AY.46.6	0.000072
S	29	T29I	aCt	aTt	1	1	AY.48	0.000465
S	29	T29I	aCt	aTt	1	1	AY.5.2	0.002463
S	29	T29T	acT	acC	1	1	AY.5.4	0.000277
S	29	T29T	acT	acC	1	1	AY.52	0.000814
S	29	T29T	acT	acC	1	1	AY.54	0.000095
S	29	T29T	acT	acC	1	1	AY.58	0.000907
S	29	T29S	aCt	aGt	1	1	AY.59	0.00053
S	29	T29I	aCt	aTt	1	1	AY.60	0.000938
S	29	T29T	acT	acC	1	1	AY.62	0.000436
S	29	T29I	aCt	aTt	1	1	AY.65	0.000533
S	29	T29I	aCt	aTt	1	1	AY.67	0.000464
S	29	T29T	acT	acC	1	1	AY.67	0.000464
S	29	T29del	ACT	---	1	1	AY.68	0.000274
S	29	T29T	acT	acC	1	1	AY.68	0.000274
S	29	T29A	Act	Gct	1	1	AY.72	0.001361
S	29	T29A	Act	Gct	1	1	AY.85	0.000427
S	29	T29I	aCt	aTt	1	1	AY.91	0.00073
S	29	T29A	Act	Gct	1	1	AY.92	0.000287
S	29	T29I	aCt	aTt	1	1	AY.92	0.000287
S	29	T29I	aCt	aTt	1	1	AY.96	0.002075
S	29	T29T	acT	acC	1	1	AY.96	0.002075
S	29	T29A	Act	Gct	1	1	AY.96	0.002075
S	29	T29I	aCt	aTt	1	1	AY.99.1	0.001553
S	29	T29S	Act	Tct	1	1	B	0.000128
S	29	T29A	Act	Gct	1	1	B	0.000128
S	29	T29A	Act	Gct	1	1	B.1.1	0.000018
S	29	T29P	Act	Cct	1	1	B.1.1	0.000018
S	29	T29S	aCt	aGt	1	1	B.1.1	0.000018
S	29	T29N	aCT	aAC	1	1	B.1.1.1	0.000327
S	29	T29I	aCt	aTt	1	1	B.1.1.1	0.000327
S	29	T29I	aCt	aTt	1	1	B.1.1.113	0.006993
S	29	T29I	aCt	aTt	1	1	B.1.1.134	0.011364
S	29	T29I	aCt	aTt	1	1	B.1.1.158	0.012195
S	29	T29I	aCt	aTt	1	1	B.1.1.176	0.000439
S	29	T29T	acT	acC	1	1	B.1.1.214	0.000055
S	29	T29I	aCt	aTt	1	1	B.1.1.218	0.007692
S	29	T29I	aCt	aTt	1	1	B.1.1.220	0.001859
S	29	T29I	aCt	aTt	1	1	B.1.1.227	0.004348
S	29	T29I	aCt	aTt	1	1	B.1.1.241	0.00207
S	29	T29T	acT	acC	1	1	B.1.1.25	0.000569
S	29	T29P	Act	Cct	1	1	B.1.1.261	0.008621
S	29	T29S	Act	Tct	1	1	B.1.1.261	0.008621
S	29	T29A	Act	Gct	1	1	B.1.1.291	0.000742
S	29	T29S	AcT	TcG	1	1	B.1.1.306	0.000438
S	29	T29del	ACT	---	1	1	B.1.1.306	0.000438
S	29	T29I	aCt	aTt	1	1	B.1.1.307	0.002532
S	29	T29I	aCt	aTt	1	1	B.1.1.309	0.005848
S	29	T29I	aCt	aTt	1	1	B.1.1.311	0.000358
S	29	T29del	ACT	---	1	1	B.1.1.315	0.008475
S	29	T29I	aCt	aTt	1	1	B.1.1.316	0.000925
S	29	T29I	aCt	aTt	1	1	B.1.1.317	0.000412
S	29	T29I	aCt	aTt	1	1	B.1.1.33	0.000421
S	29	T29I	aCt	aTt	1	1	B.1.1.353	0.020833
S	29	T29I	aCt	aTt	1	1	B.1.1.362	0.005618
S	29	T29I	aCt	aTt	1	1	B.1.1.37	0.000193
S	29	T29S	Act	Tct	1	1	B.1.1.372	0.000689
S	29	T29I	aCt	aTt	1	1	B.1.1.398	0.003226
S	29	T29del	ACT	---	1	1	B.1.1.401	0.066667
S	29	T29I	aCt	aTt	1	1	B.1.1.407	0.041667
S	29	T29T	acT	acC	1	1	B.1.1.411	0.014706
S	29	T29I	aCt	aTt	1	1	B.1.1.433	0.001425
S	29	T29del	ACT	---	1	1	B.1.1.46	0.004367
S	29	T29T	acT	acC	1	1	B.1.1.519	0.00004
S	29	T29S	aCt	aGt	1	1	B.1.1.519	0.00004
S	29	T29I	aCt	aTt	1	1	B.1.1.70	0.000341
S	29	T29I	aCt	aTt	1	1	B.1.128	0.000635
S	29	T29I	aCt	aTt	1	1	B.1.139	0.000733
S	29	T29T	acT	acC	1	1	B.1.142	0.002899
S	29	T29A	Act	Gct	1	1	B.1.143	0.021277
S	29	T29I	aCt	aTt	1	1	B.1.157	0.002985
S	29	T29A	Act	Gct	1	1	B.1.160	0.000031
S	29	T29S	Act	Tct	1	1	B.1.177	0.000013
S	29	T29N	aCt	aAt	1	1	B.1.177	0.000013
S	29	T29T	acT	acC	1	1	B.1.177.15	0.000631
S	29	T29del	ACT	---	1	1	B.1.177.17	0.000821
S	29	T29T	acT	acC	1	1	B.1.177.19	0.001431
S	29	T29A	Act	Gct	1	1	B.1.177.44	0.000519
S	29	T29S	Act	Tct	1	1	B.1.177.46	0.000918
S	29	T29I	aCt	aTt	1	1	B.1.177.48	0.003125
S	29	T29del1	acT	ac-	1	1	B.1.177.6	0.000977
S	29	T29S	aCt	aGt	1	1	B.1.177.60	0.000218
S	29	T29del	ACT	---	1	1	B.1.177.60	0.000218
S	29	T29del	ACT	---	1	1	B.1.177.68	0.015152
S	29	T29del	ACT	---	1	1	B.1.177.7	0.000165
S	29	T29T	acT	acC	1	1	B.1.177.73	0.000566
S	29	T29A	Act	Gct	1	1	B.1.177.81	0.000189
S	29	T29del	ACT	---	1	1	B.1.177.83	0.001481
S	29	T29I	aCt	aTt	1	1	B.1.177.9	0.001332
S	29	T29del	ACT	---	1	1	B.1.2	0.000009
S	29	T29I	aCt	aTt	1	1	B.1.206	0.000816
S	29	T29I	aCt	aTt	1	1	B.1.210	0.002132
S	29	T29I	aCt	aTt	1	1	B.1.221.3	0.000833
S	29	T29I	aCt	aTt	1	1	B.1.232	0.000537
S	29	T29T	acT	acC	1	1	B.1.232	0.000537
S	29	T29I	aCt	aTt	1	1	B.1.237	0.004975
S	29	T29S	aCt	aGt	1	1	B.1.258.17	0.000104
S	29	T29I	aCt	aTt	1	1	B.1.320	0.001245
S	29	T29T	acT	acA	1	1	B.1.326	0.007576
S	29	T29I	aCt	aTt	1	1	B.1.349	0.000715
S	29	T29A	Act	Gct	1	1	B.1.351	0.00003
S	29	T29I	aCt	aTt	1	1	B.1.351.3	0.000876
S	29	T29A	Act	Gct	1	1	B.1.36	0.000146
S	29	T29del	ACT	---	1	1	B.1.36	0.000146
S	29	T29I	aCt	aTt	1	1	B.1.36.1	0.00114
S	29	T29del1	acT	ac-	1	1	B.1.36.1	0.00114
S	29	T29I	aCt	aTt	1	1	B.1.36.10	0.004785
S	29	T29I	aCt	aTt	1	1	B.1.36.16	0.001425
S	29	T29I	aCt	aTt	1	1	B.1.36.18	0.00042
S	29	T29I	aCt	aTt	1	1	B.1.36.22	0.001208
S	29	T29I	aCt	aTt	1	1	B.1.36.26	0.002857
S	29	T29I	aCt	aTt	1	1	B.1.36.31	0.001751
S	29	T29T	acT	acC	1	1	B.1.36.31	0.001751
S	29	T29I	aCt	aTt	1	1	B.1.36.36	0.000602
S	29	T29I	aCt	aTt	1	1	B.1.367	0.000792
S	29	T29I	aCt	aTt	1	1	B.1.371	0.001122
S	29	T29I	aCt	aTt	1	1	B.1.399	0.001934
S	29	T29T	acT	acC	1	1	B.1.400	0.000429
S	29	T29T	acT	acC	1	1	B.1.429	0.000024
S	29	T29T	acT	acC	1	1	B.1.433	0.003195
S	29	T29I	aCt	aTt	1	1	B.1.434	0.052632
S	29	T29I	aCt	aTt	1	1	B.1.448	0.002625
S	29	T29I	aCt	aTt	1	1	B.1.460	0.017857
S	29	T29I	aCt	aTt	1	1	B.1.463	0.008065
S	29	T29I	aCt	aTt	1	1	B.1.468	0.005714
S	29	T29I	aCt	aTt	1	1	B.1.497	0.000315
S	29	T29I	aCt	aTt	1	1	B.1.509	0.000866
S	29	T29I	aCt	aTt	1	1	B.1.521	0.004975
S	29	T29I	aCt	aTt	1	1	B.1.529	0.055556
S	29	T29T	acT	acC	1	1	B.1.561	0.000397
S	29	T29I	aCt	aTt	1	1	B.1.561	0.000397
S	29	T29T	acT	acC	1	1	B.1.564.1	0.001577
S	29	T29I	aCt	aTt	1	1	B.1.565	0.00081
S	29	T29I	aCt	aTt	1	1	B.1.587	0.001898
S	29	T29I	aCt	aTt	1	1	B.1.595	0.000261
S	29	T29I	aCt	aTt	1	1	B.1.609	0.000479
S	29	T29del	ACT	---	1	1	B.1.617.2	0.000004
S	29	T29del	ACT	---	1	1	B.1.620	0.000946
S	29	T29A	Act	Gct	1	1	B.1.621	0.000089
S	29	T29A	Act	Gct	1	1	B.1.623	0.000536
S	29	T29I	aCt	aTt	1	1	B.1.635	0.017544
S	29	T29A	Act	Gct	1	1	B.4	0.002208
S	29	T29I	aCt	aTt	1	1	B.40	0.000364
S	29	T29I	aCt	aTt	1	1	B.55	0.00295
S	29	T29T	acT	acC	1	1	C.36.3	0.000567
S	29	T29T	acT	acC	1	1	C.37	0.000116
S	29	T29I	aCt	aTt	1	1	C.37.1	0.002618
S	29	T29I	aCt	aTt	1	1	D.2	0.000075
S	29	T29T	acT	acA	1	1	D.2	0.000075
S	29	T29I	aCt	aTt	1	1	N.3	0.005814
S	29	T29S	aCt	aGt	1	1	P.1	0.000016
S	29	T29I	aCt	aTt	1	1	P.1.10	0.000269
S	29	T29T	acT	acC	1	1	P.1.10.1	0.00813
S	29	T29del1	Act	-ct	1	1	P.1.12	0.000484
S	29	T29I	aCt	aTt	1	1	P.1.16	0.000374
S	29	T29I	aCt	aTt	1	1	P.1.6	0.001946
S	29	T29A	Act	Gct	1	1	P.2	0.000187
S	29	T29del	ACT	---	1	1	Q.1	0.000126
S	29	T29T	acT	acC	1	1	Q.1	0.000126
S	29	T29I	aCt	aTt	1	1	Q.3	0.000145
S	29	T29I	aCt	aTt	1	1	Q.4	0.000455
S	29	T29del1	acT	ac-	1	1	R.1	0.00009
S	29	T29I	aCt	aTt	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.