CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 4

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
M	4	S4F		nonsyn	tCc	tTc	1911	1904	0.996337	26532-26534
M	4	S4F		nonsyn	tCC	tTT	1911	7	0.003663	26532-26534
M	4	S4S		syn	tcC	tcT	1522	1422	0.934297	26532-26534
M	4	S4S		syn	tcC	tcA	1522	76	0.0499343	26532-26534
M	4	S4S		syn	tcC	tcG	1522	24	0.0157687	26532-26534
M	4	S4A		nonsyn	Tcc	Gcc	108	106	0.981481	26532-26534
M	4	S4A		nonsyn	TcC	GcA	108	1	0.00925926	26532-26534
M	4	S4A		nonsyn	TcC	GcG	108	1	0.00925926	26532-26534
M	4	S4P		nonsyn	Tcc	Ccc	99	99	1	26532-26534
M	4	S4del		del	TCC	---	68	68	1	26532-26534
M	4	S4Y		nonsyn	tCc	tAc	53	52	0.981132	26532-26534
M	4	S4Y		nonsyn	tCC	tAT	53	1	0.0188679	26532-26534
M	4	S4T		nonsyn	Tcc	Acc	6	6	1	26532-26534
M	4	S4C		nonsyn	tCc	tGc	5	5	1	26532-26534
M	4	S4del1		del	tCc	t-c	5	5	1	26532-26534
M	4	S4I		nonsyn	TCc	ATc	2	2	1	26532-26534
M	4	S4X		nonsyn	tCC	tAA	1	1	1	26532-26534
M	4	S4L		nonsyn	tCC	tTG	1	1	1	26532-26534
M	4	S4V		nonsyn	TCC	GTG	1	1	1	26532-26534

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
M	4	S4F	tCc	tTc	1904	1911	All	0.000364
M	4	S4F	tCC	tTT	7	1911	All	0.000001
M	4	S4S	tcC	tcT	1422	1522	All	0.000272
M	4	S4S	tcC	tcA	76	1522	All	0.000015
M	4	S4S	tcC	tcG	24	1522	All	0.000005
M	4	S4S	tcC	tcT	278	282	AY.20	0.010805
M	4	S4S	tcC	tcG	4	282	AY.20	0.000155
M	4	S4S	tcC	tcT	214	217	B.1.1.7	0.000192
M	4	S4S	tcC	tcA	3	217	B.1.1.7	0.000003
M	4	S4F	tCc	tTc	213	213	B.1.1.7	0.000191
M	4	S4F	tCc	tTc	182	182	AY.4	0.000283
M	4	S4F	tCc	tTc	177	177	AY.34	0.017163
M	4	S4S	tcC	tcT	149	149	B.1.243	0.010368
M	4	S4F	tCc	tTc	123	123	B.1.632	0.825503
M	4	S4A	Tcc	Gcc	106	108	All	0.00002
M	4	S4A	TcC	GcA	1	108	All	0
M	4	S4A	TcC	GcG	1	108	All	0
M	4	S4P	Tcc	Ccc	99	99	All	0.000019
M	4	S4S	tcC	tcT	79	79	B.1.1	0.001433
M	4	S4F	tCc	tTc	78	78	B.1.617.2	0.000294
M	4	S4F	tCc	tTc	72	72	B.1.177	0.000948
M	4	S4del	TCC	---	68	68	All	0.000013
M	4	S4S	tcC	tcA	36	67	B.1.617.2	0.000136
M	4	S4S	tcC	tcT	31	67	B.1.617.2	0.000117
M	4	S4S	tcC	tcT	50	64	AY.4	0.000078
M	4	S4S	tcC	tcG	11	64	AY.4	0.000017
M	4	S4S	tcC	tcA	3	64	AY.4	0.000005
M	4	S4S	tcC	tcT	63	63	AY.44	0.000383
M	4	S4S	tcC	tcT	63	63	B.1.1.404	1
M	4	S4A	Tcc	Gcc	59	59	AY.3.1	0.00503
M	4	S4Y	tCc	tAc	52	53	All	0.00001
M	4	S4Y	tCC	tAT	1	53	All	0
M	4	S4S	tcC	tcT	51	52	B.1.526	0.001199
M	4	S4S	tcC	tcA	1	52	B.1.526	0.000024
M	4	S4F	tCc	tTc	50	50	AY.103	0.00031
M	4	S4F	tCc	tTc	45	46	B.1	0.000412
M	4	S4F	tCC	tTT	1	46	B.1	0.000009
M	4	S4F	tCc	tTc	45	45	AY.25	0.000271
M	4	S4S	tcC	tcT	44	44	B.1	0.000403
M	4	S4F	tCc	tTc	43	43	B.1.160	0.001341
M	4	S4F	tCc	tTc	39	39	B.1.580	0.158537
M	4	S4P	Tcc	Ccc	38	38	B.1.1.7	0.000034
M	4	S4S	tcC	tcT	36	36	B.1.471	0.098361
M	4	S4F	tCc	tTc	32	32	AY.26	0.000906
M	4	S4F	tCc	tTc	29	29	B.1.1.519	0.001152
M	4	S4S	tcC	tcT	29	29	B.1.177	0.000382
M	4	S4S	tcC	tcT	28	28	L.3	0.099291
M	4	S4F	tCc	tTc	27	27	AY.39.1	0.00107
M	4	S4F	tCc	tTc	27	27	AY.4.2	0.000586
M	4	S4S	tcC	tcT	27	27	B.1.2	0.000238
M	4	S4F	tCc	tTc	25	25	P.1	0.000394
M	4	S4F	tCc	tTc	24	24	AY.43	0.000106
M	4	S4F	tCc	tTc	24	24	B.1.1	0.000435
M	4	S4F	tCc	tTc	24	24	B.1.2	0.000211
M	4	S4S	tcC	tcT	23	23	AY.3	0.000229
M	4	S4F	tCc	tTc	23	23	AY.44	0.00014
M	4	S4F	tCc	tTc	23	23	B.1.258	0.001531
M	4	S4A	Tcc	Gcc	22	22	B.1.177	0.00029
M	4	S4F	tCc	tTc	21	21	AY.119	0.000741
M	4	S4F	tCc	tTc	21	21	AY.23	0.001465
M	4	S4F	tCc	tTc	19	19	B.1.561	0.007543
M	4	S4F	tCc	tTc	18	18	B.1.573	0.109756
M	4	S4S	tcC	tcT	16	17	AY.103	0.000099
M	4	S4S	tcC	tcG	1	17	AY.103	0.000006
M	4	S4Y	tCc	tAc	16	16	B.1.1.317	0.006587
M	4	S4S	tcC	tcT	14	16	B.1.258	0.000932
M	4	S4S	tcC	tcA	2	16	B.1.258	0.000133
M	4	S4S	tcC	tcT	9	15	AY.43	0.00004
M	4	S4S	tcC	tcG	4	15	AY.43	0.000018
M	4	S4S	tcC	tcA	2	15	AY.43	0.000009
M	4	S4F	tCc	tTc	15	15	B.1.400	0.006435
M	4	S4F	tCc	tTc	14	14	B.1.1.214	0.000776
M	4	S4F	tCc	tTc	14	14	B.1.243	0.000974
M	4	S4F	tCc	tTc	9	13	AY.20	0.00035
M	4	S4F	tCC	tTT	4	13	AY.20	0.000155
M	4	S4F	tCc	tTc	13	13	AY.3	0.000129
M	4	S4F	tCc	tTc	13	13	B.1.351	0.000386
M	4	S4S	tcC	tcA	9	12	AY.100	0.000414
M	4	S4S	tcC	tcT	3	12	AY.100	0.000138
M	4	S4F	tCc	tTc	12	12	AY.102	0.000318
M	4	S4F	tCc	tTc	12	12	AY.29	0.000189
M	4	S4S	tcC	tcT	11	12	AY.39.1	0.000436
M	4	S4S	tcC	tcG	1	12	AY.39.1	0.00004
M	4	S4P	Tcc	Ccc	12	12	AY.4	0.000019
M	4	S4F	tCc	tTc	12	12	B	0.001534
M	4	S4S	tcC	tcT	12	12	B.1.351	0.000357
M	4	S4del	TCC	---	11	11	B.1.1.7	0.00001
M	4	S4S	tcC	tcT	9	10	AY.26	0.000255
M	4	S4S	tcC	tcA	1	10	AY.26	0.000028
M	4	S4F	tCc	tTc	10	10	AY.42	0.000402
M	4	S4F	tCc	tTc	9	9	AY.39	0.000222
M	4	S4del	TCC	---	9	9	AY.4	0.000014
M	4	S4F	tCc	tTc	9	9	AY.98.1	0.000436
M	4	S4Y	tCc	tAc	9	9	B.1.1.7	0.000008
M	4	S4F	tCc	tTc	9	9	B.1.429	0.000212
M	4	S4F	tCc	tTc	8	8	A.2.5	0.003992
M	4	S4S	tcC	tcT	8	8	B.1.177.86	0.001468
M	4	S4F	tCc	tTc	8	8	B.1.526	0.000188
M	4	S4F	tCc	tTc	7	7	AY.107	0.003262
M	4	S4S	tcC	tcT	7	7	AY.25	0.000042
M	4	S4F	tCc	tTc	7	7	AY.3.1	0.000597
M	4	S4del	TCC	---	7	7	AY.46.6	0.000505
M	4	S4Y	tCc	tAc	7	7	B.1	0.000064
M	4	S4S	tcC	tcT	7	7	B.1.1.519	0.000278
M	4	S4F	tCc	tTc	7	7	B.1.351.2	0.002118
M	4	S4F	tCc	tTc	7	7	B.1.525	0.000792
M	4	S4S	tcC	tcT	6	7	B.1.596	0.000523
M	4	S4S	tcC	tcA	1	7	B.1.596	0.000087
M	4	S4F	tCc	tTc	7	7	B.1.621	0.00062
M	4	S4T	Tcc	Acc	6	6	All	0.000001
M	4	S4S	tcC	tcA	6	6	AY.32	0.003195
M	4	S4S	tcC	tcT	5	6	AY.54	0.000477
M	4	S4S	tcC	tcA	1	6	AY.54	0.000095
M	4	S4S	tcC	tcT	6	6	AY.92	0.001724
M	4	S4S	tcC	tcT	6	6	B	0.000767
M	4	S4del	TCC	---	6	6	B.1	0.000055
M	4	S4S	tcC	tcT	6	6	B.1.160	0.000187
M	4	S4P	Tcc	Ccc	6	6	B.1.177	0.000079
M	4	S4S	tcC	tcT	6	6	P.1.15	0.001394
M	4	S4P	Tcc	Ccc	6	6	P.1.17	0.000971
M	4	S4F	tCc	tTc	6	6	P.1.7	0.001916
M	4	S4del1	tCc	t-c	5	5	All	0.000001
M	4	S4C	tCc	tGc	5	5	All	0.000001
M	4	S4F	tCc	tTc	5	5	AY.6	0.000206
M	4	S4F	tCc	tTc	5	5	B.1.108	0.02907
M	4	S4F	tCc	tTc	5	5	B.1.234	0.00066
M	4	S4F	tCc	tTc	5	5	B.1.367	0.003962
M	4	S4F	tCc	tTc	5	5	B.1.565	0.004052
M	4	S4F	tCc	tTc	5	5	B.1.596	0.000436
M	4	S4S	tcC	tcT	5	5	C.37	0.00058
M	4	S4F	tCc	tTc	5	5	P.1.1	0.001588
M	4	S4F	tCc	tTc	5	5	P.1.14	0.000239
M	4	S4A	Tcc	Gcc	5	5	P.1.15	0.001162
M	4	S4F	tCc	tTc	4	4	AY.100	0.000184
M	4	S4S	tcC	tcT	4	4	AY.102	0.000106
M	4	S4S	tcC	tcT	4	4	AY.110	0.000451
M	4	S4S	tcC	tcT	4	4	AY.119	0.000141
M	4	S4F	tCc	tTc	4	4	AY.120	0.000149
M	4	S4F	tCc	tTc	4	4	AY.27	0.000259
M	4	S4F	tCc	tTc	4	4	AY.33	0.000267
M	4	S4S	tcC	tcA	3	4	AY.46.6	0.000217
M	4	S4S	tcC	tcT	1	4	AY.46.6	0.000072
M	4	S4F	tCc	tTc	4	4	AY.57	0.002625
M	4	S4S	tcC	tcT	4	4	AY.61	0.000419
M	4	S4F	tCc	tTc	4	4	AY.98	0.000316
M	4	S4A	Tcc	Gcc	4	4	B.1.1	0.000073
M	4	S4F	tCc	tTc	4	4	B.1.1.284	0.00043
M	4	S4S	tcC	tcT	4	4	B.1.1.464	0.005891
M	4	S4F	tCc	tTc	4	4	B.1.177.4	0.000844
M	4	S4del1	tCc	t-c	4	4	B.1.2	0.000035
M	4	S4F	tCc	tTc	4	4	B.1.221	0.000284
M	4	S4F	tCc	tTc	4	4	B.1.258.17	0.000416
M	4	S4F	tCc	tTc	4	4	D.2	0.0003
M	4	S4F	tCc	tTc	4	4	N.3	0.023256
M	4	S4S	tcC	tcT	3	4	P.1	0.000047
M	4	S4S	tcC	tcG	1	4	P.1	0.000016
M	4	S4F	tCc	tTc	4	4	W.4	0.005405
M	4	S4F	tCc	tTc	2	3		0.111111
M	4	S4F	tCC	tTT	1	3		0.055556
M	4	S4F	tCc	tTc	3	3	AA.6	0.048387
M	4	S4F	tCc	tTc	3	3	AY.117	0.000254
M	4	S4F	tCc	tTc	3	3	AY.118	0.000188
M	4	S4F	tCc	tTc	3	3	AY.121	0.000406
M	4	S4F	tCc	tTc	3	3	AY.13	0.000483
M	4	S4F	tCc	tTc	3	3	AY.2	0.001068
M	4	S4del	TCC	---	3	3	AY.25	0.000018
M	4	S4S	tcC	tcT	3	3	AY.29	0.000047
M	4	S4S	tcC	tcT	3	3	AY.42	0.000121
M	4	S4A	Tcc	Gcc	3	3	AY.43	0.000013
M	4	S4Y	tCc	tAc	3	3	AY.43	0.000013
M	4	S4F	tCc	tTc	3	3	AY.46	0.000312
M	4	S4F	tCc	tTc	3	3	AY.46.5	0.000595
M	4	S4F	tCc	tTc	3	3	AY.5	0.000062
M	4	S4S	tcC	tcT	3	3	AY.6	0.000123
M	4	S4A	Tcc	Gcc	3	3	AY.61	0.000314
M	4	S4F	tCc	tTc	3	3	AY.9	0.000203
M	4	S4F	tCc	tTc	3	3	AY.93	0.000819
M	4	S4F	tCc	tTc	3	3	B.1.1.121	0.007282
M	4	S4S	tcC	tcT	3	3	B.1.1.169	0.054545
M	4	S4F	tCc	tTc	3	3	B.1.1.311	0.001074
M	4	S4F	tCc	tTc	3	3	B.1.1.411	0.044118
M	4	S4F	tCc	tTc	2	3	B.1.1.63	0.000772
M	4	S4F	tCC	tTT	1	3	B.1.1.63	0.000386
M	4	S4A	Tcc	Gcc	3	3	B.1.1.7	0.000003
M	4	S4S	tcC	tcT	3	3	B.1.177.20	0.004552
M	4	S4F	tCc	tTc	3	3	B.1.177.60	0.000655
M	4	S4F	tCc	tTc	3	3	B.1.177.81	0.000568
M	4	S4S	tcC	tcT	3	3	B.1.258.11	0.001189
M	4	S4F	tCc	tTc	3	3	B.1.36.18	0.001261
M	4	S4F	tCc	tTc	3	3	B.1.517	0.001281
M	4	S4S	tcC	tcA	3	3	B.1.525	0.000339
M	4	S4F	tCc	tTc	3	3	B.1.609	0.001438
M	4	S4F	tCc	tTc	3	3	B.4.8	0.214286
M	4	S4P	Tcc	Ccc	3	3	R.1	0.00027
M	4	S4del	TCC	---	2	2		0.111111
M	4	S4S	tcC	tcT	1	2		0.055556
M	4	S4S	tcC	tcG	1	2		0.055556
M	4	S4I	TCc	ATc	2	2	All	0
M	4	S4F	tCc	tTc	2	2	AM.4	0.007143
M	4	S4del	TCC	---	2	2	AY.100	0.000092
M	4	S4P	Tcc	Ccc	2	2	AY.120	0.000074
M	4	S4S	tcC	tcT	1	2	AY.120	0.000037
M	4	S4S	tcC	tcG	1	2	AY.120	0.000037
M	4	S4S	tcC	tcT	2	2	AY.121	0.000271
M	4	S4F	tCc	tTc	2	2	AY.34.1	0.00102
M	4	S4F	tCc	tTc	2	2	AY.35	0.000466
M	4	S4S	tcC	tcT	2	2	AY.39	0.000049
M	4	S4S	tcC	tcT	2	2	AY.4.2	0.000043
M	4	S4del	TCC	---	2	2	AY.4.5	0.000215
M	4	S4P	Tcc	Ccc	2	2	AY.43	0.000009
M	4	S4del	TCC	---	2	2	AY.43	0.000009
M	4	S4del	TCC	---	2	2	AY.44	0.000012
M	4	S4F	tCc	tTc	2	2	AY.47	0.000062
M	4	S4F	tCc	tTc	2	2	AY.48	0.00093
M	4	S4F	tCc	tTc	2	2	AY.55	0.001835
M	4	S4F	tCc	tTc	2	2	AY.75	0.000112
M	4	S4P	Tcc	Ccc	2	2	AY.9.1	0.000167
M	4	S4S	tcC	tcT	2	2	AY.9.2	0.000073
M	4	S4P	Tcc	Ccc	2	2	B.1	0.000018
M	4	S4F	tCc	tTc	2	2	B.1.1.1	0.000653
M	4	S4S	tcC	tcT	2	2	B.1.1.214	0.000111
M	4	S4S	tcC	tcT	2	2	B.1.1.28	0.000622
M	4	S4S	tcC	tcT	2	2	B.1.1.294	0.002532
M	4	S4S	tcC	tcT	2	2	B.1.1.33	0.000842
M	4	S4F	tCc	tTc	2	2	B.1.1.33	0.000842
M	4	S4S	tcC	tcA	2	2	B.1.1.47	0.010695
M	4	S4C	tCc	tGc	2	2	B.1.1.7	0.000002
M	4	S4F	tCc	tTc	2	2	B.1.128	0.001271
M	4	S4Y	tCc	tAc	2	2	B.1.160	0.000062
M	4	S4F	tCc	tTc	2	2	B.1.160.16	0.001859
M	4	S4F	tCc	tTc	2	2	B.1.160.26	0.004843
M	4	S4S	tcC	tcT	2	2	B.1.177.53	0.004785
M	4	S4S	tcC	tcT	2	2	B.1.177.8	0.001505
M	4	S4Y	tCc	tAc	2	2	B.1.2	0.000018
M	4	S4S	tcC	tcT	2	2	B.1.206	0.001631
M	4	S4S	tcC	tcT	2	2	B.1.210	0.004264
M	4	S4S	tcC	tcT	2	2	B.1.234	0.000264
M	4	S4F	tCc	tTc	2	2	B.1.240	0.000431
M	4	S4F	tCc	tTc	2	2	B.1.241	0.001623
M	4	S4P	Tcc	Ccc	2	2	B.1.243	0.000139
M	4	S4P	Tcc	Ccc	2	2	B.1.36	0.000292
M	4	S4F	tCc	tTc	2	2	B.1.396	0.001411
M	4	S4P	Tcc	Ccc	2	2	B.1.429	0.000047
M	4	S4F	tCc	tTc	2	2	B.1.438.1	0.000215
M	4	S4S	tcC	tcT	2	2	B.1.466.2	0.000782
M	4	S4F	tCc	tTc	2	2	B.1.474	0.003802
M	4	S4S	tcC	tcT	2	2	B.1.517	0.000854
M	4	S4Y	tCC	tAT	1	2	B.1.617.1	0.000129
M	4	S4S	tcC	tcA	1	2	B.1.617.1	0.000129
M	4	S4Y	tCc	tAc	1	2	B.1.617.1	0.000129
M	4	S4S	tcC	tcT	1	2	B.1.617.1	0.000129
M	4	S4P	Tcc	Ccc	2	2	B.1.617.2	0.000008
M	4	S4F	tCc	tTc	2	2	B.1.623	0.001073
M	4	S4F	tCc	tTc	2	2	B.40	0.000729
M	4	S4F	tCc	tTc	2	2	C.14	0.008658
M	4	S4del	TCC	---	2	2	P.1	0.000032
M	4	S4P	Tcc	Ccc	2	2	P.1	0.000032
M	4	S4S	tcC	tcT	2	2	P.1.14	0.000096
M	4	S4F	tCc	tTc	2	2	Q.1	0.000253
M	4	S4L	tCC	tTG	1	1		0.055556
M	4	S4F	tCc	tTc	1	1	A	0.000387
M	4	S4Y	tCc	tAc	1	1	A	0.000387
M	4	S4F	tCc	tTc	1	1	A.2.2	0.001689
M	4	S4F	tCc	tTc	1	1	A.23.1	0.000704
M	4	S4F	tCc	tTc	1	1	A.29	0.005319
M	4	S4L	tCC	tTG	1	1	All	0
M	4	S4X	tCC	tAA	1	1	All	0
M	4	S4V	TCC	GTG	1	1	All	0
M	4	S4S	tcC	tcT	1	1	AU.1	0.001266
M	4	S4F	tCc	tTc	1	1	AU.1	0.001266
M	4	S4F	tCc	tTc	1	1	AU.3	0.00211
M	4	S4F	tCc	tTc	1	1	AY.101	0.00049
M	4	S4Y	tCc	tAc	1	1	AY.103	0.000006
M	4	S4F	tCc	tTc	1	1	AY.105	0.000643
M	4	S4Y	tCc	tAc	1	1	AY.107	0.000466
M	4	S4del	TCC	---	1	1	AY.108	0.001103
M	4	S4F	tCc	tTc	1	1	AY.110	0.000113
M	4	S4F	tCc	tTc	1	1	AY.116	0.000287
M	4	S4S	tcC	tcA	1	1	AY.116	0.000287
M	4	S4del	TCC	---	1	1	AY.118	0.000063
M	4	S4F	tCc	tTc	1	1	AY.12	0.000316
M	4	S4del	TCC	---	1	1	AY.120	0.000037
M	4	S4F	tCc	tTc	1	1	AY.120.2.1	0.000498
M	4	S4F	tCc	tTc	1	1	AY.14	0.000088
M	4	S4S	tcC	tcT	1	1	AY.14	0.000088
M	4	S4S	tcC	tcT	1	1	AY.16	0.00038
M	4	S4F	tCc	tTc	1	1	AY.22	0.002092
M	4	S4F	tCc	tTc	1	1	AY.23.1	0.000417
M	4	S4S	tcC	tcT	1	1	AY.29.1	0.000221
M	4	S4F	tCc	tTc	1	1	AY.29.1	0.000221
M	4	S4S	tcC	tcT	1	1	AY.3.1	0.000085
M	4	S4F	tCc	tTc	1	1	AY.32	0.000532
M	4	S4S	tcC	tcT	1	1	AY.33	0.000067
M	4	S4C	tCc	tGc	1	1	AY.4	0.000002
M	4	S4A	Tcc	Gcc	1	1	AY.4	0.000002
M	4	S4S	tcC	tcT	1	1	AY.4.1	0.000737
M	4	S4Y	tCc	tAc	1	1	AY.4.2	0.000022
M	4	S4F	tCc	tTc	1	1	AY.4.3	0.000842
M	4	S4F	tCc	tTc	1	1	AY.4.5	0.000107
M	4	S4S	tcC	tcT	1	1	AY.4.5	0.000107
M	4	S4S	tcC	tcT	1	1	AY.40	0.000964
M	4	S4T	Tcc	Acc	1	1	AY.43	0.000004
M	4	S4S	tcC	tcT	1	1	AY.45	0.000122
M	4	S4A	Tcc	Gcc	1	1	AY.45	0.000122
M	4	S4Y	tCc	tAc	1	1	AY.45	0.000122
M	4	S4F	tCc	tTc	1	1	AY.46.6	0.000072
M	4	S4A	Tcc	Gcc	1	1	AY.47	0.000031
M	4	S4S	tcC	tcT	1	1	AY.47	0.000031
M	4	S4T	Tcc	Acc	1	1	AY.5	0.000021
M	4	S4F	tCc	tTc	1	1	AY.53	0.000288
M	4	S4P	Tcc	Ccc	1	1	AY.54	0.000095
M	4	S4F	tCc	tTc	1	1	AY.59	0.00053
M	4	S4F	tCc	tTc	1	1	AY.61	0.000105
M	4	S4Y	tCc	tAc	1	1	AY.61	0.000105
M	4	S4del	TCC	---	1	1	AY.68	0.000274
M	4	S4S	tcC	tcT	1	1	AY.69	0.000187
M	4	S4P	Tcc	Ccc	1	1	AY.7	0.000196
M	4	S4F	tCc	tTc	1	1	AY.70	0.000209
M	4	S4F	tCc	tTc	1	1	AY.72	0.001361
M	4	S4F	tCc	tTc	1	1	AY.74	0.000116
M	4	S4S	tcC	tcT	1	1	AY.74	0.000116
M	4	S4S	tcC	tcT	1	1	AY.75	0.000056
M	4	S4F	tCc	tTc	1	1	AY.77	0.001127
M	4	S4F	tCc	tTc	1	1	AY.78	0.001541
M	4	S4S	tcC	tcT	1	1	AY.85	0.000427
M	4	S4del	TCC	---	1	1	AY.9	0.000068
M	4	S4S	tcC	tcT	1	1	AY.9.1	0.000084
M	4	S4S	tcC	tcT	1	1	AY.93	0.000273
M	4	S4S	tcC	tcT	1	1	AY.98	0.000079
M	4	S4S	tcC	tcA	1	1	AY.98.1	0.000048
M	4	S4P	Tcc	Ccc	1	1	AY.98.1	0.000048
M	4	S4F	tCc	tTc	1	1	AY.99	0.001049
M	4	S4S	tcC	tcT	1	1	AY.99.2	0.000092
M	4	S4del	TCC	---	1	1	B	0.000128
M	4	S4T	Tcc	Acc	1	1	B.1	0.000009
M	4	S4A	TcC	GcA	1	1	B.1	0.000009
M	4	S4I	TCc	ATc	1	1	B.1	0.000009
M	4	S4Y	tCc	tAc	1	1	B.1.1	0.000018
M	4	S4T	Tcc	Acc	1	1	B.1.1	0.000018
M	4	S4I	TCc	ATc	1	1	B.1.1	0.000018
M	4	S4S	tcC	tcT	1	1	B.1.1.10	0.001115
M	4	S4C	tCc	tGc	1	1	B.1.1.101	0.01
M	4	S4S	tcC	tcT	1	1	B.1.1.117	0.009709
M	4	S4del	TCC	---	1	1	B.1.1.139	0.022727
M	4	S4F	tCc	tTc	1	1	B.1.1.170	0.001247
M	4	S4S	tcC	tcT	1	1	B.1.1.174	0.003378
M	4	S4F	tCc	tTc	1	1	B.1.1.176	0.000439
M	4	S4del1	tCc	t-c	1	1	B.1.1.222	0.000204
M	4	S4S	tcC	tcT	1	1	B.1.1.222	0.000204
M	4	S4Y	tCc	tAc	1	1	B.1.1.225	0.007194
M	4	S4F	tCc	tTc	1	1	B.1.1.25	0.000569
M	4	S4F	tCc	tTc	1	1	B.1.1.253	0.002506
M	4	S4F	tCc	tTc	1	1	B.1.1.28	0.000311
M	4	S4F	tCc	tTc	1	1	B.1.1.280	0.003086
M	4	S4del	TCC	---	1	1	B.1.1.288	0.001916
M	4	S4F	tCc	tTc	1	1	B.1.1.294	0.001266
M	4	S4F	tCc	tTc	1	1	B.1.1.309	0.005848
M	4	S4A	Tcc	Gcc	1	1	B.1.1.312	0.001912
M	4	S4F	tCc	tTc	1	1	B.1.1.316	0.000925
M	4	S4F	tCc	tTc	1	1	B.1.1.318	0.000302
M	4	S4F	tCc	tTc	1	1	B.1.1.322	0.008772
M	4	S4F	tCc	tTc	1	1	B.1.1.369	0.000446
M	4	S4F	tCc	tTc	1	1	B.1.1.37	0.000193
M	4	S4F	tCc	tTc	1	1	B.1.1.391	0.008547
M	4	S4F	tCc	tTc	1	1	B.1.1.402	0.011111
M	4	S4S	tcC	tcT	1	1	B.1.1.406	0.006494
M	4	S4F	tCc	tTc	1	1	B.1.1.416	0.000905
M	4	S4F	tCc	tTc	1	1	B.1.1.420	0.001006
M	4	S4P	Tcc	Ccc	1	1	B.1.1.50	0.000679
M	4	S4del	TCC	---	1	1	B.1.1.519	0.00004
M	4	S4F	tCc	tTc	1	1	B.1.1.526	0.003546
M	4	S4F	tCc	tTc	1	1	B.1.1.61	0.008772
M	4	S4F	tCc	tTc	1	1	B.1.1.70	0.000341
M	4	S4F	tCc	tTc	1	1	B.1.147	0.000756
M	4	S4F	tCc	tTc	1	1	B.1.157	0.002985
M	4	S4del	TCC	---	1	1	B.1.160	0.000031
M	4	S4F	tCc	tTc	1	1	B.1.160.15	0.00495
M	4	S4S	tcC	tcT	1	1	B.1.160.31	0.008065
M	4	S4F	tCc	tTc	1	1	B.1.170	0.00431
M	4	S4del	TCC	---	1	1	B.1.177	0.000013
M	4	S4F	tCc	tTc	1	1	B.1.177.10	0.000878
M	4	S4del	TCC	---	1	1	B.1.177.16	0.000664
M	4	S4del	TCC	---	1	1	B.1.177.17	0.000821
M	4	S4F	tCc	tTc	1	1	B.1.177.21	0.000076
M	4	S4P	Tcc	Ccc	1	1	B.1.177.21	0.000076
M	4	S4F	tCc	tTc	1	1	B.1.177.56	0.000668
M	4	S4S	tcC	tcT	1	1	B.1.177.65	0.000665
M	4	S4F	tCc	tTc	1	1	B.1.177.7	0.000165
M	4	S4F	tCc	tTc	1	1	B.1.177.73	0.000566
M	4	S4F	tCc	tTc	1	1	B.1.177.8	0.000752
M	4	S4S	tcC	tcT	1	1	B.1.177.81	0.000189
M	4	S4del	TCC	---	1	1	B.1.177.87	0.000728
M	4	S4F	tCc	tTc	1	1	B.1.177.87	0.000728
M	4	S4F	tCc	tTc	1	1	B.1.179	0.003759
M	4	S4A	Tcc	Gcc	1	1	B.1.2	0.000009
M	4	S4P	Tcc	Ccc	1	1	B.1.2	0.000009
M	4	S4V	TCC	GTG	1	1	B.1.210	0.002132
M	4	S4F	tCc	tTc	1	1	B.1.210	0.002132
M	4	S4S	tcC	tcT	1	1	B.1.221	0.000071
M	4	S4S	tcC	tcT	1	1	B.1.223	0.002778
M	4	S4F	tCc	tTc	1	1	B.1.236	0.002053
M	4	S4P	Tcc	Ccc	1	1	B.1.258	0.000067
M	4	S4F	tCc	tTc	1	1	B.1.258.14	0.00098
M	4	S4S	tcC	tcT	1	1	B.1.258.17	0.000104
M	4	S4F	tCc	tTc	1	1	B.1.298	0.002114
M	4	S4S	tcC	tcT	1	1	B.1.3	0.002618
M	4	S4Y	tCc	tAc	1	1	B.1.301	0.005917
M	4	S4F	tCc	tTc	1	1	B.1.311	0.000275
M	4	S4del	TCC	---	1	1	B.1.311	0.000275
M	4	S4F	tCc	tTc	1	1	B.1.325	0.006897
M	4	S4S	tcC	tcT	1	1	B.1.326	0.007576
M	4	S4P	Tcc	Ccc	1	1	B.1.351	0.00003
M	4	S4Y	tCc	tAc	1	1	B.1.351	0.00003
M	4	S4del	TCC	---	1	1	B.1.351.2	0.000303
M	4	S4F	tCc	tTc	1	1	B.1.351.3	0.000876
M	4	S4F	tCc	tTc	1	1	B.1.36	0.000146
M	4	S4T	Tcc	Acc	1	1	B.1.36.23	0.016393
M	4	S4S	tcC	tcT	1	1	B.1.36.29	0.000517
M	4	S4F	tCc	tTc	1	1	B.1.36.29	0.000517
M	4	S4F	tCc	tTc	1	1	B.1.36.36	0.000602
M	4	S4P	Tcc	Ccc	1	1	B.1.36.9	0.003215
M	4	S4S	tcC	tcT	1	1	B.1.369	0.000285
M	4	S4P	Tcc	Ccc	1	1	B.1.404	0.001302
M	4	S4F	tCc	tTc	1	1	B.1.409	0.000781
M	4	S4F	tCc	tTc	1	1	B.1.411	0.003704
M	4	S4T	Tcc	Acc	1	1	B.1.413	0.004255
M	4	S4F	tCc	tTc	1	1	B.1.420	0.010417
M	4	S4F	tCc	tTc	1	1	B.1.427	0.00005
M	4	S4F	tCc	tTc	1	1	B.1.428	0.00102
M	4	S4S	tcC	tcT	1	1	B.1.429	0.000024
M	4	S4F	tCc	tTc	1	1	B.1.432	0.011236
M	4	S4Y	tCc	tAc	1	1	B.1.438.1	0.000107
M	4	S4P	Tcc	Ccc	1	1	B.1.473	0.019231
M	4	S4F	tCc	tTc	1	1	B.1.478	0.011765
M	4	S4F	tCc	tTc	1	1	B.1.480	0.002488
M	4	S4S	tcC	tcT	1	1	B.1.527	0.003704
M	4	S4F	tCc	tTc	1	1	B.1.536	0.02381
M	4	S4S	tcC	tcT	1	1	B.1.551	0.00129
M	4	S4del	TCC	---	1	1	B.1.561	0.000397
M	4	S4F	tCc	tTc	1	1	B.1.575	0.000303
M	4	S4S	tcC	tcT	1	1	B.1.590	0.004545
M	4	S4F	tCc	tTc	1	1	B.1.595	0.000261
M	4	S4P	Tcc	Ccc	1	1	B.1.595	0.000261
M	4	S4Y	tCc	tAc	1	1	B.1.597	0.00463
M	4	S4S	tcC	tcT	1	1	B.1.609	0.000479
M	4	S4X	tCC	tAA	1	1	B.1.617.1	0.000129
M	4	S4del	TCC	---	1	1	B.1.617.2	0.000004
M	4	S4S	tcC	tcT	1	1	B.1.619	0.000871
M	4	S4P	Tcc	Ccc	1	1	B.1.621	0.000089
M	4	S4C	tCc	tGc	1	1	B.1.621	0.000089
M	4	S4S	tcC	tcT	1	1	B.1.621.1	0.000506
M	4	S4F	tCc	tTc	1	1	B.1.630	0.005236
M	4	S4F	tCc	tTc	1	1	B.1.637	0.000073
M	4	S4S	tcC	tcT	1	1	B.1.637	0.000073
M	4	S4S	tcC	tcT	1	1	B.1.78	0.008547
M	4	S4F	tCc	tTc	1	1	B.1.9	0.006173
M	4	S4F	tCc	tTc	1	1	B.11	0.005128
M	4	S4F	tCc	tTc	1	1	B.28	0.003279
M	4	S4F	tCc	tTc	1	1	B.3	0.000831
M	4	S4del	TCC	---	1	1	B.30	0.014706
M	4	S4F	tCc	tTc	1	1	B.4	0.002208
M	4	S4F	tCc	tTc	1	1	C.16	0.00106
M	4	S4F	tCc	tTc	1	1	C.31	0.017857
M	4	S4F	tCc	tTc	1	1	C.36	0.000911
M	4	S4P	Tcc	Ccc	1	1	D.2	0.000075
M	4	S4P	Tcc	Ccc	1	1	N.5	0.001767
M	4	S4A	Tcc	Gcc	1	1	P.1	0.000016
M	4	S4P	Tcc	Ccc	1	1	P.1.12	0.000484
M	4	S4del	TCC	---	1	1	P.1.15	0.000232
M	4	S4F	tCc	tTc	1	1	P.1.6	0.001946
M	4	S4A	Tcc	Gcc	1	1	P.2	0.000187
M	4	S4A	TcC	GcG	1	1	Q.8	0.000165
M	4	S4S	tcC	tcT	1	1	Q.8	0.000165
M	4	S4F	tCc	tTc	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.