CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 244

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	244	L244del		del	TTA	---	3081	3081	1	22292-22294
S	244	L244S		nonsyn	tTa	tCa	1328	1326	0.998494	22292-22294
S	244	L244S		nonsyn	tTA	tCT	1328	1	0.000753012	22292-22294
S	244	L244S		nonsyn	tTA	tCC	1328	1	0.000753012	22292-22294
S	244	L244L		syn	Tta	Cta	695	524	0.753957	22292-22294
S	244	L244L		syn	ttA	ttG	695	166	0.238849	22292-22294
S	244	L244L		syn	TtA	CtT	695	4	0.0057554	22292-22294
S	244	L244L		syn	TtA	CtC	695	1	0.00143885	22292-22294
S	244	L244F		nonsyn	ttA	ttT	181	132	0.729282	22292-22294
S	244	L244F		nonsyn	ttA	ttC	181	49	0.270718	22292-22294
S	244	L244V		nonsyn	Tta	Gta	60	55	0.916667	22292-22294
S	244	L244V		nonsyn	TtA	GtT	60	5	0.0833333	22292-22294
S	244	L244del2		del	tTA	t--	30	23	0.766667	22292-22294
S	244	L244del2		del	TTa	--a	30	4	0.133333	22292-22294
S	244	L244del2		del	TTA	--N	30	3	0.1	22292-22294
S	244	L244del1		del	ttA	tt-	19	16	0.842105	22292-22294
S	244	L244del1		del	Tta	-ta	19	2	0.105263	22292-22294
S	244	L244del1		del	TTA	-NN	19	1	0.0526316	22292-22294
S	244	L244I		nonsyn	Tta	Ata	13	11	0.846154	22292-22294
S	244	L244I		nonsyn	TtA	AtC	13	1	0.0769231	22292-22294
S	244	L244I		nonsyn	TtA	AtT	13	1	0.0769231	22292-22294
S	244	L244X		nonsyn	tTa	tGa	5	2	0.4	22292-22294
S	244	L244X		nonsyn	tTa	tAa	5	2	0.4	22292-22294
S	244	L244X		nonsyn	tTA	tAG	5	1	0.2	22292-22294
S	244	L244T		nonsyn	TTa	ACa	2	2	1	22292-22294
S	244	L244R		nonsyn	TTa	AGa	1	1	1	22292-22294

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	244	L244del	TTA	---	3081	3081	All	0.000589
S	244	L244S	tTa	tCa	1326	1328	All	0.000254
S	244	L244S	tTA	tCC	1	1328	All	0
S	244	L244S	tTA	tCT	1	1328	All	0
S	244	L244S	tTa	tCa	1005	1005	AY.95	0.76484
S	244	L244L	Tta	Cta	524	695	All	0.0001
S	244	L244L	ttA	ttG	166	695	All	0.000032
S	244	L244L	TtA	CtT	4	695	All	0.000001
S	244	L244L	TtA	CtC	1	695	All	0
S	244	L244del	TTA	---	409	409	B.1.1.7	0.000366
S	244	L244del	TTA	---	351	351	P.3	0.559809
S	244	L244del	TTA	---	313	313	AY.3	0.003113
S	244	L244del	TTA	---	218	218	C.1.2	0.92766
S	244	L244L	Tta	Cta	141	183	AY.4	0.000219
S	244	L244L	ttA	ttG	42	183	AY.4	0.000065
S	244	L244F	ttA	ttT	132	181	All	0.000025
S	244	L244F	ttA	ttC	49	181	All	0.000009
S	244	L244L	Tta	Cta	175	176	AY.102	0.00464
S	244	L244L	TtA	CtT	1	176	AY.102	0.000027
S	244	L244del	TTA	---	176	176	B.1.630	0.921466
S	244	L244del	TTA	---	169	169	AY.4	0.000263
S	244	L244del	TTA	---	139	139	B.1.617.2	0.000523
S	244	L244del	TTA	---	77	77	AY.4.2	0.00167
S	244	L244S	tTa	tCa	77	77	B.1.1.7	0.000069
S	244	L244del	TTA	---	72	72	AY.44	0.000438
S	244	L244L	Tta	Cta	57	71	B.1.617.2	0.000215
S	244	L244L	ttA	ttG	14	71	B.1.617.2	0.000053
S	244	L244V	Tta	Gta	55	60	All	0.000011
S	244	L244V	TtA	GtT	5	60	All	0.000001
S	244	L244del	TTA	---	59	59	B.1	0.00054
S	244	L244del	TTA	---	58	58	AY.43	0.000257
S	244	L244del	TTA	---	55	55	B.1.351	0.001635
S	244	L244del	TTA	---	51	51	AY.25	0.000307
S	244	L244del	TTA	---	46	46	AY.120	0.00171
S	244	L244del	TTA	---	46	46	B.1.1	0.000834
S	244	L244del	TTA	---	44	44	AY.103	0.000273
S	244	L244S	tTa	tCa	40	40	AY.4	0.000062
S	244	L244S	tTa	tCa	40	40	AY.4.2	0.000868
S	244	L244del	TTA	---	37	37	B.1.427	0.001868
S	244	L244del	TTA	---	37	37	P.1	0.000583
S	244	L244del	TTA	---	31	31	AY.29	0.000489
S	244	L244del2	tTA	t--	23	30	All	0.000004
S	244	L244del2	TTa	--a	4	30	All	0.000001
S	244	L244del2	TTA	--N	3	30	All	0.000001
S	244	L244L	ttA	ttG	14	26	B.1.1.7	0.000013
S	244	L244L	Tta	Cta	12	26	B.1.1.7	0.000011
S	244	L244del	TTA	---	25	25	B.1.2	0.00022
S	244	L244del	TTA	---	24	24	B.1.177	0.000316
S	244	L244S	tTa	tCa	23	23	AY.103	0.000143
S	244	L244L	Tta	Cta	15	23	B.1.2	0.000132
S	244	L244L	ttA	ttG	8	23	B.1.2	0.00007
S	244	L244F	ttA	ttC	13	23	B.1.617.2	0.000049
S	244	L244F	ttA	ttT	10	23	B.1.617.2	0.000038
S	244	L244del	TTA	---	22	22	C.40	0.611111
S	244	L244F	ttA	ttT	19	21	B.1.1.7	0.000017
S	244	L244F	ttA	ttC	2	21	B.1.1.7	0.000002
S	244	L244del	TTA	---	20	20	B.1.351.3	0.017528
S	244	L244del1	ttA	tt-	16	19	All	0.000003
S	244	L244del1	Tta	-ta	2	19	All	0
S	244	L244del1	TTA	-NN	1	19	All	0
S	244	L244S	tTa	tCa	19	19	AY.25	0.000114
S	244	L244F	ttA	ttC	16	19	AY.43	0.000071
S	244	L244F	ttA	ttT	3	19	AY.43	0.000013
S	244	L244del	TTA	---	19	19	AY.69	0.003547
S	244	L244del	TTA	---	18	18	AY.36	0.002668
S	244	L244S	tTa	tCa	18	18	B.1.617.2	0.000068
S	244	L244del	TTA	---	18	18	C.36.3.1	0.048913
S	244	L244F	ttA	ttT	16	16	AY.4	0.000025
S	244	L244L	Tta	Cta	13	16	AY.43	0.000058
S	244	L244L	ttA	ttG	3	16	AY.43	0.000013
S	244	L244L	ttA	ttG	16	16	AY.75	0.000896
S	244	L244F	ttA	ttT	16	16	B.1.177	0.000211
S	244	L244L	ttA	ttG	16	16	Q.4	0.007276
S	244	L244del	TTA	---	14	14	AY.102	0.000371
S	244	L244L	ttA	ttG	14	14	B.1.265	0.017789
S	244	L244S	tTa	tCa	14	14	B.1.427	0.000707
S	244	L244del	TTA	---	14	14	B.1.526	0.000329
S	244	L244I	Tta	Ata	11	13	All	0.000002
S	244	L244I	TtA	AtT	1	13	All	0
S	244	L244I	TtA	AtC	1	13	All	0
S	244	L244del	TTA	---	13	13	B.1.1.297	0.029083
S	244	L244del	TTA	---	13	13	B.1.214.2	0.007794
S	244	L244del	TTA	---	12	12	AY.20	0.000466
S	244	L244del	TTA	---	12	12	AY.39	0.000297
S	244	L244V	Tta	Gta	12	12	AY.4.2	0.00026
S	244	L244L	Tta	Cta	11	12	AY.44	0.000067
S	244	L244L	ttA	ttG	1	12	AY.44	0.000006
S	244	L244del	TTA	---	12	12	AY.46	0.001249
S	244	L244del	TTA	---	12	12	AY.47	0.000373
S	244	L244del	TTA	---	12	12	B.1.160	0.000374
S	244	L244del	TTA	---	12	12	C.37	0.001393
S	244	L244F	ttA	ttT	11	11	AY.4.2	0.000239
S	244	L244L	Tta	Cta	10	11	B.1.177	0.000132
S	244	L244L	TtA	CtT	1	11	B.1.177	0.000013
S	244	L244del	TTA	---	10	10	B.1.525	0.001132
S	244	L244del	TTA	---	10	10	B.1.637	0.000731
S	244	L244del2	tTA	t--	10	10	C.40	0.277778
S	244	L244del	TTA	---	10	10	P.1.15	0.002323
S	244	L244del	TTA	---	9	9	AY.119	0.000318
S	244	L244V	Tta	Gta	9	9	AY.26	0.000255
S	244	L244F	ttA	ttC	9	9	AY.34.1	0.004589
S	244	L244del	TTA	---	9	9	AY.9.2	0.000331
S	244	L244L	ttA	ttG	4	8	AY.103	0.000025
S	244	L244L	Tta	Cta	4	8	AY.103	0.000025
S	244	L244del	TTA	---	8	8	AY.3.1	0.000682
S	244	L244S	tTa	tCa	7	8	AY.44	0.000043
S	244	L244S	tTA	tCC	1	8	AY.44	0.000006
S	244	L244del	TTA	---	8	8	AY.99.2	0.000737
S	244	L244del	TTA	---	8	8	B.1.429	0.000188
S	244	L244del	TTA	---	8	8	B.1.596	0.000697
S	244	L244del	TTA	---	8	8	P.1.4	0.007812
S	244	L244del	TTA	---	7	7	AY.100	0.000322
S	244	L244L	Tta	Cta	6	7	AY.118	0.000376
S	244	L244L	ttA	ttG	1	7	AY.118	0.000063
S	244	L244del	TTA	---	7	7	AY.65	0.003731
S	244	L244L	Tta	Cta	5	7	B.1	0.000046
S	244	L244L	ttA	ttG	2	7	B.1	0.000018
S	244	L244del	TTA	---	7	7	B.1.369	0.001997
S	244	L244L	Tta	Cta	7	7	P.1	0.00011
S	244	L244del	TTA	---	6	6	AY.34	0.000582
S	244	L244del	TTA	---	6	6	AY.45	0.00073
S	244	L244del	TTA	---	6	6	AY.5	0.000124
S	244	L244del	TTA	---	6	6	AY.61	0.000629
S	244	L244S	tTa	tCa	6	6	B.1.2	0.000053
S	244	L244F	ttA	ttT	6	6	B.1.243	0.000418
S	244	L244L	Tta	Cta	6	6	B.1.429	0.000141
S	244	L244del	TTA	---	6	6	B.1.621	0.000531
S	244	L244X	tTa	tGa	2	5	All	0
S	244	L244X	tTa	tAa	2	5	All	0
S	244	L244X	tTA	tAG	1	5	All	0
S	244	L244del	TTA	---	5	5	AY.101	0.002452
S	244	L244del	TTA	---	5	5	AY.33	0.000334
S	244	L244L	Tta	Cta	3	5	AY.4.5	0.000322
S	244	L244L	ttA	ttG	2	5	AY.4.5	0.000215
S	244	L244del	TTA	---	5	5	AY.46.4	0.000823
S	244	L244del	TTA	---	5	5	AY.74	0.000578
S	244	L244S	tTa	tCa	5	5	B.1	0.000046
S	244	L244S	tTa	tCa	5	5	B.1.1	0.000091
S	244	L244S	tTa	tCa	5	5	B.1.1.317	0.002058
S	244	L244del	TTA	---	5	5	B.1.1.519	0.000199
S	244	L244V	TtA	GtT	5	5	B.1.351.1	0.192308
S	244	L244S	tTa	tCa	5	5	B.1.429	0.000118
S	244	L244del	TTA	---	5	5	P.5	0.068493
S	244	L244del	TTA	---	5	5	Q.1	0.000632
S	244	L244del	TTA	---	4	4	AY.113	0.00057
S	244	L244S	tTa	tCa	4	4	AY.116	0.001147
S	244	L244del	TTA	---	4	4	AY.26	0.000113
S	244	L244F	ttA	ttC	2	4	AY.39	0.000049
S	244	L244F	ttA	ttT	2	4	AY.39	0.000049
S	244	L244del	TTA	---	4	4	AY.9.1	0.000335
S	244	L244del	TTA	---	4	4	AY.95	0.003044
S	244	L244L	Tta	Cta	4	4	AY.98.1	0.000194
S	244	L244F	ttA	ttC	2	4	B.1	0.000018
S	244	L244F	ttA	ttT	2	4	B.1	0.000018
S	244	L244F	ttA	ttT	4	4	B.1.1.28	0.001245
S	244	L244del	TTA	---	4	4	B.1.409	0.003125
S	244	L244del	TTA	---	4	4	D.2	0.0003
S	244	L244del	TTA	---	4	4	P.1.1	0.001271
S	244	L244del	TTA	---	4	4	R.1	0.00036
S	244	L244V	Tta	Gta	3	3	AY.103	0.000019
S	244	L244L	ttA	ttG	3	3	AY.20	0.000117
S	244	L244L	Tta	Cta	3	3	AY.26	0.000085
S	244	L244del	TTA	---	3	3	AY.27	0.000194
S	244	L244del	TTA	---	3	3	AY.32	0.001597
S	244	L244L	Tta	Cta	3	3	AY.34.1	0.00153
S	244	L244del	TTA	---	3	3	AY.38	0.001498
S	244	L244del	TTA	---	3	3	AY.4.5	0.000322
S	244	L244F	ttA	ttT	3	3	AY.46	0.000312
S	244	L244L	Tta	Cta	3	3	AY.46	0.000312
S	244	L244L	Tta	Cta	3	3	AY.46.1	0.00308
S	244	L244del	TTA	---	3	3	AY.5.3	0.001012
S	244	L244del	TTA	---	3	3	AY.54	0.000286
S	244	L244L	ttA	ttG	3	3	AY.61	0.000314
S	244	L244L	Tta	Cta	3	3	AY.98	0.000237
S	244	L244del	TTA	---	3	3	B	0.000383
S	244	L244del1	ttA	tt-	3	3	B.1	0.000027
S	244	L244del	TTA	---	3	3	B.1.1.294	0.003797
S	244	L244L	Tta	Cta	3	3	B.1.1.311	0.001074
S	244	L244del	TTA	---	3	3	B.1.1.50	0.002037
S	244	L244V	Tta	Gta	3	3	B.1.1.7	0.000003
S	244	L244del1	Tta	-ta	2	3	B.1.1.7	0.000002
S	244	L244del1	TTA	-NN	1	3	B.1.1.7	0.000001
S	244	L244del	TTA	---	3	3	B.1.177.60	0.000655
S	244	L244L	Tta	Cta	3	3	B.1.177.82	0.001432
S	244	L244del	TTA	---	3	3	B.1.177.86	0.00055
S	244	L244F	ttA	ttT	3	3	B.1.2	0.000026
S	244	L244L	ttA	ttG	3	3	B.1.214.2	0.001799
S	244	L244del	TTA	---	3	3	B.1.221	0.000213
S	244	L244del	TTA	---	3	3	B.1.258	0.0002
S	244	L244del	TTA	---	3	3	B.1.36	0.000438
S	244	L244del	TTA	---	3	3	B.1.433	0.009585
S	244	L244S	tTa	tCa	3	3	B.1.526	0.000071
S	244	L244V	Tta	Gta	3	3	B.1.617.2	0.000011
S	244	L244V	Tta	Gta	3	3	B.4.5	0.035714
S	244	L244del	TTA	---	3	3	Q.2	0.00184
S	244	L244del	TTA	---	3	3	Q.8	0.000495
S	244	L244del	TTA	---	2	2		0.111111
S	244	L244del	TTA	---	2	2	A	0.000774
S	244	L244del	TTA	---	2	2	AB.1	0.016393
S	244	L244T	TTa	ACa	2	2	All	0
S	244	L244L	Tta	Cta	2	2	AY.1	0.000791
S	244	L244del	TTA	---	2	2	AY.118	0.000125
S	244	L244L	Tta	Cta	2	2	AY.119	0.000071
S	244	L244S	tTa	tCa	2	2	AY.119	0.000071
S	244	L244del	TTA	---	2	2	AY.13	0.000322
S	244	L244L	ttA	ttG	2	2	AY.14	0.000176
S	244	L244del2	TTA	--N	1	2	AY.25	0.000006
S	244	L244del2	tTA	t--	1	2	AY.25	0.000006
S	244	L244del1	ttA	tt-	2	2	AY.3	0.00002
S	244	L244del2	tTA	t--	2	2	AY.3	0.00002
S	244	L244del	TTA	---	2	2	AY.37	0.000632
S	244	L244L	Tta	Cta	2	2	AY.39	0.000049
S	244	L244V	Tta	Gta	2	2	AY.4	0.000003
S	244	L244L	ttA	ttG	1	2	AY.4.2	0.000022
S	244	L244L	Tta	Cta	1	2	AY.4.2	0.000022
S	244	L244del	TTA	---	2	2	AY.4.4	0.000818
S	244	L244del	TTA	---	2	2	AY.42	0.00008
S	244	L244F	ttA	ttC	1	2	AY.42	0.00004
S	244	L244F	ttA	ttT	1	2	AY.42	0.00004
S	244	L244del1	ttA	tt-	2	2	AY.43	0.000009
S	244	L244I	Tta	Ata	2	2	AY.43	0.000009
S	244	L244F	ttA	ttC	1	2	AY.44	0.000006
S	244	L244F	ttA	ttT	1	2	AY.44	0.000006
S	244	L244S	tTa	tCa	2	2	AY.46.6	0.000144
S	244	L244del	TTA	---	2	2	AY.46.6	0.000144
S	244	L244V	Tta	Gta	2	2	AY.47	0.000062
S	244	L244S	tTa	tCa	2	2	AY.5	0.000041
S	244	L244L	Tta	Cta	2	2	AY.5	0.000041
S	244	L244del	TTA	---	2	2	AY.5.4	0.000553
S	244	L244L	ttA	ttG	2	2	AY.53	0.000575
S	244	L244del	TTA	---	2	2	AY.6	0.000082
S	244	L244del	TTA	---	2	2	AY.7	0.000392
S	244	L244del	TTA	---	2	2	AY.75	0.000112
S	244	L244del	TTA	---	2	2	AY.92	0.000575
S	244	L244X	tTa	tAa	1	2	B.1	0.000009
S	244	L244X	tTa	tGa	1	2	B.1	0.000009
S	244	L244del2	TTA	--N	1	2	B.1	0.000009
S	244	L244del2	tTA	t--	1	2	B.1	0.000009
S	244	L244L	ttA	ttG	1	2	B.1.1	0.000018
S	244	L244L	Tta	Cta	1	2	B.1.1	0.000018
S	244	L244del	TTA	---	2	2	B.1.1.318	0.000604
S	244	L244del	TTA	---	2	2	B.1.1.432	0.002532
S	244	L244del	TTA	---	2	2	B.1.1.464	0.002946
S	244	L244V	Tta	Gta	2	2	B.1.1.519	0.000079
S	244	L244L	ttA	ttG	1	2	B.1.1.519	0.00004
S	244	L244L	Tta	Cta	1	2	B.1.1.519	0.00004
S	244	L244del	TTA	---	2	2	B.1.1.524	0.041667
S	244	L244I	Tta	Ata	1	2	B.1.1.7	0.000001
S	244	L244I	TtA	AtC	1	2	B.1.1.7	0.000001
S	244	L244del	TTA	---	2	2	B.1.1.95	0.039216
S	244	L244del	TTA	---	2	2	B.1.177.12	0.000303
S	244	L244del	TTA	---	2	2	B.1.177.16	0.001329
S	244	L244del	TTA	---	2	2	B.1.177.81	0.000379
S	244	L244del	TTA	---	2	2	B.1.332	0.006993
S	244	L244S	tTA	tCT	1	2	B.1.351.1	0.038462
S	244	L244S	tTa	tCa	1	2	B.1.351.1	0.038462
S	244	L244L	ttA	ttG	2	2	B.1.36	0.000292
S	244	L244del	TTA	---	2	2	B.1.404	0.002604
S	244	L244del	TTA	---	2	2	B.1.416	0.002538
S	244	L244F	ttA	ttT	2	2	B.1.427	0.000101
S	244	L244F	ttA	ttT	2	2	B.1.429	0.000047
S	244	L244L	Tta	Cta	2	2	B.1.517	0.000854
S	244	L244del	TTA	---	2	2	B.1.568	0.002222
S	244	L244del	TTA	---	2	2	B.1.595	0.000522
S	244	L244del	TTA	---	2	2	B.1.619	0.001742
S	244	L244L	ttA	ttG	2	2	B.1.621	0.000177
S	244	L244F	ttA	ttT	2	2	B.1.628	0.000705
S	244	L244S	tTa	tCa	2	2	B.1.628	0.000705
S	244	L244S	tTa	tCa	2	2	P.1	0.000032
S	244	L244del	TTA	---	2	2	P.1.14	0.000096
S	244	L244F	ttA	ttT	2	2	P.1.14	0.000096
S	244	L244del	TTA	---	2	2	P.1.16	0.000748
S	244	L244del	TTA	---	2	2	P.4	0.007605
S	244	L244del	TTA	---	2	2	Q.3	0.00029
S	244	L244del	TTA	---	2	2	Q.4	0.00091
S	244	L244del	TTA	---	1	1	A.2	0.000662
S	244	L244F	ttA	ttT	1	1	A.2.4	0.003367
S	244	L244del	TTA	---	1	1	A.2.5	0.000499
S	244	L244F	ttA	ttT	1	1	A.2.5	0.000499
S	244	L244del	TTA	---	1	1	A.23.1	0.000704
S	244	L244F	ttA	ttT	1	1	A.23.1	0.000704
S	244	L244L	Tta	Cta	1	1	A.3	0.002096
S	244	L244del	TTA	---	1	1	A.3	0.002096
S	244	L244del	TTA	---	1	1	AA.1	0.007246
S	244	L244R	TTa	AGa	1	1	All	0
S	244	L244del1	ttA	tt-	1	1	AY.100	0.000046
S	244	L244F	ttA	ttT	1	1	AY.101	0.00049
S	244	L244L	ttA	ttG	1	1	AY.101	0.00049
S	244	L244V	Tta	Gta	1	1	AY.102	0.000027
S	244	L244del2	tTA	t--	1	1	AY.103	0.000006
S	244	L244F	ttA	ttC	1	1	AY.103	0.000006
S	244	L244del1	ttA	tt-	1	1	AY.103	0.000006
S	244	L244I	Tta	Ata	1	1	AY.103	0.000006
S	244	L244del	TTA	---	1	1	AY.111	0.000183
S	244	L244L	Tta	Cta	1	1	AY.113	0.000142
S	244	L244del	TTA	---	1	1	AY.116	0.000287
S	244	L244del	TTA	---	1	1	AY.117	0.000085
S	244	L244F	ttA	ttT	1	1	AY.119	0.000035
S	244	L244F	ttA	ttT	1	1	AY.12	0.000316
S	244	L244S	tTa	tCa	1	1	AY.120	0.000037
S	244	L244L	ttA	ttG	1	1	AY.120	0.000037
S	244	L244del	TTA	---	1	1	AY.120.2	0.001285
S	244	L244X	tTA	tAG	1	1	AY.121	0.000135
S	244	L244del	TTA	---	1	1	AY.16	0.00038
S	244	L244S	tTa	tCa	1	1	AY.20	0.000039
S	244	L244L	Tta	Cta	1	1	AY.23	0.00007
S	244	L244del	TTA	---	1	1	AY.23	0.00007
S	244	L244L	ttA	ttG	1	1	AY.25	0.000006
S	244	L244del1	ttA	tt-	1	1	AY.25	0.000006
S	244	L244del1	ttA	tt-	1	1	AY.29	0.000016
S	244	L244del2	tTA	t--	1	1	AY.29	0.000016
S	244	L244L	Tta	Cta	1	1	AY.29.1	0.000221
S	244	L244del	TTA	---	1	1	AY.29.1	0.000221
S	244	L244V	Tta	Gta	1	1	AY.3	0.00001
S	244	L244L	Tta	Cta	1	1	AY.3	0.00001
S	244	L244F	ttA	ttT	1	1	AY.3	0.00001
S	244	L244F	ttA	ttT	1	1	AY.3.1	0.000085
S	244	L244del	TTA	---	1	1	AY.30	0.000396
S	244	L244I	Tta	Ata	1	1	AY.34	0.000097
S	244	L244S	tTa	tCa	1	1	AY.34.1	0.00051
S	244	L244del	TTA	---	1	1	AY.35	0.000233
S	244	L244S	tTa	tCa	1	1	AY.36	0.000148
S	244	L244L	Tta	Cta	1	1	AY.36	0.000148
S	244	L244I	Tta	Ata	1	1	AY.37	0.000316
S	244	L244del1	ttA	tt-	1	1	AY.4	0.000002
S	244	L244S	tTa	tCa	1	1	AY.42	0.00004
S	244	L244L	Tta	Cta	1	1	AY.42	0.00004
S	244	L244S	tTa	tCa	1	1	AY.43	0.000004
S	244	L244V	Tta	Gta	1	1	AY.43	0.000004
S	244	L244V	Tta	Gta	1	1	AY.44	0.000006
S	244	L244F	ttA	ttT	1	1	AY.45	0.000122
S	244	L244I	Tta	Ata	1	1	AY.45	0.000122
S	244	L244S	tTa	tCa	1	1	AY.45	0.000122
S	244	L244S	tTa	tCa	1	1	AY.46.4	0.000165
S	244	L244V	Tta	Gta	1	1	AY.46.6	0.000072
S	244	L244F	ttA	ttT	1	1	AY.5	0.000021
S	244	L244S	tTa	tCa	1	1	AY.52	0.000814
S	244	L244F	ttA	ttT	1	1	AY.54	0.000095
S	244	L244L	ttA	ttG	1	1	AY.55	0.000917
S	244	L244S	tTa	tCa	1	1	AY.59	0.00053
S	244	L244V	Tta	Gta	1	1	AY.59	0.00053
S	244	L244S	tTa	tCa	1	1	AY.6	0.000041
S	244	L244del	TTA	---	1	1	AY.64	0.000595
S	244	L244del	TTA	---	1	1	AY.67	0.000464
S	244	L244del	TTA	---	1	1	AY.70	0.000209
S	244	L244del	TTA	---	1	1	AY.75.1	0.00018
S	244	L244S	tTa	tCa	1	1	AY.80	0.001129
S	244	L244del	TTA	---	1	1	AY.82	0.001357
S	244	L244L	Tta	Cta	1	1	AY.84	0.000437
S	244	L244del	TTA	---	1	1	AY.84	0.000437
S	244	L244del	TTA	---	1	1	AY.88	0.000884
S	244	L244L	Tta	Cta	1	1	AY.9	0.000068
S	244	L244S	tTa	tCa	1	1	AY.9.1	0.000084
S	244	L244T	TTa	ACa	1	1	AY.9.2	0.000037
S	244	L244I	Tta	Ata	1	1	AY.9.2	0.000037
S	244	L244V	Tta	Gta	1	1	AY.9.2	0.000037
S	244	L244S	tTa	tCa	1	1	AY.9.2	0.000037
S	244	L244del	TTA	---	1	1	AY.90	0.000684
S	244	L244I	Tta	Ata	1	1	AY.96	0.002075
S	244	L244del2	tTA	t--	1	1	AY.96	0.002075
S	244	L244del	TTA	---	1	1	AY.98	0.000079
S	244	L244S	tTa	tCa	1	1	AY.99.1	0.001553
S	244	L244S	tTa	tCa	1	1	AY.99.2	0.000092
S	244	L244S	tTa	tCa	1	1	B	0.000128
S	244	L244T	TTa	ACa	1	1	B.1	0.000009
S	244	L244R	TTa	AGa	1	1	B.1	0.000009
S	244	L244V	Tta	Gta	1	1	B.1.1	0.000018
S	244	L244I	Tta	Ata	1	1	B.1.1	0.000018
S	244	L244F	ttA	ttT	1	1	B.1.1	0.000018
S	244	L244L	TtA	CtT	1	1	B.1.1.1	0.000327
S	244	L244del	TTA	---	1	1	B.1.1.1	0.000327
S	244	L244del	TTA	---	1	1	B.1.1.153	0.001095
S	244	L244del	TTA	---	1	1	B.1.1.159	0.004673
S	244	L244del	TTA	---	1	1	B.1.1.165	0.015385
S	244	L244F	ttA	ttT	1	1	B.1.1.170	0.001247
S	244	L244L	ttA	ttG	1	1	B.1.1.189	0.001513
S	244	L244L	ttA	ttG	1	1	B.1.1.204	0.00304
S	244	L244del	TTA	---	1	1	B.1.1.214	0.000055
S	244	L244L	ttA	ttG	1	1	B.1.1.214	0.000055
S	244	L244del	TTA	---	1	1	B.1.1.277	0.000759
S	244	L244del	TTA	---	1	1	B.1.1.28	0.000311
S	244	L244del	TTA	---	1	1	B.1.1.280	0.003086
S	244	L244F	ttA	ttT	1	1	B.1.1.284	0.000107
S	244	L244del	TTA	---	1	1	B.1.1.298	0.000862
S	244	L244S	tTa	tCa	1	1	B.1.1.306	0.000438
S	244	L244del	TTA	---	1	1	B.1.1.306	0.000438
S	244	L244F	ttA	ttC	1	1	B.1.1.306	0.000438
S	244	L244del	TTA	---	1	1	B.1.1.311	0.000358
S	244	L244S	tTa	tCa	1	1	B.1.1.318	0.000302
S	244	L244del	TTA	---	1	1	B.1.1.322	0.008772
S	244	L244del	TTA	---	1	1	B.1.1.33	0.000421
S	244	L244del1	ttA	tt-	1	1	B.1.1.331	0.011628
S	244	L244del	TTA	---	1	1	B.1.1.352	0.03125
S	244	L244del	TTA	---	1	1	B.1.1.368	0.003086
S	244	L244del	TTA	---	1	1	B.1.1.37	0.000193
S	244	L244del	TTA	---	1	1	B.1.1.374	0.002375
S	244	L244del	TTA	---	1	1	B.1.1.389	0.006061
S	244	L244S	tTa	tCa	1	1	B.1.1.39	0.00051
S	244	L244del	TTA	---	1	1	B.1.1.39	0.00051
S	244	L244del	TTA	---	1	1	B.1.1.402	0.011111
S	244	L244S	tTa	tCa	1	1	B.1.1.416	0.000905
S	244	L244S	tTa	tCa	1	1	B.1.1.417	0.002703
S	244	L244del	TTA	---	1	1	B.1.1.420	0.001006
S	244	L244del2	tTA	t--	1	1	B.1.1.434	0.000349
S	244	L244del	TTA	---	1	1	B.1.1.44	0.00241
S	244	L244S	tTa	tCa	1	1	B.1.1.453	0.008475
S	244	L244F	ttA	ttT	1	1	B.1.1.519	0.00004
S	244	L244del	TTA	---	1	1	B.1.1.526	0.003546
S	244	L244del	TTA	---	1	1	B.1.1.53	0.013699
S	244	L244X	tTa	tGa	1	1	B.1.1.54	0.003021
S	244	L244del2	TTa	--a	1	1	B.1.1.7	0.000001
S	244	L244X	tTa	tAa	1	1	B.1.1.7	0.000001
S	244	L244del	TTA	---	1	1	B.1.147	0.000756
S	244	L244del	TTA	---	1	1	B.1.160.29	0.004219
S	244	L244del2	TTa	--a	1	1	B.1.177	0.000013
S	244	L244V	Tta	Gta	1	1	B.1.177	0.000013
S	244	L244del	TTA	---	1	1	B.1.177.17	0.000821
S	244	L244del	TTA	---	1	1	B.1.177.21	0.000076
S	244	L244del	TTA	---	1	1	B.1.177.24	0.001295
S	244	L244L	Tta	Cta	1	1	B.1.177.4	0.000211
S	244	L244del2	TTa	--a	1	1	B.1.177.54	0.000606
S	244	L244S	tTa	tCa	1	1	B.1.177.57	0.000281
S	244	L244del	TTA	---	1	1	B.1.177.69	0.001484
S	244	L244del	TTA	---	1	1	B.1.177.7	0.000165
S	244	L244S	tTa	tCa	1	1	B.1.177.77	0.000726
S	244	L244del	TTA	---	1	1	B.1.177.87	0.000728
S	244	L244del1	ttA	tt-	1	1	B.1.177.87	0.000728
S	244	L244V	Tta	Gta	1	1	B.1.2	0.000009
S	244	L244del2	TTa	--a	1	1	B.1.2	0.000009
S	244	L244del	TTA	---	1	1	B.1.213	0.014925
S	244	L244del	TTA	---	1	1	B.1.220	0.01087
S	244	L244L	ttA	ttG	1	1	B.1.221	0.000071
S	244	L244S	tTa	tCa	1	1	B.1.221	0.000071
S	244	L244del	TTA	---	1	1	B.1.234	0.000132
S	244	L244del	TTA	---	1	1	B.1.237	0.004975
S	244	L244F	ttA	ttT	1	1	B.1.237	0.004975
S	244	L244L	Tta	Cta	1	1	B.1.240	0.000216
S	244	L244del	TTA	---	1	1	B.1.241	0.000812
S	244	L244S	tTa	tCa	1	1	B.1.243	0.00007
S	244	L244del	TTA	---	1	1	B.1.243	0.00007
S	244	L244L	Tta	Cta	1	1	B.1.258	0.000067
S	244	L244V	Tta	Gta	1	1	B.1.258	0.000067
S	244	L244del2	tTA	t--	1	1	B.1.258.14	0.00098
S	244	L244del	TTA	---	1	1	B.1.258.14	0.00098
S	244	L244S	tTa	tCa	1	1	B.1.258.14	0.00098
S	244	L244del	TTA	---	1	1	B.1.258.17	0.000104
S	244	L244S	tTa	tCa	1	1	B.1.258.17	0.000104
S	244	L244L	Tta	Cta	1	1	B.1.258.17	0.000104
S	244	L244V	Tta	Gta	1	1	B.1.332	0.003497
S	244	L244F	ttA	ttT	1	1	B.1.351	0.00003
S	244	L244S	tTa	tCa	1	1	B.1.351	0.00003
S	244	L244I	TtA	AtT	1	1	B.1.351.1	0.038462
S	244	L244L	TtA	CtC	1	1	B.1.351.1	0.038462
S	244	L244del	TTA	---	1	1	B.1.36.17	0.000494
S	244	L244L	Tta	Cta	1	1	B.1.36.19	0.009259
S	244	L244S	tTa	tCa	1	1	B.1.36.29	0.000517
S	244	L244del	TTA	---	1	1	B.1.389	0.001002
S	244	L244S	tTa	tCa	1	1	B.1.389	0.001002
S	244	L244del	TTA	---	1	1	B.1.400	0.000429
S	244	L244F	ttA	ttT	1	1	B.1.404	0.001302
S	244	L244del	TTA	---	1	1	B.1.424	0.008065
S	244	L244del	TTA	---	1	1	B.1.439	0.005917
S	244	L244del	TTA	---	1	1	B.1.445	0.011765
S	244	L244del	TTA	---	1	1	B.1.453	0.003236
S	244	L244V	Tta	Gta	1	1	B.1.462	0.007246
S	244	L244del	TTA	---	1	1	B.1.466.2	0.000391
S	244	L244del2	tTA	t--	1	1	B.1.466.2	0.000391
S	244	L244del	TTA	---	1	1	B.1.468	0.005714
S	244	L244del	TTA	---	1	1	B.1.470	0.001404
S	244	L244del	TTA	---	1	1	B.1.499	0.00105
S	244	L244del	TTA	---	1	1	B.1.517	0.000427
S	244	L244del	TTA	---	1	1	B.1.524	0.001406
S	244	L244F	ttA	ttT	1	1	B.1.524	0.001406
S	244	L244del1	ttA	tt-	1	1	B.1.525	0.000113
S	244	L244V	Tta	Gta	1	1	B.1.526	0.000024
S	244	L244F	ttA	ttT	1	1	B.1.526	0.000024
S	244	L244L	Tta	Cta	1	1	B.1.526	0.000024
S	244	L244del	TTA	---	1	1	B.1.551	0.00129
S	244	L244del	TTA	---	1	1	B.1.561	0.000397
S	244	L244F	ttA	ttC	1	1	B.1.572	0.025
S	244	L244F	ttA	ttT	1	1	B.1.575	0.000303
S	244	L244del	TTA	---	1	1	B.1.576	0.000907
S	244	L244L	Tta	Cta	1	1	B.1.577	0.000687
S	244	L244S	tTa	tCa	1	1	B.1.582	0.000491
S	244	L244del	TTA	---	1	1	B.1.589	0.007576
S	244	L244del	TTA	---	1	1	B.1.596.1	0.009346
S	244	L244del	TTA	---	1	1	B.1.599	0.00365
S	244	L244del	TTA	---	1	1	B.1.604	0.017241
S	244	L244del	TTA	---	1	1	B.1.606	0.006024
S	244	L244del	TTA	---	1	1	B.1.617.1	0.000129
S	244	L244S	tTa	tCa	1	1	B.1.617.1	0.000129
S	244	L244del2	tTA	t--	1	1	B.1.617.2	0.000004
S	244	L244I	Tta	Ata	1	1	B.1.617.2	0.000004
S	244	L244del1	ttA	tt-	1	1	B.1.617.2	0.000004
S	244	L244V	Tta	Gta	1	1	B.1.619	0.000871
S	244	L244del	TTA	---	1	1	B.1.620	0.000946
S	244	L244S	tTa	tCa	1	1	B.1.621	0.000089
S	244	L244del	TTA	---	1	1	B.1.621.1	0.000506
S	244	L244S	tTa	tCa	1	1	B.1.625	0.002353
S	244	L244F	ttA	ttT	1	1	B.1.637	0.000073
S	244	L244S	tTa	tCa	1	1	B.1.637	0.000073
S	244	L244L	Tta	Cta	1	1	B.1.639	0.021739
S	244	L244del	TTA	---	1	1	B.40	0.000364
S	244	L244F	ttA	ttT	1	1	B.55	0.00295
S	244	L244F	ttA	ttT	1	1	B.6	0.00091
S	244	L244L	ttA	ttG	1	1	B.6.6	0.000889
S	244	L244del	TTA	---	1	1	C.1	0.002392
S	244	L244del	TTA	---	1	1	C.16	0.00106
S	244	L244del	TTA	---	1	1	C.30	0.001727
S	244	L244del	TTA	---	1	1	C.35	0.000774
S	244	L244L	Tta	Cta	1	1	C.37	0.000116
S	244	L244del	TTA	---	1	1	C.4	0.01
S	244	L244del2	tTA	t--	1	1	C.6	0.037037
S	244	L244V	Tta	Gta	1	1	D.2	0.000075
S	244	L244L	Tta	Cta	1	1	D.2	0.000075
S	244	L244F	ttA	ttT	1	1	L.1	0.001905
S	244	L244F	ttA	ttT	1	1	L.3	0.003546
S	244	L244del	TTA	---	1	1	N.5	0.001767
S	244	L244del2	tTA	t--	1	1	P.1	0.000016
S	244	L244L	Tta	Cta	1	1	P.1.12	0.000484
S	244	L244del2	TTA	--N	1	1	P.1.15	0.000232
S	244	L244del	TTA	---	1	1	P.1.2	0.001156
S	244	L244del	TTA	---	1	1	P.1.6	0.001946
S	244	L244del	TTA	---	1	1	P.2	0.000187
S	244	L244S	tTa	tCa	1	1	P.2	0.000187
S	244	L244L	TtA	CtT	1	1	P.3	0.001595
S	244	L244F	ttA	ttT	1	1	Q.3	0.000145
S	244	L244del	TTA	---	1	1	Q.7	0.001111
S	244	L244L	Tta	Cta	1	1	Q.8	0.000165
S	244	L244S	tTa	tCa	1	1	U.3	0.003861

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.