CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 846

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	846	A846V		nonsyn	gCt	gTt	2937	2934	0.998979	24098-24100
S	846	A846V		nonsyn	gCT	gTC	2937	3	0.00102145	24098-24100
S	846	A846S		nonsyn	Gct	Tct	1829	1827	0.998906	24098-24100
S	846	A846S		nonsyn	GcT	TcG	1829	1	0.000546747	24098-24100
S	846	A846S		nonsyn	GcT	TcA	1829	1	0.000546747	24098-24100
S	846	A846G		nonsyn	gCt	gGt	759	759	1	24098-24100
S	846	A846A		syn	gcT	gcC	286	226	0.79021	24098-24100
S	846	A846A		syn	gcT	gcA	286	54	0.188811	24098-24100
S	846	A846A		syn	gcT	gcG	286	6	0.020979	24098-24100
S	846	A846T		nonsyn	Gct	Act	113	112	0.99115	24098-24100
S	846	A846T		nonsyn	GcT	AcC	113	1	0.00884956	24098-24100
S	846	A846del		del	GCT	---	80	80	1	24098-24100
S	846	A846D		nonsyn	gCt	gAt	14	14	1	24098-24100
S	846	A846F		nonsyn	GCt	TTt	8	8	1	24098-24100
S	846	A846P		nonsyn	Gct	Cct	8	7	0.875	24098-24100
S	846	A846P		nonsyn	GcT	CcC	8	1	0.125	24098-24100
S	846	A846del2		del	gCT	g--	6	3	0.5	24098-24100
S	846	A846del2		del	GCt	--t	6	3	0.5	24098-24100
S	846	A846del1		del	gcT	gc-	4	2	0.5	24098-24100
S	846	A846del1		del	Gct	-ct	4	2	0.5	24098-24100
S	846	A846I		nonsyn	GCt	ATt	1	1	1	24098-24100
S	846	A846N		nonsyn	GCt	AAt	1	1	1	24098-24100
S	846	A846Y		nonsyn	GCt	TAt	1	1	1	24098-24100
S	846	A846K		nonsyn	GCT	AAG	1	1	1	24098-24100

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	846	A846V	gCt	gTt	2934	2937	All	0.000561
S	846	A846V	gCT	gTC	3	2937	All	0.000001
S	846	A846S	Gct	Tct	1827	1829	All	0.000349
S	846	A846S	GcT	TcG	1	1829	All	0
S	846	A846S	GcT	TcA	1	1829	All	0
S	846	A846G	gCt	gGt	759	759	All	0.000145
S	846	A846V	gCt	gTt	667	667	AY.3.1	0.056868
S	846	A846G	gCt	gGt	655	655	AY.29	0.010332
S	846	A846V	gCt	gTt	408	408	B.1.1.7	0.000365
S	846	A846A	gcT	gcC	226	286	All	0.000043
S	846	A846A	gcT	gcA	54	286	All	0.00001
S	846	A846A	gcT	gcG	6	286	All	0.000001
S	846	A846S	Gct	Tct	277	277	AY.4	0.000431
S	846	A846S	Gct	Tct	214	214	B.1.1.7	0.000192
S	846	A846V	gCt	gTt	198	198	AY.4	0.000308
S	846	A846S	Gct	Tct	177	177	AY.25	0.001065
S	846	A846V	gCt	gTt	171	171	AY.25	0.001029
S	846	A846S	Gct	Tct	153	153	AY.43	0.000678
S	846	A846S	Gct	Tct	119	119	AY.4.2	0.002581
S	846	A846T	Gct	Act	112	113	All	0.000021
S	846	A846T	GcT	AcC	1	113	All	0
S	846	A846V	gCt	gTt	106	106	B.1.429	0.002494
S	846	A846V	gCt	gTt	98	98	B.1.617.2	0.000369
S	846	A846S	Gct	Tct	97	97	B.1.617.2	0.000365
S	846	A846S	Gct	Tct	96	96	B.1.177.17	0.078818
S	846	A846V	gCt	gTt	94	94	B.1.1.75	1
S	846	A846V	gCt	gTt	81	81	AY.43	0.000359
S	846	A846del	GCT	---	80	80	All	0.000015
S	846	A846V	gCt	gTt	77	80	B.1.2	0.000678
S	846	A846V	gCT	gTC	3	80	B.1.2	0.000026
S	846	A846V	gCt	gTt	73	73	AY.103	0.000453
S	846	A846A	gcT	gcC	61	61	B.1.617.2	0.00023
S	846	A846V	gCt	gTt	60	60	B.1.221	0.004262
S	846	A846V	gCt	gTt	57	57	B.1.1.459	0.876923
S	846	A846V	gCt	gTt	54	54	B.1.221.3	0.045
S	846	A846V	gCt	gTt	52	52	AY.44	0.000317
S	846	A846S	Gct	Tct	50	50	B.28	0.163934
S	846	A846S	Gct	Tct	44	44	AY.42	0.00177
S	846	A846V	gCt	gTt	44	44	B.1.177	0.000579
S	846	A846V	gCt	gTt	42	42	B.1.1	0.000762
S	846	A846S	Gct	Tct	39	39	AY.103	0.000242
S	846	A846A	gcT	gcC	38	38	AY.102	0.001008
S	846	A846S	Gct	Tct	35	35	B.1.2	0.000308
S	846	A846A	gcT	gcA	35	35	B.1.637	0.002558
S	846	A846G	gCt	gGt	34	34	B.1.2	0.000299
S	846	A846S	Gct	Tct	32	32	P.2	0.005972
S	846	A846V	gCt	gTt	31	31	AY.3	0.000308
S	846	A846S	Gct	Tct	31	31	B.1	0.000284
S	846	A846V	gCt	gTt	31	31	B.1.1.519	0.001231
S	846	A846V	gCt	gTt	31	31	B.1.177.2	0.140909
S	846	A846V	gCt	gTt	27	27	AY.46.6	0.00195
S	846	A846V	gCt	gTt	27	27	B.1.160	0.000842
S	846	A846del	GCT	---	26	26	B.1.1.7	0.000023
S	846	A846S	Gct	Tct	24	24	AY.120	0.000892
S	846	A846V	gCt	gTt	24	24	B.1	0.00022
S	846	A846S	Gct	Tct	23	23	B.1.351	0.000684
S	846	A846S	Gct	Tct	22	22	AY.46.6	0.001589
S	846	A846T	Gct	Act	22	22	B.1.1.7	0.00002
S	846	A846S	Gct	Tct	21	21	AY.39	0.000519
S	846	A846G	gCt	gGt	21	21	B.1.1.7	0.000019
S	846	A846S	Gct	Tct	19	19	AY.117	0.001606
S	846	A846A	gcT	gcC	13	19	B.1.1.7	0.000012
S	846	A846A	gcT	gcA	4	19	B.1.1.7	0.000004
S	846	A846A	gcT	gcG	2	19	B.1.1.7	0.000002
S	846	A846T	Gct	Act	18	19	B.1.2	0.000158
S	846	A846T	GcT	AcC	1	19	B.1.2	0.000009
S	846	A846S	Gct	Tct	18	18	AY.44	0.00011
S	846	A846V	gCt	gTt	18	18	B.1.258	0.001198
S	846	A846T	Gct	Act	17	17	AY.103	0.000106
S	846	A846S	Gct	Tct	16	16	AY.29	0.000252
S	846	A846D	gCt	gAt	14	14	All	0.000003
S	846	A846G	gCt	gGt	14	14	B.1.160	0.000437
S	846	A846V	gCt	gTt	14	14	P.1	0.000221
S	846	A846S	Gct	Tct	13	13	AY.102	0.000345
S	846	A846V	gCt	gTt	13	13	AY.120	0.000483
S	846	A846S	Gct	Tct	13	13	AY.3	0.000129
S	846	A846S	Gct	Tct	13	13	P.1	0.000205
S	846	A846A	gcT	gcC	12	12	AY.105	0.007717
S	846	A846A	gcT	gcC	12	12	AY.36	0.001779
S	846	A846T	Gct	Act	12	12	AY.4	0.000019
S	846	A846S	Gct	Tct	12	12	B.1.1	0.000218
S	846	A846S	Gct	Tct	12	12	B.1.177.87	0.008734
S	846	A846V	gCt	gTt	11	11	AY.117	0.00093
S	846	A846V	gCt	gTt	11	11	AY.20	0.000428
S	846	A846S	Gct	Tct	11	11	AY.46.5	0.002183
S	846	A846V	gCt	gTt	11	11	AY.61	0.001153
S	846	A846S	Gct	Tct	11	11	B.1.177	0.000145
S	846	A846V	gCt	gTt	10	10	B.1.1.214	0.000555
S	846	A846V	gCt	gTt	10	10	B.1.1.294	0.012658
S	846	A846V	gCt	gTt	10	10	B.1.637	0.000731
S	846	A846S	Gct	Tct	9	9	AY.120.1	0.002889
S	846	A846G	gCt	gGt	9	9	AY.29.1	0.001985
S	846	A846A	gcT	gcC	8	9	AY.39	0.000198
S	846	A846A	gcT	gcG	1	9	AY.39	0.000025
S	846	A846S	Gct	Tct	9	9	AY.4.5	0.000967
S	846	A846S	Gct	Tct	9	9	AY.47	0.00028
S	846	A846F	GCt	TTt	8	8	All	0.000002
S	846	A846P	Gct	Cct	7	8	All	0.000001
S	846	A846P	GcT	CcC	1	8	All	0
S	846	A846V	gCt	gTt	8	8	AY.5	0.000165
S	846	A846S	Gct	Tct	8	8	AY.54	0.000763
S	846	A846V	gCt	gTt	8	8	B.1.177.32	0.010796
S	846	A846V	gCt	gTt	8	8	B.1.351	0.000238
S	846	A846S	Gct	Tct	8	8	B.1.526	0.000188
S	846	A846V	gCt	gTt	7	7	AY.100	0.000322
S	846	A846T	Gct	Act	7	7	AY.120	0.00026
S	846	A846S	Gct	Tct	7	7	AY.121	0.000947
S	846	A846V	gCt	gTt	7	7	AY.39	0.000173
S	846	A846V	gCt	gTt	7	7	AY.4.2	0.000152
S	846	A846S	Gct	Tct	7	7	AY.5	0.000145
S	846	A846V	gCt	gTt	7	7	AY.6	0.000288
S	846	A846S	Gct	Tct	7	7	AY.61	0.000733
S	846	A846S	Gct	Tct	7	7	AY.98.1	0.000339
S	846	A846del2	gCT	g--	3	6	All	0.000001
S	846	A846del2	GCt	--t	3	6	All	0.000001
S	846	A846V	gCt	gTt	6	6	AY.102	0.000159
S	846	A846V	gCt	gTt	6	6	AY.29	0.000095
S	846	A846T	Gct	Act	6	6	AY.44	0.000037
S	846	A846V	gCt	gTt	6	6	AY.46	0.000624
S	846	A846A	gcT	gcA	6	6	B.1.1.63	0.002315
S	846	A846S	Gct	Tct	6	6	B.1.1.70	0.002046
S	846	A846V	gCt	gTt	6	6	B.1.243	0.000418
S	846	A846V	gCt	gTt	6	6	B.1.595	0.001566
S	846	A846A	gcT	gcC	6	6	B.6	0.00546
S	846	A846V	gCt	gTt	5	5	AY.113	0.000712
S	846	A846V	gCt	gTt	5	5	AY.121	0.000677
S	846	A846S	Gct	Tct	5	5	AY.14	0.00044
S	846	A846S	Gct	Tct	5	5	AY.34	0.000485
S	846	A846V	gCt	gTt	5	5	AY.34.1	0.00255
S	846	A846A	gcT	gcC	5	5	AY.4	0.000008
S	846	A846T	Gct	Act	5	5	AY.43	0.000022
S	846	A846G	gCt	gGt	5	5	AY.44	0.00003
S	846	A846V	gCt	gTt	5	5	AY.47	0.000156
S	846	A846V	gCt	gTt	5	5	AY.9	0.000338
S	846	A846S	Gct	Tct	5	5	B.1.1.28	0.001556
S	846	A846V	gCt	gTt	5	5	B.1.1.318	0.001509
S	846	A846A	gcT	gcC	5	5	B.1.2	0.000044
S	846	A846V	gCt	gTt	5	5	B.1.369	0.001426
S	846	A846S	Gct	Tct	5	5	B.1.429	0.000118
S	846	A846V	gCt	gTt	5	5	B.1.526	0.000118
S	846	A846V	gCt	gTt	5	5	B.1.596	0.000436
S	846	A846S	Gct	Tct	2	4		0.111111
S	846	A846S	GcT	TcG	1	4		0.055556
S	846	A846S	GcT	TcA	1	4		0.055556
S	846	A846S	Gct	Tct	4	4	AD.2	0.000876
S	846	A846del1	Gct	-ct	2	4	All	0
S	846	A846del1	gcT	gc-	2	4	All	0
S	846	A846A	gcT	gcC	4	4	AY.103	0.000025
S	846	A846V	gCt	gTt	4	4	AY.116	0.001147
S	846	A846V	gCt	gTt	4	4	AY.26	0.000113
S	846	A846V	gCt	gTt	4	4	AY.33	0.000267
S	846	A846V	gCt	gTt	4	4	AY.34	0.000388
S	846	A846del	GCT	---	4	4	AY.4.5	0.00043
S	846	A846V	gCt	gTt	4	4	AY.42	0.000161
S	846	A846del	GCT	---	4	4	AY.43	0.000018
S	846	A846V	gCt	gTt	4	4	AY.9.2	0.000147
S	846	A846V	gCt	gTt	4	4	AY.96	0.008299
S	846	A846A	gcT	gcC	2	4	B.1	0.000018
S	846	A846A	gcT	gcA	2	4	B.1	0.000018
S	846	A846V	gCt	gTt	4	4	B.1.1.161	0.014134
S	846	A846A	gcT	gcC	4	4	B.1.1.174	0.013514
S	846	A846V	gCt	gTt	4	4	B.1.1.317	0.001647
S	846	A846F	GCt	TTt	4	4	B.1.1.459	0.061538
S	846	A846S	Gct	Tct	4	4	B.1.1.519	0.000159
S	846	A846D	gCt	gAt	4	4	B.1.1.7	0.000004
S	846	A846V	gCt	gTt	4	4	B.1.177.45	0.001525
S	846	A846S	Gct	Tct	4	4	B.1.223	0.011111
S	846	A846V	gCt	gTt	4	4	B.1.389	0.004008
S	846	A846S	Gct	Tct	4	4	P.1.7	0.001277
S	846	A846V	gCt	gTt	4	4	R.1	0.00036
S	846	A846A	gcT	gcA	1	3		0.055556
S	846	A846A	gcT	gcC	1	3		0.055556
S	846	A846A	gcT	gcG	1	3		0.055556
S	846	A846V	gCt	gTt	3	3	A.2.5	0.001497
S	846	A846V	gCt	gTt	3	3	AY.23	0.000209
S	846	A846A	gcT	gcC	3	3	AY.26	0.000085
S	846	A846A	gcT	gcC	3	3	AY.33	0.0002
S	846	A846S	Gct	Tct	3	3	AY.39.1	0.000119
S	846	A846V	gCt	gTt	3	3	AY.39.1	0.000119
S	846	A846del	GCT	---	3	3	AY.4	0.000005
S	846	A846A	gcT	gcC	3	3	AY.44	0.000018
S	846	A846V	gCt	gTt	3	3	AY.45	0.000365
S	846	A846V	gCt	gTt	3	3	AY.5.4	0.00083
S	846	A846S	Gct	Tct	3	3	AY.53	0.000863
S	846	A846V	gCt	gTt	3	3	AY.75	0.000168
S	846	A846V	gCt	gTt	3	3	AY.9.1	0.000251
S	846	A846V	gCt	gTt	3	3	AY.92	0.000862
S	846	A846A	gcT	gcC	3	3	AY.93	0.000819
S	846	A846S	Gct	Tct	3	3	AY.99.2	0.000276
S	846	A846V	gCt	gTt	3	3	B	0.000383
S	846	A846A	gcT	gcC	2	3	B.1.1	0.000036
S	846	A846A	gcT	gcA	1	3	B.1.1	0.000018
S	846	A846V	gCt	gTt	3	3	B.1.1.10	0.003344
S	846	A846V	gCt	gTt	3	3	B.1.162	0.015075
S	846	A846V	gCt	gTt	3	3	B.1.177.81	0.000568
S	846	A846S	Gct	Tct	3	3	B.1.221	0.000213
S	846	A846V	gCt	gTt	3	3	B.1.232	0.001612
S	846	A846V	gCt	gTt	3	3	B.1.234	0.000396
S	846	A846V	gCt	gTt	3	3	B.1.311	0.000824
S	846	A846A	gcT	gcC	2	3	B.1.351	0.000059
S	846	A846A	gcT	gcG	1	3	B.1.351	0.00003
S	846	A846S	Gct	Tct	3	3	B.1.36	0.000438
S	846	A846V	gCt	gTt	3	3	B.1.36.17	0.001482
S	846	A846V	gCt	gTt	3	3	B.1.575	0.00091
S	846	A846V	gCt	gTt	3	3	B.1.612	0.007958
S	846	A846T	Gct	Act	3	3	B.1.617.2	0.000011
S	846	A846V	gCt	gTt	3	3	B.1.618	0.012097
S	846	A846F	GCt	TTt	3	3	P.1	0.000047
S	846	A846V	gCt	gTt	3	3	W.1	0.026087
S	846	A846del	GCT	---	2	2		0.111111
S	846	A846S	Gct	Tct	2	2	A.23.1	0.001408
S	846	A846V	gCt	gTt	2	2	A.28	0.005291
S	846	A846A	gcT	gcC	2	2	AU.1	0.002532
S	846	A846V	gCt	gTt	2	2	AY.109	0.001479
S	846	A846V	gCt	gTt	2	2	AY.111	0.000366
S	846	A846S	Gct	Tct	2	2	AY.111	0.000366
S	846	A846S	Gct	Tct	2	2	AY.113	0.000285
S	846	A846V	gCt	gTt	2	2	AY.118	0.000125
S	846	A846S	Gct	Tct	2	2	AY.119	0.000071
S	846	A846V	gCt	gTt	2	2	AY.119	0.000071
S	846	A846V	gCt	gTt	2	2	AY.14	0.000176
S	846	A846S	Gct	Tct	2	2	AY.23	0.000139
S	846	A846T	Gct	Act	2	2	AY.25	0.000012
S	846	A846A	gcT	gcC	2	2	AY.25	0.000012
S	846	A846S	Gct	Tct	2	2	AY.32	0.001065
S	846	A846S	Gct	Tct	2	2	AY.35	0.000466
S	846	A846S	Gct	Tct	2	2	AY.36	0.000296
S	846	A846S	Gct	Tct	2	2	AY.38	0.000999
S	846	A846G	gCt	gGt	2	2	AY.4	0.000003
S	846	A846S	Gct	Tct	2	2	AY.4.4	0.000818
S	846	A846V	gCt	gTt	2	2	AY.4.5	0.000215
S	846	A846A	gcT	gcG	1	2	AY.43	0.000004
S	846	A846A	gcT	gcC	1	2	AY.43	0.000004
S	846	A846P	GcT	CcC	1	2	AY.44	0.000006
S	846	A846P	Gct	Cct	1	2	AY.44	0.000006
S	846	A846A	gcT	gcC	2	2	AY.45	0.000243
S	846	A846V	gCt	gTt	2	2	AY.46.2	0.001271
S	846	A846S	Gct	Tct	2	2	AY.46.4	0.000329
S	846	A846S	Gct	Tct	2	2	AY.5.4	0.000553
S	846	A846V	gCt	gTt	2	2	AY.59	0.001059
S	846	A846A	gcT	gcC	2	2	AY.6	0.000082
S	846	A846S	Gct	Tct	2	2	AY.60	0.001876
S	846	A846V	gCt	gTt	2	2	AY.69	0.000373
S	846	A846S	Gct	Tct	2	2	AY.7.1	0.000225
S	846	A846V	gCt	gTt	2	2	AY.74	0.000231
S	846	A846V	gCt	gTt	2	2	AY.84	0.000875
S	846	A846S	Gct	Tct	2	2	AY.9	0.000135
S	846	A846S	Gct	Tct	2	2	AY.9.2	0.000073
S	846	A846V	gCt	gTt	2	2	AY.98	0.000158
S	846	A846del	GCT	---	2	2	B.1	0.000018
S	846	A846G	gCt	gGt	2	2	B.1	0.000018
S	846	A846del	GCT	---	2	2	B.1.1	0.000036
S	846	A846S	Gct	Tct	2	2	B.1.1.214	0.000111
S	846	A846A	gcT	gcC	2	2	B.1.1.222	0.000408
S	846	A846del	GCT	---	2	2	B.1.1.236	0.013793
S	846	A846V	gCt	gTt	2	2	B.1.1.284	0.000215
S	846	A846S	Gct	Tct	2	2	B.1.1.306	0.000877
S	846	A846V	gCt	gTt	2	2	B.1.1.434	0.000697
S	846	A846P	Gct	Cct	2	2	B.1.1.7	0.000002
S	846	A846A	gcT	gcC	2	2	B.1.157	0.00597
S	846	A846S	Gct	Tct	2	2	B.1.170	0.008621
S	846	A846del	GCT	---	2	2	B.1.177	0.000026
S	846	A846del1	gcT	gc-	1	2	B.1.177	0.000013
S	846	A846del1	Gct	-ct	1	2	B.1.177	0.000013
S	846	A846V	gCt	gTt	2	2	B.1.177.12	0.000303
S	846	A846del	GCT	---	2	2	B.1.177.4	0.000422
S	846	A846del	GCT	---	2	2	B.1.177.54	0.001213
S	846	A846V	gCt	gTt	2	2	B.1.177.57	0.000562
S	846	A846V	gCt	gTt	2	2	B.1.177.62	0.002384
S	846	A846V	gCt	gTt	2	2	B.1.177.65	0.001331
S	846	A846V	gCt	gTt	2	2	B.1.177.7	0.00033
S	846	A846T	Gct	Act	2	2	B.1.177.75	0.002081
S	846	A846S	Gct	Tct	2	2	B.1.177.81	0.000379
S	846	A846V	gCt	gTt	2	2	B.1.177.86	0.000367
S	846	A846S	Gct	Tct	2	2	B.1.221.3	0.001667
S	846	A846V	gCt	gTt	2	2	B.1.224	0.05
S	846	A846V	gCt	gTt	2	2	B.1.236	0.004107
S	846	A846S	Gct	Tct	2	2	B.1.240	0.000431
S	846	A846V	gCt	gTt	2	2	B.1.258.17	0.000208
S	846	A846S	Gct	Tct	2	2	B.1.311	0.000549
S	846	A846V	gCt	gTt	2	2	B.1.36.18	0.00084
S	846	A846S	Gct	Tct	2	2	B.1.36.29	0.001035
S	846	A846V	gCt	gTt	2	2	B.1.427	0.000101
S	846	A846S	Gct	Tct	2	2	B.1.427	0.000101
S	846	A846V	gCt	gTt	2	2	B.1.433	0.00639
S	846	A846V	gCt	gTt	2	2	B.1.466.2	0.000782
S	846	A846A	gcT	gcC	2	2	B.1.526	0.000047
S	846	A846T	Gct	Act	2	2	B.1.561	0.000794
S	846	A846V	gCt	gTt	2	2	B.1.561	0.000794
S	846	A846V	gCt	gTt	2	2	B.1.617.1	0.000258
S	846	A846G	gCt	gGt	2	2	B.1.617.2	0.000008
S	846	A846S	Gct	Tct	2	2	B.1.637	0.000146
S	846	A846V	gCt	gTt	2	2	C.37	0.000232
S	846	A846V	gCt	gTt	2	2	D.2	0.00015
S	846	A846V	gCt	gTt	2	2	N.5	0.003534
S	846	A846G	gCt	gGt	2	2	P.1.17	0.000324
S	846	A846S	Gct	Tct	2	2	Q.1	0.000253
S	846	A846V	gCt	gTt	2	2	Q.1	0.000253
S	846	A846S	Gct	Tct	2	2	Q.4	0.00091
S	846	A846G	gCt	gGt	1	1		0.055556
S	846	A846F	GCt	TTt	1	1		0.055556
S	846	A846I	GCt	ATt	1	1		0.055556
S	846	A846N	GCt	AAt	1	1		0.055556
S	846	A846V	gCt	gTt	1	1		0.055556
S	846	A846T	Gct	Act	1	1		0.055556
S	846	A846D	gCt	gAt	1	1		0.055556
S	846	A846Y	GCt	TAt	1	1		0.055556
S	846	A846D	gCt	gAt	1	1	A	0.000387
S	846	A846V	gCt	gTt	1	1	A	0.000387
S	846	A846del	GCT	---	1	1	A	0.000387
S	846	A846S	Gct	Tct	1	1	A	0.000387
S	846	A846V	gCt	gTt	1	1	A.2.5.1	0.004808
S	846	A846V	gCt	gTt	1	1	A.21	0.00277
S	846	A846S	Gct	Tct	1	1	A.4	0.012821
S	846	A846V	gCt	gTt	1	1	AE.8	0.000489
S	846	A846del	GCT	---	1	1	AH.3	0.003802
S	846	A846K	GCT	AAG	1	1	All	0
S	846	A846I	GCt	ATt	1	1	All	0
S	846	A846N	GCt	AAt	1	1	All	0
S	846	A846Y	GCt	TAt	1	1	All	0
S	846	A846V	gCt	gTt	1	1	AM.2	0.111111
S	846	A846V	gCt	gTt	1	1	AM.4	0.003571
S	846	A846T	Gct	Act	1	1	AY.102	0.000027
S	846	A846S	Gct	Tct	1	1	AY.106	0.000335
S	846	A846S	Gct	Tct	1	1	AY.114	0.000231
S	846	A846del	GCT	---	1	1	AY.117	0.000085
S	846	A846G	gCt	gGt	1	1	AY.117	0.000085
S	846	A846T	Gct	Act	1	1	AY.118	0.000063
S	846	A846S	Gct	Tct	1	1	AY.118	0.000063
S	846	A846G	gCt	gGt	1	1	AY.120	0.000037
S	846	A846del	GCT	---	1	1	AY.120	0.000037
S	846	A846V	gCt	gTt	1	1	AY.120.1	0.000321
S	846	A846V	gCt	gTt	1	1	AY.120.2	0.001285
S	846	A846A	gcT	gcC	1	1	AY.121	0.000135
S	846	A846S	Gct	Tct	1	1	AY.16	0.00038
S	846	A846D	gCt	gAt	1	1	AY.20	0.000039
S	846	A846A	gcT	gcC	1	1	AY.20	0.000039
S	846	A846S	Gct	Tct	1	1	AY.20	0.000039
S	846	A846V	gCt	gTt	1	1	AY.24	0.000431
S	846	A846G	gCt	gGt	1	1	AY.25	0.000006
S	846	A846del	GCT	---	1	1	AY.25	0.000006
S	846	A846V	gCt	gTt	1	1	AY.27	0.000065
S	846	A846D	gCt	gAt	1	1	AY.29	0.000016
S	846	A846A	gcT	gcC	1	1	AY.29.1	0.000221
S	846	A846del	GCT	---	1	1	AY.3.1	0.000085
S	846	A846A	gcT	gcC	1	1	AY.32	0.000532
S	846	A846V	gCt	gTt	1	1	AY.32	0.000532
S	846	A846S	Gct	Tct	1	1	AY.33	0.000067
S	846	A846del	GCT	---	1	1	AY.36	0.000148
S	846	A846P	Gct	Cct	1	1	AY.39	0.000025
S	846	A846D	gCt	gAt	1	1	AY.4	0.000002
S	846	A846del2	GCt	--t	1	1	AY.4	0.000002
S	846	A846P	Gct	Cct	1	1	AY.4	0.000002
S	846	A846del1	gcT	gc-	1	1	AY.4	0.000002
S	846	A846A	gcT	gcC	1	1	AY.4.5	0.000107
S	846	A846G	gCt	gGt	1	1	AY.43	0.000004
S	846	A846D	gCt	gAt	1	1	AY.44	0.000006
S	846	A846S	Gct	Tct	1	1	AY.45	0.000122
S	846	A846A	gcT	gcC	1	1	AY.46	0.000104
S	846	A846S	Gct	Tct	1	1	AY.46	0.000104
S	846	A846del2	gCT	g--	1	1	AY.46.2	0.000635
S	846	A846del	GCT	---	1	1	AY.46.2	0.000635
S	846	A846A	gcT	gcC	1	1	AY.47	0.000031
S	846	A846T	Gct	Act	1	1	AY.47	0.000031
S	846	A846del	GCT	---	1	1	AY.5	0.000021
S	846	A846A	gcT	gcC	1	1	AY.5.3	0.000337
S	846	A846S	Gct	Tct	1	1	AY.5.3	0.000337
S	846	A846A	gcT	gcC	1	1	AY.51	0.000909
S	846	A846V	gCt	gTt	1	1	AY.54	0.000095
S	846	A846V	gCt	gTt	1	1	AY.55	0.000917
S	846	A846S	Gct	Tct	1	1	AY.55	0.000917
S	846	A846V	gCt	gTt	1	1	AY.58	0.000907
S	846	A846D	gCt	gAt	1	1	AY.6	0.000041
S	846	A846V	gCt	gTt	1	1	AY.60	0.000938
S	846	A846T	Gct	Act	1	1	AY.61	0.000105
S	846	A846V	gCt	gTt	1	1	AY.68	0.000274
S	846	A846S	Gct	Tct	1	1	AY.70	0.000209
S	846	A846V	gCt	gTt	1	1	AY.71	0.000475
S	846	A846S	Gct	Tct	1	1	AY.75	0.000056
S	846	A846del	GCT	---	1	1	AY.75	0.000056
S	846	A846A	gcT	gcC	1	1	AY.75.1	0.00018
S	846	A846S	Gct	Tct	1	1	AY.75.1	0.00018
S	846	A846V	gCt	gTt	1	1	AY.79	0.001211
S	846	A846A	gcT	gcC	1	1	AY.86	0.00083
S	846	A846V	gCt	gTt	1	1	AY.87	0.000833
S	846	A846V	gCt	gTt	1	1	AY.88	0.000884
S	846	A846A	gcT	gcC	1	1	AY.9	0.000068
S	846	A846T	Gct	Act	1	1	AY.9	0.000068
S	846	A846S	Gct	Tct	1	1	AY.9.1	0.000084
S	846	A846S	Gct	Tct	1	1	AY.91	0.00073
S	846	A846S	Gct	Tct	1	1	AY.93	0.000273
S	846	A846G	gCt	gGt	1	1	AY.98	0.000079
S	846	A846S	Gct	Tct	1	1	AY.98	0.000079
S	846	A846V	gCt	gTt	1	1	AY.98.1	0.000048
S	846	A846del	GCT	---	1	1	AY.98.1	0.000048
S	846	A846A	gcT	gcC	1	1	AY.98.1	0.000048
S	846	A846del	GCT	---	1	1	AY.99.1	0.001553
S	846	A846A	gcT	gcA	1	1	B	0.000128
S	846	A846S	Gct	Tct	1	1	B	0.000128
S	846	A846D	gCt	gAt	1	1	B.1	0.000009
S	846	A846T	Gct	Act	1	1	B.1	0.000009
S	846	A846P	Gct	Cct	1	1	B.1	0.000009
S	846	A846G	gCt	gGt	1	1	B.1.1	0.000018
S	846	A846del2	GCt	--t	1	1	B.1.1	0.000018
S	846	A846V	gCt	gTt	1	1	B.1.1.117	0.009709
S	846	A846G	gCt	gGt	1	1	B.1.1.138	0.006061
S	846	A846del	GCT	---	1	1	B.1.1.159	0.004673
S	846	A846V	gCt	gTt	1	1	B.1.1.166	0.033333
S	846	A846V	gCt	gTt	1	1	B.1.1.170	0.001247
S	846	A846S	Gct	Tct	1	1	B.1.1.189	0.001513
S	846	A846V	gCt	gTt	1	1	B.1.1.25	0.000569
S	846	A846V	gCt	gTt	1	1	B.1.1.277	0.000759
S	846	A846A	gcT	gcC	1	1	B.1.1.277	0.000759
S	846	A846V	gCt	gTt	1	1	B.1.1.306	0.000438
S	846	A846del	GCT	---	1	1	B.1.1.312	0.001912
S	846	A846G	gCt	gGt	1	1	B.1.1.318	0.000302
S	846	A846S	Gct	Tct	1	1	B.1.1.318	0.000302
S	846	A846V	gCt	gTt	1	1	B.1.1.326	0.001761
S	846	A846V	gCt	gTt	1	1	B.1.1.349	0.010309
S	846	A846V	gCt	gTt	1	1	B.1.1.368	0.003086
S	846	A846V	gCt	gTt	1	1	B.1.1.37	0.000193
S	846	A846A	gcT	gcC	1	1	B.1.1.370	0.012658
S	846	A846S	Gct	Tct	1	1	B.1.1.374	0.002375
S	846	A846V	gCt	gTt	1	1	B.1.1.391	0.008547
S	846	A846V	gCt	gTt	1	1	B.1.1.406	0.006494
S	846	A846V	gCt	gTt	1	1	B.1.1.416	0.000905
S	846	A846A	gcT	gcC	1	1	B.1.1.432	0.001266
S	846	A846A	gcT	gcC	1	1	B.1.1.448	0.002033
S	846	A846T	Gct	Act	1	1	B.1.1.51	0.001718
S	846	A846P	Gct	Cct	1	1	B.1.1.514	0.038462
S	846	A846T	Gct	Act	1	1	B.1.1.519	0.00004
S	846	A846V	gCt	gTt	1	1	B.1.1.528	0.004808
S	846	A846K	GCT	AAG	1	1	B.1.1.7	0.000001
S	846	A846del1	Gct	-ct	1	1	B.1.1.7	0.000001
S	846	A846del2	GCt	--t	1	1	B.1.1.7	0.000001
S	846	A846S	Gct	Tct	1	1	B.1.160	0.000031
S	846	A846V	gCt	gTt	1	1	B.1.160.16	0.000929
S	846	A846A	gcT	gcA	1	1	B.1.177	0.000013
S	846	A846del2	gCT	g--	1	1	B.1.177	0.000013
S	846	A846V	gCt	gTt	1	1	B.1.177.10	0.000878
S	846	A846del	GCT	---	1	1	B.1.177.17	0.000821
S	846	A846del	GCT	---	1	1	B.1.177.18	0.00116
S	846	A846S	Gct	Tct	1	1	B.1.177.32	0.00135
S	846	A846A	gcT	gcC	1	1	B.1.177.44	0.000519
S	846	A846V	gCt	gTt	1	1	B.1.177.52	0.001757
S	846	A846V	gCt	gTt	1	1	B.1.177.53	0.002392
S	846	A846del2	gCT	g--	1	1	B.1.177.54	0.000606
S	846	A846V	gCt	gTt	1	1	B.1.177.56	0.000668
S	846	A846del	GCT	---	1	1	B.1.177.58	0.001332
S	846	A846del	GCT	---	1	1	B.1.177.60	0.000218
S	846	A846S	Gct	Tct	1	1	B.1.177.60	0.000218
S	846	A846del	GCT	---	1	1	B.1.177.63	0.002703
S	846	A846T	Gct	Act	1	1	B.1.177.65	0.000665
S	846	A846S	Gct	Tct	1	1	B.1.177.7	0.000165
S	846	A846T	Gct	Act	1	1	B.1.177.73	0.000566
S	846	A846del	GCT	---	1	1	B.1.179	0.003759
S	846	A846del	GCT	---	1	1	B.1.2	0.000009
S	846	A846T	Gct	Act	1	1	B.1.221	0.000071
S	846	A846A	gcT	gcC	1	1	B.1.221	0.000071
S	846	A846G	gCt	gGt	1	1	B.1.221	0.000071
S	846	A846S	Gct	Tct	1	1	B.1.234	0.000132
S	846	A846G	gCt	gGt	1	1	B.1.241	0.000812
S	846	A846A	gcT	gcC	1	1	B.1.243	0.00007
S	846	A846del	GCT	---	1	1	B.1.258	0.000067
S	846	A846S	Gct	Tct	1	1	B.1.258.11	0.000396
S	846	A846S	Gct	Tct	1	1	B.1.258.17	0.000104
S	846	A846V	gCt	gTt	1	1	B.1.3	0.002618
S	846	A846D	gCt	gAt	1	1	B.1.321	0.034483
S	846	A846V	gCt	gTt	1	1	B.1.324	0.001605
S	846	A846V	gCt	gTt	1	1	B.1.329	0.000608
S	846	A846A	gcT	gcC	1	1	B.1.350	0.002933
S	846	A846del	GCT	---	1	1	B.1.351	0.00003
S	846	A846T	Gct	Act	1	1	B.1.351	0.00003
S	846	A846V	gCt	gTt	1	1	B.1.36	0.000146
S	846	A846S	Gct	Tct	1	1	B.1.36.18	0.00042
S	846	A846del	GCT	---	1	1	B.1.36.18	0.00042
S	846	A846S	Gct	Tct	1	1	B.1.36.19	0.009259
S	846	A846V	gCt	gTt	1	1	B.1.36.26	0.002857
S	846	A846V	gCt	gTt	1	1	B.1.36.29	0.000517
S	846	A846A	gcT	gcC	1	1	B.1.36.37	0.002778
S	846	A846S	Gct	Tct	1	1	B.1.362	0.001541
S	846	A846G	gCt	gGt	1	1	B.1.362	0.001541
S	846	A846S	Gct	Tct	1	1	B.1.369	0.000285
S	846	A846V	gCt	gTt	1	1	B.1.377	0.004566
S	846	A846V	gCt	gTt	1	1	B.1.385	0.010638
S	846	A846S	Gct	Tct	1	1	B.1.396	0.000706
S	846	A846T	Gct	Act	1	1	B.1.396	0.000706
S	846	A846V	gCt	gTt	1	1	B.1.400	0.000429
S	846	A846S	Gct	Tct	1	1	B.1.404	0.001302
S	846	A846G	gCt	gGt	1	1	B.1.409	0.000781
S	846	A846V	gCt	gTt	1	1	B.1.428	0.00102
S	846	A846V	gCt	gTt	1	1	B.1.438.1	0.000107
S	846	A846V	gCt	gTt	1	1	B.1.469	0.00361
S	846	A846S	Gct	Tct	1	1	B.1.504	0.03125
S	846	A846S	Gct	Tct	1	1	B.1.517	0.000427
S	846	A846T	Gct	Act	1	1	B.1.525	0.000113
S	846	A846V	gCt	gTt	1	1	B.1.525	0.000113
S	846	A846V	gCt	gTt	1	1	B.1.538	0.008065
S	846	A846V	gCt	gTt	1	1	B.1.551	0.00129
S	846	A846V	gCt	gTt	1	1	B.1.564	0.000426
S	846	A846S	Gct	Tct	1	1	B.1.565	0.00081
S	846	A846S	Gct	Tct	1	1	B.1.575	0.000303
S	846	A846S	Gct	Tct	1	1	B.1.596	0.000087
S	846	A846del	GCT	---	1	1	B.1.617.2	0.000004
S	846	A846D	gCt	gAt	1	1	B.1.617.2	0.000004
S	846	A846S	Gct	Tct	1	1	B.1.620	0.000946
S	846	A846V	gCt	gTt	1	1	B.1.621	0.000089
S	846	A846A	gcT	gcA	1	1	B.1.621	0.000089
S	846	A846S	Gct	Tct	1	1	B.1.621	0.000089
S	846	A846S	Gct	Tct	1	1	B.1.9.4	0.006135
S	846	A846V	gCt	gTt	1	1	B.1.93	0.000934
S	846	A846V	gCt	gTt	1	1	B.12	0.00641
S	846	A846V	gCt	gTt	1	1	B.55	0.00295
S	846	A846V	gCt	gTt	1	1	C.36	0.000911
S	846	A846V	gCt	gTt	1	1	C.36.3	0.000567
S	846	A846S	Gct	Tct	1	1	C.37	0.000116
S	846	A846T	Gct	Act	1	1	D.2	0.000075
S	846	A846A	gcT	gcA	1	1	D.2	0.000075
S	846	A846V	gCt	gTt	1	1	D.5	0.004975
S	846	A846A	gcT	gcC	1	1	P.1	0.000016
S	846	A846S	Gct	Tct	1	1	P.1.1	0.000318
S	846	A846del	GCT	---	1	1	P.1.13	0.000898
S	846	A846V	gCt	gTt	1	1	P.1.14	0.000048
S	846	A846del	GCT	---	1	1	P.1.15	0.000232
S	846	A846A	gcT	gcA	1	1	P.1.17	0.000162
S	846	A846S	Gct	Tct	1	1	P.1.17	0.000162
S	846	A846V	gCt	gTt	1	1	P.1.2	0.001156
S	846	A846V	gCt	gTt	1	1	P.2	0.000187
S	846	A846V	gCt	gTt	1	1	P.6	0.003145
S	846	A846S	Gct	Tct	1	1	P.7	0.004367
S	846	A846A	gcT	gcC	1	1	Q.1	0.000126
S	846	A846del	GCT	---	1	1	Q.2	0.000613
S	846	A846V	gCt	gTt	1	1	Q.3	0.000145
S	846	A846S	Gct	Tct	1	1	Q.3	0.000145
S	846	A846V	gCt	gTt	1	1	Q.4	0.000455
S	846	A846del	GCT	---	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.