CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 3

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	3	V3G		nonsyn	gTt	gGt	1884	1884	1	21569-21571
S	3	V3V		syn	gtT	gtC	457	259	0.56674	21569-21571
S	3	V3V		syn	gtT	gtG	457	187	0.40919	21569-21571
S	3	V3V		syn	gtT	gtA	457	11	0.02407	21569-21571
S	3	V3I		nonsyn	Gtt	Att	213	213	1	21569-21571
S	3	V3F		nonsyn	Gtt	Ttt	137	137	1	21569-21571
S	3	V3A		nonsyn	gTt	gCt	107	105	0.981308	21569-21571
S	3	V3A		nonsyn	gTT	gCA	107	1	0.00934579	21569-21571
S	3	V3A		nonsyn	gTT	gCC	107	1	0.00934579	21569-21571
S	3	V3del		del	GTT	---	52	52	1	21569-21571
S	3	V3del1		del	gTt	g-t	26	24	0.923077	21569-21571
S	3	V3del1		del	Gtt	-tt	26	2	0.0769231	21569-21571
S	3	V3L		nonsyn	Gtt	Ctt	9	6	0.666667	21569-21571
S	3	V3L		nonsyn	GtT	TtA	9	3	0.333333	21569-21571
S	3	V3C		nonsyn	GTt	TGt	8	8	1	21569-21571
S	3	V3Y		nonsyn	GTt	TAt	6	6	1	21569-21571
S	3	V3D		nonsyn	gTt	gAt	5	5	1	21569-21571
S	3	V3del2		del	gTT	g--	5	4	0.8	21569-21571
S	3	V3del2		del	GTt	--t	5	1	0.2	21569-21571
S	3	V3E		nonsyn	gTT	gAA	3	3	1	21569-21571
S	3	V3X		nonsyn	GTT	TAA	2	2	1	21569-21571
S	3	V3H		nonsyn	GTt	CAt	1	1	1	21569-21571
S	3	V3R		nonsyn	GTt	CGt	1	1	1	21569-21571
S	3	V3S		nonsyn	GTt	AGt	1	1	1	21569-21571

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	3	V3G	gTt	gGt	1884	1884	All	0.00036
S	3	V3G	gTt	gGt	459	459	B.1.1.241	0.950311
S	3	V3V	gtT	gtC	259	457	All	0.00005
S	3	V3V	gtT	gtG	187	457	All	0.000036
S	3	V3V	gtT	gtA	11	457	All	0.000002
S	3	V3G	gTt	gGt	249	249	B.1.1.7	0.000223
S	3	V3G	gTt	gGt	248	248	AH.3	0.942966
S	3	V3V	gtT	gtC	220	229	B.1.1.7	0.000197
S	3	V3V	gtT	gtG	7	229	B.1.1.7	0.000006
S	3	V3V	gtT	gtA	2	229	B.1.1.7	0.000002
S	3	V3I	Gtt	Att	213	213	All	0.000041
S	3	V3G	gTt	gGt	158	158	B.1.617.1	0.020377
S	3	V3F	Gtt	Ttt	137	137	All	0.000026
S	3	V3A	gTt	gCt	105	107	All	0.00002
S	3	V3A	gTT	gCC	1	107	All	0
S	3	V3A	gTT	gCA	1	107	All	0
S	3	V3V	gtT	gtG	98	98	B.1.1.70	0.033424
S	3	V3G	gTt	gGt	81	81	AY.4	0.000126
S	3	V3G	gTt	gGt	79	79	AH.2	0.951807
S	3	V3G	gTt	gGt	70	70	B.1.1.519	0.00278
S	3	V3I	Gtt	Att	68	68	AY.4	0.000106
S	3	V3G	gTt	gGt	62	62	AY.43	0.000275
S	3	V3G	gTt	gGt	55	55	B.1	0.000504
S	3	V3del	GTT	---	52	52	All	0.00001
S	3	V3I	Gtt	Att	44	44	B.1.1.7	0.000039
S	3	V3G	gTt	gGt	40	40	B.1.2	0.000352
S	3	V3V	gtT	gtG	40	40	B.1.526	0.00094
S	3	V3A	gTt	gCt	38	38	AY.43	0.000168
S	3	V3A	gTt	gCt	35	35	B.1.617.2	0.000132
S	3	V3G	gTt	gGt	31	31	B.1.617.2	0.000117
S	3	V3G	gTt	gGt	27	27	AY.103	0.000168
S	3	V3del1	gTt	g-t	24	26	All	0.000005
S	3	V3del1	Gtt	-tt	2	26	All	0
S	3	V3G	gTt	gGt	26	26	B.1.526	0.000611
S	3	V3G	gTt	gGt	22	22	B.1.177	0.00029
S	3	V3G	gTt	gGt	21	21	B.1.1	0.000381
S	3	V3F	Gtt	Ttt	21	21	B.1.617.2	0.000079
S	3	V3G	gTt	gGt	20	20	AY.25	0.00012
S	3	V3G	gTt	gGt	20	20	AY.29	0.000315
S	3	V3F	Gtt	Ttt	18	18	B.1.1.7	0.000016
S	3	V3I	Gtt	Att	17	17	P.1	0.000268
S	3	V3F	Gtt	Ttt	16	16	AY.4	0.000025
S	3	V3G	gTt	gGt	11	11	AY.44	0.000067
S	3	V3V	gtT	gtG	9	10	AY.25	0.000054
S	3	V3V	gtT	gtC	1	10	AY.25	0.000006
S	3	V3G	gTt	gGt	10	10	AY.3	0.000099
S	3	V3G	gTt	gGt	10	10	AY.59	0.005297
S	3	V3L	Gtt	Ctt	6	9	All	0.000001
S	3	V3L	GtT	TtA	3	9	All	0.000001
S	3	V3F	Gtt	Ttt	9	9	AY.43	0.00004
S	3	V3G	gTt	gGt	9	9	B.1.1.239	0.290323
S	3	V3G	gTt	gGt	9	9	B.1.351	0.000268
S	3	V3C	GTt	TGt	8	8	All	0.000002
S	3	V3G	gTt	gGt	8	8	B.1.596	0.000697
S	3	V3G	gTt	gGt	7	7	AH.1	1
S	3	V3I	Gtt	Att	7	7	AY.103	0.000043
S	3	V3G	gTt	gGt	7	7	AY.27	0.000453
S	3	V3I	Gtt	Att	7	7	AY.44	0.000043
S	3	V3V	gtT	gtG	6	7	B.1.2	0.000053
S	3	V3V	gtT	gtC	1	7	B.1.2	0.000009
S	3	V3I	Gtt	Att	7	7	B.1.617.2	0.000026
S	3	V3Y	GTt	TAt	6	6	All	0.000001
S	3	V3V	gtT	gtG	5	6	AY.29	0.000079
S	3	V3V	gtT	gtC	1	6	AY.29	0.000016
S	3	V3del	GTT	---	6	6	AY.33	0.000401
S	3	V3V	gtT	gtG	4	6	B.1	0.000037
S	3	V3V	gtT	gtC	2	6	B.1	0.000018
S	3	V3G	gTt	gGt	6	6	B.1.160	0.000187
S	3	V3I	Gtt	Att	6	6	B.1.177.82	0.002864
S	3	V3F	Gtt	Ttt	6	6	B.1.2	0.000053
S	3	V3G	gTt	gGt	6	6	B.1.258	0.000399
S	3	V3G	gTt	gGt	6	6	P.1	0.000095
S	3	V3A	gTt	gCt	6	6	P.1.17.1	0.005249
S	3	V3G	gTt	gGt	6	6	Q.8	0.000989
S	3	V3D	gTt	gAt	5	5	All	0.000001
S	3	V3del2	gTT	g--	4	5	All	0.000001
S	3	V3del2	GTt	--t	1	5	All	0
S	3	V3F	Gtt	Ttt	5	5	AY.25	0.00003
S	3	V3I	Gtt	Att	5	5	AY.3	0.00005
S	3	V3I	Gtt	Att	5	5	AY.30	0.001979
S	3	V3G	gTt	gGt	5	5	AY.48	0.002326
S	3	V3F	Gtt	Ttt	5	5	AY.66	0.005348
S	3	V3F	Gtt	Ttt	5	5	AY.75	0.00028
S	3	V3G	gTt	gGt	5	5	B.1.1.274	0.025253
S	3	V3V	gtT	gtC	3	5	B.1.617.2	0.000011
S	3	V3V	gtT	gtG	2	5	B.1.617.2	0.000008
S	3	V3G	gTt	gGt	4	4	AY.54	0.000381
S	3	V3V	gtT	gtC	3	4	B.1.1	0.000054
S	3	V3V	gtT	gtG	1	4	B.1.1	0.000018
S	3	V3A	gTt	gCt	4	4	B.1.1.7	0.000004
S	3	V3I	Gtt	Att	4	4	B.1.427	0.000202
S	3	V3G	gTt	gGt	4	4	B.1.429	0.000094
S	3	V3del	GTT	---	4	4	B.1.526	0.000094
S	3	V3del	GTT	---	4	4	B.1.617.2	0.000015
S	3	V3V	gtT	gtC	4	4	C.37	0.000464
S	3	V3E	gTT	gAA	3	3	All	0.000001
S	3	V3I	Gtt	Att	3	3	AY.29	0.000047
S	3	V3V	gtT	gtG	2	3	AY.3	0.00002
S	3	V3V	gtT	gtC	1	3	AY.3	0.00001
S	3	V3I	Gtt	Att	3	3	AY.33	0.0002
S	3	V3V	gtT	gtC	2	3	AY.4	0.000003
S	3	V3V	gtT	gtA	1	3	AY.4	0.000002
S	3	V3del1	gTt	g-t	2	3	AY.43	0.000009
S	3	V3del1	Gtt	-tt	1	3	AY.43	0.000004
S	3	V3V	gtT	gtG	3	3	AY.44	0.000018
S	3	V3G	gTt	gGt	3	3	AY.45	0.000365
S	3	V3F	Gtt	Ttt	3	3	AY.45	0.000365
S	3	V3V	gtT	gtC	3	3	AY.46.6	0.000217
S	3	V3G	gTt	gGt	3	3	AY.72	0.004082
S	3	V3del	GTT	---	3	3	B.1	0.000027
S	3	V3F	Gtt	Ttt	3	3	B.1	0.000027
S	3	V3I	Gtt	Att	3	3	B.1.1	0.000054
S	3	V3del	GTT	---	3	3	B.1.1	0.000054
S	3	V3G	gTt	gGt	3	3	B.1.1.222	0.000612
S	3	V3del	GTT	---	3	3	B.1.1.7	0.000003
S	3	V3G	gTt	gGt	3	3	B.1.177.21	0.000229
S	3	V3G	gTt	gGt	3	3	B.1.177.73	0.001699
S	3	V3G	gTt	gGt	3	3	B.1.36.38	0.004926
S	3	V3I	Gtt	Att	3	3	B.1.525	0.000339
S	3	V3G	gTt	gGt	3	3	B.1.609	0.001438
S	3	V3del	GTT	---	3	3	P.1	0.000047
S	3	V3V	gtT	gtC	3	3	P.1	0.000047
S	3	V3V	gtT	gtA	2	2		0.111111
S	3	V3X	GTT	TAA	2	2		0.111111
S	3	V3Y	GTt	TAt	2	2		0.111111
S	3	V3del1	gTt	g-t	2	2		0.111111
S	3	V3D	gTt	gAt	2	2		0.111111
S	3	V3F	Gtt	Ttt	2	2		0.111111
S	3	V3L	GtT	TtA	2	2		0.111111
S	3	V3E	gTT	gAA	2	2		0.111111
S	3	V3G	gTt	gGt	2	2	A.1	0.000564
S	3	V3X	GTT	TAA	2	2	All	0
S	3	V3G	gTt	gGt	2	2	AY.100	0.000092
S	3	V3F	Gtt	Ttt	2	2	AY.103	0.000012
S	3	V3V	gtT	gtA	1	2	AY.103	0.000006
S	3	V3V	gtT	gtC	1	2	AY.103	0.000006
S	3	V3G	gTt	gGt	2	2	AY.110	0.000225
S	3	V3F	Gtt	Ttt	2	2	AY.113	0.000285
S	3	V3I	Gtt	Att	2	2	AY.118	0.000125
S	3	V3F	Gtt	Ttt	2	2	AY.118	0.000125
S	3	V3G	gTt	gGt	2	2	AY.119	0.000071
S	3	V3A	gTt	gCt	2	2	AY.23	0.000139
S	3	V3del	GTT	---	2	2	AY.25	0.000012
S	3	V3G	gTt	gGt	2	2	AY.26	0.000057
S	3	V3I	Gtt	Att	2	2	AY.3.1	0.000171
S	3	V3A	gTt	gCt	2	2	AY.36	0.000296
S	3	V3G	gTt	gGt	2	2	AY.39.1	0.000079
S	3	V3I	Gtt	Att	2	2	AY.4.2	0.000043
S	3	V3del	GTT	---	2	2	AY.43	0.000009
S	3	V3A	gTt	gCt	2	2	AY.44	0.000012
S	3	V3del1	gTt	g-t	2	2	AY.44	0.000012
S	3	V3G	gTt	gGt	2	2	AY.5	0.000041
S	3	V3G	gTt	gGt	2	2	AY.5.3	0.000675
S	3	V3G	gTt	gGt	2	2	AY.5.4	0.000553
S	3	V3F	Gtt	Ttt	2	2	AY.9.2	0.000073
S	3	V3I	Gtt	Att	2	2	B.1	0.000018
S	3	V3del2	gTT	g--	2	2	B.1	0.000018
S	3	V3L	Gtt	Ctt	2	2	B.1.1	0.000036
S	3	V3G	gTt	gGt	2	2	B.1.1.294	0.002532
S	3	V3C	GTt	TGt	2	2	B.1.1.33	0.000842
S	3	V3G	gTt	gGt	2	2	B.1.1.406	0.012987
S	3	V3V	gtT	gtC	2	2	B.1.1.46	0.008734
S	3	V3V	gtT	gtA	2	2	B.1.1.519	0.000079
S	3	V3del1	gTt	g-t	2	2	B.1.1.7	0.000002
S	3	V3V	gtT	gtG	1	2	B.1.160	0.000031
S	3	V3V	gtT	gtC	1	2	B.1.160	0.000031
S	3	V3V	gtT	gtG	2	2	B.1.177	0.000026
S	3	V3I	Gtt	Att	2	2	B.1.177	0.000026
S	3	V3del1	gTt	g-t	2	2	B.1.2	0.000018
S	3	V3A	gTt	gCt	2	2	B.1.2	0.000018
S	3	V3del	GTT	---	2	2	B.1.2	0.000018
S	3	V3V	gtT	gtC	2	2	B.1.243	0.000139
S	3	V3G	gTt	gGt	2	2	B.1.427	0.000101
S	3	V3G	gTt	gGt	2	2	B.1.459	0.008163
S	3	V3del	GTT	---	2	2	B.1.525	0.000226
S	3	V3F	Gtt	Ttt	2	2	B.1.526	0.000047
S	3	V3F	Gtt	Ttt	2	2	B.1.575	0.000607
S	3	V3del1	gTt	g-t	2	2	B.1.627	0.00404
S	3	V3G	gTt	gGt	2	2	D.2	0.00015
S	3	V3G	gTt	gGt	2	2	N.5	0.003534
S	3	V3del1	gTt	g-t	2	2	P.1	0.000032
S	3	V3A	gTt	gCt	2	2	P.1	0.000032
S	3	V3C	GTt	TGt	2	2	P.2	0.000373
S	3	V3V	gtT	gtG	1	1	A.2	0.000662
S	3	V3V	gtT	gtG	1	1	A.2.2	0.001689
S	3	V3del	GTT	---	1	1	A.2.4	0.003367
S	3	V3V	gtT	gtC	1	1	A.5	0.001923
S	3	V3H	GTt	CAt	1	1	All	0
S	3	V3S	GTt	AGt	1	1	All	0
S	3	V3R	GTt	CGt	1	1	All	0
S	3	V3A	gTt	gCt	1	1	AY.1	0.000396
S	3	V3del	GTT	---	1	1	AY.100	0.000046
S	3	V3G	gTt	gGt	1	1	AY.102	0.000027
S	3	V3del	GTT	---	1	1	AY.103	0.000006
S	3	V3I	Gtt	Att	1	1	AY.105	0.000643
S	3	V3G	gTt	gGt	1	1	AY.113	0.000142
S	3	V3G	gTt	gGt	1	1	AY.116	0.000287
S	3	V3G	gTt	gGt	1	1	AY.117	0.000085
S	3	V3G	gTt	gGt	1	1	AY.118	0.000063
S	3	V3F	Gtt	Ttt	1	1	AY.119	0.000035
S	3	V3I	Gtt	Att	1	1	AY.119	0.000035
S	3	V3F	Gtt	Ttt	1	1	AY.120	0.000037
S	3	V3G	gTt	gGt	1	1	AY.120	0.000037
S	3	V3V	gtT	gtC	1	1	AY.121	0.000135
S	3	V3G	gTt	gGt	1	1	AY.16	0.00038
S	3	V3G	gTt	gGt	1	1	AY.16.1	0.00047
S	3	V3V	gtT	gtG	1	1	AY.23	0.00007
S	3	V3I	Gtt	Att	1	1	AY.23	0.00007
S	3	V3I	Gtt	Att	1	1	AY.23.1	0.000417
S	3	V3I	Gtt	Att	1	1	AY.26	0.000028
S	3	V3F	Gtt	Ttt	1	1	AY.26	0.000028
S	3	V3F	Gtt	Ttt	1	1	AY.3	0.00001
S	3	V3Y	GTt	TAt	1	1	AY.34	0.000097
S	3	V3C	GTt	TGt	1	1	AY.36	0.000148
S	3	V3G	gTt	gGt	1	1	AY.37	0.000316
S	3	V3D	gTt	gAt	1	1	AY.4	0.000002
S	3	V3V	gtT	gtG	1	1	AY.4.2	0.000022
S	3	V3G	gTt	gGt	1	1	AY.4.2	0.000022
S	3	V3V	gtT	gtA	1	1	AY.4.2.1	0.000149
S	3	V3del	GTT	---	1	1	AY.4.3	0.000842
S	3	V3del	GTT	---	1	1	AY.42	0.00004
S	3	V3I	Gtt	Att	1	1	AY.43	0.000004
S	3	V3Y	GTt	TAt	1	1	AY.43	0.000004
S	3	V3A	gTt	gCt	1	1	AY.46.2	0.000635
S	3	V3F	Gtt	Ttt	1	1	AY.46.4	0.000165
S	3	V3G	gTt	gGt	1	1	AY.47	0.000031
S	3	V3A	gTt	gCt	1	1	AY.47	0.000031
S	3	V3I	Gtt	Att	1	1	AY.47	0.000031
S	3	V3F	Gtt	Ttt	1	1	AY.5	0.000021
S	3	V3V	gtT	gtC	1	1	AY.5	0.000021
S	3	V3V	gtT	gtA	1	1	AY.5.3	0.000337
S	3	V3F	Gtt	Ttt	1	1	AY.54	0.000095
S	3	V3del	GTT	---	1	1	AY.54	0.000095
S	3	V3I	Gtt	Att	1	1	AY.57	0.000656
S	3	V3G	gTt	gGt	1	1	AY.60	0.000938
S	3	V3G	gTt	gGt	1	1	AY.61	0.000105
S	3	V3del1	gTt	g-t	1	1	AY.63	0.000387
S	3	V3I	Gtt	Att	1	1	AY.66	0.00107
S	3	V3del	GTT	---	1	1	AY.68	0.000274
S	3	V3V	gtT	gtA	1	1	AY.69	0.000187
S	3	V3G	gTt	gGt	1	1	AY.75	0.000056
S	3	V3A	gTt	gCt	1	1	AY.77	0.001127
S	3	V3F	Gtt	Ttt	1	1	AY.85	0.000427
S	3	V3G	gTt	gGt	1	1	AY.9.2	0.000037
S	3	V3A	gTt	gCt	1	1	AY.9.2.1	0.001976
S	3	V3del	GTT	---	1	1	AY.98	0.000079
S	3	V3F	Gtt	Ttt	1	1	AY.98	0.000079
S	3	V3A	gTt	gCt	1	1	AY.98.1	0.000048
S	3	V3G	gTt	gGt	1	1	AY.98.1	0.000048
S	3	V3I	Gtt	Att	1	1	AY.98.1	0.000048
S	3	V3L	Gtt	Ctt	1	1	AY.98.1	0.000048
S	3	V3F	Gtt	Ttt	1	1	AY.98.1	0.000048
S	3	V3I	Gtt	Att	1	1	AY.99.2	0.000092
S	3	V3G	gTt	gGt	1	1	AY.99.2	0.000092
S	3	V3I	Gtt	Att	1	1	B	0.000128
S	3	V3del1	gTt	g-t	1	1	B.1	0.000009
S	3	V3D	gTt	gAt	1	1	B.1.1	0.000018
S	3	V3del2	gTT	g--	1	1	B.1.1	0.000018
S	3	V3A	gTt	gCt	1	1	B.1.1	0.000018
S	3	V3F	Gtt	Ttt	1	1	B.1.1	0.000018
S	3	V3F	Gtt	Ttt	1	1	B.1.1.1	0.000327
S	3	V3del1	gTt	g-t	1	1	B.1.1.170	0.001247
S	3	V3del1	gTt	g-t	1	1	B.1.1.210	0.005714
S	3	V3V	gtT	gtC	1	1	B.1.1.214	0.000055
S	3	V3G	gTt	gGt	1	1	B.1.1.214	0.000055
S	3	V3G	gTt	gGt	1	1	B.1.1.243	0.004082
S	3	V3G	gTt	gGt	1	1	B.1.1.253	0.002506
S	3	V3G	gTt	gGt	1	1	B.1.1.273	0.006757
S	3	V3C	GTt	TGt	1	1	B.1.1.28	0.000311
S	3	V3G	gTt	gGt	1	1	B.1.1.28	0.000311
S	3	V3V	gtT	gtC	1	1	B.1.1.306	0.000438
S	3	V3G	gTt	gGt	1	1	B.1.1.311	0.000358
S	3	V3del	GTT	---	1	1	B.1.1.315	0.008475
S	3	V3V	gtT	gtC	1	1	B.1.1.317	0.000412
S	3	V3G	gTt	gGt	1	1	B.1.1.401	0.066667
S	3	V3I	Gtt	Att	1	1	B.1.1.411	0.014706
S	3	V3del	GTT	---	1	1	B.1.1.46	0.004367
S	3	V3del1	gTt	g-t	1	1	B.1.1.486	0.001577
S	3	V3A	gTt	gCt	1	1	B.1.1.519	0.00004
S	3	V3del1	gTt	g-t	1	1	B.1.1.519	0.00004
S	3	V3E	gTT	gAA	1	1	B.1.1.7	0.000001
S	3	V3del2	GTt	--t	1	1	B.1.1.7	0.000001
S	3	V3F	Gtt	Ttt	1	1	B.1.111	0.001175
S	3	V3G	gTt	gGt	1	1	B.1.131	0.008772
S	3	V3F	Gtt	Ttt	1	1	B.1.160	0.000031
S	3	V3H	GTt	CAt	1	1	B.1.160	0.000031
S	3	V3A	gTt	gCt	1	1	B.1.160	0.000031
S	3	V3Y	GTt	TAt	1	1	B.1.160	0.000031
S	3	V3D	gTt	gAt	1	1	B.1.160	0.000031
S	3	V3L	Gtt	Ctt	1	1	B.1.160	0.000031
S	3	V3C	GTt	TGt	1	1	B.1.160	0.000031
S	3	V3I	Gtt	Att	1	1	B.1.160	0.000031
S	3	V3R	GTt	CGt	1	1	B.1.160	0.000031
S	3	V3V	gtT	gtG	1	1	B.1.160.29	0.004219
S	3	V3F	Gtt	Ttt	1	1	B.1.160.9	0.007194
S	3	V3F	Gtt	Ttt	1	1	B.1.177	0.000013
S	3	V3F	Gtt	Ttt	1	1	B.1.177.44	0.000519
S	3	V3A	gTt	gCt	1	1	B.1.177.46	0.000918
S	3	V3G	gTt	gGt	1	1	B.1.177.54	0.000606
S	3	V3G	gTt	gGt	1	1	B.1.177.60	0.000218
S	3	V3F	Gtt	Ttt	1	1	B.1.177.65	0.000665
S	3	V3del	GTT	---	1	1	B.1.177.68	0.015152
S	3	V3A	gTt	gCt	1	1	B.1.177.7	0.000165
S	3	V3G	gTt	gGt	1	1	B.1.177.77	0.000726
S	3	V3del	GTT	---	1	1	B.1.177.83	0.001481
S	3	V3G	gTt	gGt	1	1	B.1.177.87	0.000728
S	3	V3del2	gTT	g--	1	1	B.1.2	0.000009
S	3	V3G	gTt	gGt	1	1	B.1.221	0.000071
S	3	V3del1	gTt	g-t	1	1	B.1.234	0.000132
S	3	V3G	gTt	gGt	1	1	B.1.240	0.000216
S	3	V3F	Gtt	Ttt	1	1	B.1.240	0.000216
S	3	V3G	gTt	gGt	1	1	B.1.243	0.00007
S	3	V3del1	gTt	g-t	1	1	B.1.258	0.000067
S	3	V3F	Gtt	Ttt	1	1	B.1.258.11	0.000396
S	3	V3del	GTT	---	1	1	B.1.258.16	0.001637
S	3	V3F	Gtt	Ttt	1	1	B.1.265	0.001271
S	3	V3I	Gtt	Att	1	1	B.1.279	0.000514
S	3	V3del1	Gtt	-tt	1	1	B.1.289	0.00266
S	3	V3F	Gtt	Ttt	1	1	B.1.3	0.002618
S	3	V3I	Gtt	Att	1	1	B.1.332	0.003497
S	3	V3del1	gTt	g-t	1	1	B.1.351	0.00003
S	3	V3G	gTt	gGt	1	1	B.1.351.3	0.000876
S	3	V3A	gTt	gCt	1	1	B.1.36	0.000146
S	3	V3F	Gtt	Ttt	1	1	B.1.36.16	0.001425
S	3	V3F	Gtt	Ttt	1	1	B.1.36.28	0.005747
S	3	V3F	Gtt	Ttt	1	1	B.1.36.29	0.000517
S	3	V3G	gTt	gGt	1	1	B.1.36.31	0.001751
S	3	V3G	gTt	gGt	1	1	B.1.36.8	0.001
S	3	V3F	Gtt	Ttt	1	1	B.1.369	0.000285
S	3	V3G	gTt	gGt	1	1	B.1.416.1	0.001563
S	3	V3V	gtT	gtC	1	1	B.1.427	0.00005
S	3	V3G	gTt	gGt	1	1	B.1.428	0.00102
S	3	V3F	Gtt	Ttt	1	1	B.1.429	0.000024
S	3	V3L	Gtt	Ctt	1	1	B.1.429	0.000024
S	3	V3del	GTT	---	1	1	B.1.453	0.003236
S	3	V3G	gTt	gGt	1	1	B.1.468	0.005714
S	3	V3G	gTt	gGt	1	1	B.1.470	0.001404
S	3	V3F	Gtt	Ttt	1	1	B.1.471	0.002732
S	3	V3G	gTt	gGt	1	1	B.1.515	0.014493
S	3	V3G	gTt	gGt	1	1	B.1.517	0.000427
S	3	V3G	gTt	gGt	1	1	B.1.528	0.047619
S	3	V3V	gtT	gtG	1	1	B.1.561	0.000397
S	3	V3I	Gtt	Att	1	1	B.1.565	0.00081
S	3	V3G	gTt	gGt	1	1	B.1.575	0.000303
S	3	V3F	Gtt	Ttt	1	1	B.1.596	0.000087
S	3	V3V	gtT	gtG	1	1	B.1.609	0.000479
S	3	V3Y	GTt	TAt	1	1	B.1.617.2	0.000004
S	3	V3del1	gTt	g-t	1	1	B.1.617.2	0.000004
S	3	V3A	gTT	gCC	1	1	B.1.617.3	0.002985
S	3	V3del	GTT	---	1	1	B.1.620	0.000946
S	3	V3G	gTt	gGt	1	1	B.1.623	0.000536
S	3	V3G	gTt	gGt	1	1	B.1.637	0.000073
S	3	V3V	gtT	gtC	1	1	B.40	0.000364
S	3	V3G	gTt	gGt	1	1	B.6	0.00091
S	3	V3G	gTt	gGt	1	1	C.1.2	0.004255
S	3	V3G	gTt	gGt	1	1	C.37	0.000116
S	3	V3G	gTt	gGt	1	1	N.4	0.004255
S	3	V3C	GTt	TGt	1	1	P.1	0.000016
S	3	V3F	Gtt	Ttt	1	1	P.1	0.000016
S	3	V3L	GtT	TtA	1	1	P.1	0.000016
S	3	V3del	GTT	---	1	1	P.1.1	0.000318
S	3	V3del	GTT	---	1	1	P.1.10	0.000269
S	3	V3F	Gtt	Ttt	1	1	P.1.10	0.000269
S	3	V3G	gTt	gGt	1	1	P.1.13	0.000898
S	3	V3A	gTT	gCA	1	1	P.1.14	0.000048
S	3	V3I	Gtt	Att	1	1	P.1.16	0.000374
S	3	V3G	gTt	gGt	1	1	P.1.16	0.000374
S	3	V3F	Gtt	Ttt	1	1	P.1.17	0.000162
S	3	V3L	Gtt	Ctt	1	1	P.1.2	0.001156
S	3	V3I	Gtt	Att	1	1	P.2	0.000187
S	3	V3G	gTt	gGt	1	1	P.2	0.000187
S	3	V3S	GTt	AGt	1	1	P.2	0.000187
S	3	V3V	gtT	gtC	1	1	Q.1	0.000126
S	3	V3I	Gtt	Att	1	1	Q.7	0.001111
S	3	V3I	Gtt	Att	1	1	Q.8	0.000165
S	3	V3del	GTT	---	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.