CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 70

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	70	V70L		nonsyn	Gtt	Ctt	19660	19656	0.999797	26730-26732
M	70	V70L		nonsyn	GtT	CtG	19660	2	0.000101729	26730-26732
M	70	V70L		nonsyn	GtT	CtC	19660	2	0.000101729	26730-26732
M	70	V70F		nonsyn	Gtt	Ttt	4425	4425	1	26730-26732
M	70	V70V		syn	gtT	gtC	1102	1091	0.990018	26730-26732
M	70	V70V		syn	gtT	gtG	1102	9	0.00816697	26730-26732
M	70	V70V		syn	gtT	gtA	1102	2	0.00181488	26730-26732
M	70	V70I		nonsyn	Gtt	Att	933	930	0.996785	26730-26732
M	70	V70I		nonsyn	GtT	AtC	933	2	0.00214362	26730-26732
M	70	V70I		nonsyn	GtT	AtA	933	1	0.00107181	26730-26732
M	70	V70A		nonsyn	gTt	gCt	200	196	0.98	26730-26732
M	70	V70A		nonsyn	gTT	gCC	200	2	0.01	26730-26732
M	70	V70A		nonsyn	gTT	gCG	200	2	0.01	26730-26732
M	70	V70del		del	GTT	---	71	71	1	26730-26732
M	70	V70T		nonsyn	GTt	ACt	8	3	0.375	26730-26732
M	70	V70T		nonsyn	GTT	ACC	8	2	0.25	26730-26732
M	70	V70T		nonsyn	GTT	ACG	8	2	0.25	26730-26732
M	70	V70T		nonsyn	GTT	ACA	8	1	0.125	26730-26732
M	70	V70P		nonsyn	GTT	CCC	6	2	0.333333	26730-26732
M	70	V70P		nonsyn	GTT	CCG	6	2	0.333333	26730-26732
M	70	V70P		nonsyn	GTt	CCt	6	2	0.333333	26730-26732
M	70	V70D		nonsyn	gTt	gAt	5	3	0.6	26730-26732
M	70	V70D		nonsyn	gTT	gAC	5	2	0.4	26730-26732
M	70	V70H		nonsyn	GTt	CAt	4	2	0.5	26730-26732
M	70	V70H		nonsyn	GTT	CAC	4	2	0.5	26730-26732
M	70	V70N		nonsyn	GTt	AAt	4	2	0.5	26730-26732
M	70	V70N		nonsyn	GTT	AAC	4	2	0.5	26730-26732
M	70	V70del1		del	Gtt	-tt	3	3	1	26730-26732
M	70	V70G		nonsyn	gTt	gGt	3	3	1	26730-26732
M	70	V70E		nonsyn	gTT	gAG	2	2	1	26730-26732
M	70	V70Q		nonsyn	GTT	CAG	2	2	1	26730-26732
M	70	V70M		nonsyn	GtT	AtG	2	2	1	26730-26732
M	70	V70K		nonsyn	GTT	AAG	2	2	1	26730-26732
M	70	V70del2		del	gTT	g--	1	1	1	26730-26732

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	70	V70L	Gtt	Ctt	19656	19660	All	0.003759
M	70	V70L	GtT	CtG	2	19660	All	0
M	70	V70L	GtT	CtC	2	19660	All	0
M	70	V70L	Gtt	Ctt	12256	12256	B.1.1.7	0.010972
M	70	V70L	Gtt	Ctt	6873	6873	Q.3	0.996809
M	70	V70F	Gtt	Ttt	4425	4425	All	0.000846
M	70	V70V	gtT	gtC	1091	1102	All	0.000209
M	70	V70V	gtT	gtG	9	1102	All	0.000002
M	70	V70V	gtT	gtA	2	1102	All	0
M	70	V70I	Gtt	Att	930	933	All	0.000178
M	70	V70I	GtT	AtC	2	933	All	0
M	70	V70I	GtT	AtA	1	933	All	0
M	70	V70F	Gtt	Ttt	838	838	B.1.1.207	0.990544
M	70	V70V	gtT	gtC	811	811	AY.98	0.064065
M	70	V70F	Gtt	Ttt	591	591	AY.4	0.00092
M	70	V70F	Gtt	Ttt	403	403	B.1.1.7	0.000361
M	70	V70F	Gtt	Ttt	369	369	B.1.1	0.006694
M	70	V70I	Gtt	Att	348	348	B.1.1.48	1
M	70	V70F	Gtt	Ttt	265	265	B.1.617.2	0.000998
M	70	V70A	gTt	gCt	196	200	All	0.000037
M	70	V70A	gTT	gCC	2	200	All	0
M	70	V70A	gTT	gCG	2	200	All	0
M	70	V70F	Gtt	Ttt	131	131	B.1	0.0012
M	70	V70V	gtT	gtC	112	112	B.1.2	0.000986
M	70	V70L	Gtt	Ctt	105	105	AY.118	0.006578
M	70	V70I	Gtt	Att	94	94	AY.44	0.000572
M	70	V70F	Gtt	Ttt	89	89	B.1.1.344	0.956989
M	70	V70F	Gtt	Ttt	87	87	R.1	0.007831
M	70	V70F	Gtt	Ttt	84	84	AY.25	0.000505
M	70	V70F	Gtt	Ttt	81	81	AY.3	0.000806
M	70	V70F	Gtt	Ttt	79	79	AY.43	0.00035
M	70	V70L	Gtt	Ctt	73	73	B.1.1	0.001324
M	70	V70I	Gtt	Att	72	72	B.1.1.7	0.000064
M	70	V70del	GTT	---	71	71	All	0.000014
M	70	V70F	Gtt	Ttt	69	69	P.1	0.001087
M	70	V70F	Gtt	Ttt	67	67	AY.100	0.003082
M	70	V70F	Gtt	Ttt	67	67	AY.103	0.000416
M	70	V70F	Gtt	Ttt	66	66	B.1.2	0.000581
M	70	V70F	Gtt	Ttt	59	59	B.1.177	0.000777
M	70	V70F	Gtt	Ttt	58	58	AY.44	0.000353
M	70	V70I	Gtt	Att	57	57	B.1.1	0.001034
M	70	V70A	gTt	gCt	56	56	AY.119	0.001977
M	70	V70del	GTT	---	49	49	B.1.177.21	0.003747
M	70	V70F	Gtt	Ttt	46	46	B.1.1.63	0.017747
M	70	V70I	Gtt	Att	46	46	B.1.36.36	0.027694
M	70	V70F	Gtt	Ttt	44	44	AY.42	0.00177
M	70	V70F	Gtt	Ttt	44	44	B.1.1.519	0.001747
M	70	V70L	Gtt	Ctt	44	44	B.1.596	0.003834
M	70	V70L	Gtt	Ctt	41	41	B.1.2	0.000361
M	70	V70F	Gtt	Ttt	39	39	B.1.617.1	0.00503
M	70	V70I	Gtt	Att	38	38	AY.103	0.000236
M	70	V70V	gtT	gtC	38	38	B.1.617.2	0.000143
M	70	V70F	Gtt	Ttt	37	37	AY.27	0.002395
M	70	V70L	Gtt	Ctt	34	34	B.1.617.2	0.000128
M	70	V70I	Gtt	Att	33	33	B.1.177.81	0.006248
M	70	V70A	gTt	gCt	30	30	B.1.1.7	0.000027
M	70	V70A	gTt	gCt	30	30	B.1.429	0.000706
M	70	V70L	Gtt	Ctt	28	28	B.1.1.326	0.049296
M	70	V70F	Gtt	Ttt	27	27	AY.4.2	0.000586
M	70	V70F	Gtt	Ttt	26	26	B.1.596	0.002266
M	70	V70F	Gtt	Ttt	25	25	AY.119	0.000883
M	70	V70V	gtT	gtC	24	24	AY.102	0.000636
M	70	V70F	Gtt	Ttt	24	24	B.1.160	0.000749
M	70	V70F	Gtt	Ttt	23	23	B.1.177.77	0.016703
M	70	V70F	Gtt	Ttt	22	22	AY.39	0.000544
M	70	V70L	Gtt	Ctt	22	22	AY.4	0.000034
M	70	V70I	Gtt	Att	21	21	A.1	0.005919
M	70	V70L	Gtt	Ctt	21	21	B.1	0.000192
M	70	V70L	Gtt	Ctt	21	21	Q.8	0.003463
M	70	V70F	Gtt	Ttt	19	19	AY.102	0.000504
M	70	V70F	Gtt	Ttt	19	19	AY.61	0.001991
M	70	V70F	Gtt	Ttt	18	18	AY.29	0.000284
M	70	V70F	Gtt	Ttt	18	18	AY.98.1	0.000872
M	70	V70F	Gtt	Ttt	18	18	B.1.258	0.001198
M	70	V70I	Gtt	Att	17	17	AY.119	0.0006
M	70	V70I	Gtt	Att	17	17	B.1.617.2	0.000064
M	70	V70V	gtT	gtC	16	16	B.1.1.7	0.000014
M	70	V70I	Gtt	Att	16	16	B.1.2	0.000141
M	70	V70I	Gtt	Att	15	15	AY.3	0.000149
M	70	V70I	Gtt	Att	15	15	AY.4	0.000023
M	70	V70F	Gtt	Ttt	14	14	AY.20	0.000544
M	70	V70F	Gtt	Ttt	14	14	B.1.279	0.007191
M	70	V70F	Gtt	Ttt	13	13	AY.14	0.001144
M	70	V70L	Gtt	Ctt	13	13	AY.29	0.000205
M	70	V70V	gtT	gtC	13	13	AY.43	0.000058
M	70	V70F	Gtt	Ttt	13	13	B.1.1.189	0.019667
M	70	V70L	Gtt	Ctt	13	13	C.36	0.01184
M	70	V70L	Gtt	Ctt	12	12	B.1.177	0.000158
M	70	V70V	gtT	gtC	11	11	AY.4	0.000017
M	70	V70F	Gtt	Ttt	11	11	B.1.1.311	0.00394
M	70	V70F	Gtt	Ttt	11	11	P.1.14	0.000526
M	70	V70del	GTT	---	10	10	B.1.1.7	0.000009
M	70	V70F	Gtt	Ttt	10	10	B.1.526	0.000235
M	70	V70V	gtT	gtC	10	10	C.14	0.04329
M	70	V70L	Gtt	Ctt	9	9	AY.113	0.001282
M	70	V70F	Gtt	Ttt	9	9	AY.113	0.001282
M	70	V70F	Gtt	Ttt	9	9	AY.121	0.001218
M	70	V70F	Gtt	Ttt	9	9	AY.23	0.000628
M	70	V70L	Gtt	Ctt	9	9	B.1.1.275	0.101124
M	70	V70F	Gtt	Ttt	9	9	B.1.258.17	0.000936
M	70	V70F	Gtt	Ttt	9	9	B.1.497	0.002833
M	70	V70F	Gtt	Ttt	9	9	P.1.15	0.002091
M	70	V70F	Gtt	Ttt	9	9	V.2	0.290323
M	70	V70T	GTt	ACt	3	8	All	0.000001
M	70	V70T	GTT	ACG	2	8	All	0
M	70	V70T	GTT	ACC	2	8	All	0
M	70	V70T	GTT	ACA	1	8	All	0
M	70	V70F	Gtt	Ttt	8	8	AY.26	0.000226
M	70	V70F	Gtt	Ttt	8	8	AY.33	0.000534
M	70	V70I	Gtt	Att	8	8	AY.43	0.000035
M	70	V70F	Gtt	Ttt	8	8	AY.47	0.000249
M	70	V70F	Gtt	Ttt	8	8	B.1.1.348	0.006369
M	70	V70I	Gtt	Att	8	8	B.1.177.60	0.001747
M	70	V70A	gTt	gCt	8	8	B.1.2	0.00007
M	70	V70I	Gtt	Att	8	8	B.1.258	0.000532
M	70	V70F	Gtt	Ttt	8	8	P.1.7	0.002554
M	70	V70I	Gtt	Att	7	7	AY.25	0.000042
M	70	V70A	gTt	gCt	7	7	AY.4	0.000011
M	70	V70F	Gtt	Ttt	7	7	AY.46.6	0.000505
M	70	V70F	Gtt	Ttt	7	7	AY.75	0.000392
M	70	V70F	Gtt	Ttt	7	7	AY.99.2	0.000645
M	70	V70F	Gtt	Ttt	7	7	B.1.1.507	0.06087
M	70	V70A	gTt	gCt	7	7	B.1.258	0.000466
M	70	V70F	Gtt	Ttt	7	7	B.1.427	0.000353
M	70	V70F	Gtt	Ttt	7	7	B.1.525	0.000792
M	70	V70F	Gtt	Ttt	7	7	B.1.628	0.002467
M	70	V70L	Gtt	Ctt	7	7	P.1	0.00011
M	70	V70I	Gtt	Att	4	6		0.222222
M	70	V70P	GTT	CCC	2	6		0.111111
M	70	V70T	GTT	ACG	2	6		0.111111
M	70	V70P	GTT	CCG	2	6		0.111111
M	70	V70T	GTt	ACt	2	6		0.111111
M	70	V70I	GtT	AtC	2	6		0.111111
M	70	V70L	GtT	CtC	2	6		0.111111
M	70	V70T	GTT	ACC	2	6		0.111111
M	70	V70P	GTt	CCt	2	6		0.111111
M	70	V70L	GtT	CtG	2	6		0.111111
M	70	V70A	gTT	gCC	2	6		0.111111
M	70	V70A	gTT	gCG	2	6		0.111111
M	70	V70L	Gtt	Ctt	2	6		0.111111
M	70	V70A	gTt	gCt	2	6		0.111111
M	70	V70P	GTT	CCC	2	6	All	0
M	70	V70P	GTt	CCt	2	6	All	0
M	70	V70P	GTT	CCG	2	6	All	0
M	70	V70I	Gtt	Att	6	6	AY.13	0.000966
M	70	V70F	Gtt	Ttt	6	6	AY.29.1	0.001323
M	70	V70F	Gtt	Ttt	6	6	AY.6	0.000247
M	70	V70I	Gtt	Att	6	6	B.1	0.000055
M	70	V70A	gTt	gCt	6	6	B.1	0.000055
M	70	V70F	Gtt	Ttt	6	6	B.1.1.214	0.000333
M	70	V70V	gtT	gtC	6	6	B.1.177.60	0.001311
M	70	V70A	gTt	gCt	6	6	B.1.568	0.006667
M	70	V70F	Gtt	Ttt	6	6	B.1.609	0.002876
M	70	V70A	gTt	gCt	6	6	B.1.617.2	0.000023
M	70	V70F	Gtt	Ttt	6	6	B.1.621	0.000531
M	70	V70A	gTt	gCt	6	6	B.6.6	0.005333
M	70	V70D	gTt	gAt	3	5	All	0.000001
M	70	V70D	gTT	gAC	2	5	All	0
M	70	V70V	gtT	gtC	5	5	AY.106	0.001674
M	70	V70F	Gtt	Ttt	5	5	AY.111	0.000916
M	70	V70V	gtT	gtC	5	5	AY.25	0.00003
M	70	V70F	Gtt	Ttt	5	5	AY.53	0.001438
M	70	V70F	Gtt	Ttt	5	5	AY.93	0.001365
M	70	V70F	Gtt	Ttt	5	5	B	0.000639
M	70	V70V	gtT	gtC	5	5	B.1.1.322	0.04386
M	70	V70F	Gtt	Ttt	5	5	B.1.243	0.000348
M	70	V70F	Gtt	Ttt	5	5	B.1.252	0.033113
M	70	V70F	Gtt	Ttt	5	5	B.1.351.2	0.001513
M	70	V70D	gTT	gAC	2	4		0.111111
M	70	V70N	GTT	AAC	2	4		0.111111
M	70	V70N	GTt	AAt	2	4		0.111111
M	70	V70V	gtT	gtG	2	4		0.111111
M	70	V70H	GTt	CAt	2	4		0.111111
M	70	V70H	GTT	CAC	2	4		0.111111
M	70	V70V	gtT	gtC	2	4		0.111111
M	70	V70D	gTt	gAt	2	4		0.111111
M	70	V70F	Gtt	Ttt	4	4	A	0.001548
M	70	V70H	GTT	CAC	2	4	All	0
M	70	V70N	GTT	AAC	2	4	All	0
M	70	V70N	GTt	AAt	2	4	All	0
M	70	V70H	GTt	CAt	2	4	All	0
M	70	V70I	Gtt	Att	4	4	AY.102	0.000106
M	70	V70F	Gtt	Ttt	4	4	AY.114	0.000924
M	70	V70F	Gtt	Ttt	4	4	AY.117	0.000338
M	70	V70I	Gtt	Att	4	4	AY.20	0.000155
M	70	V70F	Gtt	Ttt	4	4	AY.3.1	0.000341
M	70	V70F	Gtt	Ttt	4	4	AY.34	0.000388
M	70	V70I	Gtt	Att	4	4	AY.36	0.000593
M	70	V70F	Gtt	Ttt	4	4	AY.4.4	0.001637
M	70	V70F	Gtt	Ttt	4	4	AY.45	0.000487
M	70	V70F	Gtt	Ttt	4	4	AY.46	0.000416
M	70	V70I	Gtt	Att	4	4	AY.6	0.000165
M	70	V70I	Gtt	Att	4	4	AY.64	0.002381
M	70	V70V	gtT	gtC	4	4	B.1	0.000037
M	70	V70F	Gtt	Ttt	4	4	B.1.1.25	0.002274
M	70	V70F	Gtt	Ttt	4	4	B.1.1.284	0.00043
M	70	V70F	Gtt	Ttt	4	4	B.1.1.301	0.004717
M	70	V70F	Gtt	Ttt	4	4	B.1.1.37	0.000771
M	70	V70L	Gtt	Ctt	4	4	B.1.1.39	0.002039
M	70	V70F	Gtt	Ttt	4	4	B.1.1.462	0.034483
M	70	V70V	gtT	gtC	4	4	B.1.1.519	0.000159
M	70	V70F	Gtt	Ttt	4	4	B.1.1.61	0.035088
M	70	V70F	Gtt	Ttt	4	4	B.1.139	0.002933
M	70	V70F	Gtt	Ttt	4	4	B.1.177.60	0.000874
M	70	V70F	Gtt	Ttt	4	4	B.1.214.2	0.002398
M	70	V70F	Gtt	Ttt	4	4	B.1.240	0.000862
M	70	V70L	Gtt	Ctt	4	4	B.1.429	0.000094
M	70	V70L	Gtt	Ctt	4	4	B.1.576	0.003626
M	70	V70F	Gtt	Ttt	4	4	B.1.637	0.000292
M	70	V70F	Gtt	Ttt	4	4	C.35	0.003096
M	70	V70del1	Gtt	-tt	3	3	All	0.000001
M	70	V70G	gTt	gGt	3	3	All	0.000001
M	70	V70I	Gtt	Att	3	3	AY.100	0.000138
M	70	V70F	Gtt	Ttt	3	3	AY.105	0.001929
M	70	V70F	Gtt	Ttt	3	3	AY.116	0.00086
M	70	V70F	Gtt	Ttt	3	3	AY.120	0.000112
M	70	V70L	Gtt	Ctt	3	3	AY.25	0.000018
M	70	V70A	gTt	gCt	3	3	AY.30	0.001187
M	70	V70V	gtT	gtC	3	3	AY.33	0.0002
M	70	V70I	Gtt	Att	3	3	AY.39	0.000074
M	70	V70L	Gtt	Ctt	3	3	AY.43	0.000013
M	70	V70F	Gtt	Ttt	3	3	AY.46.1	0.00308
M	70	V70F	Gtt	Ttt	3	3	AY.5	0.000062
M	70	V70F	Gtt	Ttt	3	3	AY.75.1	0.000541
M	70	V70F	Gtt	Ttt	3	3	AY.9	0.000203
M	70	V70F	Gtt	Ttt	3	3	AY.9.2	0.00011
M	70	V70I	Gtt	Att	3	3	B.1.1.306	0.001315
M	70	V70I	Gtt	Att	3	3	B.1.177	0.00004
M	70	V70A	gTt	gCt	3	3	B.1.221	0.000213
M	70	V70L	Gtt	Ctt	3	3	B.1.243	0.000209
M	70	V70I	Gtt	Att	3	3	B.1.243	0.000209
M	70	V70I	Gtt	Att	3	3	B.1.298	0.006342
M	70	V70L	Gtt	Ctt	3	3	B.1.351	0.000089
M	70	V70F	Gtt	Ttt	3	3	B.1.351	0.000089
M	70	V70F	Gtt	Ttt	3	3	B.1.36	0.000438
M	70	V70F	Gtt	Ttt	3	3	B.1.415.1	0.022727
M	70	V70L	Gtt	Ctt	3	3	B.1.427	0.000151
M	70	V70F	Gtt	Ttt	3	3	B.1.429	0.000071
M	70	V70V	gtT	gtC	3	3	B.1.575	0.00091
M	70	V70F	Gtt	Ttt	3	3	B.1.587	0.005693
M	70	V70F	Gtt	Ttt	3	3	B.1.627	0.006061
M	70	V70F	Gtt	Ttt	3	3	B.4	0.006623
M	70	V70V	gtT	gtG	3	3	B.40	0.001093
M	70	V70I	Gtt	Att	3	3	C.37	0.000348
M	70	V70I	Gtt	Att	3	3	P.1	0.000047
M	70	V70F	Gtt	Ttt	3	3	P.1.13	0.002695
M	70	V70L	Gtt	Ctt	3	3	Q.4	0.001364
M	70	V70K	GTT	AAG	2	2		0.111111
M	70	V70del	GTT	---	2	2		0.111111
M	70	V70M	GtT	AtG	2	2		0.111111
M	70	V70Q	GTT	CAG	2	2		0.111111
M	70	V70E	gTT	gAG	2	2		0.111111
M	70	V70Q	GTT	CAG	2	2	All	0
M	70	V70M	GtT	AtG	2	2	All	0
M	70	V70E	gTT	gAG	2	2	All	0
M	70	V70K	GTT	AAG	2	2	All	0
M	70	V70F	Gtt	Ttt	2	2	AY.118	0.000125
M	70	V70F	Gtt	Ttt	2	2	AY.16	0.000759
M	70	V70V	gtT	gtC	2	2	AY.23	0.000139
M	70	V70A	gTt	gCt	2	2	AY.25	0.000012
M	70	V70I	Gtt	Att	2	2	AY.26	0.000057
M	70	V70L	Gtt	Ctt	2	2	AY.29.1	0.000441
M	70	V70V	gtT	gtC	2	2	AY.34	0.000194
M	70	V70F	Gtt	Ttt	2	2	AY.37	0.000632
M	70	V70F	Gtt	Ttt	2	2	AY.4.5	0.000215
M	70	V70L	Gtt	Ctt	2	2	AY.44	0.000012
M	70	V70A	gTt	gCt	2	2	AY.44	0.000012
M	70	V70I	Gtt	Att	2	2	AY.45	0.000243
M	70	V70F	Gtt	Ttt	2	2	AY.46.5	0.000397
M	70	V70I	Gtt	Att	2	2	AY.47	0.000062
M	70	V70L	Gtt	Ctt	2	2	AY.47	0.000062
M	70	V70I	Gtt	Att	2	2	AY.5	0.000041
M	70	V70F	Gtt	Ttt	2	2	AY.5.4	0.000553
M	70	V70F	Gtt	Ttt	2	2	AY.55	0.001835
M	70	V70F	Gtt	Ttt	2	2	AY.59	0.001059
M	70	V70F	Gtt	Ttt	2	2	AY.69	0.000373
M	70	V70F	Gtt	Ttt	2	2	AY.7	0.000392
M	70	V70I	Gtt	Att	2	2	AY.73	0.001331
M	70	V70L	Gtt	Ctt	2	2	AY.74	0.000231
M	70	V70F	Gtt	Ttt	2	2	AY.84	0.000875
M	70	V70F	Gtt	Ttt	2	2	AY.92	0.000575
M	70	V70F	Gtt	Ttt	2	2	AY.99	0.002099
M	70	V70F	Gtt	Ttt	2	2	B.1.1.1	0.000653
M	70	V70L	Gtt	Ctt	2	2	B.1.1.161	0.007067
M	70	V70I	Gtt	Att	2	2	B.1.1.174	0.006757
M	70	V70F	Gtt	Ttt	2	2	B.1.1.216	0.001781
M	70	V70F	Gtt	Ttt	2	2	B.1.1.279	0.002242
M	70	V70A	gTt	gCt	2	2	B.1.1.28	0.000622
M	70	V70F	Gtt	Ttt	2	2	B.1.1.326	0.003521
M	70	V70F	Gtt	Ttt	2	2	B.1.1.369	0.000892
M	70	V70F	Gtt	Ttt	2	2	B.1.1.398	0.006452
M	70	V70F	Gtt	Ttt	2	2	B.1.1.410	0.074074
M	70	V70L	Gtt	Ctt	2	2	B.1.1.519	0.000079
M	70	V70A	gTt	gCt	2	2	B.1.160	0.000062
M	70	V70F	Gtt	Ttt	2	2	B.1.160.8	0.002577
M	70	V70T	GTT	ACA	1	2	B.1.177.21	0.000076
M	70	V70T	GTt	ACt	1	2	B.1.177.21	0.000076
M	70	V70F	Gtt	Ttt	2	2	B.1.177.33	0.003289
M	70	V70F	Gtt	Ttt	2	2	B.1.177.81	0.000379
M	70	V70F	Gtt	Ttt	2	2	B.1.177.87	0.001456
M	70	V70F	Gtt	Ttt	2	2	B.1.210	0.004264
M	70	V70F	Gtt	Ttt	2	2	B.1.221	0.000142
M	70	V70F	Gtt	Ttt	2	2	B.1.234	0.000264
M	70	V70I	Gtt	Att	2	2	B.1.351	0.000059
M	70	V70I	Gtt	Att	2	2	B.1.36	0.000292
M	70	V70F	Gtt	Ttt	2	2	B.1.517	0.000854
M	70	V70V	gtT	gtG	2	2	B.1.526	0.000047
M	70	V70L	Gtt	Ctt	2	2	B.1.537	0.04
M	70	V70F	Gtt	Ttt	2	2	B.1.564	0.000852
M	70	V70F	Gtt	Ttt	2	2	B.1.595	0.000522
M	70	V70I	Gtt	Att	2	2	B.1.596	0.000174
M	70	V70I	Gtt	Att	2	2	B.1.621	0.000177
M	70	V70L	Gtt	Ctt	2	2	B.1.621.1	0.001012
M	70	V70V	gtT	gtC	2	2	B.1.625	0.004706
M	70	V70L	Gtt	Ctt	2	2	B.1.637	0.000146
M	70	V70F	Gtt	Ttt	2	2	C.36	0.001821
M	70	V70F	Gtt	Ttt	2	2	C.37	0.000232
M	70	V70A	gTt	gCt	2	2	P.1	0.000032
M	70	V70V	gtT	gtC	2	2	P.1	0.000032
M	70	V70F	Gtt	Ttt	2	2	P.1.16	0.000748
M	70	V70G	gTt	gGt	1	1		0.055556
M	70	V70V	gtT	gtG	1	1	A	0.000387
M	70	V70A	gTt	gCt	1	1	A.2	0.000662
M	70	V70F	Gtt	Ttt	1	1	A.2.2	0.001689
M	70	V70F	Gtt	Ttt	1	1	A.2.4	0.003367
M	70	V70L	Gtt	Ctt	1	1	A.5	0.001923
M	70	V70del2	gTT	g--	1	1	All	0
M	70	V70F	Gtt	Ttt	1	1	AP.1	0.001502
M	70	V70L	Gtt	Ctt	1	1	AY.102	0.000027
M	70	V70L	Gtt	Ctt	1	1	AY.103	0.000006
M	70	V70V	gtT	gtC	1	1	AY.103	0.000006
M	70	V70A	gTt	gCt	1	1	AY.103	0.000006
M	70	V70F	Gtt	Ttt	1	1	AY.107	0.000466
M	70	V70del	GTT	---	1	1	AY.120	0.000037
M	70	V70V	gtT	gtC	1	1	AY.120	0.000037
M	70	V70G	gTt	gGt	1	1	AY.14	0.000088
M	70	V70A	gTt	gCt	1	1	AY.14	0.000088
M	70	V70A	gTt	gCt	1	1	AY.20	0.000039
M	70	V70F	Gtt	Ttt	1	1	AY.22	0.002092
M	70	V70I	Gtt	Att	1	1	AY.23	0.00007
M	70	V70I	Gtt	Att	1	1	AY.23.1	0.000417
M	70	V70I	Gtt	Att	1	1	AY.27	0.000065
M	70	V70V	gtT	gtC	1	1	AY.29	0.000016
M	70	V70L	Gtt	Ctt	1	1	AY.3	0.00001
M	70	V70A	gTt	gCt	1	1	AY.3	0.00001
M	70	V70F	Gtt	Ttt	1	1	AY.34.1	0.00051
M	70	V70F	Gtt	Ttt	1	1	AY.38	0.000499
M	70	V70V	gtT	gtC	1	1	AY.39	0.000025
M	70	V70F	Gtt	Ttt	1	1	AY.39.1	0.00004
M	70	V70F	Gtt	Ttt	1	1	AY.4.3	0.000842
M	70	V70L	Gtt	Ctt	1	1	AY.4.3	0.000842
M	70	V70A	gTt	gCt	1	1	AY.42	0.00004
M	70	V70del	GTT	---	1	1	AY.43	0.000004
M	70	V70V	gtT	gtC	1	1	AY.44	0.000006
M	70	V70I	Gtt	Att	1	1	AY.46	0.000104
M	70	V70V	gtT	gtC	1	1	AY.5	0.000021
M	70	V70L	Gtt	Ctt	1	1	AY.5	0.000021
M	70	V70F	Gtt	Ttt	1	1	AY.5.3	0.000337
M	70	V70I	Gtt	Att	1	1	AY.50	0.000799
M	70	V70A	gTt	gCt	1	1	AY.53	0.000288
M	70	V70I	Gtt	Att	1	1	AY.61	0.000105
M	70	V70F	Gtt	Ttt	1	1	AY.62	0.000436
M	70	V70F	Gtt	Ttt	1	1	AY.64	0.000595
M	70	V70F	Gtt	Ttt	1	1	AY.67	0.000464
M	70	V70F	Gtt	Ttt	1	1	AY.7.1	0.000113
M	70	V70I	Gtt	Att	1	1	AY.70	0.000209
M	70	V70F	Gtt	Ttt	1	1	AY.70	0.000209
M	70	V70I	Gtt	Att	1	1	AY.74	0.000116
M	70	V70D	gTt	gAt	1	1	AY.75	0.000056
M	70	V70I	Gtt	Att	1	1	AY.75	0.000056
M	70	V70F	Gtt	Ttt	1	1	AY.77	0.001127
M	70	V70V	gtT	gtC	1	1	AY.78	0.001541
M	70	V70F	Gtt	Ttt	1	1	AY.89	0.004902
M	70	V70I	Gtt	Att	1	1	AY.9	0.000068
M	70	V70F	Gtt	Ttt	1	1	AY.9.1	0.000084
M	70	V70I	Gtt	Att	1	1	AY.92	0.000287
M	70	V70F	Gtt	Ttt	1	1	AY.94	0.000443
M	70	V70F	Gtt	Ttt	1	1	AY.95	0.000761
M	70	V70F	Gtt	Ttt	1	1	AY.97	0.001701
M	70	V70V	gtT	gtC	1	1	AY.98.1	0.000048
M	70	V70V	gtT	gtA	1	1	AY.99.2	0.000092
M	70	V70I	Gtt	Att	1	1	AZ.2	0.000821
M	70	V70F	Gtt	Ttt	1	1	AZ.3	0.00152
M	70	V70L	Gtt	Ctt	1	1	B	0.000128
M	70	V70I	Gtt	Att	1	1	B	0.000128
M	70	V70del	GTT	---	1	1	B.1	0.000009
M	70	V70V	gtT	gtC	1	1	B.1.1	0.000018
M	70	V70A	gTt	gCt	1	1	B.1.1	0.000018
M	70	V70L	Gtt	Ctt	1	1	B.1.1.1	0.000327
M	70	V70F	Gtt	Ttt	1	1	B.1.1.174	0.003378
M	70	V70F	Gtt	Ttt	1	1	B.1.1.205	0.003717
M	70	V70I	Gtt	Att	1	1	B.1.1.216	0.00089
M	70	V70L	Gtt	Ctt	1	1	B.1.1.222	0.000204
M	70	V70F	Gtt	Ttt	1	1	B.1.1.222	0.000204
M	70	V70I	Gtt	Att	1	1	B.1.1.254	0.011236
M	70	V70F	Gtt	Ttt	1	1	B.1.1.261	0.008621
M	70	V70I	Gtt	Att	1	1	B.1.1.266	0.012195
M	70	V70F	Gtt	Ttt	1	1	B.1.1.274	0.005051
M	70	V70F	Gtt	Ttt	1	1	B.1.1.277	0.000759
M	70	V70I	Gtt	Att	1	1	B.1.1.305	0.003861
M	70	V70F	Gtt	Ttt	1	1	B.1.1.306	0.000438
M	70	V70F	Gtt	Ttt	1	1	B.1.1.307	0.002532
M	70	V70F	Gtt	Ttt	1	1	B.1.1.317	0.000412
M	70	V70L	Gtt	Ctt	1	1	B.1.1.329	0.003846
M	70	V70I	Gtt	Att	1	1	B.1.1.33	0.000421
M	70	V70F	Gtt	Ttt	1	1	B.1.1.33	0.000421
M	70	V70I	Gtt	Att	1	1	B.1.1.333	0.001076
M	70	V70del	GTT	---	1	1	B.1.1.372	0.000689
M	70	V70L	Gtt	Ctt	1	1	B.1.1.375	0.011905
M	70	V70F	Gtt	Ttt	1	1	B.1.1.41	0.006329
M	70	V70I	Gtt	Att	1	1	B.1.1.416	0.000905
M	70	V70F	Gtt	Ttt	1	1	B.1.1.44	0.00241
M	70	V70I	Gtt	Att	1	1	B.1.1.467	0.019231
M	70	V70F	Gtt	Ttt	1	1	B.1.1.50	0.000679
M	70	V70A	gTt	gCt	1	1	B.1.1.506	0.037037
M	70	V70A	gTt	gCt	1	1	B.1.1.519	0.00004
M	70	V70L	Gtt	Ctt	1	1	B.1.1.524	0.020833
M	70	V70I	Gtt	Att	1	1	B.1.1.526	0.003546
M	70	V70del2	gTT	g--	1	1	B.1.1.7	0.000001
M	70	V70del1	Gtt	-tt	1	1	B.1.1.7	0.000001
M	70	V70L	Gtt	Ctt	1	1	B.1.1.8	0.003584
M	70	V70F	Gtt	Ttt	1	1	B.1.104	0.00369
M	70	V70A	gTt	gCt	1	1	B.1.111	0.001175
M	70	V70I	Gtt	Att	1	1	B.1.128	0.000635
M	70	V70L	Gtt	Ctt	1	1	B.1.139	0.000733
M	70	V70F	Gtt	Ttt	1	1	B.1.158	0.02381
M	70	V70L	Gtt	Ctt	1	1	B.1.160.28	0.002924
M	70	V70I	GtT	AtA	1	1	B.1.161	0.017241
M	70	V70F	Gtt	Ttt	1	1	B.1.177.19	0.001431
M	70	V70F	Gtt	Ttt	1	1	B.1.177.21	0.000076
M	70	V70F	Gtt	Ttt	1	1	B.1.177.23	0.003236
M	70	V70F	Gtt	Ttt	1	1	B.1.177.43	0.001477
M	70	V70F	Gtt	Ttt	1	1	B.1.177.54	0.000606
M	70	V70F	Gtt	Ttt	1	1	B.1.177.57	0.000281
M	70	V70F	Gtt	Ttt	1	1	B.1.177.65	0.000665
M	70	V70L	Gtt	Ctt	1	1	B.1.177.7	0.000165
M	70	V70L	Gtt	Ctt	1	1	B.1.177.73	0.000566
M	70	V70V	gtT	gtA	1	1	B.1.177.73	0.000566
M	70	V70A	gTt	gCt	1	1	B.1.177.73	0.000566
M	70	V70L	Gtt	Ctt	1	1	B.1.177.81	0.000189
M	70	V70I	Gtt	Att	1	1	B.1.177.82	0.000477
M	70	V70F	Gtt	Ttt	1	1	B.1.179	0.003759
M	70	V70L	Gtt	Ctt	1	1	B.1.189	0.004292
M	70	V70del1	Gtt	-tt	1	1	B.1.2	0.000009
M	70	V70A	gTt	gCt	1	1	B.1.215	0.009615
M	70	V70F	Gtt	Ttt	1	1	B.1.232	0.000537
M	70	V70A	gTt	gCt	1	1	B.1.234	0.000132
M	70	V70F	Gtt	Ttt	1	1	B.1.236	0.002053
M	70	V70L	Gtt	Ctt	1	1	B.1.240	0.000216
M	70	V70V	gtT	gtC	1	1	B.1.258	0.000067
M	70	V70I	Gtt	Att	1	1	B.1.258.11	0.000396
M	70	V70del	GTT	---	1	1	B.1.258.11	0.000396
M	70	V70F	Gtt	Ttt	1	1	B.1.311	0.000275
M	70	V70F	Gtt	Ttt	1	1	B.1.356	0.001727
M	70	V70L	Gtt	Ctt	1	1	B.1.36	0.000146
M	70	V70F	Gtt	Ttt	1	1	B.1.36.35	0.002604
M	70	V70F	Gtt	Ttt	1	1	B.1.367	0.000792
M	70	V70L	Gtt	Ctt	1	1	B.1.375	0.00082
M	70	V70F	Gtt	Ttt	1	1	B.1.378	0.006849
M	70	V70F	Gtt	Ttt	1	1	B.1.383	0.009009
M	70	V70F	Gtt	Ttt	1	1	B.1.393	0.028571
M	70	V70I	Gtt	Att	1	1	B.1.396	0.000706
M	70	V70A	gTt	gCt	1	1	B.1.396	0.000706
M	70	V70F	Gtt	Ttt	1	1	B.1.416	0.001269
M	70	V70F	Gtt	Ttt	1	1	B.1.418	0.015873
M	70	V70A	gTt	gCt	1	1	B.1.427	0.00005
M	70	V70V	gtT	gtG	1	1	B.1.429	0.000024
M	70	V70F	Gtt	Ttt	1	1	B.1.438.1	0.000107
M	70	V70F	Gtt	Ttt	1	1	B.1.444	0.015873
M	70	V70del	GTT	---	1	1	B.1.577	0.000687
M	70	V70F	Gtt	Ttt	1	1	B.1.582	0.000491
M	70	V70F	Gtt	Ttt	1	1	B.1.589	0.007576
M	70	V70del	GTT	---	1	1	B.1.596	0.000087
M	70	V70V	gtT	gtC	1	1	B.1.596	0.000087
M	70	V70G	gTt	gGt	1	1	B.1.617.2	0.000004
M	70	V70del	GTT	---	1	1	B.1.617.2	0.000004
M	70	V70F	Gtt	Ttt	1	1	B.1.619	0.000871
M	70	V70F	Gtt	Ttt	1	1	B.1.625	0.002353
M	70	V70del	GTT	---	1	1	B.1.627	0.00202
M	70	V70L	Gtt	Ctt	1	1	B.1.628	0.000352
M	70	V70F	Gtt	Ttt	1	1	B.1.638	0.052632
M	70	V70F	Gtt	Ttt	1	1	B.27	0.015385
M	70	V70F	Gtt	Ttt	1	1	B.28	0.003279
M	70	V70I	Gtt	Att	1	1	B.3	0.000831
M	70	V70L	Gtt	Ctt	1	1	B.40	0.000364
M	70	V70F	Gtt	Ttt	1	1	B.6	0.00091
M	70	V70I	Gtt	Att	1	1	B.6.6	0.000889
M	70	V70F	Gtt	Ttt	1	1	B.6.6	0.000889
M	70	V70F	Gtt	Ttt	1	1	C.36.3	0.000567
M	70	V70del1	Gtt	-tt	1	1	D.2	0.000075
M	70	V70F	Gtt	Ttt	1	1	D.2	0.000075
M	70	V70F	Gtt	Ttt	1	1	N.1	0.016949
M	70	V70F	Gtt	Ttt	1	1	N.4	0.004255
M	70	V70F	Gtt	Ttt	1	1	N.5	0.001767
M	70	V70F	Gtt	Ttt	1	1	P.1.12	0.000484
M	70	V70del	GTT	---	1	1	P.1.15	0.000232
M	70	V70L	Gtt	Ctt	1	1	P.1.7	0.000319
M	70	V70F	Gtt	Ttt	1	1	P.2	0.000187
M	70	V70I	Gtt	Att	1	1	P.6	0.003145
M	70	V70F	Gtt	Ttt	1	1	Q.3	0.000145
M	70	V70F	Gtt	Ttt	1	1	Q.4	0.000455
M	70	V70I	Gtt	Att	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.