CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 17

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	17	L17F		nonsyn	Ctt	Ttt	2936	2936	1	26571-26573
M	17	L17I		nonsyn	Ctt	Att	1102	1101	0.999093	26571-26573
M	17	L17I		nonsyn	CtT	AtA	1102	1	0.000907441	26571-26573
M	17	L17L		syn	ctT	ctC	509	431	0.846758	26571-26573
M	17	L17L		syn	ctT	ctA	509	73	0.143418	26571-26573
M	17	L17L		syn	ctT	ctG	509	3	0.00589391	26571-26573
M	17	L17L		syn	CtT	TtA	509	1	0.00196464	26571-26573
M	17	L17L		syn	CtT	TtG	509	1	0.00196464	26571-26573
M	17	L17del		del	CTT	---	57	57	1	26571-26573
M	17	L17V		nonsyn	Ctt	Gtt	20	20	1	26571-26573
M	17	L17P		nonsyn	cTt	cCt	15	14	0.933333	26571-26573
M	17	L17P		nonsyn	cTT	cCC	15	1	0.0666667	26571-26573
M	17	L17del2		del	CTt	--t	9	7	0.777778	26571-26573
M	17	L17del2		del	cTT	c--	9	2	0.222222	26571-26573
M	17	L17del1		del	CTT	-NN	5	2	0.4	26571-26573
M	17	L17del1		del	Ctt	-tt	5	2	0.4	26571-26573
M	17	L17del1		del	cTt	c-t	5	1	0.2	26571-26573
M	17	L17H		nonsyn	cTt	cAt	3	3	1	26571-26573
M	17	L17S		nonsyn	CTT	TCG	3	1	0.333333	26571-26573
M	17	L17S		nonsyn	CTt	TCt	3	1	0.333333	26571-26573
M	17	L17S		nonsyn	CTt	AGt	3	1	0.333333	26571-26573
M	17	L17Y		nonsyn	CTt	TAt	2	2	1	26571-26573
M	17	L17A		nonsyn	CTt	GCt	1	1	1	26571-26573
M	17	L17K		nonsyn	CTT	AAG	1	1	1	26571-26573
M	17	L17Q		nonsyn	cTT	cAA	1	1	1	26571-26573
M	17	L17R		nonsyn	cTt	cGt	1	1	1	26571-26573

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	17	L17F	Ctt	Ttt	2936	2936	All	0.000562
M	17	L17I	Ctt	Att	1101	1102	All	0.000211
M	17	L17I	CtT	AtA	1	1102	All	0
M	17	L17I	Ctt	Att	681	681	B.1.1.279	0.763453
M	17	L17F	Ctt	Ttt	586	586	B.1.429	0.013788
M	17	L17L	ctT	ctC	431	509	All	0.000082
M	17	L17L	ctT	ctA	73	509	All	0.000014
M	17	L17L	ctT	ctG	3	509	All	0.000001
M	17	L17L	CtT	TtG	1	509	All	0
M	17	L17L	CtT	TtA	1	509	All	0
M	17	L17F	Ctt	Ttt	496	496	B.1.1.7	0.000444
M	17	L17F	Ctt	Ttt	255	255	AY.9.2	0.009366
M	17	L17I	Ctt	Att	245	245	B.1.1.7	0.000219
M	17	L17L	ctT	ctC	164	164	AY.4	0.000255
M	17	L17F	Ctt	Ttt	135	135	AY.103	0.000838
M	17	L17F	Ctt	Ttt	126	126	AY.4	0.000196
M	17	L17F	Ctt	Ttt	102	102	B.1.177	0.001343
M	17	L17F	Ctt	Ttt	93	93	B.1.617.2	0.00035
M	17	L17F	Ctt	Ttt	92	92	B.1.2	0.00081
M	17	L17L	ctT	ctC	68	73	B.1.1.7	0.000061
M	17	L17L	ctT	ctA	4	73	B.1.1.7	0.000004
M	17	L17L	CtT	TtG	1	73	B.1.1.7	0.000001
M	17	L17F	Ctt	Ttt	68	68	D.2	0.005103
M	17	L17del	CTT	---	57	57	All	0.000011
M	17	L17L	ctT	ctA	49	51	AY.33	0.003272
M	17	L17L	ctT	ctC	2	51	AY.33	0.000134
M	17	L17L	ctT	ctC	51	51	AY.43	0.000226
M	17	L17F	Ctt	Ttt	51	51	B.1	0.000467
M	17	L17F	Ctt	Ttt	49	49	AY.5	0.001012
M	17	L17F	Ctt	Ttt	46	46	B.1.460	0.821429
M	17	L17F	Ctt	Ttt	45	45	AY.44	0.000274
M	17	L17F	Ctt	Ttt	44	44	P.1	0.000693
M	17	L17F	Ctt	Ttt	38	38	AY.3	0.000378
M	17	L17L	ctT	ctC	37	37	B.1.617.2	0.000139
M	17	L17I	Ctt	Att	32	32	B.1.1	0.000581
M	17	L17F	Ctt	Ttt	31	31	AY.43	0.000137
M	17	L17F	Ctt	Ttt	30	30	AY.25	0.00018
M	17	L17F	Ctt	Ttt	23	23	AY.100	0.001058
M	17	L17F	Ctt	Ttt	21	21	B.1.621	0.001859
M	17	L17V	Ctt	Gtt	20	20	All	0.000004
M	17	L17F	Ctt	Ttt	18	18	AY.47	0.00056
M	17	L17I	Ctt	Att	17	17	B.1.1.337	0.061151
M	17	L17F	Ctt	Ttt	17	17	B.1.351	0.000505
M	17	L17I	Ctt	Att	16	16	AY.4	0.000025
M	17	L17F	Ctt	Ttt	16	16	B.1.1.284	0.001718
M	17	L17F	Ctt	Ttt	16	16	B.1.1.316	0.014801
M	17	L17P	cTt	cCt	14	15	All	0.000003
M	17	L17P	cTT	cCC	1	15	All	0
M	17	L17F	Ctt	Ttt	15	15	AY.29	0.000237
M	17	L17I	Ctt	Att	15	15	B.1.525	0.001697
M	17	L17F	Ctt	Ttt	14	14	B.1.1.432	0.017722
M	17	L17I	Ctt	Att	14	14	B.1.2	0.000123
M	17	L17F	Ctt	Ttt	14	14	B.1.240	0.003018
M	17	L17L	ctT	ctC	13	13	AY.102	0.000345
M	17	L17I	Ctt	Att	13	13	B.1.427	0.000656
M	17	L17F	Ctt	Ttt	13	13	B.1.427	0.000656
M	17	L17F	Ctt	Ttt	13	13	B.1.637	0.00095
M	17	L17F	Ctt	Ttt	12	12	AY.27	0.000777
M	17	L17F	Ctt	Ttt	12	12	B.1.526	0.000282
M	17	L17F	Ctt	Ttt	12	12	B.1.619	0.010453
M	17	L17F	Ctt	Ttt	12	12	P.1.14	0.000574
M	17	L17L	ctT	ctC	10	11	AY.3	0.000099
M	17	L17L	ctT	ctA	1	11	AY.3	0.00001
M	17	L17F	Ctt	Ttt	10	10	AY.26	0.000283
M	17	L17F	Ctt	Ttt	10	10	B.1.1	0.000181
M	17	L17F	Ctt	Ttt	10	10	B.1.1.214	0.000555
M	17	L17F	Ctt	Ttt	10	10	B.1.160	0.000312
M	17	L17F	Ctt	Ttt	10	10	B.1.36.31	0.017513
M	17	L17L	ctT	ctA	10	10	B.1.427	0.000505
M	17	L17F	Ctt	Ttt	10	10	R.1	0.0009
M	17	L17del2	CTt	--t	7	9	All	0.000001
M	17	L17del2	cTT	c--	2	9	All	0
M	17	L17F	Ctt	Ttt	9	9	AY.102	0.000239
M	17	L17F	Ctt	Ttt	9	9	AY.34	0.000873
M	17	L17F	Ctt	Ttt	9	9	AY.39	0.000222
M	17	L17I	Ctt	Att	9	9	B.1	0.000082
M	17	L17F	Ctt	Ttt	9	9	B.1.1.28	0.002801
M	17	L17F	Ctt	Ttt	9	9	B.1.221	0.000639
M	17	L17F	Ctt	Ttt	9	9	C.37	0.001045
M	17	L17F	Ctt	Ttt	8	8	B.1.1.519	0.000318
M	17	L17F	Ctt	Ttt	8	8	B.1.258	0.000532
M	17	L17I	Ctt	Att	8	8	B.1.451	0.065574
M	17	L17F	Ctt	Ttt	8	8	Q.8	0.001319
M	17	L17F	Ctt	Ttt	7	7	AY.4.2	0.000152
M	17	L17L	ctT	ctC	6	7	AY.44	0.000037
M	17	L17L	ctT	ctG	1	7	AY.44	0.000006
M	17	L17V	Ctt	Gtt	7	7	B.1.177.60	0.001529
M	17	L17F	Ctt	Ttt	7	7	B.1.177.86	0.001284
M	17	L17F	Ctt	Ttt	7	7	Q.1	0.000884
M	17	L17I	Ctt	Att	6	6	AY.25	0.000036
M	17	L17F	Ctt	Ttt	6	6	AY.74	0.000694
M	17	L17F	Ctt	Ttt	6	6	AY.75	0.000336
M	17	L17L	ctT	ctC	6	6	B.1	0.000055
M	17	L17F	Ctt	Ttt	6	6	B.1.1.280	0.018519
M	17	L17del	CTT	---	6	6	B.1.1.7	0.000005
M	17	L17F	Ctt	Ttt	6	6	B.1.146	0.025424
M	17	L17F	Ctt	Ttt	6	6	B.1.177.4	0.001266
M	17	L17L	ctT	ctC	6	6	B.1.177.5	0.007453
M	17	L17F	Ctt	Ttt	6	6	B.1.243	0.000418
M	17	L17F	Ctt	Ttt	6	6	B.1.36	0.000875
M	17	L17L	ctT	ctC	6	6	P.1	0.000095
M	17	L17del1	Ctt	-tt	2	5	All	0
M	17	L17del1	CTT	-NN	2	5	All	0
M	17	L17del1	cTt	c-t	1	5	All	0
M	17	L17I	Ctt	Att	5	5	AY.3	0.00005
M	17	L17F	Ctt	Ttt	5	5	AY.46.5	0.000992
M	17	L17F	Ctt	Ttt	5	5	AY.6	0.000206
M	17	L17F	Ctt	Ttt	5	5	AY.98.1	0.000242
M	17	L17F	Ctt	Ttt	5	5	B.1.1.25	0.002843
M	17	L17F	Ctt	Ttt	5	5	B.1.234	0.00066
M	17	L17F	Ctt	Ttt	5	5	B.1.582	0.002453
M	17	L17F	Ctt	Ttt	5	5	P.1.17	0.000809
M	17	L17L	ctT	ctC	4	4	AY.103	0.000025
M	17	L17I	Ctt	Att	4	4	AY.109	0.002959
M	17	L17F	Ctt	Ttt	4	4	AY.116	0.001147
M	17	L17F	Ctt	Ttt	4	4	AY.20	0.000155
M	17	L17L	ctT	ctC	4	4	AY.25	0.000024
M	17	L17L	ctT	ctC	4	4	AY.42	0.000161
M	17	L17del	CTT	---	4	4	B.1	0.000037
M	17	L17L	ctT	ctC	2	4	B.1.1	0.000036
M	17	L17L	CtT	TtA	1	4	B.1.1	0.000018
M	17	L17L	ctT	ctA	1	4	B.1.1	0.000018
M	17	L17F	Ctt	Ttt	4	4	B.1.108	0.023256
M	17	L17F	Ctt	Ttt	4	4	B.1.177.12	0.000607
M	17	L17F	Ctt	Ttt	4	4	B.1.337	0.022346
M	17	L17L	ctT	ctC	4	4	B.1.516	0.007828
M	17	L17I	Ctt	Att	4	4	P.1	0.000063
M	17	L17F	Ctt	Ttt	3	3	A.2.5	0.001497
M	17	L17H	cTt	cAt	3	3	All	0.000001
M	17	L17S	CTt	TCt	1	3	All	0
M	17	L17S	CTt	AGt	1	3	All	0
M	17	L17S	CTT	TCG	1	3	All	0
M	17	L17F	Ctt	Ttt	3	3	AY.110	0.000338
M	17	L17F	Ctt	Ttt	3	3	AY.23	0.000209
M	17	L17V	Ctt	Gtt	3	3	AY.25	0.000018
M	17	L17del	CTT	---	3	3	AY.25	0.000018
M	17	L17L	ctT	ctC	2	3	AY.26	0.000057
M	17	L17L	ctT	ctA	1	3	AY.26	0.000028
M	17	L17F	Ctt	Ttt	3	3	AY.29.1	0.000662
M	17	L17F	Ctt	Ttt	3	3	AY.39.1	0.000119
M	17	L17del	CTT	---	3	3	AY.4	0.000005
M	17	L17F	Ctt	Ttt	3	3	AY.46.6	0.000217
M	17	L17F	Ctt	Ttt	3	3	AY.54	0.000286
M	17	L17F	Ctt	Ttt	3	3	AY.99.2	0.000276
M	17	L17L	ctT	ctA	3	3	B.1.1.189	0.004539
M	17	L17I	Ctt	Att	3	3	B.1.1.25	0.001706
M	17	L17F	Ctt	Ttt	3	3	B.1.1.370	0.037975
M	17	L17F	Ctt	Ttt	3	3	B.1.1.382	0.107143
M	17	L17F	Ctt	Ttt	3	3	B.1.258.17	0.000312
M	17	L17V	Ctt	Gtt	3	3	B.1.351	0.000089
M	17	L17F	Ctt	Ttt	3	3	B.1.36.27	0.00229
M	17	L17F	Ctt	Ttt	3	3	B.1.363	0.038961
M	17	L17F	Ctt	Ttt	3	3	B.1.438.1	0.000322
M	17	L17L	ctT	ctC	3	3	B.1.438.1	0.000322
M	17	L17I	Ctt	Att	3	3	B.1.448	0.007874
M	17	L17F	Ctt	Ttt	3	3	B.1.595	0.000783
M	17	L17I	Ctt	Att	3	3	C.36	0.002732
M	17	L17F	Ctt	Ttt	3	3	P.1.10	0.000808
M	17	L17F	Ctt	Ttt	3	3	P.1.7	0.000958
M	17	L17F	Ctt	Ttt	3	3	P.7	0.0131
M	17	L17del	CTT	---	2	2		0.111111
M	17	L17Y	CTt	TAt	2	2	All	0
M	17	L17I	Ctt	Att	2	2	AY.102	0.000053
M	17	L17del	CTT	---	2	2	AY.103	0.000012
M	17	L17F	Ctt	Ttt	2	2	AY.105	0.001286
M	17	L17F	Ctt	Ttt	2	2	AY.106	0.00067
M	17	L17F	Ctt	Ttt	2	2	AY.113	0.000285
M	17	L17L	ctT	ctC	2	2	AY.117	0.000169
M	17	L17F	Ctt	Ttt	2	2	AY.119	0.000071
M	17	L17I	Ctt	Att	2	2	AY.121	0.000271
M	17	L17F	Ctt	Ttt	2	2	AY.16	0.000759
M	17	L17del1	CTT	-NN	1	2	AY.25	0.000006
M	17	L17del1	Ctt	-tt	1	2	AY.25	0.000006
M	17	L17V	Ctt	Gtt	2	2	AY.29	0.000032
M	17	L17F	Ctt	Ttt	2	2	AY.35	0.000466
M	17	L17L	ctT	ctC	2	2	AY.39	0.000049
M	17	L17del	CTT	---	2	2	AY.4.5	0.000215
M	17	L17F	Ctt	Ttt	2	2	AY.4.5	0.000215
M	17	L17del2	CTt	--t	2	2	AY.43	0.000009
M	17	L17del	CTT	---	2	2	AY.43	0.000009
M	17	L17F	Ctt	Ttt	2	2	AY.5.3	0.000675
M	17	L17F	Ctt	Ttt	2	2	AY.5.4	0.000553
M	17	L17L	ctT	ctC	2	2	AY.91	0.001461
M	17	L17V	Ctt	Gtt	2	2	B.1.1	0.000036
M	17	L17F	Ctt	Ttt	2	2	B.1.1.301	0.002358
M	17	L17F	Ctt	Ttt	2	2	B.1.1.448	0.004065
M	17	L17F	Ctt	Ttt	2	2	B.1.1.486	0.003155
M	17	L17P	cTt	cCt	2	2	B.1.1.7	0.000002
M	17	L17del2	CTt	--t	2	2	B.1.1.7	0.000002
M	17	L17H	cTt	cAt	2	2	B.1.1.7	0.000002
M	17	L17F	Ctt	Ttt	2	2	B.1.177.10	0.001756
M	17	L17del2	cTT	c--	2	2	B.1.2	0.000018
M	17	L17P	cTt	cCt	2	2	B.1.2	0.000018
M	17	L17L	ctT	ctC	2	2	B.1.234	0.000264
M	17	L17F	Ctt	Ttt	2	2	B.1.36.8	0.002
M	17	L17F	Ctt	Ttt	2	2	B.1.524	0.002813
M	17	L17L	ctT	ctC	2	2	B.1.526	0.000047
M	17	L17F	Ctt	Ttt	2	2	B.1.561	0.000794
M	17	L17F	Ctt	Ttt	2	2	B.1.577	0.001375
M	17	L17F	Ctt	Ttt	2	2	B.1.596	0.000174
M	17	L17P	cTt	cCt	2	2	B.1.617.2	0.000008
M	17	L17F	Ctt	Ttt	2	2	C.1	0.004785
M	17	L17F	Ctt	Ttt	2	2	C.35	0.001548
M	17	L17L	ctT	ctG	1	2	C.37	0.000116
M	17	L17L	ctT	ctA	1	2	C.37	0.000116
M	17	L17del	CTT	---	2	2	P.1	0.000032
M	17	L17F	Ctt	Ttt	2	2	P.1.15	0.000465
M	17	L17I	Ctt	Att	2	2	Q.8	0.00033
M	17	L17F	Ctt	Ttt	1	1	A	0.000387
M	17	L17L	ctT	ctC	1	1	A.1	0.000282
M	17	L17F	Ctt	Ttt	1	1	A.2.4	0.003367
M	17	L17S	CTt	TCt	1	1	A.21	0.00277
M	17	L17del	CTT	---	1	1	A.23.1	0.000704
M	17	L17F	Ctt	Ttt	1	1	AD.2	0.000219
M	17	L17F	Ctt	Ttt	1	1	AE.1	0.011364
M	17	L17K	CTT	AAG	1	1	All	0
M	17	L17A	CTt	GCt	1	1	All	0
M	17	L17R	cTt	cGt	1	1	All	0
M	17	L17Q	cTT	cAA	1	1	All	0
M	17	L17del	CTT	---	1	1	AY.100	0.000046
M	17	L17P	cTt	cCt	1	1	AY.103	0.000006
M	17	L17F	Ctt	Ttt	1	1	AY.104	0.001984
M	17	L17del	CTT	---	1	1	AY.108	0.001103
M	17	L17F	Ctt	Ttt	1	1	AY.111	0.000183
M	17	L17L	ctT	ctC	1	1	AY.113	0.000142
M	17	L17F	Ctt	Ttt	1	1	AY.114	0.000231
M	17	L17L	ctT	ctC	1	1	AY.116	0.000287
M	17	L17L	ctT	ctC	1	1	AY.116.1	0.000311
M	17	L17del2	CTt	--t	1	1	AY.118	0.000063
M	17	L17F	Ctt	Ttt	1	1	AY.118	0.000063
M	17	L17del	CTT	---	1	1	AY.120	0.000037
M	17	L17L	ctT	ctC	1	1	AY.121	0.000135
M	17	L17F	Ctt	Ttt	1	1	AY.14	0.000088
M	17	L17F	Ctt	Ttt	1	1	AY.2	0.000356
M	17	L17del2	CTt	--t	1	1	AY.25	0.000006
M	17	L17P	cTt	cCt	1	1	AY.25	0.000006
M	17	L17del	CTT	---	1	1	AY.3	0.00001
M	17	L17L	ctT	ctC	1	1	AY.34.1	0.00051
M	17	L17F	Ctt	Ttt	1	1	AY.37	0.000316
M	17	L17del	CTT	---	1	1	AY.39	0.000025
M	17	L17K	CTT	AAG	1	1	AY.4	0.000002
M	17	L17del1	Ctt	-tt	1	1	AY.4	0.000002
M	17	L17V	Ctt	Gtt	1	1	AY.4	0.000002
M	17	L17del	CTT	---	1	1	AY.4.2	0.000022
M	17	L17I	Ctt	Att	1	1	AY.41	0.000294
M	17	L17F	Ctt	Ttt	1	1	AY.42	0.00004
M	17	L17del1	CTT	-NN	1	1	AY.44	0.000006
M	17	L17del	CTT	---	1	1	AY.44	0.000006
M	17	L17P	cTT	cCC	1	1	AY.44	0.000006
M	17	L17I	Ctt	Att	1	1	AY.44	0.000006
M	17	L17F	Ctt	Ttt	1	1	AY.45	0.000122
M	17	L17F	Ctt	Ttt	1	1	AY.46	0.000104
M	17	L17del	CTT	---	1	1	AY.46.6	0.000072
M	17	L17del	CTT	---	1	1	AY.5	0.000021
M	17	L17I	Ctt	Att	1	1	AY.5	0.000021
M	17	L17del	CTT	---	1	1	AY.5.3	0.000337
M	17	L17F	Ctt	Ttt	1	1	AY.55	0.000917
M	17	L17P	cTt	cCt	1	1	AY.55	0.000917
M	17	L17I	Ctt	Att	1	1	AY.55	0.000917
M	17	L17L	ctT	ctA	1	1	AY.59	0.00053
M	17	L17F	Ctt	Ttt	1	1	AY.61	0.000105
M	17	L17F	Ctt	Ttt	1	1	AY.63	0.000387
M	17	L17L	ctT	ctC	1	1	AY.67	0.000464
M	17	L17del	CTT	---	1	1	AY.68	0.000274
M	17	L17F	Ctt	Ttt	1	1	AY.7	0.000196
M	17	L17F	Ctt	Ttt	1	1	AY.7.2	0.000559
M	17	L17del	CTT	---	1	1	AY.74	0.000116
M	17	L17L	ctT	ctC	1	1	AY.74	0.000116
M	17	L17del	CTT	---	1	1	AY.75	0.000056
M	17	L17F	Ctt	Ttt	1	1	AY.75.1	0.00018
M	17	L17I	Ctt	Att	1	1	AY.75.1	0.00018
M	17	L17F	Ctt	Ttt	1	1	AY.82	0.001357
M	17	L17L	ctT	ctC	1	1	AY.84	0.000437
M	17	L17L	ctT	ctA	1	1	AY.87	0.000833
M	17	L17F	Ctt	Ttt	1	1	AY.89	0.004902
M	17	L17del	CTT	---	1	1	AY.9	0.000068
M	17	L17F	Ctt	Ttt	1	1	AY.9	0.000068
M	17	L17S	CTT	TCG	1	1	AY.9.2	0.000037
M	17	L17L	ctT	ctC	1	1	AY.9.2	0.000037
M	17	L17L	ctT	ctC	1	1	AY.98	0.000079
M	17	L17L	ctT	ctC	1	1	AY.98.1	0.000048
M	17	L17L	ctT	ctC	1	1	AY.99	0.001049
M	17	L17F	Ctt	Ttt	1	1	B	0.000128
M	17	L17Y	CTt	TAt	1	1	B.1	0.000009
M	17	L17P	cTt	cCt	1	1	B.1	0.000009
M	17	L17R	cTt	cGt	1	1	B.1	0.000009
M	17	L17V	Ctt	Gtt	1	1	B.1	0.000009
M	17	L17F	Ctt	Ttt	1	1	B.1.1.1	0.000327
M	17	L17del	CTT	---	1	1	B.1.1.139	0.022727
M	17	L17F	Ctt	Ttt	1	1	B.1.1.192	0.002309
M	17	L17F	Ctt	Ttt	1	1	B.1.1.222	0.000204
M	17	L17I	Ctt	Att	1	1	B.1.1.263	0.001558
M	17	L17L	ctT	ctC	1	1	B.1.1.263	0.001558
M	17	L17F	Ctt	Ttt	1	1	B.1.1.266	0.012195
M	17	L17del	CTT	---	1	1	B.1.1.288	0.001916
M	17	L17F	Ctt	Ttt	1	1	B.1.1.305	0.003861
M	17	L17F	Ctt	Ttt	1	1	B.1.1.311	0.000358
M	17	L17del	CTT	---	1	1	B.1.1.312	0.001912
M	17	L17F	Ctt	Ttt	1	1	B.1.1.317	0.000412
M	17	L17F	Ctt	Ttt	1	1	B.1.1.338	0.017241
M	17	L17F	Ctt	Ttt	1	1	B.1.1.37	0.000193
M	17	L17S	CTt	AGt	1	1	B.1.1.398	0.003226
M	17	L17F	Ctt	Ttt	1	1	B.1.1.40	0.034483
M	17	L17I	Ctt	Att	1	1	B.1.1.413	0.006897
M	17	L17I	Ctt	Att	1	1	B.1.1.416	0.000905
M	17	L17del	CTT	---	1	1	B.1.1.432	0.001266
M	17	L17F	Ctt	Ttt	1	1	B.1.1.434	0.000349
M	17	L17F	Ctt	Ttt	1	1	B.1.1.447	0.035714
M	17	L17F	Ctt	Ttt	1	1	B.1.1.464	0.001473
M	17	L17L	ctT	ctC	1	1	B.1.1.464	0.001473
M	17	L17F	Ctt	Ttt	1	1	B.1.1.63	0.000386
M	17	L17A	CTt	GCt	1	1	B.1.1.7	0.000001
M	17	L17Y	CTt	TAt	1	1	B.1.1.7	0.000001
M	17	L17del1	cTt	c-t	1	1	B.1.1.7	0.000001
M	17	L17F	Ctt	Ttt	1	1	B.1.110.3	0.000718
M	17	L17F	Ctt	Ttt	1	1	B.1.160.22	0.006757
M	17	L17F	Ctt	Ttt	1	1	B.1.160.28	0.002924
M	17	L17del	CTT	---	1	1	B.1.161	0.017241
M	17	L17P	cTt	cCt	1	1	B.1.177	0.000013
M	17	L17I	Ctt	Att	1	1	B.1.177	0.000013
M	17	L17del	CTT	---	1	1	B.1.177.10	0.000878
M	17	L17del2	CTt	--t	1	1	B.1.177.16	0.000664
M	17	L17F	Ctt	Ttt	1	1	B.1.177.50	0.004695
M	17	L17L	ctT	ctC	1	1	B.1.177.53	0.002392
M	17	L17F	Ctt	Ttt	1	1	B.1.177.65	0.000665
M	17	L17F	Ctt	Ttt	1	1	B.1.177.7	0.000165
M	17	L17L	ctT	ctC	1	1	B.1.177.81	0.000189
M	17	L17del	CTT	---	1	1	B.1.177.83	0.001481
M	17	L17del	CTT	---	1	1	B.1.2	0.000009
M	17	L17L	ctT	ctC	1	1	B.1.206	0.000816
M	17	L17F	Ctt	Ttt	1	1	B.1.210	0.002132
M	17	L17F	Ctt	Ttt	1	1	B.1.214.2	0.0006
M	17	L17F	Ctt	Ttt	1	1	B.1.222	0.001692
M	17	L17del	CTT	---	1	1	B.1.23	0.006061
M	17	L17F	Ctt	Ttt	1	1	B.1.237	0.004975
M	17	L17L	ctT	ctC	1	1	B.1.240	0.000216
M	17	L17L	ctT	ctC	1	1	B.1.258	0.000067
M	17	L17del	CTT	---	1	1	B.1.258	0.000067
M	17	L17del	CTT	---	1	1	B.1.258.16	0.001637
M	17	L17L	ctT	ctC	1	1	B.1.258.17	0.000104
M	17	L17I	Ctt	Att	1	1	B.1.258.3	0.001675
M	17	L17L	ctT	ctG	1	1	B.1.338	0.008621
M	17	L17F	Ctt	Ttt	1	1	B.1.349	0.000715
M	17	L17I	Ctt	Att	1	1	B.1.351	0.00003
M	17	L17L	ctT	ctC	1	1	B.1.351	0.00003
M	17	L17I	Ctt	Att	1	1	B.1.36.10	0.004785
M	17	L17L	ctT	ctC	1	1	B.1.36.17	0.000494
M	17	L17F	Ctt	Ttt	1	1	B.1.36.18	0.00042
M	17	L17F	Ctt	Ttt	1	1	B.1.36.29	0.000517
M	17	L17del	CTT	---	1	1	B.1.369	0.000285
M	17	L17F	Ctt	Ttt	1	1	B.1.377	0.004566
M	17	L17F	Ctt	Ttt	1	1	B.1.389	0.001002
M	17	L17F	Ctt	Ttt	1	1	B.1.396	0.000706
M	17	L17F	Ctt	Ttt	1	1	B.1.399	0.001934
M	17	L17F	Ctt	Ttt	1	1	B.1.400	0.000429
M	17	L17F	Ctt	Ttt	1	1	B.1.422	0.000812
M	17	L17F	Ctt	Ttt	1	1	B.1.426	0.001009
M	17	L17del	CTT	---	1	1	B.1.433	0.003195
M	17	L17F	Ctt	Ttt	1	1	B.1.480	0.002488
M	17	L17I	Ctt	Att	1	1	B.1.490	0.1
M	17	L17F	Ctt	Ttt	1	1	B.1.509	0.000866
M	17	L17Q	cTT	cAA	1	1	B.1.525	0.000113
M	17	L17I	Ctt	Att	1	1	B.1.526	0.000024
M	17	L17L	ctT	ctC	1	1	B.1.551	0.00129
M	17	L17L	ctT	ctC	1	1	B.1.564	0.000426
M	17	L17F	Ctt	Ttt	1	1	B.1.581	0.009434
M	17	L17I	Ctt	Att	1	1	B.1.609	0.000479
M	17	L17L	ctT	ctA	1	1	B.1.609	0.000479
M	17	L17F	Ctt	Ttt	1	1	B.1.612	0.002653
M	17	L17I	CtT	AtA	1	1	B.1.617.1	0.000129
M	17	L17H	cTt	cAt	1	1	B.1.617.2	0.000004
M	17	L17del	CTT	---	1	1	B.1.617.2	0.000004
M	17	L17I	Ctt	Att	1	1	B.1.617.2	0.000004
M	17	L17F	Ctt	Ttt	1	1	B.1.88.1	0.004808
M	17	L17F	Ctt	Ttt	1	1	B.3	0.000831
M	17	L17P	cTt	cCt	1	1	B.4	0.002208
M	17	L17F	Ctt	Ttt	1	1	B.40	0.000364
M	17	L17F	Ctt	Ttt	1	1	C.16	0.00106
M	17	L17L	ctT	ctC	1	1	D.2	0.000075
M	17	L17P	cTt	cCt	1	1	P.1	0.000016
M	17	L17V	Ctt	Gtt	1	1	P.1.12	0.000484
M	17	L17I	Ctt	Att	1	1	P.1.12	0.000484
M	17	L17L	ctT	ctC	1	1	P.1.14	0.000048
M	17	L17del	CTT	---	1	1	P.1.15	0.000232
M	17	L17F	Ctt	Ttt	1	1	P.1.16	0.000374
M	17	L17L	ctT	ctC	1	1	P.1.17.1	0.000875
M	17	L17L	ctT	ctC	1	1	Q.1	0.000126
M	17	L17del	CTT	---	1	1	Q.2	0.000613
M	17	L17F	Ctt	Ttt	1	1	Q.3	0.000145
M	17	L17F	Ctt	Ttt	1	1	Q.4	0.000455
M	17	L17P	cTt	cCt	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.