CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 40

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
ORF1ab/nsp2	40	D40D	D220D	syn	gaC	gaT	5359	5359	1	923-925
ORF1ab/nsp2	40	D40Y	D220Y	nonsyn	Gac	Tac	945	943	0.997884	923-925
ORF1ab/nsp2	40	D40Y	D220Y	nonsyn	GaC	TaT	945	2	0.0021164	923-925
ORF1ab/nsp2	40	D40N	D220N	nonsyn	Gac	Aac	695	694	0.998561	923-925
ORF1ab/nsp2	40	D40N	D220N	nonsyn	GaC	AaT	695	1	0.00143885	923-925
ORF1ab/nsp2	40	D40E	D220E	nonsyn	gaC	gaA	83	82	0.987952	923-925
ORF1ab/nsp2	40	D40E	D220E	nonsyn	gaC	gaG	83	1	0.0120482	923-925
ORF1ab/nsp2	40	D40G	D220G	nonsyn	gAc	gGc	70	70	1	923-925
ORF1ab/nsp2	40	D40del	D220del	del	GAC	---	45	45	1	923-925
ORF1ab/nsp2	40	D40A	D220A	nonsyn	gAc	gCc	11	11	1	923-925
ORF1ab/nsp2	40	D40H	D220H	nonsyn	Gac	Cac	3	3	1	923-925
ORF1ab/nsp2	40	D40F	D220F	nonsyn	GAc	TTc	1	1	1	923-925

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
ORF1ab/nsp2	40	D40D	gaC	gaT	5359	5359	All	0.001025
ORF1ab/nsp2	40	D40D	gaC	gaT	1918	1918	AY.101	0.940657
ORF1ab/nsp2	40	D40Y	Gac	Tac	943	945	All	0.00018
ORF1ab/nsp2	40	D40Y	GaC	TaT	2	945	All	0
ORF1ab/nsp2	40	D40D	gaC	gaT	840	840	B.1.617.2	0.003163
ORF1ab/nsp2	40	D40N	Gac	Aac	694	695	All	0.000133
ORF1ab/nsp2	40	D40N	GaC	AaT	1	695	All	0
ORF1ab/nsp2	40	D40D	gaC	gaT	521	521	AY.43	0.002308
ORF1ab/nsp2	40	D40Y	Gac	Tac	471	471	AY.103	0.002924
ORF1ab/nsp2	40	D40D	gaC	gaT	422	422	B.1.1.7	0.000378
ORF1ab/nsp2	40	D40D	gaC	gaT	401	401	AY.4	0.000624
ORF1ab/nsp2	40	D40Y	Gac	Tac	362	363	AY.4	0.000563
ORF1ab/nsp2	40	D40Y	GaC	TaT	1	363	AY.4	0.000002
ORF1ab/nsp2	40	D40N	Gac	Aac	360	360	AY.4	0.00056
ORF1ab/nsp2	40	D40D	gaC	gaT	154	154	AY.106	0.051574
ORF1ab/nsp2	40	D40D	gaC	gaT	143	143	A.23.1	0.100704
ORF1ab/nsp2	40	D40D	gaC	gaT	129	129	AY.39.1	0.00511
ORF1ab/nsp2	40	D40D	gaC	gaT	88	88	AY.26	0.002491
ORF1ab/nsp2	40	D40E	gaC	gaA	82	83	All	0.000016
ORF1ab/nsp2	40	D40E	gaC	gaG	1	83	All	0
ORF1ab/nsp2	40	D40D	gaC	gaT	73	73	B.1.2	0.000643
ORF1ab/nsp2	40	D40G	gAc	gGc	70	70	All	0.000013
ORF1ab/nsp2	40	D40N	Gac	Aac	54	54	B.1.1.7	0.000048
ORF1ab/nsp2	40	D40D	gaC	gaT	53	53	B.1	0.000485
ORF1ab/nsp2	40	D40D	gaC	gaT	51	51	AY.103	0.000317
ORF1ab/nsp2	40	D40del	GAC	---	45	45	All	0.000009
ORF1ab/nsp2	40	D40N	Gac	Aac	43	43	B.1.617.2	0.000162
ORF1ab/nsp2	40	D40N	Gac	Aac	39	39	AY.44	0.000237
ORF1ab/nsp2	40	D40D	gaC	gaT	37	37	R.1	0.00333
ORF1ab/nsp2	40	D40Y	Gac	Tac	33	33	AY.44	0.000201
ORF1ab/nsp2	40	D40D	gaC	gaT	32	32	AY.25	0.000192
ORF1ab/nsp2	40	D40G	gAc	gGc	29	29	AY.4	0.000045
ORF1ab/nsp2	40	D40D	gaC	gaT	29	29	B.1.177	0.000382
ORF1ab/nsp2	40	D40D	gaC	gaT	28	28	P.1	0.000441
ORF1ab/nsp2	40	D40D	gaC	gaT	23	23	B.1.526	0.000541
ORF1ab/nsp2	40	D40Y	Gac	Tac	21	21	B.1.1.7	0.000019
ORF1ab/nsp2	40	D40D	gaC	gaT	20	20	AY.20	0.000777
ORF1ab/nsp2	40	D40D	gaC	gaT	19	19	AY.44	0.000116
ORF1ab/nsp2	40	D40N	Gac	Aac	17	17	AY.5	0.000351
ORF1ab/nsp2	40	D40D	gaC	gaT	17	17	B.1.1	0.000308
ORF1ab/nsp2	40	D40D	gaC	gaT	16	16	B.1.575	0.004854
ORF1ab/nsp2	40	D40D	gaC	gaT	15	15	AY.120	0.000558
ORF1ab/nsp2	40	D40N	Gac	Aac	15	15	AY.25	0.00009
ORF1ab/nsp2	40	D40del	GAC	---	15	15	B.1.1.7	0.000013
ORF1ab/nsp2	40	D40D	gaC	gaT	14	14	AY.47	0.000435
ORF1ab/nsp2	40	D40D	gaC	gaT	14	14	B.1.111	0.016451
ORF1ab/nsp2	40	D40D	gaC	gaT	13	13	B.1.177.60	0.00284
ORF1ab/nsp2	40	D40G	gAc	gGc	12	12	B.1.177	0.000158
ORF1ab/nsp2	40	D40A	gAc	gCc	11	11	All	0.000002
ORF1ab/nsp2	40	D40E	gaC	gaA	11	11	AY.5	0.000227
ORF1ab/nsp2	40	D40N	Gac	Aac	10	10	B.1.2	0.000088
ORF1ab/nsp2	40	D40E	gaC	gaA	9	10	B.1.2	0.000079
ORF1ab/nsp2	40	D40E	gaC	gaG	1	10	B.1.2	0.000009
ORF1ab/nsp2	40	D40N	Gac	Aac	8	9	B.1	0.000073
ORF1ab/nsp2	40	D40N	GaC	AaT	1	9	B.1	0.000009
ORF1ab/nsp2	40	D40E	gaC	gaA	9	9	B.1.1.7	0.000008
ORF1ab/nsp2	40	D40D	gaC	gaT	9	9	B.1.351	0.000268
ORF1ab/nsp2	40	D40N	Gac	Aac	8	8	AY.47	0.000249
ORF1ab/nsp2	40	D40D	gaC	gaT	8	8	AY.55	0.007339
ORF1ab/nsp2	40	D40D	gaC	gaT	8	8	B.1.258	0.000532
ORF1ab/nsp2	40	D40N	Gac	Aac	8	8	B.1.258.17	0.000832
ORF1ab/nsp2	40	D40D	gaC	gaT	8	8	B.1.609	0.003835
ORF1ab/nsp2	40	D40Y	Gac	Tac	7	7	AY.3	0.00007
ORF1ab/nsp2	40	D40D	gaC	gaT	7	7	AY.3	0.00007
ORF1ab/nsp2	40	D40N	Gac	Aac	7	7	AY.43	0.000031
ORF1ab/nsp2	40	D40D	gaC	gaT	7	7	AY.75	0.000392
ORF1ab/nsp2	40	D40N	Gac	Aac	7	7	B.1.1	0.000127
ORF1ab/nsp2	40	D40D	gaC	gaT	7	7	B.1.1.327	0.7
ORF1ab/nsp2	40	D40E	gaC	gaA	7	7	B.1.1.519	0.000278
ORF1ab/nsp2	40	D40E	gaC	gaA	7	7	B.1.617.2	0.000026
ORF1ab/nsp2	40	D40D	gaC	gaT	7	7	C.37	0.000812
ORF1ab/nsp2	40	D40N	Gac	Aac	6	6	AY.103	0.000037
ORF1ab/nsp2	40	D40E	gaC	gaA	6	6	AY.119	0.000212
ORF1ab/nsp2	40	D40D	gaC	gaT	6	6	AY.33	0.000401
ORF1ab/nsp2	40	D40E	gaC	gaA	6	6	AY.4	0.000009
ORF1ab/nsp2	40	D40D	gaC	gaT	6	6	AY.41	0.001764
ORF1ab/nsp2	40	D40N	Gac	Aac	6	6	B.1.428	0.006122
ORF1ab/nsp2	40	D40D	gaC	gaT	6	6	B.1.596	0.000523
ORF1ab/nsp2	40	D40Y	Gac	Tac	6	6	B.1.617.2	0.000023
ORF1ab/nsp2	40	D40D	gaC	gaT	6	6	B.1.621	0.000531
ORF1ab/nsp2	40	D40N	Gac	Aac	6	6	P.1	0.000095
ORF1ab/nsp2	40	D40D	gaC	gaT	6	6	P.1.7	0.001916
ORF1ab/nsp2	40	D40D	gaC	gaT	6	6	Q.8	0.000989
ORF1ab/nsp2	40	D40D	gaC	gaT	5	5	AY.117	0.000423
ORF1ab/nsp2	40	D40N	Gac	Aac	5	5	AY.20	0.000194
ORF1ab/nsp2	40	D40N	Gac	Aac	5	5	AY.29	0.000079
ORF1ab/nsp2	40	D40D	gaC	gaT	5	5	AY.34	0.000485
ORF1ab/nsp2	40	D40D	gaC	gaT	5	5	AY.46.6	0.000361
ORF1ab/nsp2	40	D40D	gaC	gaT	5	5	AY.99.2	0.000461
ORF1ab/nsp2	40	D40del	GAC	---	5	5	B.1.1.33	0.002104
ORF1ab/nsp2	40	D40N	Gac	Aac	5	5	B.1.177	0.000066
ORF1ab/nsp2	40	D40D	gaC	gaT	5	5	B.1.243	0.000348
ORF1ab/nsp2	40	D40D	gaC	gaT	5	5	B.1.397	0.024272
ORF1ab/nsp2	40	D40N	Gac	Aac	5	5	B.1.526	0.000118
ORF1ab/nsp2	40	D40Y	Gac	Tac	5	5	B.1.526	0.000118
ORF1ab/nsp2	40	D40D	gaC	gaT	5	5	B.1.564	0.002129
ORF1ab/nsp2	40	D40N	Gac	Aac	5	5	B.1.621	0.000443
ORF1ab/nsp2	40	D40D	gaC	gaT	4	4	AY.111	0.000733
ORF1ab/nsp2	40	D40N	Gac	Aac	4	4	AY.14	0.000352
ORF1ab/nsp2	40	D40D	gaC	gaT	4	4	AY.42	0.000161
ORF1ab/nsp2	40	D40Y	Gac	Tac	3	4	AY.43	0.000013
ORF1ab/nsp2	40	D40Y	GaC	TaT	1	4	AY.43	0.000004
ORF1ab/nsp2	40	D40D	gaC	gaT	4	4	AY.45	0.000487
ORF1ab/nsp2	40	D40D	gaC	gaT	4	4	AY.46	0.000416
ORF1ab/nsp2	40	D40G	gAc	gGc	4	4	AY.5.3	0.00135
ORF1ab/nsp2	40	D40D	gaC	gaT	4	4	AY.6	0.000165
ORF1ab/nsp2	40	D40del	GAC	---	4	4	B.1.1.348	0.003185
ORF1ab/nsp2	40	D40N	Gac	Aac	4	4	B.1.177.87	0.002911
ORF1ab/nsp2	40	D40N	Gac	Aac	4	4	B.1.265	0.005083
ORF1ab/nsp2	40	D40D	gaC	gaT	4	4	B.1.429	0.000094
ORF1ab/nsp2	40	D40D	gaC	gaT	4	4	B.1.497	0.001259
ORF1ab/nsp2	40	D40G	gAc	gGc	4	4	P.1	0.000063
ORF1ab/nsp2	40	D40H	Gac	Cac	3	3	All	0.000001
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	AY.102	0.00008
ORF1ab/nsp2	40	D40E	gaC	gaA	3	3	AY.102	0.00008
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	AY.119	0.000106
ORF1ab/nsp2	40	D40E	gaC	gaA	3	3	AY.25	0.000018
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	AY.29	0.000047
ORF1ab/nsp2	40	D40N	Gac	Aac	3	3	AY.3	0.00003
ORF1ab/nsp2	40	D40E	gaC	gaA	3	3	AY.4.2.1	0.000447
ORF1ab/nsp2	40	D40G	gAc	gGc	3	3	AY.44	0.000018
ORF1ab/nsp2	40	D40N	Gac	Aac	3	3	AY.75.1	0.000541
ORF1ab/nsp2	40	D40N	Gac	Aac	3	3	AY.9.2	0.00011
ORF1ab/nsp2	40	D40Y	Gac	Tac	3	3	AY.98.1	0.000145
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	B.1.1.176	0.001318
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	B.1.1.25	0.001706
ORF1ab/nsp2	40	D40N	Gac	Aac	3	3	B.1.1.519	0.000119
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	B.1.351.2	0.000908
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	B.1.400	0.001287
ORF1ab/nsp2	40	D40N	Gac	Aac	3	3	B.1.466.2	0.001174
ORF1ab/nsp2	40	D40A	gAc	gCc	3	3	B.1.617.2	0.000011
ORF1ab/nsp2	40	D40G	gAc	gGc	3	3	B.1.617.2	0.000011
ORF1ab/nsp2	40	D40D	gaC	gaT	3	3	D.2	0.000225
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	AU.1	0.002532
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.113	0.000285
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	AY.120	0.000074
ORF1ab/nsp2	40	D40E	gaC	gaA	2	2	AY.23	0.000139
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	AY.23	0.000139
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	AY.27	0.000129
ORF1ab/nsp2	40	D40Y	Gac	Tac	2	2	AY.29	0.000032
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.3.1	0.000171
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.30	0.000791
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.32	0.001065
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.39	0.000049
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	AY.39.1	0.000079
ORF1ab/nsp2	40	D40del	GAC	---	2	2	AY.4	0.000003
ORF1ab/nsp2	40	D40E	gaC	gaA	2	2	AY.4.2	0.000043
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.4.2	0.000043
ORF1ab/nsp2	40	D40E	gaC	gaA	2	2	AY.5.4	0.000553
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.53	0.000575
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	AY.54	0.000191
ORF1ab/nsp2	40	D40H	Gac	Cac	2	2	AY.6	0.000082
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.9.2	0.000073
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	AY.92	0.000575
ORF1ab/nsp2	40	D40Y	Gac	Tac	2	2	AY.94	0.000885
ORF1ab/nsp2	40	D40Y	Gac	Tac	2	2	AY.99.2	0.000184
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B	0.000256
ORF1ab/nsp2	40	D40E	gaC	gaA	2	2	B.1	0.000018
ORF1ab/nsp2	40	D40Y	Gac	Tac	2	2	B.1	0.000018
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	B.1.1.214	0.000111
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.1.28	0.000622
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	B.1.1.391	0.017094
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.1.409	0.005666
ORF1ab/nsp2	40	D40E	gaC	gaA	2	2	B.1.177	0.000026
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.177.15	0.001262
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.258.11	0.000793
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.258.17	0.000208
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.302	0.026667
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.36	0.000292
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	B.1.369	0.00057
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	B.1.413	0.008511
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.427	0.000101
ORF1ab/nsp2	40	D40N	Gac	Aac	2	2	B.1.429	0.000047
ORF1ab/nsp2	40	D40Y	Gac	Tac	2	2	B.1.429	0.000047
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.617.1	0.000258
ORF1ab/nsp2	40	D40del	GAC	---	2	2	B.1.617.2	0.000008
ORF1ab/nsp2	40	D40D	gaC	gaT	2	2	B.1.628	0.000705
ORF1ab/nsp2	40	D40Y	Gac	Tac	2	2	C.37	0.000232
ORF1ab/nsp2	40	D40del	GAC	---	2	2	N.4	0.008511
ORF1ab/nsp2	40	D40del	GAC	---	2	2	N.6	0.014184
ORF1ab/nsp2	40	D40Y	Gac	Tac	2	2	P.1.14	0.000096
ORF1ab/nsp2	40	D40del	GAC	---	2	2	P.2	0.000373
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1		0.055556
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	A	0.000387
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	A.1	0.000282
ORF1ab/nsp2	40	D40del	GAC	---	1	1	A.2.2	0.001689
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	A.2.5	0.000499
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AD.2	0.000219
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AE.8	0.000489
ORF1ab/nsp2	40	D40F	GAc	TTc	1	1	All	0
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	AU.2	0.002421
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.100	0.000046
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	AY.102	0.000027
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.108	0.001103
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.110	0.000113
ORF1ab/nsp2	40	D40del	GAC	---	1	1	AY.111	0.000183
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	AY.113	0.000142
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	AY.116	0.000287
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.116	0.000287
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.116.1	0.000311
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	AY.118	0.000063
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.118	0.000063
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	AY.119	0.000035
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1	AY.20	0.000039
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.21	0.001898
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.23	0.00007
ORF1ab/nsp2	40	D40del	GAC	---	1	1	AY.25	0.000006
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	AY.26	0.000028
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1	AY.29	0.000016
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	AY.29	0.000016
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.30	0.000396
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.36	0.000148
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	AY.37	0.000316
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	AY.4	0.000002
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1	AY.4.5	0.000107
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.4.5	0.000107
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.40	0.000964
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	AY.42	0.00004
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.42	0.00004
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	AY.43	0.000004
ORF1ab/nsp2	40	D40del	GAC	---	1	1	AY.43	0.000004
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	AY.43	0.000004
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1	AY.44	0.000006
ORF1ab/nsp2	40	D40H	Gac	Cac	1	1	AY.44	0.000006
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	AY.44	0.000006
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.45	0.000122
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1	AY.46	0.000104
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	AY.46.1	0.001027
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.46.4	0.000165
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.46.5	0.000198
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.5	0.000021
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.5.3	0.000337
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	AY.54	0.000095
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1	AY.61	0.000105
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.66	0.00107
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	AY.67	0.000464
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.68	0.000274
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	AY.68	0.000274
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.7	0.000196
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.89	0.004902
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.9.1	0.000084
ORF1ab/nsp2	40	D40E	gaC	gaA	1	1	AY.9.1	0.000084
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.92	0.000287
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AY.96	0.002075
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	AY.98.1	0.000048
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	AY.98.1	0.000048
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	AZ.2	0.000821
ORF1ab/nsp2	40	D40del	GAC	---	1	1	B.1	0.000009
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	B.1	0.000009
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	B.1.1	0.000018
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.1.10	0.001115
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	B.1.1.161	0.003534
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.1.243	0.004082
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.1.294	0.001266
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.1.317	0.000412
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.1.354	0.004386
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.1.378	0.007299
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.1.409	0.002833
ORF1ab/nsp2	40	D40del	GAC	---	1	1	B.1.1.420	0.001006
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.1.420	0.001006
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	B.1.1.434	0.000349
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.1.519	0.00004
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.1.519	0.00004
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.1.526	0.003546
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.1.63	0.000386
ORF1ab/nsp2	40	D40F	GAc	TTc	1	1	B.1.1.63	0.000386
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	B.1.1.7	0.000001
ORF1ab/nsp2	40	D40A	gAc	gCc	1	1	B.1.1.7	0.000001
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.139	0.000733
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.160	0.000031
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.177	0.000013
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.177.44	0.000519
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.177.54	0.000606
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.177.57	0.000281
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.177.57	0.000281
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.177.58	0.001332
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	B.1.177.81	0.000189
ORF1ab/nsp2	40	D40del	GAC	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.177.83	0.001481
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.2	0.000009
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	B.1.221	0.000071
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.221.1	0.002907
ORF1ab/nsp2	40	D40del	GAC	---	1	1	B.1.23	0.006061
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.234	0.000132
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.240	0.000216
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.240	0.000216
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.243	0.00007
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.258	0.000067
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.265	0.001271
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.305	0.002151
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.311	0.000275
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.324	0.001605
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.338	0.008621
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.350	0.002933
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.351	0.00003
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.36.1	0.00114
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.36.10	0.004785
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.36.18	0.00042
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.36.19	0.009259
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.36.31	0.001751
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.36.7	0.004
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.396	0.000706
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.422	0.000812
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.427	0.00005
ORF1ab/nsp2	40	D40del	GAC	---	1	1	B.1.429	0.000024
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.466.2	0.000391
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.505	0.004386
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.516	0.001957
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.517	0.000427
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.560	0.00463
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.561	0.000397
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.564.1	0.001577
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.580	0.004065
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.595	0.000261
ORF1ab/nsp2	40	D40del	GAC	---	1	1	B.1.617.3	0.002985
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.619.1	0.000641
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	B.1.621.1	0.000506
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.628	0.000352
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.1.637	0.000073
ORF1ab/nsp2	40	D40Y	Gac	Tac	1	1	B.1.93	0.000934
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	B.6	0.00091
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	C.1	0.002392
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	C.12	0.007194
ORF1ab/nsp2	40	D40del	GAC	---	1	1	C.35	0.000774
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	C.36.3	0.000567
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	C.36.3	0.000567
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	P.1.10	0.000269
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	P.1.14	0.000048
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	P.1.15	0.000232
ORF1ab/nsp2	40	D40G	gAc	gGc	1	1	P.1.15	0.000232
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	P.1.17	0.000162
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	P.3	0.001595
ORF1ab/nsp2	40	D40N	Gac	Aac	1	1	Q.1	0.000126
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	Q.1	0.000126
ORF1ab/nsp2	40	D40D	gaC	gaT	1	1	Q.3	0.000145

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.