CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 268

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	268	D268del	D448del	del	GAC	---	2740	2740	1	1607-1609
ORF1ab/nsp2	268	D268D	D448D	syn	gaC	gaT	2272	2272	1	1607-1609
ORF1ab/nsp2	268	D268G	D448G	nonsyn	gAc	gGc	230	228	0.991304	1607-1609
ORF1ab/nsp2	268	D268G	D448G	nonsyn	gAC	gGT	230	1	0.00434783	1607-1609
ORF1ab/nsp2	268	D268G	D448G	nonsyn	gAC	gGA	230	1	0.00434783	1607-1609
ORF1ab/nsp2	268	D268N	D448N	nonsyn	Gac	Aac	201	200	0.995025	1607-1609
ORF1ab/nsp2	268	D268N	D448N	nonsyn	GaC	AaT	201	1	0.00497512	1607-1609
ORF1ab/nsp2	268	D268E	D448E	nonsyn	gaC	gaA	96	94	0.979167	1607-1609
ORF1ab/nsp2	268	D268E	D448E	nonsyn	gaC	gaG	96	2	0.0208333	1607-1609
ORF1ab/nsp2	268	D268Y	D448Y	nonsyn	Gac	Tac	53	53	1	1607-1609
ORF1ab/nsp2	268	D268A	D448A	nonsyn	gAc	gCc	27	27	1	1607-1609
ORF1ab/nsp2	268	D268V	D448V	nonsyn	gAc	gTc	7	6	0.857143	1607-1609
ORF1ab/nsp2	268	D268V	D448V	nonsyn	gAC	gTG	7	1	0.142857	1607-1609
ORF1ab/nsp2	268	D268H	D448H	nonsyn	Gac	Cac	5	5	1	1607-1609
ORF1ab/nsp2	268	D268S	D448S	nonsyn	GAc	AGc	3	2	0.666667	1607-1609
ORF1ab/nsp2	268	D268S	D448S	nonsyn	GAc	TCc	3	1	0.333333	1607-1609
ORF1ab/nsp2	268	D268del1	D448del1	del	Gac	-ac	2	2	1	1607-1609
ORF1ab/nsp2	268	D268F	D448F	nonsyn	GAc	TTc	1	1	1	1607-1609
ORF1ab/nsp2	268	D268I	D448I	nonsyn	GAc	ATc	1	1	1	1607-1609
ORF1ab/nsp2	268	D268T	D448T	nonsyn	GAc	ACc	1	1	1	1607-1609

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	268	D268del	GAC	---	2740	2740	All	0.000524
ORF1ab/nsp2	268	D268D	gaC	gaT	2272	2272	All	0.000435
ORF1ab/nsp2	268	D268D	gaC	gaT	1180	1180	B.1.1.7	0.001056
ORF1ab/nsp2	268	D268del	GAC	---	646	646	B	0.082566
ORF1ab/nsp2	268	D268del	GAC	---	312	312	B.23	0.912281
ORF1ab/nsp2	268	D268del	GAC	---	257	257	B.45	0.984674
ORF1ab/nsp2	268	D268G	gAc	gGc	228	230	All	0.000044
ORF1ab/nsp2	268	D268G	gAC	gGA	1	230	All	0
ORF1ab/nsp2	268	D268G	gAC	gGT	1	230	All	0
ORF1ab/nsp2	268	D268del	GAC	---	228	228	B.55	0.672566
ORF1ab/nsp2	268	D268N	Gac	Aac	200	201	All	0.000038
ORF1ab/nsp2	268	D268N	GaC	AaT	1	201	All	0
ORF1ab/nsp2	268	D268del	GAC	---	176	176	B.11	0.902564
ORF1ab/nsp2	268	D268del	GAC	---	128	128	C.23	0.744186
ORF1ab/nsp2	268	D268del	GAC	---	117	117	B.10	0.966942
ORF1ab/nsp2	268	D268N	Gac	Aac	104	104	B.1	0.000953
ORF1ab/nsp2	268	D268E	gaC	gaA	94	96	All	0.000018
ORF1ab/nsp2	268	D268E	gaC	gaG	2	96	All	0
ORF1ab/nsp2	268	D268del	GAC	---	88	88	B.52	0.888889
ORF1ab/nsp2	268	D268D	gaC	gaT	82	82	AY.4	0.000128
ORF1ab/nsp2	268	D268del	GAC	---	67	67	B.1.617.2	0.000252
ORF1ab/nsp2	268	D268D	gaC	gaT	65	65	B.1.617.2	0.000245
ORF1ab/nsp2	268	D268D	gaC	gaT	60	60	AY.20	0.002332
ORF1ab/nsp2	268	D268del	GAC	---	60	60	P.1.1	0.01906
ORF1ab/nsp2	268	D268del	GAC	---	58	58	B.27	0.892308
ORF1ab/nsp2	268	D268D	gaC	gaT	57	57	B.1	0.000522
ORF1ab/nsp2	268	D268del	GAC	---	56	56	B.57	0.848485
ORF1ab/nsp2	268	D268G	gAc	gGc	55	55	AY.44	0.000335
ORF1ab/nsp2	268	D268del	GAC	---	55	55	B.15	0.964912
ORF1ab/nsp2	268	D268Y	Gac	Tac	53	53	All	0.00001
ORF1ab/nsp2	268	D268E	gaC	gaA	53	53	AY.25	0.000319
ORF1ab/nsp2	268	D268D	gaC	gaT	52	52	AY.25	0.000313
ORF1ab/nsp2	268	D268G	gAc	gGc	48	48	B.1.177	0.000632
ORF1ab/nsp2	268	D268D	gaC	gaT	46	46	AY.103	0.000286
ORF1ab/nsp2	268	D268del	GAC	---	46	46	B.1.177.86	0.008439
ORF1ab/nsp2	268	D268G	gAc	gGc	46	46	B.1.617.2	0.000173
ORF1ab/nsp2	268	D268D	gaC	gaT	45	45	AY.44	0.000274
ORF1ab/nsp2	268	D268del	GAC	---	43	43	B.1	0.000394
ORF1ab/nsp2	268	D268del	GAC	---	43	43	B.26	0.632353
ORF1ab/nsp2	268	D268D	gaC	gaT	41	41	AY.26	0.001161
ORF1ab/nsp2	268	D268D	gaC	gaT	39	39	B.1.2	0.000343
ORF1ab/nsp2	268	D268del	GAC	---	38	38	B.1.1	0.000689
ORF1ab/nsp2	268	D268D	gaC	gaT	38	38	B.1.160	0.001185
ORF1ab/nsp2	268	D268del	GAC	---	38	38	B.47	0.77551
ORF1ab/nsp2	268	D268D	gaC	gaT	36	36	B.1.1	0.000653
ORF1ab/nsp2	268	D268del	GAC	---	33	33	B.1.1.7	0.00003
ORF1ab/nsp2	268	D268D	gaC	gaT	31	31	P.1	0.000488
ORF1ab/nsp2	268	D268del	GAC	---	29	29	AY.98	0.002291
ORF1ab/nsp2	268	D268A	gAc	gCc	27	27	All	0.000005
ORF1ab/nsp2	268	D268D	gaC	gaT	25	25	AY.43	0.000111
ORF1ab/nsp2	268	D268D	gaC	gaT	25	25	B.1.1.222	0.0051
ORF1ab/nsp2	268	D268D	gaC	gaT	25	25	B.1.177	0.000329
ORF1ab/nsp2	268	D268G	gAc	gGc	22	22	B.1.2	0.000194
ORF1ab/nsp2	268	D268D	gaC	gaT	20	20	AY.6	0.000823
ORF1ab/nsp2	268	D268del	GAC	---	20	20	B.49	1
ORF1ab/nsp2	268	D268del	GAC	---	20	20	P.1	0.000315
ORF1ab/nsp2	268	D268D	gaC	gaT	20	20	Q.1	0.002527
ORF1ab/nsp2	268	D268G	gAc	gGc	19	19	B.1.1.7	0.000017
ORF1ab/nsp2	268	D268D	gaC	gaT	19	19	C.37	0.002205
ORF1ab/nsp2	268	D268D	gaC	gaT	18	18	AY.9.2	0.000661
ORF1ab/nsp2	268	D268D	gaC	gaT	17	17	AY.39	0.00042
ORF1ab/nsp2	268	D268Y	Gac	Tac	15	15	D.2	0.001126
ORF1ab/nsp2	268	D268D	gaC	gaT	13	13	AY.2	0.00463
ORF1ab/nsp2	268	D268D	gaC	gaT	12	12	AY.102	0.000318
ORF1ab/nsp2	268	D268E	gaC	gaA	11	11	AY.4	0.000017
ORF1ab/nsp2	268	D268D	gaC	gaT	11	11	AY.47	0.000342
ORF1ab/nsp2	268	D268del	GAC	---	11	11	B.1.2	0.000097
ORF1ab/nsp2	268	D268D	gaC	gaT	10	10	A.27	0.016556
ORF1ab/nsp2	268	D268del	GAC	---	10	10	AY.3	0.000099
ORF1ab/nsp2	268	D268del	GAC	---	10	10	AY.4	0.000016
ORF1ab/nsp2	268	D268D	gaC	gaT	10	10	B.1.221	0.00071
ORF1ab/nsp2	268	D268D	gaC	gaT	10	10	P.1.4	0.009766
ORF1ab/nsp2	268	D268del	GAC	---	9	9	AY.44	0.000055
ORF1ab/nsp2	268	D268D	gaC	gaT	9	9	B.1.369	0.002567
ORF1ab/nsp2	268	D268N	Gac	Aac	8	8	AY.103	0.00005
ORF1ab/nsp2	268	D268D	gaC	gaT	8	8	AY.117	0.000676
ORF1ab/nsp2	268	D268del	GAC	---	8	8	AY.20	0.000311
ORF1ab/nsp2	268	D268del	GAC	---	8	8	B.1.1.1	0.002614
ORF1ab/nsp2	268	D268D	gaC	gaT	8	8	B.1.177.4	0.001688
ORF1ab/nsp2	268	D268N	Gac	Aac	8	8	B.1.617.2	0.00003
ORF1ab/nsp2	268	D268del	GAC	---	8	8	C.37	0.000929
ORF1ab/nsp2	268	D268V	gAc	gTc	6	7	All	0.000001
ORF1ab/nsp2	268	D268V	gAC	gTG	1	7	All	0
ORF1ab/nsp2	268	D268D	gaC	gaT	7	7	AY.29	0.00011
ORF1ab/nsp2	268	D268N	Gac	Aac	7	7	AY.4	0.000011
ORF1ab/nsp2	268	D268N	Gac	Aac	7	7	B.1.1.7	0.000006
ORF1ab/nsp2	268	D268del	GAC	---	7	7	B.1.258	0.000466
ORF1ab/nsp2	268	D268D	gaC	gaT	7	7	B.1.351	0.000208
ORF1ab/nsp2	268	D268D	gaC	gaT	7	7	B.1.526	0.000165
ORF1ab/nsp2	268	D268G	gAc	gGc	6	6	AY.103	0.000037
ORF1ab/nsp2	268	D268D	gaC	gaT	6	6	AY.33	0.000401
ORF1ab/nsp2	268	D268E	gaC	gaA	6	6	AY.36	0.000889
ORF1ab/nsp2	268	D268Y	Gac	Tac	6	6	AY.4	0.000009
ORF1ab/nsp2	268	D268Y	Gac	Tac	6	6	B.1	0.000055
ORF1ab/nsp2	268	D268del	GAC	---	6	6	B.1.1.434	0.002091
ORF1ab/nsp2	268	D268H	Gac	Cac	5	5	All	0.000001
ORF1ab/nsp2	268	D268del	GAC	---	5	5	AY.103	0.000031
ORF1ab/nsp2	268	D268D	gaC	gaT	5	5	AY.119	0.000177
ORF1ab/nsp2	268	D268G	gAc	gGc	5	5	AY.119	0.000177
ORF1ab/nsp2	268	D268del	GAC	---	5	5	AY.26	0.000142
ORF1ab/nsp2	268	D268D	gaC	gaT	5	5	AY.71	0.002375
ORF1ab/nsp2	268	D268D	gaC	gaT	5	5	B.1.1.214	0.000277
ORF1ab/nsp2	268	D268D	gaC	gaT	5	5	B.1.1.519	0.000199
ORF1ab/nsp2	268	D268A	gAc	gCc	5	5	B.1.1.7	0.000004
ORF1ab/nsp2	268	D268N	Gac	Aac	5	5	B.1.177	0.000066
ORF1ab/nsp2	268	D268D	gaC	gaT	5	5	B.1.243	0.000348
ORF1ab/nsp2	268	D268D	gaC	gaT	5	5	B.1.628	0.001762
ORF1ab/nsp2	268	D268D	gaC	gaT	5	5	P.2	0.000933
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	AY.100	0.000184
ORF1ab/nsp2	268	D268N	Gac	Aac	4	4	AY.25	0.000024
ORF1ab/nsp2	268	D268E	gaC	gaA	4	4	AY.26	0.000113
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	AY.39.1	0.000158
ORF1ab/nsp2	268	D268A	gAc	gCc	4	4	AY.4	0.000006
ORF1ab/nsp2	268	D268N	Gac	Aac	4	4	AY.43	0.000018
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	AY.65	0.002132
ORF1ab/nsp2	268	D268del	GAC	---	4	4	AY.9.2	0.000147
ORF1ab/nsp2	268	D268A	gAc	gCc	4	4	AY.92	0.001149
ORF1ab/nsp2	268	D268N	Gac	Aac	4	4	B	0.000511
ORF1ab/nsp2	268	D268del	GAC	---	4	4	B.1.1.33	0.001684
ORF1ab/nsp2	268	D268G	gAc	gGc	4	4	B.1.177.58	0.005326
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	B.1.239	0.004884
ORF1ab/nsp2	268	D268N	Gac	Aac	4	4	B.1.258	0.000266
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	B.1.258.17	0.000416
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	B.1.425	0.011976
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	B.1.525	0.000453
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	B.1.582	0.001963
ORF1ab/nsp2	268	D268D	gaC	gaT	4	4	B.1.637	0.000292
ORF1ab/nsp2	268	D268S	GAc	AGc	2	3	All	0
ORF1ab/nsp2	268	D268S	GAc	TCc	1	3	All	0
ORF1ab/nsp2	268	D268del	GAC	---	3	3	AY.110	0.000338
ORF1ab/nsp2	268	D268E	gaC	gaA	3	3	AY.111	0.000549
ORF1ab/nsp2	268	D268G	gAc	gGc	3	3	AY.120	0.000112
ORF1ab/nsp2	268	D268N	Gac	Aac	3	3	AY.29	0.000047
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	AY.3	0.00003
ORF1ab/nsp2	268	D268del	GAC	---	3	3	AY.39	0.000074
ORF1ab/nsp2	268	D268Y	Gac	Tac	3	3	AY.44	0.000018
ORF1ab/nsp2	268	D268N	Gac	Aac	2	3	AY.44	0.000012
ORF1ab/nsp2	268	D268N	GaC	AaT	1	3	AY.44	0.000006
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	AY.98	0.000237
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	AY.99.1	0.004658
ORF1ab/nsp2	268	D268Y	Gac	Tac	3	3	AY.99.2	0.000276
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	AZ.1	0.002602
ORF1ab/nsp2	268	D268N	Gac	Aac	3	3	B.1.1	0.000054
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	B.1.1.241	0.006211
ORF1ab/nsp2	268	D268del	GAC	---	3	3	B.1.1.348	0.002389
ORF1ab/nsp2	268	D268E	gaC	gaA	3	3	B.1.1.7	0.000003
ORF1ab/nsp2	268	D268E	gaC	gaA	3	3	B.1.2	0.000026
ORF1ab/nsp2	268	D268N	Gac	Aac	3	3	B.1.243.1	0.066667
ORF1ab/nsp2	268	D268del	GAC	---	3	3	B.1.284	0.039474
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	B.1.429	0.000071
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	D.2	0.000225
ORF1ab/nsp2	268	D268D	gaC	gaT	3	3	P.1.16	0.001122
ORF1ab/nsp2	268	D268Y	Gac	Tac	2	2		0.111111
ORF1ab/nsp2	268	D268del1	Gac	-ac	2	2	All	0
ORF1ab/nsp2	268	D268Y	Gac	Tac	2	2	AY.103	0.000012
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	AY.107	0.000932
ORF1ab/nsp2	268	D268A	gAc	gCc	2	2	AY.25	0.000012
ORF1ab/nsp2	268	D268del	GAC	---	2	2	AY.29	0.000032
ORF1ab/nsp2	268	D268G	gAc	gGc	2	2	AY.4	0.000003
ORF1ab/nsp2	268	D268E	gaC	gaA	2	2	AY.43	0.000009
ORF1ab/nsp2	268	D268E	gaC	gaA	2	2	AY.47	0.000062
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	AY.5	0.000041
ORF1ab/nsp2	268	D268del	GAC	---	2	2	AY.54	0.000191
ORF1ab/nsp2	268	D268N	Gac	Aac	2	2	AY.75	0.000112
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	AY.83	0.003448
ORF1ab/nsp2	268	D268del	GAC	---	2	2	AY.85	0.000854
ORF1ab/nsp2	268	D268V	gAC	gTG	1	2	AY.85	0.000427
ORF1ab/nsp2	268	D268V	gAc	gTc	1	2	AY.85	0.000427
ORF1ab/nsp2	268	D268del	GAC	---	2	2	AY.9	0.000135
ORF1ab/nsp2	268	D268N	Gac	Aac	2	2	AY.9	0.000135
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	AY.9.1	0.000167
ORF1ab/nsp2	268	D268Y	Gac	Tac	2	2	B.1.1	0.000036
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.1.157	0.001826
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.1.1.28	0.000622
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.1.326	0.003521
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.1.329	0.007692
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.1.1.37	0.000386
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.1.388	0.090909
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.1.1.521	0.010695
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.1.525	0.010929
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.1.1.63	0.000772
ORF1ab/nsp2	268	D268Y	Gac	Tac	2	2	B.1.1.7	0.000002
ORF1ab/nsp2	268	D268N	Gac	Aac	2	2	B.1.160	0.000062
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.160.29	0.008439
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.177.21	0.000153
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.177.32	0.002699
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.177.81	0.000379
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.1.177.81	0.000379
ORF1ab/nsp2	268	D268N	Gac	Aac	2	2	B.1.2	0.000018
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.1.221	0.000142
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.234	0.000264
ORF1ab/nsp2	268	D268N	Gac	Aac	2	2	B.1.234	0.000264
ORF1ab/nsp2	268	D268G	gAc	gGc	2	2	B.1.243	0.000139
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.258	0.000133
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.311	0.000549
ORF1ab/nsp2	268	D268N	Gac	Aac	2	2	B.1.429	0.000047
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.450	0.022727
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.561	0.000794
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.575	0.000607
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.577	0.001375
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.1.595	0.000522
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.596	0.000174
ORF1ab/nsp2	268	D268A	gAc	gCc	2	2	B.1.617.2	0.000008
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.621	0.000177
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.1.93	0.001867
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	B.3	0.001661
ORF1ab/nsp2	268	D268del	GAC	---	2	2	B.4	0.004415
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	C.8	0.008929
ORF1ab/nsp2	268	D268del	GAC	---	2	2	D.2	0.00015
ORF1ab/nsp2	268	D268del	GAC	---	2	2	N.6	0.014184
ORF1ab/nsp2	268	D268D	gaC	gaT	2	2	P.1.12	0.000968
ORF1ab/nsp2	268	D268del	GAC	---	2	2	P.2	0.000373
ORF1ab/nsp2	268	D268T	GAc	ACc	1	1		0.055556
ORF1ab/nsp2	268	D268V	gAc	gTc	1	1		0.055556
ORF1ab/nsp2	268	D268S	GAc	TCc	1	1		0.055556
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1		0.055556
ORF1ab/nsp2	268	D268F	GAc	TTc	1	1		0.055556
ORF1ab/nsp2	268	D268I	GAc	ATc	1	1		0.055556
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1		0.055556
ORF1ab/nsp2	268	D268del	GAC	---	1	1	A	0.000387
ORF1ab/nsp2	268	D268H	Gac	Cac	1	1	A.2.2	0.001689
ORF1ab/nsp2	268	D268del	GAC	---	1	1	A.2.3	0.004739
ORF1ab/nsp2	268	D268del	GAC	---	1	1	A.5	0.001923
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	AD.2	0.000219
ORF1ab/nsp2	268	D268T	GAc	ACc	1	1	All	0
ORF1ab/nsp2	268	D268F	GAc	TTc	1	1	All	0
ORF1ab/nsp2	268	D268I	GAc	ATc	1	1	All	0
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	AY.100	0.000046
ORF1ab/nsp2	268	D268E	gaC	gaA	1	1	AY.103	0.000006
ORF1ab/nsp2	268	D268S	GAc	AGc	1	1	AY.103	0.000006
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	AY.105	0.000643
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.111	0.000183
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.113	0.000142
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	AY.116	0.000287
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.116.1	0.000311
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.118	0.000063
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.120	0.000037
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.13	0.000161
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.16	0.00038
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.16.1	0.00047
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	AY.2	0.000356
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.2	0.000356
ORF1ab/nsp2	268	D268G	gAC	gGT	1	1	AY.20	0.000039
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.24	0.000431
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.25	0.000006
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	AY.25	0.000006
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.27	0.000065
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	AY.29	0.000016
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	AY.3	0.00001
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	AY.3	0.00001
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	AY.3	0.00001
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.34	0.000097
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.35	0.000233
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.36	0.000148
ORF1ab/nsp2	268	D268S	GAc	AGc	1	1	AY.39	0.000025
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.39.1	0.00004
ORF1ab/nsp2	268	D268E	gaC	gaA	1	1	AY.39.1	0.00004
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.4.2	0.000022
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.4.2	0.000022
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.4.3	0.000842
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.4.5	0.000107
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	AY.42	0.00004
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.42	0.00004
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	AY.43	0.000004
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.45	0.000122
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.46.3	0.000934
ORF1ab/nsp2	268	D268H	Gac	Cac	1	1	AY.46.6	0.000072
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	AY.47	0.000031
ORF1ab/nsp2	268	D268E	gaC	gaA	1	1	AY.5	0.000021
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	AY.5	0.000021
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	AY.5	0.000021
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.5.3	0.000337
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.6	0.000041
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.60	0.000938
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	AY.61	0.000105
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.65	0.000533
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.68	0.000274
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.69	0.000187
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.69	0.000187
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.7.2	0.000559
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.70	0.000209
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.70	0.000209
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.72	0.001361
ORF1ab/nsp2	268	D268del	GAC	---	1	1	AY.75	0.000056
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.75.1	0.00018
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.78	0.001541
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.82	0.001357
ORF1ab/nsp2	268	D268G	gAC	gGA	1	1	AY.85	0.000427
ORF1ab/nsp2	268	D268E	gaC	gaG	1	1	AY.85	0.000427
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	AY.9.2	0.000037
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.94	0.000443
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	AY.98.1	0.000048
ORF1ab/nsp2	268	D268del1	Gac	-ac	1	1	B	0.000128
ORF1ab/nsp2	268	D268E	gaC	gaA	1	1	B.1	0.000009
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1	0.000009
ORF1ab/nsp2	268	D268H	Gac	Cac	1	1	B.1	0.000009
ORF1ab/nsp2	268	D268V	gAc	gTc	1	1	B.1	0.000009
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	B.1.1	0.000018
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.1	0.000018
ORF1ab/nsp2	268	D268H	Gac	Cac	1	1	B.1.1	0.000018
ORF1ab/nsp2	268	D268V	gAc	gTc	1	1	B.1.1	0.000018
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.1.1.134	0.011364
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.153	0.001095
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.176	0.000439
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.1.176	0.000439
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.1.189	0.001513
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.1.194	0.00495
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.1.220	0.001859
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	B.1.1.25	0.000569
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.263	0.001558
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.1.274	0.005051
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	B.1.1.284	0.000107
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.284	0.000107
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.1.284	0.000107
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.1.294	0.001266
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.299	0.012195
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.301	0.001179
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.317	0.000412
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.368	0.003086
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.37	0.000193
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.371	0.010417
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.1.375	0.011905
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.1.461	0.012048
ORF1ab/nsp2	268	D268V	gAc	gTc	1	1	B.1.1.7	0.000001
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.111	0.001175
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.127	0.002198
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.146	0.004237
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.157	0.002985
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.157	0.002985
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.177	0.000013
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.1.177	0.000013
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.177.12	0.000152
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	B.1.177.43	0.001477
ORF1ab/nsp2	268	D268E	gaC	gaA	1	1	B.1.177.53	0.002392
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.177.60	0.000218
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.177.73	0.000566
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.177.87	0.000728
ORF1ab/nsp2	268	D268V	gAc	gTc	1	1	B.1.2	0.000009
ORF1ab/nsp2	268	D268H	Gac	Cac	1	1	B.1.2	0.000009
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.214.2	0.0006
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.221	0.000071
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.221	0.000071
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.1.240	0.000216
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.240	0.000216
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.243	0.00007
ORF1ab/nsp2	268	D268E	gaC	gaA	1	1	B.1.258	0.000067
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.258.3	0.001675
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.35	0.008475
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.351	0.00003
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.1.351	0.00003
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.36	0.000146
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.36	0.000146
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.36.29	0.000517
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.36.29	0.000517
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.36.31	0.001751
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.36.8	0.001
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.375	0.00082
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.382	0.008929
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.396	0.000706
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.408	0.00369
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.1.409	0.000781
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.416.1	0.001563
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.426	0.001009
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.427	0.00005
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.428	0.00102
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.1.429	0.000024
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.437	0.020833
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.438.1	0.000107
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.450	0.011364
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.459	0.004082
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.470	0.001404
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.471	0.002732
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.471	0.002732
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.497	0.000315
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.500	0.052632
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.541	0.004425
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.564	0.000426
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.576	0.000907
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.580	0.004065
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.596	0.000087
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.617.1	0.000129
ORF1ab/nsp2	268	D268E	gaC	gaA	1	1	B.1.617.1	0.000129
ORF1ab/nsp2	268	D268G	gAc	gGc	1	1	B.1.621	0.000089
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.621	0.000089
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.621	0.000089
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.1.623	0.000536
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.627	0.00202
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.1.78	0.008547
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.1.9.5	0.005682
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.1.93	0.000934
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.11	0.005128
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	B.31	0.003731
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	B.40	0.000364
ORF1ab/nsp2	268	D268del1	Gac	-ac	1	1	B.47	0.020408
ORF1ab/nsp2	268	D268del	GAC	---	1	1	B.5	0.038462
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	B.55	0.00295
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	B.6	0.00091
ORF1ab/nsp2	268	D268del	GAC	---	1	1	C.1	0.002392
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	C.27	0.018519
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	C.37	0.000116
ORF1ab/nsp2	268	D268E	gaC	gaG	1	1	D.2	0.000075
ORF1ab/nsp2	268	D268Y	Gac	Tac	1	1	D.3	0.005917
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	D.5	0.004975
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	K.1	0.02381
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	N.5	0.001767
ORF1ab/nsp2	268	D268A	gAc	gCc	1	1	P.1.1	0.000318
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	P.1.14	0.000048
ORF1ab/nsp2	268	D268del	GAC	---	1	1	P.1.15	0.000232
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	P.1.17	0.000162
ORF1ab/nsp2	268	D268del	GAC	---	1	1	Q.1	0.000126
ORF1ab/nsp2	268	D268N	Gac	Aac	1	1	Q.3	0.000145
ORF1ab/nsp2	268	D268D	gaC	gaT	1	1	Q.4	0.000455
ORF1ab/nsp2	268	D268del	GAC	---	1	1	R.1	0.00009
ORF1ab/nsp2	268	D268del	GAC	---	1	1	Y.1	0.012821

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.