CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 222

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
ORF3a	222	D222D		syn	gaC	gaT	8889	8889	1	26056-26058
ORF3a	222	D222Y		nonsyn	Gac	Tac	3049	3044	0.99836	26056-26058
ORF3a	222	D222Y		nonsyn	GaC	TaT	3049	5	0.00163988	26056-26058
ORF3a	222	D222G		nonsyn	gAc	gGc	522	518	0.992337	26056-26058
ORF3a	222	D222G		nonsyn	gAC	gGT	522	4	0.00766284	26056-26058
ORF3a	222	D222N		nonsyn	Gac	Aac	267	267	1	26056-26058
ORF3a	222	D222A		nonsyn	gAc	gCc	238	238	1	26056-26058
ORF3a	222	D222E		nonsyn	gaC	gaA	68	50	0.735294	26056-26058
ORF3a	222	D222E		nonsyn	gaC	gaG	68	18	0.264706	26056-26058
ORF3a	222	D222del		del	GAC	---	31	31	1	26056-26058
ORF3a	222	D222H		nonsyn	Gac	Cac	14	14	1	26056-26058
ORF3a	222	D222del2		del	gAC	g--	1	1	1	26056-26058
ORF3a	222	D222V		nonsyn	gAc	gTc	1	1	1	26056-26058
ORF3a	222	D222X		nonsyn	GaC	TaA	1	1	1	26056-26058

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
ORF3a	222	D222D	gaC	gaT	8889	8889	All	0.0017
ORF3a	222	D222D	gaC	gaT	3616	3616	B.1.1.7	0.003237
ORF3a	222	D222Y	Gac	Tac	3044	3049	All	0.000582
ORF3a	222	D222Y	GaC	TaT	5	3049	All	0.000001
ORF3a	222	D222Y	Gac	Tac	972	974	AY.1	0.384646
ORF3a	222	D222Y	GaC	TaT	2	974	AY.1	0.000791
ORF3a	222	D222Y	Gac	Tac	713	713	B.1.1.7	0.000638
ORF3a	222	D222D	gaC	gaT	608	608	AY.4	0.000946
ORF3a	222	D222G	gAc	gGc	518	522	All	0.000099
ORF3a	222	D222G	gAC	gGT	4	522	All	0.000001
ORF3a	222	D222D	gaC	gaT	509	509	AY.42	0.020477
ORF3a	222	D222Y	Gac	Tac	494	496	B.1.1.141	0.993964
ORF3a	222	D222Y	GaC	TaT	2	496	B.1.1.141	0.004024
ORF3a	222	D222D	gaC	gaT	471	471	AY.102	0.012488
ORF3a	222	D222D	gaC	gaT	392	392	AY.46.4	0.064484
ORF3a	222	D222G	gAc	gGc	371	373	AY.4	0.000577
ORF3a	222	D222G	gAC	gGT	2	373	AY.4	0.000003
ORF3a	222	D222Y	Gac	Tac	285	285	B.1.621	0.025228
ORF3a	222	D222D	gaC	gaT	282	282	B.1.617.2	0.001062
ORF3a	222	D222N	Gac	Aac	267	267	All	0.000051
ORF3a	222	D222D	gaC	gaT	245	245	AY.44	0.001491
ORF3a	222	D222A	gAc	gCc	238	238	All	0.000046
ORF3a	222	D222D	gaC	gaT	232	232	B.1.551	0.299355
ORF3a	222	D222D	gaC	gaT	223	223	B.1.2	0.001964
ORF3a	222	D222D	gaC	gaT	140	140	AY.39	0.00346
ORF3a	222	D222D	gaC	gaT	119	119	B.1.177.60	0.025994
ORF3a	222	D222D	gaC	gaT	112	112	AY.3	0.001114
ORF3a	222	D222N	Gac	Aac	111	111	B.1.1.7	0.000099
ORF3a	222	D222D	gaC	gaT	106	106	B.1	0.000971
ORF3a	222	D222D	gaC	gaT	92	92	AY.25	0.000553
ORF3a	222	D222D	gaC	gaT	88	88	AY.43	0.00039
ORF3a	222	D222D	gaC	gaT	86	86	AY.103	0.000534
ORF3a	222	D222A	gAc	gCc	86	86	B.1.1.7	0.000077
ORF3a	222	D222D	gaC	gaT	79	79	P.1	0.001245
ORF3a	222	D222E	gaC	gaA	50	68	All	0.00001
ORF3a	222	D222E	gaC	gaG	18	68	All	0.000003
ORF3a	222	D222D	gaC	gaT	68	68	AY.20	0.002643
ORF3a	222	D222D	gaC	gaT	68	68	B.1.1.255	0.206061
ORF3a	222	D222D	gaC	gaT	65	65	B.1.427	0.003282
ORF3a	222	D222Y	Gac	Tac	54	55	B.1.1	0.00098
ORF3a	222	D222Y	GaC	TaT	1	55	B.1.1	0.000018
ORF3a	222	D222D	gaC	gaT	51	51	B.1.160	0.001591
ORF3a	222	D222Y	Gac	Tac	50	50	AY.46.5	0.009921
ORF3a	222	D222D	gaC	gaT	44	44	Q.8	0.007256
ORF3a	222	D222D	gaC	gaT	42	42	B.1.1.253	0.105263
ORF3a	222	D222Y	Gac	Tac	42	42	B.1.470	0.058989
ORF3a	222	D222Y	Gac	Tac	37	37	AY.69	0.006907
ORF3a	222	D222D	gaC	gaT	37	37	B.1.1	0.000671
ORF3a	222	D222Y	Gac	Tac	37	37	B.1.617.2	0.000139
ORF3a	222	D222D	gaC	gaT	36	36	B.1.177	0.000474
ORF3a	222	D222D	gaC	gaT	35	35	AY.47	0.001089
ORF3a	222	D222Y	Gac	Tac	35	35	B.1	0.000321
ORF3a	222	D222G	gAc	gGc	35	35	B.1.1.7	0.000031
ORF3a	222	D222Y	Gac	Tac	34	34	B.1.1.83	0.092141
ORF3a	222	D222G	gAc	gGc	34	34	B.1.177	0.000448
ORF3a	222	D222D	gaC	gaT	33	33	B.1.351	0.000981
ORF3a	222	D222del	GAC	---	31	31	All	0.000006
ORF3a	222	D222Y	Gac	Tac	28	28	AY.117	0.002366
ORF3a	222	D222A	gAc	gCc	27	27	AY.5	0.000558
ORF3a	222	D222A	gAc	gCc	27	27	B.1.2	0.000238
ORF3a	222	D222D	gaC	gaT	26	26	AY.39.1	0.00103
ORF3a	222	D222D	gaC	gaT	26	26	B.1.429	0.000612
ORF3a	222	D222D	gaC	gaT	24	24	AY.27	0.001553
ORF3a	222	D222D	gaC	gaT	24	24	AY.46	0.002498
ORF3a	222	D222Y	Gac	Tac	22	22	AY.103	0.000137
ORF3a	222	D222D	gaC	gaT	22	22	AY.118	0.001378
ORF3a	222	D222E	gaC	gaA	21	21	AY.4.2	0.000455
ORF3a	222	D222Y	Gac	Tac	21	21	B.1.1.222	0.004284
ORF3a	222	D222D	gaC	gaT	21	21	B.1.243	0.001461
ORF3a	222	D222D	gaC	gaT	20	20	B.1.1.519	0.000794
ORF3a	222	D222N	Gac	Aac	19	19	AY.23	0.001325
ORF3a	222	D222D	gaC	gaT	18	18	AY.26	0.00051
ORF3a	222	D222N	Gac	Aac	18	18	B.1.621	0.001593
ORF3a	222	D222D	gaC	gaT	17	17	B.1.633	0.708333
ORF3a	222	D222D	gaC	gaT	16	16	AY.36	0.002371
ORF3a	222	D222D	gaC	gaT	16	16	B.1.221	0.001137
ORF3a	222	D222D	gaC	gaT	16	16	B.1.526	0.000376
ORF3a	222	D222D	gaC	gaT	15	15	AY.113	0.002136
ORF3a	222	D222D	gaC	gaT	15	15	AY.121	0.00203
ORF3a	222	D222D	gaC	gaT	15	15	AY.54	0.00143
ORF3a	222	D222D	gaC	gaT	15	15	AY.75	0.00084
ORF3a	222	D222D	gaC	gaT	15	15	B.1.177.7	0.002473
ORF3a	222	D222Y	Gac	Tac	15	15	B.1.2	0.000132
ORF3a	222	D222A	gAc	gCc	15	15	B.1.596	0.001307
ORF3a	222	D222N	Gac	Aac	15	15	B.1.617.2	0.000056
ORF3a	222	D222Y	Gac	Tac	15	15	P.1	0.000236
ORF3a	222	D222D	gaC	gaT	15	15	P.2	0.0028
ORF3a	222	D222H	Gac	Cac	14	14	All	0.000003
ORF3a	222	D222Y	Gac	Tac	14	14	B.1.110.3	0.010057
ORF3a	222	D222D	gaC	gaT	14	14	B.1.596	0.00122
ORF3a	222	D222G	gAc	gGc	14	14	B.1.617.2	0.000053
ORF3a	222	D222N	Gac	Aac	14	14	P.1	0.000221
ORF3a	222	D222Y	Gac	Tac	13	13	AY.102	0.000345
ORF3a	222	D222E	gaC	gaG	13	13	AY.103	0.000081
ORF3a	222	D222D	gaC	gaT	13	13	AY.106	0.004354
ORF3a	222	D222D	gaC	gaT	13	13	AY.5	0.000268
ORF3a	222	D222D	gaC	gaT	13	13	AY.70	0.002711
ORF3a	222	D222G	gAc	gGc	13	13	B.1.160	0.000405
ORF3a	222	D222D	gaC	gaT	12	12	AY.119	0.000424
ORF3a	222	D222N	Gac	Aac	12	12	AY.4	0.000019
ORF3a	222	D222D	gaC	gaT	12	12	B.1.1.222	0.002448
ORF3a	222	D222D	gaC	gaT	12	12	B.1.1.526	0.042553
ORF3a	222	D222D	gaC	gaT	12	12	B.1.637	0.000877
ORF3a	222	D222D	gaC	gaT	12	12	C.37	0.001393
ORF3a	222	D222D	gaC	gaT	12	12	P.1.14	0.000574
ORF3a	222	D222Y	Gac	Tac	11	11	AY.33	0.000735
ORF3a	222	D222A	gAc	gCc	11	11	AY.4	0.000017
ORF3a	222	D222D	gaC	gaT	11	11	AY.4.2	0.000239
ORF3a	222	D222D	gaC	gaT	11	11	AY.4.5	0.001182
ORF3a	222	D222E	gaC	gaA	11	11	AY.69	0.002053
ORF3a	222	D222D	gaC	gaT	11	11	AY.9.2	0.000404
ORF3a	222	D222D	gaC	gaT	11	11	B.1.1.214	0.00061
ORF3a	222	D222D	gaC	gaT	11	11	B.1.1.220	0.020446
ORF3a	222	D222D	gaC	gaT	10	10	AY.14	0.00088
ORF3a	222	D222Y	Gac	Tac	10	10	AY.4	0.000016
ORF3a	222	D222D	gaC	gaT	10	10	B.1.1.176	0.004394
ORF3a	222	D222D	gaC	gaT	10	10	B.1.111	0.011751
ORF3a	222	D222Y	Gac	Tac	10	10	B.1.36	0.001459
ORF3a	222	D222D	gaC	gaT	10	10	R.1	0.0009
ORF3a	222	D222D	gaC	gaT	9	9	AY.100	0.000414
ORF3a	222	D222D	gaC	gaT	9	9	AY.34.1	0.004589
ORF3a	222	D222N	Gac	Aac	9	9	AY.43	0.00004
ORF3a	222	D222D	gaC	gaT	9	9	AY.98	0.000711
ORF3a	222	D222D	gaC	gaT	9	9	B.1.1.50	0.00611
ORF3a	222	D222D	gaC	gaT	9	9	B.1.438.1	0.000965
ORF3a	222	D222D	gaC	gaT	9	9	B.1.525	0.001018
ORF3a	222	D222Y	Gac	Tac	8	8	AY.119	0.000282
ORF3a	222	D222D	gaC	gaT	8	8	AY.120	0.000297
ORF3a	222	D222Y	Gac	Tac	8	8	AY.20	0.000311
ORF3a	222	D222D	gaC	gaT	8	8	AY.99.2	0.000737
ORF3a	222	D222D	gaC	gaT	8	8	B	0.001022
ORF3a	222	D222D	gaC	gaT	8	8	B.1.177.32	0.010796
ORF3a	222	D222D	gaC	gaT	8	8	B.1.177.86	0.001468
ORF3a	222	D222D	gaC	gaT	8	8	B.1.36	0.001167
ORF3a	222	D222D	gaC	gaT	8	8	B.1.577	0.005498
ORF3a	222	D222D	gaC	gaT	8	8	B.1.623	0.004292
ORF3a	222	D222D	gaC	gaT	7	7	AY.98.1	0.000339
ORF3a	222	D222A	gAc	gCc	7	7	B.1	0.000064
ORF3a	222	D222D	gaC	gaT	7	7	B.1.234	0.000924
ORF3a	222	D222D	gaC	gaT	7	7	B.1.311	0.001922
ORF3a	222	D222D	gaC	gaT	7	7	B.1.351.2	0.002118
ORF3a	222	D222N	Gac	Aac	7	7	B.1.416.1	0.010937
ORF3a	222	D222D	gaC	gaT	7	7	P.1.17	0.001132
ORF3a	222	D222del	GAC	---	6	6		0.333333
ORF3a	222	D222D	gaC	gaT	6	6	AY.117	0.000507
ORF3a	222	D222D	gaC	gaT	6	6	AY.61	0.000629
ORF3a	222	D222D	gaC	gaT	6	6	AY.76	0.028986
ORF3a	222	D222Y	Gac	Tac	6	6	AY.85	0.002563
ORF3a	222	D222D	gaC	gaT	6	6	AY.88	0.005305
ORF3a	222	D222G	gAc	gGc	6	6	B.1.1.243	0.02449
ORF3a	222	D222D	gaC	gaT	6	6	B.1.396	0.004234
ORF3a	222	D222Y	Gac	Tac	6	6	B.1.597	0.027778
ORF3a	222	D222E	gaC	gaA	6	6	B.1.617.1	0.000774
ORF3a	222	D222D	gaC	gaT	6	6	B.1.621	0.000531
ORF3a	222	D222D	gaC	gaT	6	6	Q.3	0.00087
ORF3a	222	D222D	gaC	gaT	5	5	AY.19	0.005701
ORF3a	222	D222N	Gac	Aac	5	5	AY.44	0.00003
ORF3a	222	D222D	gaC	gaT	5	5	AY.45	0.000608
ORF3a	222	D222G	gAc	gGc	5	5	AY.61	0.000524
ORF3a	222	D222D	gaC	gaT	5	5	B.1.1.153	0.005476
ORF3a	222	D222A	gAc	gCc	5	5	B.1.1.25	0.002843
ORF3a	222	D222N	Gac	Aac	5	5	B.1.177	0.000066
ORF3a	222	D222A	gAc	gCc	5	5	B.1.234	0.00066
ORF3a	222	D222D	gaC	gaT	5	5	B.1.369	0.001426
ORF3a	222	D222D	gaC	gaT	5	5	B.1.421	0.037313
ORF3a	222	D222G	gAc	gGc	5	5	B.1.427	0.000252
ORF3a	222	D222D	gaC	gaT	5	5	B.1.582	0.002453
ORF3a	222	D222Y	Gac	Tac	5	5	B.1.609	0.002397
ORF3a	222	D222D	gaC	gaT	5	5	Q.1	0.000632
ORF3a	222	D222G	gAc	gGc	4	4	AY.20	0.000155
ORF3a	222	D222D	gaC	gaT	4	4	AY.33	0.000267
ORF3a	222	D222Y	Gac	Tac	4	4	AY.44	0.000024
ORF3a	222	D222A	gAc	gCc	4	4	B.1.1	0.000073
ORF3a	222	D222D	gaC	gaT	4	4	B.1.1.294	0.005063
ORF3a	222	D222A	gAc	gCc	4	4	B.1.1.306	0.001754
ORF3a	222	D222D	gaC	gaT	4	4	B.1.1.33	0.001684
ORF3a	222	D222Y	Gac	Tac	4	4	B.1.1.398	0.012903
ORF3a	222	D222Y	Gac	Tac	4	4	B.1.177	0.000053
ORF3a	222	D222N	Gac	Aac	4	4	B.1.177.12	0.000607
ORF3a	222	D222D	gaC	gaT	4	4	B.1.36.1	0.004561
ORF3a	222	D222del	GAC	---	4	4	B.1.525	0.000453
ORF3a	222	D222Y	Gac	Tac	4	4	B.1.526	0.000094
ORF3a	222	D222H	Gac	Cac	3	3	AY.100	0.000138
ORF3a	222	D222Y	Gac	Tac	3	3	AY.114	0.000693
ORF3a	222	D222Y	Gac	Tac	3	3	AY.118	0.000188
ORF3a	222	D222D	gaC	gaT	3	3	AY.13	0.000483
ORF3a	222	D222G	gAc	gGc	3	3	AY.25	0.000018
ORF3a	222	D222D	gaC	gaT	3	3	AY.29	0.000047
ORF3a	222	D222G	gAc	gGc	3	3	AY.29	0.000047
ORF3a	222	D222G	gAc	gGc	3	3	AY.3	0.00003
ORF3a	222	D222D	gaC	gaT	3	3	AY.34	0.000291
ORF3a	222	D222del	GAC	---	3	3	AY.43	0.000013
ORF3a	222	D222G	gAc	gGc	3	3	AY.43	0.000013
ORF3a	222	D222A	gAc	gCc	3	3	AY.44	0.000018
ORF3a	222	D222D	gaC	gaT	3	3	AY.5.3	0.001012
ORF3a	222	D222D	gaC	gaT	3	3	AY.66	0.003209
ORF3a	222	D222Y	Gac	Tac	3	3	AY.75.1	0.000541
ORF3a	222	D222N	Gac	Aac	3	3	AY.95	0.002283
ORF3a	222	D222N	Gac	Aac	3	3	B.1	0.000027
ORF3a	222	D222G	gAc	gGc	3	3	B.1	0.000027
ORF3a	222	D222H	Gac	Cac	3	3	B.1	0.000027
ORF3a	222	D222D	gaC	gaT	3	3	B.1.1.232	0.005445
ORF3a	222	D222D	gaC	gaT	3	3	B.1.1.25	0.001706
ORF3a	222	D222D	gaC	gaT	3	3	B.1.1.28	0.000934
ORF3a	222	D222D	gaC	gaT	3	3	B.1.1.348	0.002389
ORF3a	222	D222D	gaC	gaT	3	3	B.1.1.372	0.002066
ORF3a	222	D222E	gaC	gaA	3	3	B.1.1.7	0.000003
ORF3a	222	D222del	GAC	---	3	3	B.1.1.7	0.000003
ORF3a	222	D222G	gAc	gGc	3	3	B.1.1.70	0.001023
ORF3a	222	D222A	gAc	gCc	3	3	B.1.177	0.00004
ORF3a	222	D222D	gaC	gaT	3	3	B.1.177.40	0.015464
ORF3a	222	D222D	gaC	gaT	3	3	B.1.177.67	0.022901
ORF3a	222	D222N	Gac	Aac	3	3	B.1.177.81	0.000568
ORF3a	222	D222D	gaC	gaT	3	3	B.1.517	0.001281
ORF3a	222	D222D	gaC	gaT	3	3	B.1.523	0.007353
ORF3a	222	D222H	Gac	Cac	3	3	B.1.530	0.021429
ORF3a	222	D222D	gaC	gaT	3	3	B.1.564	0.001278
ORF3a	222	D222E	gaC	gaA	3	3	B.1.617.2	0.000011
ORF3a	222	D222D	gaC	gaT	3	3	B.52	0.030303
ORF3a	222	D222D	gaC	gaT	3	3	P.1.15	0.000697
ORF3a	222	D222Y	Gac	Tac	3	3	P.2	0.00056
ORF3a	222	D222A	gAc	gCc	3	3	Q.8	0.000495
ORF3a	222	D222D	gaC	gaT	2	2	AY.105	0.001286
ORF3a	222	D222N	Gac	Aac	2	2	AY.106	0.00067
ORF3a	222	D222N	Gac	Aac	2	2	AY.110	0.000225
ORF3a	222	D222D	gaC	gaT	2	2	AY.16.1	0.00094
ORF3a	222	D222Y	Gac	Tac	2	2	AY.25	0.000012
ORF3a	222	D222Y	Gac	Tac	2	2	AY.3	0.00002
ORF3a	222	D222D	gaC	gaT	2	2	AY.3.1	0.000171
ORF3a	222	D222A	gAc	gCc	2	2	AY.33	0.000134
ORF3a	222	D222D	gaC	gaT	2	2	AY.4.2.1	0.000298
ORF3a	222	D222Y	Gac	Tac	2	2	AY.43	0.000009
ORF3a	222	D222Y	Gac	Tac	2	2	AY.45	0.000243
ORF3a	222	D222Y	Gac	Tac	2	2	AY.47	0.000062
ORF3a	222	D222Y	Gac	Tac	2	2	AY.54	0.000191
ORF3a	222	D222D	gaC	gaT	2	2	AY.59	0.001059
ORF3a	222	D222D	gaC	gaT	2	2	AY.6	0.000082
ORF3a	222	D222Y	Gac	Tac	2	2	AY.62	0.000871
ORF3a	222	D222E	gaC	gaA	2	2	AY.63	0.000774
ORF3a	222	D222D	gaC	gaT	2	2	AY.64	0.00119
ORF3a	222	D222D	gaC	gaT	2	2	AY.74	0.000231
ORF3a	222	D222D	gaC	gaT	2	2	AY.75.1	0.000361
ORF3a	222	D222D	gaC	gaT	2	2	AY.84	0.000875
ORF3a	222	D222N	Gac	Aac	2	2	AY.87	0.001665
ORF3a	222	D222D	gaC	gaT	2	2	AY.9.1	0.000167
ORF3a	222	D222D	gaC	gaT	2	2	B.1.1.409	0.005666
ORF3a	222	D222D	gaC	gaT	2	2	B.1.1.432	0.002532
ORF3a	222	D222D	gaC	gaT	2	2	B.1.1.442	0.037037
ORF3a	222	D222D	gaC	gaT	2	2	B.1.110.3	0.001437
ORF3a	222	D222Y	Gac	Tac	2	2	B.1.118	0.013423
ORF3a	222	D222D	gaC	gaT	2	2	B.1.157	0.00597
ORF3a	222	D222N	Gac	Aac	2	2	B.1.160	0.000062
ORF3a	222	D222D	gaC	gaT	2	2	B.1.177.21	0.000153
ORF3a	222	D222D	gaC	gaT	2	2	B.1.177.4	0.000422
ORF3a	222	D222D	gaC	gaT	2	2	B.1.177.73	0.001133
ORF3a	222	D222D	gaC	gaT	2	2	B.1.177.82	0.000955
ORF3a	222	D222D	gaC	gaT	2	2	B.1.221.1	0.005814
ORF3a	222	D222D	gaC	gaT	2	2	B.1.223	0.005556
ORF3a	222	D222D	gaC	gaT	2	2	B.1.232	0.001075
ORF3a	222	D222E	gaC	gaA	2	2	B.1.234	0.000264
ORF3a	222	D222D	gaC	gaT	2	2	B.1.236	0.004107
ORF3a	222	D222D	gaC	gaT	2	2	B.1.258.17	0.000208
ORF3a	222	D222D	gaC	gaT	2	2	B.1.323	0.041667
ORF3a	222	D222A	gAc	gCc	2	2	B.1.351	0.000059
ORF3a	222	D222A	gAc	gCc	2	2	B.1.351.3	0.001753
ORF3a	222	D222A	gAc	gCc	2	2	B.1.36	0.000292
ORF3a	222	D222D	gaC	gaT	2	2	B.1.398	0.005952
ORF3a	222	D222D	gaC	gaT	2	2	B.1.404	0.002604
ORF3a	222	D222N	Gac	Aac	2	2	B.1.429	0.000047
ORF3a	222	D222Y	Gac	Tac	2	2	B.1.466.2	0.000782
ORF3a	222	D222D	gaC	gaT	2	2	B.1.466.2	0.000782
ORF3a	222	D222E	gaC	gaG	2	2	B.1.526	0.000047
ORF3a	222	D222D	gaC	gaT	2	2	B.1.575	0.000607
ORF3a	222	D222G	gAC	gGT	2	2	B.1.582	0.000981
ORF3a	222	D222A	gAc	gCc	2	2	B.1.582	0.000981
ORF3a	222	D222N	Gac	Aac	2	2	B.1.588	0.00182
ORF3a	222	D222D	gaC	gaT	2	2	B.1.595	0.000522
ORF3a	222	D222A	gAc	gCc	2	2	B.1.595	0.000522
ORF3a	222	D222Y	Gac	Tac	2	2	B.1.603	0.021277
ORF3a	222	D222D	gaC	gaT	2	2	B.1.617.1	0.000258
ORF3a	222	D222Y	Gac	Tac	2	2	B.1.632	0.013423
ORF3a	222	D222D	gaC	gaT	2	2	B.4	0.004415
ORF3a	222	D222D	gaC	gaT	2	2	C.36.3	0.001134
ORF3a	222	D222D	gaC	gaT	2	2	D.2	0.00015
ORF3a	222	D222D	gaC	gaT	2	2	P.1.12	0.000968
ORF3a	222	D222D	gaC	gaT	2	2	P.4	0.007605
ORF3a	222	D222Y	Gac	Tac	2	2	Q.1	0.000253
ORF3a	222	D222D	gaC	gaT	2	2	Q.4	0.00091
ORF3a	222	D222D	gaC	gaT	1	1	A	0.000387
ORF3a	222	D222H	Gac	Cac	1	1	A.1	0.000282
ORF3a	222	D222D	gaC	gaT	1	1	A.1	0.000282
ORF3a	222	D222D	gaC	gaT	1	1	A.2	0.000662
ORF3a	222	D222D	gaC	gaT	1	1	A.2.5	0.000499
ORF3a	222	D222Y	Gac	Tac	1	1	A.23	0.010526
ORF3a	222	D222D	gaC	gaT	1	1	AD.2	0.000219
ORF3a	222	D222Y	Gac	Tac	1	1	AE.8	0.000489
ORF3a	222	D222D	gaC	gaT	1	1	AH.3	0.003802
ORF3a	222	D222X	GaC	TaA	1	1	All	0
ORF3a	222	D222V	gAc	gTc	1	1	All	0
ORF3a	222	D222del2	gAC	g--	1	1	All	0
ORF3a	222	D222G	gAc	gGc	1	1	AY.100	0.000046
ORF3a	222	D222N	Gac	Aac	1	1	AY.103	0.000006
ORF3a	222	D222H	Gac	Cac	1	1	AY.103	0.000006
ORF3a	222	D222D	gaC	gaT	1	1	AY.111	0.000183
ORF3a	222	D222Y	Gac	Tac	1	1	AY.113	0.000142
ORF3a	222	D222D	gaC	gaT	1	1	AY.114	0.000231
ORF3a	222	D222D	gaC	gaT	1	1	AY.116	0.000287
ORF3a	222	D222Y	Gac	Tac	1	1	AY.116	0.000287
ORF3a	222	D222N	Gac	Aac	1	1	AY.118	0.000063
ORF3a	222	D222D	gaC	gaT	1	1	AY.12	0.000316
ORF3a	222	D222del	GAC	---	1	1	AY.120	0.000037
ORF3a	222	D222D	gaC	gaT	1	1	AY.120.1	0.000321
ORF3a	222	D222Y	Gac	Tac	1	1	AY.13	0.000161
ORF3a	222	D222G	gAc	gGc	1	1	AY.13	0.000161
ORF3a	222	D222Y	Gac	Tac	1	1	AY.16	0.00038
ORF3a	222	D222D	gaC	gaT	1	1	AY.16	0.00038
ORF3a	222	D222Y	Gac	Tac	1	1	AY.22	0.002092
ORF3a	222	D222Y	Gac	Tac	1	1	AY.23	0.00007
ORF3a	222	D222A	gAc	gCc	1	1	AY.24	0.000431
ORF3a	222	D222N	Gac	Aac	1	1	AY.25	0.000006
ORF3a	222	D222N	Gac	Aac	1	1	AY.26	0.000028
ORF3a	222	D222G	gAc	gGc	1	1	AY.26	0.000028
ORF3a	222	D222Y	Gac	Tac	1	1	AY.26	0.000028
ORF3a	222	D222Y	Gac	Tac	1	1	AY.29	0.000016
ORF3a	222	D222D	gaC	gaT	1	1	AY.29.1	0.000221
ORF3a	222	D222N	Gac	Aac	1	1	AY.3	0.00001
ORF3a	222	D222Y	Gac	Tac	1	1	AY.32	0.000532
ORF3a	222	D222N	Gac	Aac	1	1	AY.34	0.000097
ORF3a	222	D222Y	Gac	Tac	1	1	AY.34	0.000097
ORF3a	222	D222Y	Gac	Tac	1	1	AY.34.1	0.00051
ORF3a	222	D222D	gaC	gaT	1	1	AY.35	0.000233
ORF3a	222	D222Y	Gac	Tac	1	1	AY.37	0.000316
ORF3a	222	D222G	gAc	gGc	1	1	AY.39	0.000025
ORF3a	222	D222E	gaC	gaA	1	1	AY.39	0.000025
ORF3a	222	D222Y	Gac	Tac	1	1	AY.39	0.000025
ORF3a	222	D222X	GaC	TaA	1	1	AY.39	0.000025
ORF3a	222	D222N	Gac	Aac	1	1	AY.39	0.000025
ORF3a	222	D222N	Gac	Aac	1	1	AY.39.1	0.00004
ORF3a	222	D222E	gaC	gaG	1	1	AY.4	0.000002
ORF3a	222	D222G	gAc	gGc	1	1	AY.42	0.00004
ORF3a	222	D222E	gaC	gaA	1	1	AY.44	0.000006
ORF3a	222	D222Y	Gac	Tac	1	1	AY.46	0.000104
ORF3a	222	D222N	Gac	Aac	1	1	AY.46	0.000104
ORF3a	222	D222G	gAc	gGc	1	1	AY.46.2	0.000635
ORF3a	222	D222Y	Gac	Tac	1	1	AY.46.4	0.000165
ORF3a	222	D222del	GAC	---	1	1	AY.46.6	0.000072
ORF3a	222	D222D	gaC	gaT	1	1	AY.48	0.000465
ORF3a	222	D222D	gaC	gaT	1	1	AY.49	0.003195
ORF3a	222	D222N	Gac	Aac	1	1	AY.5	0.000021
ORF3a	222	D222Y	Gac	Tac	1	1	AY.5	0.000021
ORF3a	222	D222D	gaC	gaT	1	1	AY.5.2	0.002463
ORF3a	222	D222D	gaC	gaT	1	1	AY.5.4	0.000277
ORF3a	222	D222N	Gac	Aac	1	1	AY.54	0.000095
ORF3a	222	D222Y	Gac	Tac	1	1	AY.6	0.000041
ORF3a	222	D222del	GAC	---	1	1	AY.67	0.000464
ORF3a	222	D222D	gaC	gaT	1	1	AY.67	0.000464
ORF3a	222	D222D	gaC	gaT	1	1	AY.68	0.000274
ORF3a	222	D222del	GAC	---	1	1	AY.68	0.000274
ORF3a	222	D222N	Gac	Aac	1	1	AY.68	0.000274
ORF3a	222	D222V	gAc	gTc	1	1	AY.69	0.000187
ORF3a	222	D222A	gAc	gCc	1	1	AY.69	0.000187
ORF3a	222	D222Y	Gac	Tac	1	1	AY.73	0.000665
ORF3a	222	D222Y	Gac	Tac	1	1	AY.82	0.001357
ORF3a	222	D222D	gaC	gaT	1	1	AY.83	0.001724
ORF3a	222	D222Y	Gac	Tac	1	1	AY.84	0.000437
ORF3a	222	D222del	GAC	---	1	1	AY.85	0.000427
ORF3a	222	D222D	gaC	gaT	1	1	AY.9	0.000068
ORF3a	222	D222N	Gac	Aac	1	1	AY.9.1	0.000084
ORF3a	222	D222Y	Gac	Tac	1	1	AY.94	0.000443
ORF3a	222	D222D	gaC	gaT	1	1	AY.94	0.000443
ORF3a	222	D222Y	Gac	Tac	1	1	AY.95	0.000761
ORF3a	222	D222D	gaC	gaT	1	1	AY.95	0.000761
ORF3a	222	D222D	gaC	gaT	1	1	AY.96	0.002075
ORF3a	222	D222D	gaC	gaT	1	1	AY.97	0.001701
ORF3a	222	D222Y	Gac	Tac	1	1	AY.98	0.000079
ORF3a	222	D222Y	Gac	Tac	1	1	AY.99	0.001049
ORF3a	222	D222Y	Gac	Tac	1	1	AY.99.2	0.000092
ORF3a	222	D222E	gaC	gaG	1	1	B	0.000128
ORF3a	222	D222A	gAc	gCc	1	1	B	0.000128
ORF3a	222	D222del	GAC	---	1	1	B.1	0.000009
ORF3a	222	D222N	Gac	Aac	1	1	B.1.1	0.000018
ORF3a	222	D222N	Gac	Aac	1	1	B.1.1.1	0.000327
ORF3a	222	D222A	gAc	gCc	1	1	B.1.1.135	0.004695
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.161	0.003534
ORF3a	222	D222A	gAc	gCc	1	1	B.1.1.171	0.003676
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.186	0.003436
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.216	0.00089
ORF3a	222	D222N	Gac	Aac	1	1	B.1.1.220	0.001859
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.1.220	0.001859
ORF3a	222	D222H	Gac	Cac	1	1	B.1.1.222	0.000204
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.1.269	0.001353
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.1.272	0.005208
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.277	0.000759
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.279	0.001121
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.284	0.000107
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.301	0.001179
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.306	0.000438
ORF3a	222	D222del	GAC	---	1	1	B.1.1.311	0.000358
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.312	0.001912
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.315	0.008475
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.316	0.000925
ORF3a	222	D222N	Gac	Aac	1	1	B.1.1.316	0.000925
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.318	0.000302
ORF3a	222	D222A	gAc	gCc	1	1	B.1.1.320	0.018182
ORF3a	222	D222A	gAc	gCc	1	1	B.1.1.33	0.000421
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.334	0.016393
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.356	0.008547
ORF3a	222	D222N	Gac	Aac	1	1	B.1.1.369	0.000446
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.1.397	0.002252
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.413	0.006897
ORF3a	222	D222A	gAc	gCc	1	1	B.1.1.416	0.000905
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.464	0.001473
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.466	0.008696
ORF3a	222	D222G	gAc	gGc	1	1	B.1.1.52	0.012195
ORF3a	222	D222D	gaC	gaT	1	1	B.1.1.521	0.005348
ORF3a	222	D222D	gaC	gaT	1	1	B.1.139	0.000733
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.160	0.000031
ORF3a	222	D222H	Gac	Cac	1	1	B.1.160	0.000031
ORF3a	222	D222A	gAc	gCc	1	1	B.1.160	0.000031
ORF3a	222	D222D	gaC	gaT	1	1	B.1.160.11	0.005714
ORF3a	222	D222D	gaC	gaT	1	1	B.1.160.26	0.002421
ORF3a	222	D222del	GAC	---	1	1	B.1.177	0.000013
ORF3a	222	D222E	gaC	gaG	1	1	B.1.177	0.000013
ORF3a	222	D222D	gaC	gaT	1	1	B.1.177.17	0.000821
ORF3a	222	D222A	gAc	gCc	1	1	B.1.177.20	0.001517
ORF3a	222	D222D	gaC	gaT	1	1	B.1.177.23	0.003236
ORF3a	222	D222D	gaC	gaT	1	1	B.1.177.43	0.001477
ORF3a	222	D222N	Gac	Aac	1	1	B.1.177.45	0.000381
ORF3a	222	D222D	gaC	gaT	1	1	B.1.177.45	0.000381
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.177.54	0.000606
ORF3a	222	D222D	gaC	gaT	1	1	B.1.177.6	0.000977
ORF3a	222	D222N	Gac	Aac	1	1	B.1.177.69	0.001484
ORF3a	222	D222del	GAC	---	1	1	B.1.177.73	0.000566
ORF3a	222	D222D	gaC	gaT	1	1	B.1.177.79	0.002342
ORF3a	222	D222D	gaC	gaT	1	1	B.1.177.81	0.000189
ORF3a	222	D222A	gAc	gCc	1	1	B.1.177.86	0.000183
ORF3a	222	D222del	GAC	---	1	1	B.1.2	0.000009
ORF3a	222	D222G	gAc	gGc	1	1	B.1.2	0.000009
ORF3a	222	D222D	gaC	gaT	1	1	B.1.206	0.000816
ORF3a	222	D222A	gAc	gCc	1	1	B.1.214.2	0.0006
ORF3a	222	D222A	gAc	gCc	1	1	B.1.221	0.000071
ORF3a	222	D222D	gaC	gaT	1	1	B.1.240	0.000216
ORF3a	222	D222A	gAc	gCc	1	1	B.1.240	0.000216
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.240	0.000216
ORF3a	222	D222G	gAc	gGc	1	1	B.1.243	0.00007
ORF3a	222	D222A	gAc	gCc	1	1	B.1.243	0.00007
ORF3a	222	D222D	gaC	gaT	1	1	B.1.258	0.000067
ORF3a	222	D222del	GAC	---	1	1	B.1.258	0.000067
ORF3a	222	D222N	Gac	Aac	1	1	B.1.258	0.000067
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.258	0.000067
ORF3a	222	D222A	gAc	gCc	1	1	B.1.311	0.000275
ORF3a	222	D222D	gaC	gaT	1	1	B.1.313	0.006579
ORF3a	222	D222N	Gac	Aac	1	1	B.1.323	0.020833
ORF3a	222	D222N	Gac	Aac	1	1	B.1.351	0.00003
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.351	0.00003
ORF3a	222	D222A	gAc	gCc	1	1	B.1.36.10	0.004785
ORF3a	222	D222D	gaC	gaT	1	1	B.1.36.17	0.000494
ORF3a	222	D222D	gaC	gaT	1	1	B.1.36.18	0.00042
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.36.29	0.000517
ORF3a	222	D222D	gaC	gaT	1	1	B.1.36.29	0.000517
ORF3a	222	D222D	gaC	gaT	1	1	B.1.36.7	0.004
ORF3a	222	D222D	gaC	gaT	1	1	B.1.375	0.00082
ORF3a	222	D222D	gaC	gaT	1	1	B.1.409	0.000781
ORF3a	222	D222D	gaC	gaT	1	1	B.1.411	0.003704
ORF3a	222	D222G	gAc	gGc	1	1	B.1.429	0.000024
ORF3a	222	D222D	gaC	gaT	1	1	B.1.462	0.007246
ORF3a	222	D222G	gAc	gGc	1	1	B.1.465	0.003802
ORF3a	222	D222D	gaC	gaT	1	1	B.1.470	0.001404
ORF3a	222	D222D	gaC	gaT	1	1	B.1.474	0.001901
ORF3a	222	D222H	Gac	Cac	1	1	B.1.497	0.000315
ORF3a	222	D222D	gaC	gaT	1	1	B.1.508	0.025641
ORF3a	222	D222A	gAc	gCc	1	1	B.1.517	0.000427
ORF3a	222	D222G	gAc	gGc	1	1	B.1.525	0.000113
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.533	0.009615
ORF3a	222	D222A	gAc	gCc	1	1	B.1.544	0.006024
ORF3a	222	D222A	gAc	gCc	1	1	B.1.565	0.00081
ORF3a	222	D222D	gaC	gaT	1	1	B.1.566	0.019231
ORF3a	222	D222A	gAc	gCc	1	1	B.1.574	0.002151
ORF3a	222	D222D	gaC	gaT	1	1	B.1.576	0.000907
ORF3a	222	D222del	GAC	---	1	1	B.1.577	0.000687
ORF3a	222	D222A	gAc	gCc	1	1	B.1.577	0.000687
ORF3a	222	D222D	gaC	gaT	1	1	B.1.580	0.004065
ORF3a	222	D222D	gaC	gaT	1	1	B.1.594	0.03125
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.596	0.000087
ORF3a	222	D222D	gaC	gaT	1	1	B.1.597	0.00463
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.598	0.016949
ORF3a	222	D222A	gAc	gCc	1	1	B.1.609	0.000479
ORF3a	222	D222D	gaC	gaT	1	1	B.1.609	0.000479
ORF3a	222	D222A	gAc	gCc	1	1	B.1.617.1	0.000129
ORF3a	222	D222del	GAC	---	1	1	B.1.617.2	0.000004
ORF3a	222	D222A	gAc	gCc	1	1	B.1.617.2	0.000004
ORF3a	222	D222D	gaC	gaT	1	1	B.1.617.3	0.002985
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.621.1	0.000506
ORF3a	222	D222A	gAc	gCc	1	1	B.1.621.1	0.000506
ORF3a	222	D222Y	Gac	Tac	1	1	B.1.623	0.000536
ORF3a	222	D222G	gAc	gGc	1	1	B.1.628	0.000352
ORF3a	222	D222D	gaC	gaT	1	1	B.1.628	0.000352
ORF3a	222	D222N	Gac	Aac	1	1	B.1.637	0.000073
ORF3a	222	D222N	Gac	Aac	1	1	B.12	0.00641
ORF3a	222	D222D	gaC	gaT	1	1	B.40	0.000364
ORF3a	222	D222Y	Gac	Tac	1	1	B.6.6	0.000889
ORF3a	222	D222D	gaC	gaT	1	1	C.36.1	0.004149
ORF3a	222	D222Y	Gac	Tac	1	1	C.36.3	0.000567
ORF3a	222	D222Y	Gac	Tac	1	1	D.2	0.000075
ORF3a	222	D222D	gaC	gaT	1	1	L.3	0.003546
ORF3a	222	D222del2	gAC	g--	1	1	P.1.1	0.000318
ORF3a	222	D222N	Gac	Aac	1	1	P.1.10	0.000269
ORF3a	222	D222Y	Gac	Tac	1	1	P.1.12	0.000484
ORF3a	222	D222N	Gac	Aac	1	1	P.1.12	0.000484
ORF3a	222	D222D	gaC	gaT	1	1	P.3	0.001595
ORF3a	222	D222del	GAC	---	1	1	Q.1	0.000126
ORF3a	222	D222del	GAC	---	1	1	R.1	0.00009
ORF3a	222	D222Y	Gac	Tac	1	1	U.3	0.003861

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.