CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 42

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	42	P42L		nonsyn	cCt	cTt	64133	64111	0.999657	25516-25518
ORF3a	42	P42L		nonsyn	cCT	cTC	64133	21	0.000327445	25516-25518
ORF3a	42	P42L		nonsyn	cCT	cTA	64133	1	0.0000155926	25516-25518
ORF3a	42	P42H		nonsyn	cCt	cAt	5056	5056	1	25516-25518
ORF3a	42	P42P		syn	ccT	ccC	4974	4683	0.941496	25516-25518
ORF3a	42	P42P		syn	ccT	ccG	4974	212	0.0426216	25516-25518
ORF3a	42	P42P		syn	ccT	ccA	4974	79	0.0158826	25516-25518
ORF3a	42	P42S		nonsyn	Cct	Tct	4964	4964	1	25516-25518
ORF3a	42	P42del		del	CCT	---	997	997	1	25516-25518
ORF3a	42	P42R		nonsyn	cCt	cGt	220	220	1	25516-25518
ORF3a	42	P42del1		del	ccT	cc-	180	179	0.994444	25516-25518
ORF3a	42	P42del1		del	Cct	-ct	180	1	0.00555556	25516-25518
ORF3a	42	P42T		nonsyn	Cct	Act	75	75	1	25516-25518
ORF3a	42	P42A		nonsyn	Cct	Gct	54	54	1	25516-25518
ORF3a	42	P42F		nonsyn	CCt	TTt	12	12	1	25516-25518
ORF3a	42	P42del2		del	cCT	c--	6	5	0.833333	25516-25518
ORF3a	42	P42del2		del	CCT	--N	6	1	0.166667	25516-25518
ORF3a	42	P42Y		nonsyn	CCt	TAt	1	1	1	25516-25518

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	42	P42L	cCt	cTt	64111	64133	All	0.012262
ORF3a	42	P42L	cCT	cTC	21	64133	All	0.000004
ORF3a	42	P42L	cCT	cTA	1	64133	All	0
ORF3a	42	P42L	cCt	cTt	41835	41852	B.1.526	0.983312
ORF3a	42	P42L	cCT	cTC	16	41852	B.1.526	0.000376
ORF3a	42	P42L	cCT	cTA	1	41852	B.1.526	0.000024
ORF3a	42	P42L	cCt	cTt	13412	13417	B.1.637	0.980051
ORF3a	42	P42L	cCT	cTC	5	13417	B.1.637	0.000365
ORF3a	42	P42H	cCt	cAt	5056	5056	All	0.000967
ORF3a	42	P42P	ccT	ccC	4683	4974	All	0.000896
ORF3a	42	P42P	ccT	ccG	212	4974	All	0.000041
ORF3a	42	P42P	ccT	ccA	79	4974	All	0.000015
ORF3a	42	P42S	Cct	Tct	4964	4964	All	0.000949
ORF3a	42	P42H	cCt	cAt	4630	4630	B.1.1.7	0.004145
ORF3a	42	P42S	Cct	Tct	2813	2813	AY.12	0.889064
ORF3a	42	P42P	ccT	ccC	2738	2742	B.1.617.2	0.01031
ORF3a	42	P42P	ccT	ccG	4	2742	B.1.617.2	0.000015
ORF3a	42	P42L	cCt	cTt	2121	2121	AY.103	0.013169
ORF3a	42	P42L	cCt	cTt	1214	1214	B.1	0.01112
ORF3a	42	P42L	cCt	cTt	1060	1060	AY.4	0.00165
ORF3a	42	P42del	CCT	---	997	997	All	0.000191
ORF3a	42	P42L	cCt	cTt	924	924	B.1.1.7	0.000827
ORF3a	42	P42P	ccT	ccC	785	785	AY.102	0.020813
ORF3a	42	P42S	Cct	Tct	600	600	B.1.1.7	0.000537
ORF3a	42	P42L	cCt	cTt	316	316	AY.25	0.001901
ORF3a	42	P42P	ccT	ccC	232	242	B.1.1.7	0.000208
ORF3a	42	P42P	ccT	ccG	5	242	B.1.1.7	0.000004
ORF3a	42	P42P	ccT	ccA	5	242	B.1.1.7	0.000004
ORF3a	42	P42S	Cct	Tct	234	234	AY.4	0.000364
ORF3a	42	P42L	cCt	cTt	224	224	B.1.617.2	0.000843
ORF3a	42	P42R	cCt	cGt	220	220	All	0.000042
ORF3a	42	P42L	cCt	cTt	214	214	AY.120	0.007956
ORF3a	42	P42L	cCt	cTt	194	194	AY.9.2	0.007126
ORF3a	42	P42del	CCT	---	192	192	AY.26	0.005436
ORF3a	42	P42del1	ccT	cc-	179	180	All	0.000034
ORF3a	42	P42del1	Cct	-ct	1	180	All	0
ORF3a	42	P42del	CCT	---	153	153	B.1.630	0.801047
ORF3a	42	P42L	cCt	cTt	150	150	B.1.1	0.002721
ORF3a	42	P42L	cCt	cTt	144	144	AY.3	0.001432
ORF3a	42	P42S	Cct	Tct	135	135	AY.43	0.000598
ORF3a	42	P42P	ccT	ccC	71	131	AY.44	0.000432
ORF3a	42	P42P	ccT	ccG	58	131	AY.44	0.000353
ORF3a	42	P42P	ccT	ccA	2	131	AY.44	0.000012
ORF3a	42	P42P	ccT	ccC	124	124	AY.39	0.003064
ORF3a	42	P42L	cCt	cTt	118	118	AY.26	0.003341
ORF3a	42	P42S	Cct	Tct	117	117	B.1.617.2	0.000441
ORF3a	42	P42del1	ccT	cc-	109	109	B.1.617.3	0.325373
ORF3a	42	P42L	cCt	cTt	107	107	AY.43	0.000474
ORF3a	42	P42R	cCt	cGt	106	106	AY.4	0.000165
ORF3a	42	P42P	ccT	ccC	99	102	AY.43	0.000439
ORF3a	42	P42P	ccT	ccA	2	102	AY.43	0.000009
ORF3a	42	P42P	ccT	ccG	1	102	AY.43	0.000004
ORF3a	42	P42L	cCt	cTt	99	99	B.1.177	0.001304
ORF3a	42	P42L	cCt	cTt	95	95	AY.109	0.070266
ORF3a	42	P42H	cCt	cAt	95	95	B.1.1.528	0.456731
ORF3a	42	P42L	cCt	cTt	93	93	AY.39	0.002298
ORF3a	42	P42L	cCt	cTt	90	90	AY.6	0.003702
ORF3a	42	P42L	cCt	cTt	89	89	B.1.2	0.000784
ORF3a	42	P42L	cCt	cTt	88	88	AY.29	0.001388
ORF3a	42	P42H	cCt	cAt	87	87	AY.4	0.000135
ORF3a	42	P42del	CCT	---	87	87	B.1.2	0.000766
ORF3a	42	P42S	Cct	Tct	76	76	AY.44	0.000463
ORF3a	42	P42T	Cct	Act	75	75	All	0.000014
ORF3a	42	P42L	cCt	cTt	73	73	P.1	0.00115
ORF3a	42	P42L	cCt	cTt	71	71	B.1.561	0.028186
ORF3a	42	P42del	CCT	---	68	68	AY.43	0.000301
ORF3a	42	P42S	Cct	Tct	66	66	AY.25	0.000397
ORF3a	42	P42R	cCt	cGt	66	66	B.1.177	0.000869
ORF3a	42	P42S	Cct	Tct	61	61	AY.103	0.000379
ORF3a	42	P42del	CCT	---	61	61	B.1.1.7	0.000055
ORF3a	42	P42P	ccT	ccC	59	59	AY.106	0.019759
ORF3a	42	P42P	ccT	ccC	58	58	AY.117	0.004902
ORF3a	42	P42P	ccT	ccC	58	58	AY.34.1	0.029577
ORF3a	42	P42P	ccT	ccG	51	57	B.1	0.000467
ORF3a	42	P42P	ccT	ccC	5	57	B.1	0.000046
ORF3a	42	P42P	ccT	ccA	1	57	B.1	0.000009
ORF3a	42	P42S	Cct	Tct	57	57	B.1.427	0.002878
ORF3a	42	P42S	Cct	Tct	55	55	B.1.177	0.000724
ORF3a	42	P42A	Cct	Gct	54	54	All	0.00001
ORF3a	42	P42del	CCT	---	54	54	B.1.177.82	0.025776
ORF3a	42	P42L	cCt	cTt	50	50	AY.119	0.001765
ORF3a	42	P42P	ccT	ccG	37	49	AY.4	0.000058
ORF3a	42	P42P	ccT	ccC	12	49	AY.4	0.000019
ORF3a	42	P42S	Cct	Tct	49	49	B.1.2	0.000431
ORF3a	42	P42S	Cct	Tct	47	47	B.1	0.00043
ORF3a	42	P42H	cCt	cAt	47	47	B.1.177.35	0.032481
ORF3a	42	P42L	cCt	cTt	46	46	B.1.351	0.001367
ORF3a	42	P42S	Cct	Tct	42	42	AY.3	0.000418
ORF3a	42	P42del	CCT	---	42	42	AY.42	0.00169
ORF3a	42	P42S	Cct	Tct	42	42	B.1.429	0.000988
ORF3a	42	P42L	cCt	cTt	40	40	A	0.01548
ORF3a	42	P42L	cCt	cTt	40	40	AY.44	0.000243
ORF3a	42	P42L	cCt	cTt	39	39	B.1.623	0.020923
ORF3a	42	P42L	cCt	cTt	38	38	AY.99.2	0.003502
ORF3a	42	P42A	Cct	Gct	37	37	B.1.617.2	0.000139
ORF3a	42	P42L	cCt	cTt	36	36	AY.20	0.001399
ORF3a	42	P42del	CCT	---	36	36	B.1.177	0.000474
ORF3a	42	P42L	cCt	cTt	36	36	P.1.7	0.011494
ORF3a	42	P42P	ccT	ccA	35	35	B.1.1.519	0.00139
ORF3a	42	P42P	ccT	ccC	35	35	B.1.258.11	0.013872
ORF3a	42	P42del	CCT	---	34	34	AY.4	0.000053
ORF3a	42	P42L	cCt	cTt	33	33	AY.117	0.002789
ORF3a	42	P42S	Cct	Tct	33	33	AY.39	0.000815
ORF3a	42	P42S	Cct	Tct	33	33	AY.84	0.014436
ORF3a	42	P42L	cCt	cTt	33	33	B.1.346	0.04325
ORF3a	42	P42P	ccT	ccC	32	32	B.1.177	0.000421
ORF3a	42	P42S	Cct	Tct	29	29	B.1.160	0.000904
ORF3a	42	P42P	ccT	ccG	29	29	B.1.601	0.878788
ORF3a	42	P42L	cCt	cTt	27	27	AY.101	0.013242
ORF3a	42	P42L	cCt	cTt	27	27	B.1.160	0.000842
ORF3a	42	P42L	cCt	cTt	26	26	AY.45	0.003164
ORF3a	42	P42S	Cct	Tct	26	26	AY.61	0.002724
ORF3a	42	P42L	cCt	cTt	26	26	B.1.177.32	0.035088
ORF3a	42	P42del	CCT	---	26	26	B.1.617.2	0.000098
ORF3a	42	P42L	cCt	cTt	25	25	AY.4.2	0.000542
ORF3a	42	P42L	cCt	cTt	25	25	B	0.003195
ORF3a	42	P42L	cCt	cTt	25	25	B.1.402	0.245098
ORF3a	42	P42S	Cct	Tct	25	25	P.1	0.000394
ORF3a	42	P42S	Cct	Tct	24	24	AY.46.6	0.001733
ORF3a	42	P42T	Cct	Act	24	24	AY.9.1	0.002009
ORF3a	42	P42del	CCT	---	24	24	B.1.1	0.000435
ORF3a	42	P42L	cCt	cTt	24	24	B.1.177.73	0.01359
ORF3a	42	P42S	Cct	Tct	24	24	B.1.221	0.001705
ORF3a	42	P42P	ccT	ccC	23	23	AY.120	0.000855
ORF3a	42	P42S	Cct	Tct	22	22	AY.5.3	0.007422
ORF3a	42	P42L	cCt	cTt	22	22	B.1.177.7	0.003627
ORF3a	42	P42L	cCt	cTt	22	22	B.1.429	0.000518
ORF3a	42	P42H	cCt	cAt	21	21	AY.25	0.000126
ORF3a	42	P42L	cCt	cTt	21	21	AY.34	0.002036
ORF3a	42	P42L	cCt	cTt	21	21	B.1.1.312	0.040153
ORF3a	42	P42L	cCt	cTt	21	21	B.1.264.1	1
ORF3a	42	P42S	Cct	Tct	21	21	B.1.621	0.001859
ORF3a	42	P42P	ccT	ccC	17	20	AY.103	0.000106
ORF3a	42	P42P	ccT	ccA	3	20	AY.103	0.000019
ORF3a	42	P42H	cCt	cAt	20	20	B.1.2	0.000176
ORF3a	42	P42del	CCT	---	19	19	AY.25	0.000114
ORF3a	42	P42P	ccT	ccA	14	19	AY.25	0.000084
ORF3a	42	P42P	ccT	ccC	4	19	AY.25	0.000024
ORF3a	42	P42P	ccT	ccG	1	19	AY.25	0.000006
ORF3a	42	P42L	cCt	cTt	19	19	B.1.1.507	0.165217
ORF3a	42	P42L	cCt	cTt	18	18	AY.35	0.004195
ORF3a	42	P42P	ccT	ccC	17	17	AY.46	0.001769
ORF3a	42	P42L	cCt	cTt	16	16	AY.116.1	0.004983
ORF3a	42	P42S	Cct	Tct	16	16	AY.26	0.000453
ORF3a	42	P42P	ccT	ccC	16	16	AY.59	0.008475
ORF3a	42	P42H	cCt	cAt	16	16	B.1.617.2	0.00006
ORF3a	42	P42P	ccT	ccC	15	15	AY.77	0.016911
ORF3a	42	P42L	cCt	cTt	15	15	B.1.596	0.001307
ORF3a	42	P42del	CCT	---	15	15	B.1.637	0.001096
ORF3a	42	P42del	CCT	---	15	15	P.1	0.000236
ORF3a	42	P42L	cCt	cTt	15	15	P.1.17	0.002426
ORF3a	42	P42S	Cct	Tct	14	14	AY.119	0.000494
ORF3a	42	P42P	ccT	ccC	14	14	AY.45	0.001704
ORF3a	42	P42P	ccT	ccC	14	14	AY.73	0.009315
ORF3a	42	P42L	cCt	cTt	14	14	B.1.1.10	0.015608
ORF3a	42	P42H	cCt	cAt	14	14	B.1.177	0.000184
ORF3a	42	P42P	ccT	ccC	13	14	B.1.2	0.000114
ORF3a	42	P42P	ccT	ccG	1	14	B.1.2	0.000009
ORF3a	42	P42L	cCt	cTt	14	14	B.1.240	0.003018
ORF3a	42	P42S	Cct	Tct	14	14	B.1.409	0.010937
ORF3a	42	P42L	cCt	cTt	14	14	Q.1	0.001769
ORF3a	42	P42L	cCt	cTt	13	13	AY.100	0.000598
ORF3a	42	P42S	Cct	Tct	13	13	AY.102	0.000345
ORF3a	42	P42P	ccT	ccC	13	13	AY.23	0.000907
ORF3a	42	P42P	ccT	ccC	13	13	AY.33	0.000868
ORF3a	42	P42S	Cct	Tct	13	13	AY.39.1	0.000515
ORF3a	42	P42L	cCt	cTt	13	13	AY.47	0.000404
ORF3a	42	P42del	CCT	---	13	13	AY.98.1	0.00063
ORF3a	42	P42S	Cct	Tct	13	13	B.1.621.1	0.006576
ORF3a	42	P42F	CCt	TTt	12	12	All	0.000002
ORF3a	42	P42L	cCt	cTt	12	12	AY.102	0.000318
ORF3a	42	P42P	ccT	ccC	12	12	AY.111	0.002198
ORF3a	42	P42P	ccT	ccC	12	12	AY.116	0.003441
ORF3a	42	P42P	ccT	ccG	12	12	B.1.1.33	0.005051
ORF3a	42	P42L	cCt	cTt	12	12	B.1.1.519	0.000477
ORF3a	42	P42L	cCt	cTt	12	12	B.1.466.2	0.004695
ORF3a	42	P42del1	ccT	cc-	11	11	AY.4	0.000017
ORF3a	42	P42P	ccT	ccC	11	11	AY.98	0.000869
ORF3a	42	P42H	cCt	cAt	11	11	AY.99.2	0.001014
ORF3a	42	P42L	cCt	cTt	11	11	B.1.399	0.021277
ORF3a	42	P42R	cCt	cGt	11	11	B.1.637	0.000804
ORF3a	42	P42L	cCt	cTt	10	10	AY.14	0.00088
ORF3a	42	P42del	CCT	---	10	10	AY.3	0.000099
ORF3a	42	P42L	cCt	cTt	10	10	AY.39.1	0.000396
ORF3a	42	P42P	ccT	ccC	10	10	AY.5	0.000206
ORF3a	42	P42L	cCt	cTt	10	10	AY.5.4	0.002767
ORF3a	42	P42H	cCt	cAt	10	10	B.1.258.17	0.00104
ORF3a	42	P42L	cCt	cTt	10	10	C.37	0.001161
ORF3a	42	P42L	cCt	cTt	10	10	P.1.10	0.002695
ORF3a	42	P42R	cCt	cGt	9	9	AY.117	0.000761
ORF3a	42	P42S	Cct	Tct	9	9	AY.34	0.000873
ORF3a	42	P42L	cCt	cTt	9	9	AY.46.5	0.001786
ORF3a	42	P42L	cCt	cTt	9	9	AY.5	0.000186
ORF3a	42	P42del	CCT	---	9	9	B.1.258	0.000599
ORF3a	42	P42del1	ccT	cc-	9	9	P.1.1	0.002859
ORF3a	42	P42P	ccT	ccC	8	8	AY.120.1	0.002568
ORF3a	42	P42P	ccT	ccC	8	8	AY.6	0.000329
ORF3a	42	P42L	cCt	cTt	8	8	B.1.110.3	0.005747
ORF3a	42	P42H	cCt	cAt	8	8	B.1.160	0.00025
ORF3a	42	P42L	cCt	cTt	8	8	B.1.214.2	0.004796
ORF3a	42	P42S	Cct	Tct	8	8	B.1.258.17	0.000832
ORF3a	42	P42S	Cct	Tct	8	8	B.1.36.1	0.009122
ORF3a	42	P42S	Cct	Tct	8	8	B.1.36.8	0.008
ORF3a	42	P42F	CCt	TTt	8	8	B.1.526	0.000188
ORF3a	42	P42L	cCt	cTt	8	8	B.1.621	0.000708
ORF3a	42	P42L	cCt	cTt	8	8	P.1.14	0.000382
ORF3a	42	P42del	CCT	---	7	7	AY.103	0.000043
ORF3a	42	P42del	CCT	---	7	7	AY.39	0.000173
ORF3a	42	P42T	Cct	Act	7	7	AY.43	0.000031
ORF3a	42	P42L	cCt	cTt	7	7	AY.46	0.000729
ORF3a	42	P42H	cCt	cAt	7	7	AY.47	0.000218
ORF3a	42	P42P	ccT	ccC	7	7	AY.84	0.003062
ORF3a	42	P42L	cCt	cTt	7	7	B.1.1.39	0.003568
ORF3a	42	P42P	ccT	ccC	7	7	B.1.177.75	0.007284
ORF3a	42	P42L	cCt	cTt	7	7	B.1.554	0.030837
ORF3a	42	P42L	cCt	cTt	7	7	B.1.617.1	0.000903
ORF3a	42	P42S	Cct	Tct	7	7	B.1.617.1	0.000903
ORF3a	42	P42del2	cCT	c--	5	6	All	0.000001
ORF3a	42	P42del2	CCT	--N	1	6	All	0
ORF3a	42	P42S	Cct	Tct	6	6	AY.120	0.000223
ORF3a	42	P42H	cCt	cAt	6	6	AY.39	0.000148
ORF3a	42	P42H	cCt	cAt	6	6	AY.4.2.1	0.000894
ORF3a	42	P42S	Cct	Tct	6	6	AY.4.5	0.000645
ORF3a	42	P42H	cCt	cAt	6	6	AY.43	0.000027
ORF3a	42	P42H	cCt	cAt	6	6	AY.44	0.000037
ORF3a	42	P42del	CCT	---	6	6	AY.44	0.000037
ORF3a	42	P42L	cCt	cTt	6	6	AY.62	0.002614
ORF3a	42	P42S	Cct	Tct	6	6	AY.74	0.000694
ORF3a	42	P42H	cCt	cAt	6	6	B.1	0.000055
ORF3a	42	P42P	ccT	ccC	6	6	B.1.1.222	0.001224
ORF3a	42	P42L	cCt	cTt	6	6	B.1.243	0.000418
ORF3a	42	P42L	cCt	cTt	6	6	B.1.625	0.014118
ORF3a	42	P42L	cCt	cTt	6	6	B.1.636	0.040268
ORF3a	42	P42L	cCt	cTt	5	5	AY.110	0.000563
ORF3a	42	P42S	Cct	Tct	5	5	AY.117	0.000423
ORF3a	42	P42H	cCt	cAt	5	5	AY.118	0.000313
ORF3a	42	P42S	Cct	Tct	5	5	AY.29	0.000079
ORF3a	42	P42L	cCt	cTt	5	5	AY.33	0.000334
ORF3a	42	P42S	Cct	Tct	5	5	AY.33	0.000334
ORF3a	42	P42P	ccT	ccG	3	5	AY.4.2	0.000065
ORF3a	42	P42P	ccT	ccA	2	5	AY.4.2	0.000043
ORF3a	42	P42S	Cct	Tct	5	5	AY.46	0.00052
ORF3a	42	P42P	ccT	ccC	5	5	AY.46.4	0.000823
ORF3a	42	P42del1	ccT	cc-	5	5	AY.5	0.000103
ORF3a	42	P42P	ccT	ccC	5	5	AY.53	0.001438
ORF3a	42	P42S	Cct	Tct	5	5	AY.8	0.00303
ORF3a	42	P42del	CCT	---	5	5	B.1	0.000046
ORF3a	42	P42P	ccT	ccC	3	5	B.1.1	0.000054
ORF3a	42	P42P	ccT	ccA	1	5	B.1.1	0.000018
ORF3a	42	P42P	ccT	ccG	1	5	B.1.1	0.000018
ORF3a	42	P42L	cCt	cTt	5	5	B.1.1.220	0.009294
ORF3a	42	P42T	Cct	Act	5	5	B.1.1.7	0.000004
ORF3a	42	P42R	cCt	cGt	5	5	B.1.2	0.000044
ORF3a	42	P42L	cCt	cTt	5	5	B.1.221	0.000355
ORF3a	42	P42P	ccT	ccA	5	5	B.1.234	0.00066
ORF3a	42	P42L	cCt	cTt	5	5	B.1.427	0.000252
ORF3a	42	P42del	CCT	---	5	5	B.1.438.1	0.000536
ORF3a	42	P42L	cCt	cTt	5	5	B.1.544	0.03012
ORF3a	42	P42S	Cct	Tct	5	5	P.1.13	0.004492
ORF3a	42	P42L	cCt	cTt	5	5	P.2	0.000933
ORF3a	42	P42L	cCt	cTt	5	5	Q.8	0.000825
ORF3a	42	P42S	Cct	Tct	4	4		0.222222
ORF3a	42	P42L	cCt	cTt	4	4	AD.2	0.000876
ORF3a	42	P42P	ccT	ccC	4	4	AY.118	0.000251
ORF3a	42	P42L	cCt	cTt	4	4	AY.118	0.000251
ORF3a	42	P42P	ccT	ccC	4	4	AY.119	0.000141
ORF3a	42	P42L	cCt	cTt	4	4	AY.121	0.000541
ORF3a	42	P42S	Cct	Tct	4	4	AY.20	0.000155
ORF3a	42	P42T	Cct	Act	4	4	AY.20	0.000155
ORF3a	42	P42L	cCt	cTt	4	4	AY.23	0.000279
ORF3a	42	P42del1	ccT	cc-	3	4	AY.25	0.000018
ORF3a	42	P42del1	Cct	-ct	1	4	AY.25	0.000006
ORF3a	42	P42P	ccT	ccC	4	4	AY.36	0.000593
ORF3a	42	P42del	CCT	---	4	4	AY.4.2	0.000087
ORF3a	42	P42H	cCt	cAt	4	4	AY.5	0.000083
ORF3a	42	P42S	Cct	Tct	4	4	AY.52	0.003257
ORF3a	42	P42L	cCt	cTt	4	4	AY.55	0.00367
ORF3a	42	P42L	cCt	cTt	4	4	AY.75	0.000224
ORF3a	42	P42S	Cct	Tct	4	4	AY.75	0.000224
ORF3a	42	P42L	cCt	cTt	4	4	AY.85	0.001709
ORF3a	42	P42L	cCt	cTt	4	4	AY.98.1	0.000194
ORF3a	42	P42R	cCt	cGt	4	4	B.1	0.000037
ORF3a	42	P42H	cCt	cAt	4	4	B.1.1	0.000073
ORF3a	42	P42L	cCt	cTt	4	4	B.1.1.416	0.00362
ORF3a	42	P42S	Cct	Tct	4	4	B.1.1.63	0.001543
ORF3a	42	P42del1	ccT	cc-	4	4	B.1.1.7	0.000004
ORF3a	42	P42L	cCt	cTt	4	4	B.1.177.42	0.003578
ORF3a	42	P42P	ccT	ccC	4	4	B.1.221	0.000284
ORF3a	42	P42L	cCt	cTt	4	4	B.1.258.17	0.000416
ORF3a	42	P42A	Cct	Gct	4	4	B.1.351	0.000119
ORF3a	42	P42L	cCt	cTt	4	4	B.1.36.7	0.016
ORF3a	42	P42S	Cct	Tct	4	4	B.1.369	0.001141
ORF3a	42	P42P	ccT	ccC	4	4	B.1.617.1	0.000516
ORF3a	42	P42del1	ccT	cc-	4	4	B.1.617.2	0.000015
ORF3a	42	P42T	Cct	Act	4	4	B.1.617.2	0.000015
ORF3a	42	P42L	cCt	cTt	4	4	B.1.618	0.016129
ORF3a	42	P42L	cCt	cTt	4	4	D.2	0.0003
ORF3a	42	P42L	cCt	cTt	4	4	N.6	0.028369
ORF3a	42	P42L	cCt	cTt	4	4	P.1.1	0.001271
ORF3a	42	P42del	CCT	---	4	4	P.1.9	0.019231
ORF3a	42	P42S	Cct	Tct	3	3	AY.106	0.001005
ORF3a	42	P42P	ccT	ccC	3	3	AY.110	0.000338
ORF3a	42	P42S	Cct	Tct	3	3	AY.113	0.000427
ORF3a	42	P42S	Cct	Tct	3	3	AY.116	0.00086
ORF3a	42	P42del1	ccT	cc-	3	3	AY.118	0.000188
ORF3a	42	P42H	cCt	cAt	3	3	AY.119	0.000106
ORF3a	42	P42del	CCT	---	3	3	AY.120	0.000112
ORF3a	42	P42S	Cct	Tct	3	3	AY.14	0.000264
ORF3a	42	P42del	CCT	---	3	3	AY.20	0.000117
ORF3a	42	P42L	cCt	cTt	3	3	AY.27	0.000194
ORF3a	42	P42T	Cct	Act	3	3	AY.29	0.000047
ORF3a	42	P42T	Cct	Act	3	3	AY.3	0.00003
ORF3a	42	P42del1	ccT	cc-	3	3	AY.3	0.00003
ORF3a	42	P42L	cCt	cTt	3	3	AY.32	0.001597
ORF3a	42	P42del	CCT	---	3	3	AY.39.1	0.000119
ORF3a	42	P42del	CCT	---	3	3	AY.4.5	0.000322
ORF3a	42	P42P	ccT	ccC	3	3	AY.4.5	0.000322
ORF3a	42	P42del	CCT	---	3	3	AY.40	0.002893
ORF3a	42	P42P	ccT	ccC	3	3	AY.41	0.000882
ORF3a	42	P42L	cCt	cTt	3	3	AY.42	0.000121
ORF3a	42	P42del1	ccT	cc-	3	3	AY.44	0.000018
ORF3a	42	P42del	CCT	---	3	3	AY.45	0.000365
ORF3a	42	P42H	cCt	cAt	3	3	AY.5.3	0.001012
ORF3a	42	P42P	ccT	ccC	3	3	AY.5.4	0.00083
ORF3a	42	P42L	cCt	cTt	3	3	AY.60	0.002814
ORF3a	42	P42L	cCt	cTt	3	3	AY.61	0.000314
ORF3a	42	P42P	ccT	ccC	2	3	AY.74	0.000231
ORF3a	42	P42P	ccT	ccA	1	3	AY.74	0.000116
ORF3a	42	P42del	CCT	---	3	3	AY.75	0.000168
ORF3a	42	P42P	ccT	ccC	3	3	AY.87	0.002498
ORF3a	42	P42H	cCt	cAt	3	3	AY.88	0.002653
ORF3a	42	P42P	ccT	ccC	3	3	AY.9.2	0.00011
ORF3a	42	P42T	Cct	Act	3	3	AY.9.2	0.00011
ORF3a	42	P42P	ccT	ccC	3	3	AY.93	0.000819
ORF3a	42	P42S	Cct	Tct	3	3	AY.95	0.002283
ORF3a	42	P42del	CCT	---	3	3	AY.98	0.000237
ORF3a	42	P42S	Cct	Tct	3	3	AY.98.1	0.000145
ORF3a	42	P42del1	ccT	cc-	3	3	B.1.1	0.000054
ORF3a	42	P42S	Cct	Tct	3	3	B.1.1	0.000054
ORF3a	42	P42P	ccT	ccC	3	3	B.1.1.115	0.026786
ORF3a	42	P42P	ccT	ccG	3	3	B.1.1.258	0.009772
ORF3a	42	P42S	Cct	Tct	3	3	B.1.1.28	0.000934
ORF3a	42	P42L	cCt	cTt	3	3	B.1.1.316	0.002775
ORF3a	42	P42L	cCt	cTt	3	3	B.1.1.317	0.001235
ORF3a	42	P42L	cCt	cTt	3	3	B.1.1.63	0.001157
ORF3a	42	P42del	CCT	---	3	3	B.1.160.24	0.013274
ORF3a	42	P42S	Cct	Tct	3	3	B.1.177.7	0.000495
ORF3a	42	P42T	Cct	Act	3	3	B.1.2	0.000026
ORF3a	42	P42del1	ccT	cc-	3	3	B.1.2	0.000026
ORF3a	42	P42S	Cct	Tct	3	3	B.1.258	0.0002
ORF3a	42	P42L	cCt	cTt	3	3	B.1.324	0.004815
ORF3a	42	P42H	cCt	cAt	3	3	B.1.351	0.000089
ORF3a	42	P42S	Cct	Tct	3	3	B.1.351	0.000089
ORF3a	42	P42del	CCT	---	3	3	B.1.427	0.000151
ORF3a	42	P42L	cCt	cTt	3	3	B.1.533	0.028846
ORF3a	42	P42L	cCt	cTt	3	3	B.1.549	0.021583
ORF3a	42	P42L	cCt	cTt	3	3	B.1.575	0.00091
ORF3a	42	P42R	cCt	cGt	3	3	B.1.617.2	0.000011
ORF3a	42	P42L	cCt	cTt	3	3	B.1.628	0.001057
ORF3a	42	P42L	cCt	cTt	3	3	B.40	0.001093
ORF3a	42	P42P	ccT	ccA	3	3	D.2	0.000225
ORF3a	42	P42P	ccT	ccC	3	3	P.1	0.000047
ORF3a	42	P42P	ccT	ccG	2	3	P.2	0.000373
ORF3a	42	P42P	ccT	ccC	1	3	P.2	0.000187
ORF3a	42	P42P	ccT	ccC	3	3	Q.8	0.000495
ORF3a	42	P42del	CCT	---	3	3	U.3	0.011583
ORF3a	42	P42L	cCt	cTt	2	2	A.23.1	0.001408
ORF3a	42	P42A	Cct	Gct	2	2	A.25	0.036364
ORF3a	42	P42P	ccT	ccC	2	2	AY.1	0.000791
ORF3a	42	P42del1	ccT	cc-	2	2	AY.100	0.000092
ORF3a	42	P42del1	ccT	cc-	2	2	AY.103	0.000012
ORF3a	42	P42P	ccT	ccC	2	2	AY.105	0.001286
ORF3a	42	P42S	Cct	Tct	2	2	AY.107	0.000932
ORF3a	42	P42S	Cct	Tct	2	2	AY.111	0.000366
ORF3a	42	P42L	cCt	cTt	2	2	AY.113	0.000285
ORF3a	42	P42F	CCt	TTt	2	2	AY.12	0.000632
ORF3a	42	P42P	ccT	ccC	2	2	AY.121	0.000271
ORF3a	42	P42del	CCT	---	2	2	AY.13	0.000322
ORF3a	42	P42L	cCt	cTt	2	2	AY.13	0.000322
ORF3a	42	P42L	cCt	cTt	2	2	AY.16.1	0.00094
ORF3a	42	P42S	Cct	Tct	2	2	AY.23	0.000139
ORF3a	42	P42S	Cct	Tct	2	2	AY.27	0.000129
ORF3a	42	P42P	ccT	ccC	1	2	AY.27	0.000065
ORF3a	42	P42P	ccT	ccG	1	2	AY.27	0.000065
ORF3a	42	P42L	cCt	cTt	2	2	AY.28	0.003781
ORF3a	42	P42del	CCT	---	2	2	AY.29	0.000032
ORF3a	42	P42L	cCt	cTt	2	2	AY.30	0.000791
ORF3a	42	P42H	cCt	cAt	2	2	AY.33	0.000134
ORF3a	42	P42P	ccT	ccC	2	2	AY.34	0.000194
ORF3a	42	P42T	Cct	Act	2	2	AY.39	0.000049
ORF3a	42	P42del1	ccT	cc-	2	2	AY.39.1	0.000079
ORF3a	42	P42T	Cct	Act	2	2	AY.4	0.000003
ORF3a	42	P42H	cCt	cAt	2	2	AY.4.2	0.000043
ORF3a	42	P42S	Cct	Tct	2	2	AY.4.4	0.000818
ORF3a	42	P42S	Cct	Tct	2	2	AY.40	0.001929
ORF3a	42	P42H	cCt	cAt	2	2	AY.42	0.00008
ORF3a	42	P42del1	ccT	cc-	2	2	AY.43	0.000009
ORF3a	42	P42R	cCt	cGt	2	2	AY.44	0.000012
ORF3a	42	P42del	CCT	---	2	2	AY.46	0.000208
ORF3a	42	P42P	ccT	ccC	2	2	AY.46.1	0.002053
ORF3a	42	P42del	CCT	---	2	2	AY.46.2	0.001271
ORF3a	42	P42L	cCt	cTt	2	2	AY.48	0.00093
ORF3a	42	P42P	ccT	ccC	2	2	AY.5.3	0.000675
ORF3a	42	P42L	cCt	cTt	2	2	AY.53	0.000575
ORF3a	42	P42del	CCT	---	2	2	AY.6	0.000082
ORF3a	42	P42S	Cct	Tct	2	2	AY.62	0.000871
ORF3a	42	P42S	Cct	Tct	2	2	AY.63	0.000774
ORF3a	42	P42del	CCT	---	2	2	AY.67	0.000929
ORF3a	42	P42P	ccT	ccC	2	2	AY.68	0.000547
ORF3a	42	P42L	cCt	cTt	2	2	AY.69	0.000373
ORF3a	42	P42P	ccT	ccC	2	2	AY.70	0.000417
ORF3a	42	P42L	cCt	cTt	2	2	AY.74	0.000231
ORF3a	42	P42P	ccT	ccC	2	2	AY.75	0.000112
ORF3a	42	P42del2	cCT	c--	2	2	AY.75	0.000112
ORF3a	42	P42L	cCt	cTt	2	2	AY.75.1	0.000361
ORF3a	42	P42S	Cct	Tct	2	2	AY.75.1	0.000361
ORF3a	42	P42P	ccT	ccC	2	2	AY.75.1	0.000361
ORF3a	42	P42P	ccT	ccC	2	2	AY.78	0.003082
ORF3a	42	P42del	CCT	---	2	2	AY.81	0.003984
ORF3a	42	P42L	cCt	cTt	2	2	AY.88	0.001768
ORF3a	42	P42S	Cct	Tct	2	2	AY.9.1	0.000167
ORF3a	42	P42L	cCt	cTt	2	2	AY.90	0.001369
ORF3a	42	P42L	cCt	cTt	2	2	AY.91	0.001461
ORF3a	42	P42S	Cct	Tct	2	2	AY.92	0.000575
ORF3a	42	P42P	ccT	ccC	2	2	AY.96	0.004149
ORF3a	42	P42L	cCt	cTt	2	2	AY.96	0.004149
ORF3a	42	P42L	cCt	cTt	2	2	AY.98	0.000158
ORF3a	42	P42S	Cct	Tct	2	2	AY.98	0.000158
ORF3a	42	P42S	Cct	Tct	2	2	B	0.000256
ORF3a	42	P42del1	ccT	cc-	2	2	B.1	0.000018
ORF3a	42	P42T	Cct	Act	2	2	B.1	0.000018
ORF3a	42	P42S	Cct	Tct	2	2	B.1.1.207	0.002364
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.222	0.000408
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.25	0.001137
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.273	0.013514
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.277	0.001517
ORF3a	42	P42P	ccT	ccC	2	2	B.1.1.288	0.003831
ORF3a	42	P42S	Cct	Tct	2	2	B.1.1.305	0.007722
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.307	0.005063
ORF3a	42	P42S	Cct	Tct	2	2	B.1.1.317	0.000823
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.318	0.000604
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.369	0.000892
ORF3a	42	P42S	Cct	Tct	2	2	B.1.1.37	0.000386
ORF3a	42	P42del	CCT	---	2	2	B.1.1.519	0.000079
ORF3a	42	P42S	Cct	Tct	2	2	B.1.1.519	0.000079
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.528	0.009615
ORF3a	42	P42R	cCt	cGt	2	2	B.1.1.7	0.000002
ORF3a	42	P42A	Cct	Gct	2	2	B.1.1.7	0.000002
ORF3a	42	P42S	Cct	Tct	2	2	B.1.160.16	0.001859
ORF3a	42	P42del	CCT	---	2	2	B.1.160.33	0.00885
ORF3a	42	P42P	ccT	ccC	2	2	B.1.177.21	0.000153
ORF3a	42	P42T	Cct	Act	2	2	B.1.177.32	0.002699
ORF3a	42	P42P	ccT	ccC	2	2	B.1.177.41	0.005
ORF3a	42	P42del	CCT	---	2	2	B.1.177.60	0.000437
ORF3a	42	P42L	cCt	cTt	2	2	B.1.214	0.007326
ORF3a	42	P42L	cCt	cTt	2	2	B.1.234	0.000264
ORF3a	42	P42L	cCt	cTt	2	2	B.1.235	0.005038
ORF3a	42	P42L	cCt	cTt	2	2	B.1.243.1	0.044444
ORF3a	42	P42R	cCt	cGt	2	2	B.1.247	0.029851
ORF3a	42	P42L	cCt	cTt	2	2	B.1.280	0.014286
ORF3a	42	P42L	cCt	cTt	2	2	B.1.311	0.000549
ORF3a	42	P42L	cCt	cTt	2	2	B.1.336	0.004878
ORF3a	42	P42P	ccT	ccC	2	2	B.1.351	0.000059
ORF3a	42	P42L	cCt	cTt	2	2	B.1.356	0.003454
ORF3a	42	P42L	cCt	cTt	2	2	B.1.36.18	0.00084
ORF3a	42	P42T	Cct	Act	2	2	B.1.36.36	0.001204
ORF3a	42	P42L	cCt	cTt	2	2	B.1.367	0.001585
ORF3a	42	P42L	cCt	cTt	2	2	B.1.369	0.00057
ORF3a	42	P42L	cCt	cTt	2	2	B.1.375	0.001639
ORF3a	42	P42L	cCt	cTt	2	2	B.1.413	0.008511
ORF3a	42	P42L	cCt	cTt	2	2	B.1.438.1	0.000215
ORF3a	42	P42H	cCt	cAt	2	2	B.1.462	0.014493
ORF3a	42	P42del	CCT	---	2	2	B.1.471	0.005464
ORF3a	42	P42del	CCT	---	2	2	B.1.525	0.000226
ORF3a	42	P42L	cCt	cTt	2	2	B.1.576	0.001813
ORF3a	42	P42L	cCt	cTt	2	2	B.1.577	0.001375
ORF3a	42	P42del	CCT	---	2	2	B.1.621	0.000177
ORF3a	42	P42L	cCt	cTt	2	2	B.1.635	0.035088
ORF3a	42	P42L	cCt	cTt	2	2	B.3.1	0.003317
ORF3a	42	P42del	CCT	---	2	2	D.2	0.00015
ORF3a	42	P42S	Cct	Tct	2	2	D.2	0.00015
ORF3a	42	P42R	cCt	cGt	2	2	P.1	0.000032
ORF3a	42	P42L	cCt	cTt	2	2	P.1.15	0.000465
ORF3a	42	P42S	Cct	Tct	1	1	A.11	0.058824
ORF3a	42	P42P	ccT	ccG	1	1	A.2	0.000662
ORF3a	42	P42del	CCT	---	1	1	A.2.3	0.004739
ORF3a	42	P42S	Cct	Tct	1	1	A.2.5	0.000499
ORF3a	42	P42P	ccT	ccC	1	1	A.27	0.001656
ORF3a	42	P42A	Cct	Gct	1	1	AA.4	0.009091
ORF3a	42	P42del	CCT	---	1	1	AH.3	0.003802
ORF3a	42	P42Y	CCt	TAt	1	1	All	0
ORF3a	42	P42L	cCt	cTt	1	1	AP.1	0.001502
ORF3a	42	P42del1	ccT	cc-	1	1	AP.1	0.001502
ORF3a	42	P42L	cCt	cTt	1	1	AT.1	0.005128
ORF3a	42	P42L	cCt	cTt	1	1	AY.1	0.000396
ORF3a	42	P42L	cCt	cTt	1	1	AY.10	0.00053
ORF3a	42	P42S	Cct	Tct	1	1	AY.100	0.000046
ORF3a	42	P42P	ccT	ccC	1	1	AY.100	0.000046
ORF3a	42	P42R	cCt	cGt	1	1	AY.100	0.000046
ORF3a	42	P42del	CCT	---	1	1	AY.102	0.000027
ORF3a	42	P42H	cCt	cAt	1	1	AY.102	0.000027
ORF3a	42	P42del2	CCT	--N	1	1	AY.103	0.000006
ORF3a	42	P42A	Cct	Gct	1	1	AY.103	0.000006
ORF3a	42	P42H	cCt	cAt	1	1	AY.103	0.000006
ORF3a	42	P42L	cCt	cTt	1	1	AY.104	0.001984
ORF3a	42	P42L	cCt	cTt	1	1	AY.105	0.000643
ORF3a	42	P42P	ccT	ccA	1	1	AY.107	0.000466
ORF3a	42	P42L	cCt	cTt	1	1	AY.108	0.001103
ORF3a	42	P42S	Cct	Tct	1	1	AY.109	0.00074
ORF3a	42	P42H	cCt	cAt	1	1	AY.111	0.000183
ORF3a	42	P42del	CCT	---	1	1	AY.111	0.000183
ORF3a	42	P42del	CCT	---	1	1	AY.113	0.000142
ORF3a	42	P42P	ccT	ccC	1	1	AY.114	0.000231
ORF3a	42	P42L	cCt	cTt	1	1	AY.114	0.000231
ORF3a	42	P42del	CCT	---	1	1	AY.114	0.000231
ORF3a	42	P42S	Cct	Tct	1	1	AY.116.1	0.000311
ORF3a	42	P42del	CCT	---	1	1	AY.117	0.000085
ORF3a	42	P42S	Cct	Tct	1	1	AY.118	0.000063
ORF3a	42	P42del	CCT	---	1	1	AY.118	0.000063
ORF3a	42	P42del1	ccT	cc-	1	1	AY.119	0.000035
ORF3a	42	P42A	Cct	Gct	1	1	AY.119	0.000035
ORF3a	42	P42L	cCt	cTt	1	1	AY.120.2	0.001285
ORF3a	42	P42A	Cct	Gct	1	1	AY.121	0.000135
ORF3a	42	P42S	Cct	Tct	1	1	AY.13	0.000161
ORF3a	42	P42del1	ccT	cc-	1	1	AY.14	0.000088
ORF3a	42	P42P	ccT	ccC	1	1	AY.16	0.00038
ORF3a	42	P42L	cCt	cTt	1	1	AY.16	0.00038
ORF3a	42	P42H	cCt	cAt	1	1	AY.16	0.00038
ORF3a	42	P42P	ccT	ccC	1	1	AY.19	0.00114
ORF3a	42	P42H	cCt	cAt	1	1	AY.2	0.000356
ORF3a	42	P42S	Cct	Tct	1	1	AY.22	0.002092
ORF3a	42	P42H	cCt	cAt	1	1	AY.23	0.00007
ORF3a	42	P42del	CCT	---	1	1	AY.23	0.00007
ORF3a	42	P42del2	cCT	c--	1	1	AY.23	0.00007
ORF3a	42	P42S	Cct	Tct	1	1	AY.23.1	0.000417
ORF3a	42	P42P	ccT	ccC	1	1	AY.26	0.000028
ORF3a	42	P42H	cCt	cAt	1	1	AY.26	0.000028
ORF3a	42	P42H	cCt	cAt	1	1	AY.27	0.000065
ORF3a	42	P42del	CCT	---	1	1	AY.28	0.00189
ORF3a	42	P42H	cCt	cAt	1	1	AY.29	0.000016
ORF3a	42	P42P	ccT	ccC	1	1	AY.29	0.000016
ORF3a	42	P42del	CCT	---	1	1	AY.29.1	0.000221
ORF3a	42	P42L	cCt	cTt	1	1	AY.29.1	0.000221
ORF3a	42	P42H	cCt	cAt	1	1	AY.3	0.00001
ORF3a	42	P42L	cCt	cTt	1	1	AY.3.1	0.000085
ORF3a	42	P42del	CCT	---	1	1	AY.33	0.000067
ORF3a	42	P42L	cCt	cTt	1	1	AY.37	0.000316
ORF3a	42	P42del	CCT	---	1	1	AY.38	0.000499
ORF3a	42	P42S	Cct	Tct	1	1	AY.38	0.000499
ORF3a	42	P42A	Cct	Gct	1	1	AY.39	0.000025
ORF3a	42	P42H	cCt	cAt	1	1	AY.39.1	0.00004
ORF3a	42	P42S	Cct	Tct	1	1	AY.39.1.1	0.000725
ORF3a	42	P42A	Cct	Gct	1	1	AY.4	0.000002
ORF3a	42	P42S	Cct	Tct	1	1	AY.4.2	0.000022
ORF3a	42	P42L	cCt	cTt	1	1	AY.4.5	0.000107
ORF3a	42	P42R	cCt	cGt	1	1	AY.4.5	0.000107
ORF3a	42	P42S	Cct	Tct	1	1	AY.41	0.000294
ORF3a	42	P42P	ccT	ccC	1	1	AY.42	0.00004
ORF3a	42	P42T	Cct	Act	1	1	AY.44	0.000006
ORF3a	42	P42S	Cct	Tct	1	1	AY.45	0.000122
ORF3a	42	P42L	cCt	cTt	1	1	AY.46.2	0.000635
ORF3a	42	P42P	ccT	ccC	1	1	AY.46.2	0.000635
ORF3a	42	P42S	Cct	Tct	1	1	AY.46.3	0.000934
ORF3a	42	P42L	cCt	cTt	1	1	AY.46.4	0.000165
ORF3a	42	P42S	Cct	Tct	1	1	AY.46.4	0.000165
ORF3a	42	P42L	cCt	cTt	1	1	AY.46.6	0.000072
ORF3a	42	P42P	ccT	ccC	1	1	AY.46.6	0.000072
ORF3a	42	P42P	ccT	ccG	1	1	AY.47	0.000031
ORF3a	42	P42P	ccT	ccC	1	1	AY.48	0.000465
ORF3a	42	P42P	ccT	ccC	1	1	AY.49	0.003195
ORF3a	42	P42S	Cct	Tct	1	1	AY.5	0.000021
ORF3a	42	P42del	CCT	---	1	1	AY.5	0.000021
ORF3a	42	P42S	Cct	Tct	1	1	AY.5.4	0.000277
ORF3a	42	P42P	ccT	ccC	1	1	AY.50	0.000799
ORF3a	42	P42L	cCt	cTt	1	1	AY.50	0.000799
ORF3a	42	P42S	Cct	Tct	1	1	AY.54	0.000095
ORF3a	42	P42L	cCt	cTt	1	1	AY.54	0.000095
ORF3a	42	P42P	ccT	ccC	1	1	AY.55	0.000917
ORF3a	42	P42L	cCt	cTt	1	1	AY.56	0.001605
ORF3a	42	P42P	ccT	ccC	1	1	AY.57	0.000656
ORF3a	42	P42P	ccT	ccC	1	1	AY.58	0.000907
ORF3a	42	P42del	CCT	---	1	1	AY.59	0.00053
ORF3a	42	P42R	cCt	cGt	1	1	AY.6	0.000041
ORF3a	42	P42S	Cct	Tct	1	1	AY.6	0.000041
ORF3a	42	P42P	ccT	ccC	1	1	AY.61	0.000105
ORF3a	42	P42del	CCT	---	1	1	AY.65	0.000533
ORF3a	42	P42L	cCt	cTt	1	1	AY.67	0.000464
ORF3a	42	P42P	ccT	ccC	1	1	AY.67	0.000464
ORF3a	42	P42S	Cct	Tct	1	1	AY.68	0.000274
ORF3a	42	P42del	CCT	---	1	1	AY.7	0.000196
ORF3a	42	P42P	ccT	ccC	1	1	AY.71	0.000475
ORF3a	42	P42L	cCt	cTt	1	1	AY.73	0.000665
ORF3a	42	P42del	CCT	---	1	1	AY.75.1	0.00018
ORF3a	42	P42L	cCt	cTt	1	1	AY.76	0.004831
ORF3a	42	P42L	cCt	cTt	1	1	AY.78	0.001541
ORF3a	42	P42L	cCt	cTt	1	1	AY.82	0.001357
ORF3a	42	P42del	CCT	---	1	1	AY.84	0.000437
ORF3a	42	P42P	ccT	ccC	1	1	AY.89	0.004902
ORF3a	42	P42L	cCt	cTt	1	1	AY.89	0.004902
ORF3a	42	P42del1	ccT	cc-	1	1	AY.9	0.000068
ORF3a	42	P42S	Cct	Tct	1	1	AY.9	0.000068
ORF3a	42	P42L	cCt	cTt	1	1	AY.9	0.000068
ORF3a	42	P42L	cCt	cTt	1	1	AY.9.1	0.000084
ORF3a	42	P42del	CCT	---	1	1	AY.9.2	0.000037
ORF3a	42	P42del	CCT	---	1	1	AY.90	0.000684
ORF3a	42	P42del	CCT	---	1	1	AY.91	0.00073
ORF3a	42	P42S	Cct	Tct	1	1	AY.91	0.00073
ORF3a	42	P42H	cCt	cAt	1	1	AY.91	0.00073
ORF3a	42	P42P	ccT	ccC	1	1	AY.92	0.000287
ORF3a	42	P42L	cCt	cTt	1	1	AY.92	0.000287
ORF3a	42	P42del	CCT	---	1	1	AY.93	0.000273
ORF3a	42	P42P	ccT	ccG	1	1	AY.94	0.000443
ORF3a	42	P42L	cCt	cTt	1	1	AY.95	0.000761
ORF3a	42	P42del1	ccT	cc-	1	1	AY.98	0.000079
ORF3a	42	P42Y	CCt	TAt	1	1	AY.99	0.001049
ORF3a	42	P42S	Cct	Tct	1	1	AY.99	0.001049
ORF3a	42	P42P	ccT	ccC	1	1	AY.99	0.001049
ORF3a	42	P42del	CCT	---	1	1	AY.99.2	0.000092
ORF3a	42	P42P	ccT	ccA	1	1	AY.99.2	0.000092
ORF3a	42	P42S	Cct	Tct	1	1	AZ.1	0.000867
ORF3a	42	P42del	CCT	---	1	1	B	0.000128
ORF3a	42	P42P	ccT	ccA	1	1	B	0.000128
ORF3a	42	P42T	Cct	Act	1	1	B.1.1	0.000018
ORF3a	42	P42del2	cCT	c--	1	1	B.1.1	0.000018
ORF3a	42	P42H	cCt	cAt	1	1	B.1.1.101	0.01
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.117	0.009709
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.139	0.022727
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.141	0.002012
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.159	0.004673
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.176	0.000439
ORF3a	42	P42P	ccT	ccC	1	1	B.1.1.192	0.002309
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.192	0.002309
ORF3a	42	P42del1	ccT	cc-	1	1	B.1.1.214	0.000055
ORF3a	42	P42del	CCT	---	1	1	B.1.1.225	0.007194
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.243	0.004082
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.266	0.012195
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.27	0.00565
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.279	0.001121
ORF3a	42	P42del	CCT	---	1	1	B.1.1.28	0.000311
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.294	0.001266
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.301	0.001179
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.305	0.003861
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.306	0.000438
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.306	0.000438
ORF3a	42	P42H	cCt	cAt	1	1	B.1.1.306	0.000438
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.308	0.011765
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.311	0.000358
ORF3a	42	P42H	cCt	cAt	1	1	B.1.1.318	0.000302
ORF3a	42	P42del	CCT	---	1	1	B.1.1.33	0.000421
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.33	0.000421
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.34	0.013158
ORF3a	42	P42H	cCt	cAt	1	1	B.1.1.34	0.013158
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.354	0.004386
ORF3a	42	P42P	ccT	ccC	1	1	B.1.1.355	0.015385
ORF3a	42	P42P	ccT	ccC	1	1	B.1.1.369	0.000446
ORF3a	42	P42P	ccT	ccC	1	1	B.1.1.371	0.010417
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.372	0.000689
ORF3a	42	P42P	ccT	ccC	1	1	B.1.1.388	0.045455
ORF3a	42	P42R	cCt	cGt	1	1	B.1.1.39	0.00051
ORF3a	42	P42P	ccT	ccC	1	1	B.1.1.39	0.00051
ORF3a	42	P42del	CCT	---	1	1	B.1.1.409	0.002833
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.434	0.000349
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.44	0.00241
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.448	0.002033
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.464	0.001473
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.50	0.000679
ORF3a	42	P42F	CCt	TTt	1	1	B.1.1.519	0.00004
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.523	0.001563
ORF3a	42	P42S	Cct	Tct	1	1	B.1.1.524	0.020833
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.524	0.020833
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.70	0.000341
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.89	0.006061
ORF3a	42	P42H	cCt	cAt	1	1	B.1.1.89	0.006061
ORF3a	42	P42L	cCt	cTt	1	1	B.1.110	0.004525
ORF3a	42	P42L	cCt	cTt	1	1	B.1.128	0.000635
ORF3a	42	P42L	cCt	cTt	1	1	B.1.157	0.002985
ORF3a	42	P42del	CCT	---	1	1	B.1.160	0.000031
ORF3a	42	P42P	ccT	ccC	1	1	B.1.160	0.000031
ORF3a	42	P42L	cCt	cTt	1	1	B.1.160.23	0.004831
ORF3a	42	P42P	ccT	ccA	1	1	B.1.177.10	0.000878
ORF3a	42	P42S	Cct	Tct	1	1	B.1.177.11	0.001698
ORF3a	42	P42del1	ccT	cc-	1	1	B.1.177.21	0.000076
ORF3a	42	P42R	cCt	cGt	1	1	B.1.177.21	0.000076
ORF3a	42	P42L	cCt	cTt	1	1	B.1.177.35	0.000691
ORF3a	42	P42S	Cct	Tct	1	1	B.1.177.4	0.000211
ORF3a	42	P42H	cCt	cAt	1	1	B.1.177.42	0.000894
ORF3a	42	P42S	Cct	Tct	1	1	B.1.177.44	0.000519
ORF3a	42	P42L	cCt	cTt	1	1	B.1.177.57	0.000281
ORF3a	42	P42del	CCT	---	1	1	B.1.177.6	0.000977
ORF3a	42	P42S	Cct	Tct	1	1	B.1.177.73	0.000566
ORF3a	42	P42P	ccT	ccC	1	1	B.1.177.81	0.000189
ORF3a	42	P42L	cCt	cTt	1	1	B.1.190	0.01
ORF3a	42	P42L	cCt	cTt	1	1	B.1.195	0.005025
ORF3a	42	P42F	CCt	TTt	1	1	B.1.2	0.000009
ORF3a	42	P42P	ccT	ccC	1	1	B.1.210	0.002132
ORF3a	42	P42T	Cct	Act	1	1	B.1.221	0.000071
ORF3a	42	P42del	CCT	---	1	1	B.1.221	0.000071
ORF3a	42	P42T	Cct	Act	1	1	B.1.234	0.000132
ORF3a	42	P42L	cCt	cTt	1	1	B.1.237	0.004975
ORF3a	42	P42H	cCt	cAt	1	1	B.1.239	0.001221
ORF3a	42	P42S	Cct	Tct	1	1	B.1.240	0.000216
ORF3a	42	P42del	CCT	---	1	1	B.1.241	0.000812
ORF3a	42	P42S	Cct	Tct	1	1	B.1.243	0.00007
ORF3a	42	P42H	cCt	cAt	1	1	B.1.258	0.000067
ORF3a	42	P42L	cCt	cTt	1	1	B.1.258	0.000067
ORF3a	42	P42L	cCt	cTt	1	1	B.1.293	0.0125
ORF3a	42	P42L	cCt	cTt	1	1	B.1.320	0.001245
ORF3a	42	P42L	cCt	cTt	1	1	B.1.338	0.008621
ORF3a	42	P42S	Cct	Tct	1	1	B.1.346	0.001311
ORF3a	42	P42A	Cct	Gct	1	1	B.1.349	0.000715
ORF3a	42	P42S	Cct	Tct	1	1	B.1.350	0.002933
ORF3a	42	P42L	cCt	cTt	1	1	B.1.350	0.002933
ORF3a	42	P42L	cCt	cTt	1	1	B.1.351.2	0.000303
ORF3a	42	P42L	cCt	cTt	1	1	B.1.36	0.000146
ORF3a	42	P42S	Cct	Tct	1	1	B.1.36	0.000146
ORF3a	42	P42T	Cct	Act	1	1	B.1.36	0.000146
ORF3a	42	P42R	cCt	cGt	1	1	B.1.36.1	0.00114
ORF3a	42	P42S	Cct	Tct	1	1	B.1.36.16	0.001425
ORF3a	42	P42H	cCt	cAt	1	1	B.1.36.18	0.00042
ORF3a	42	P42del2	cCT	c--	1	1	B.1.36.24	0.006173
ORF3a	42	P42S	Cct	Tct	1	1	B.1.36.36	0.000602
ORF3a	42	P42L	cCt	cTt	1	1	B.1.36.38	0.001642
ORF3a	42	P42P	ccT	ccC	1	1	B.1.36.39	0.002217
ORF3a	42	P42P	ccT	ccC	1	1	B.1.367	0.000792
ORF3a	42	P42S	Cct	Tct	1	1	B.1.396	0.000706
ORF3a	42	P42A	Cct	Gct	1	1	B.1.398	0.002976
ORF3a	42	P42S	Cct	Tct	1	1	B.1.399	0.001934
ORF3a	42	P42S	Cct	Tct	1	1	B.1.413	0.004255
ORF3a	42	P42L	cCt	cTt	1	1	B.1.428	0.00102
ORF3a	42	P42del1	ccT	cc-	1	1	B.1.429	0.000024
ORF3a	42	P42L	cCt	cTt	1	1	B.1.436	0.001029
ORF3a	42	P42S	Cct	Tct	1	1	B.1.438.1	0.000107
ORF3a	42	P42S	Cct	Tct	1	1	B.1.456	0.003268
ORF3a	42	P42T	Cct	Act	1	1	B.1.466.2	0.000391
ORF3a	42	P42L	cCt	cTt	1	1	B.1.470	0.001404
ORF3a	42	P42S	Cct	Tct	1	1	B.1.470	0.001404
ORF3a	42	P42L	cCt	cTt	1	1	B.1.497	0.000315
ORF3a	42	P42L	cCt	cTt	1	1	B.1.499	0.00105
ORF3a	42	P42S	Cct	Tct	1	1	B.1.499.1	0.111111
ORF3a	42	P42S	Cct	Tct	1	1	B.1.509	0.000866
ORF3a	42	P42T	Cct	Act	1	1	B.1.517	0.000427
ORF3a	42	P42L	cCt	cTt	1	1	B.1.524	0.001406
ORF3a	42	P42H	cCt	cAt	1	1	B.1.525	0.000113
ORF3a	42	P42L	cCt	cTt	1	1	B.1.525	0.000113
ORF3a	42	P42S	Cct	Tct	1	1	B.1.548	0.035714
ORF3a	42	P42L	cCt	cTt	1	1	B.1.550	0.013699
ORF3a	42	P42L	cCt	cTt	1	1	B.1.551	0.00129
ORF3a	42	P42L	cCt	cTt	1	1	B.1.558	0.004566
ORF3a	42	P42S	Cct	Tct	1	1	B.1.560	0.00463
ORF3a	42	P42del	CCT	---	1	1	B.1.563	0.016949
ORF3a	42	P42L	cCt	cTt	1	1	B.1.565	0.00081
ORF3a	42	P42H	cCt	cAt	1	1	B.1.566	0.019231
ORF3a	42	P42L	cCt	cTt	1	1	B.1.567	0.003333
ORF3a	42	P42L	cCt	cTt	1	1	B.1.568	0.001111
ORF3a	42	P42L	cCt	cTt	1	1	B.1.574	0.002151
ORF3a	42	P42L	cCt	cTt	1	1	B.1.580	0.004065
ORF3a	42	P42S	Cct	Tct	1	1	B.1.587	0.001898
ORF3a	42	P42S	Cct	Tct	1	1	B.1.595	0.000261
ORF3a	42	P42L	cCt	cTt	1	1	B.1.595	0.000261
ORF3a	42	P42del1	ccT	cc-	1	1	B.1.596	0.000087
ORF3a	42	P42S	Cct	Tct	1	1	B.1.596	0.000087
ORF3a	42	P42H	cCt	cAt	1	1	B.1.596	0.000087
ORF3a	42	P42P	ccT	ccC	1	1	B.1.596	0.000087
ORF3a	42	P42H	cCt	cAt	1	1	B.1.599	0.00365
ORF3a	42	P42S	Cct	Tct	1	1	B.1.605	0.005952
ORF3a	42	P42P	ccT	ccA	1	1	B.1.621	0.000089
ORF3a	42	P42S	Cct	Tct	1	1	B.1.628	0.000352
ORF3a	42	P42L	cCt	cTt	1	1	B.1.638	0.052632
ORF3a	42	P42del	CCT	---	1	1	B.1.638	0.052632
ORF3a	42	P42R	cCt	cGt	1	1	B.1.9	0.006173
ORF3a	42	P42L	cCt	cTt	1	1	B.1.9	0.006173
ORF3a	42	P42L	cCt	cTt	1	1	B.4	0.002208
ORF3a	42	P42L	cCt	cTt	1	1	B.53	0.011765
ORF3a	42	P42S	Cct	Tct	1	1	B.55	0.00295
ORF3a	42	P42L	cCt	cTt	1	1	B.55	0.00295
ORF3a	42	P42T	Cct	Act	1	1	B.6	0.00091
ORF3a	42	P42H	cCt	cAt	1	1	B.6	0.00091
ORF3a	42	P42P	ccT	ccC	1	1	C.2.1	0.006667
ORF3a	42	P42L	cCt	cTt	1	1	C.36.3	0.000567
ORF3a	42	P42del	CCT	---	1	1	C.37	0.000116
ORF3a	42	P42P	ccT	ccC	1	1	C.37	0.000116
ORF3a	42	P42S	Cct	Tct	1	1	N.5	0.001767
ORF3a	42	P42L	cCt	cTt	1	1	P.1.12	0.000484
ORF3a	42	P42L	cCt	cTt	1	1	P.1.13	0.000898
ORF3a	42	P42S	Cct	Tct	1	1	P.1.14	0.000048
ORF3a	42	P42del	CCT	---	1	1	P.1.14	0.000048
ORF3a	42	P42del	CCT	---	1	1	P.1.15	0.000232
ORF3a	42	P42R	cCt	cGt	1	1	P.1.15	0.000232
ORF3a	42	P42del	CCT	---	1	1	P.1.16	0.000374
ORF3a	42	P42L	cCt	cTt	1	1	P.1.4	0.000977
ORF3a	42	P42del	CCT	---	1	1	P.1.6	0.001946
ORF3a	42	P42S	Cct	Tct	1	1	Q.1	0.000126
ORF3a	42	P42A	Cct	Gct	1	1	Q.1	0.000126
ORF3a	42	P42T	Cct	Act	1	1	Q.3	0.000145
ORF3a	42	P42H	cCt	cAt	1	1	Q.8	0.000165
ORF3a	42	P42L	cCt	cTt	1	1	R.1	0.00009
ORF3a	42	P42S	Cct	Tct	1	1	W.3	0.005263

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.