CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 106

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	106	L106L		syn	ctC	ctT	53136	52777	0.993244	25708-25710
ORF3a	106	L106L		syn	ctC	ctA	53136	214	0.0040274	25708-25710
ORF3a	106	L106L		syn	ctC	ctG	53136	133	0.00250301	25708-25710
ORF3a	106	L106L		syn	CtC	TtG	53136	10	0.000188196	25708-25710
ORF3a	106	L106L		syn	CtC	TtA	53136	2	0.0000376393	25708-25710
ORF3a	106	L106F		nonsyn	Ctc	Ttc	12426	12389	0.997022	25708-25710
ORF3a	106	L106F		nonsyn	CtC	TtT	12426	37	0.00297763	25708-25710
ORF3a	106	L106del		del	CTC	---	425	425	1	25708-25710
ORF3a	106	L106I		nonsyn	Ctc	Atc	385	382	0.992208	25708-25710
ORF3a	106	L106I		nonsyn	CtC	AtT	385	2	0.00519481	25708-25710
ORF3a	106	L106I		nonsyn	CtC	AtA	385	1	0.0025974	25708-25710
ORF3a	106	L106P		nonsyn	cTc	cCc	337	334	0.991098	25708-25710
ORF3a	106	L106P		nonsyn	cTC	cCT	337	2	0.00593472	25708-25710
ORF3a	106	L106P		nonsyn	cTC	cCG	337	1	0.00296736	25708-25710
ORF3a	106	L106V		nonsyn	Ctc	Gtc	326	324	0.993865	25708-25710
ORF3a	106	L106V		nonsyn	CtC	GtG	326	1	0.00306748	25708-25710
ORF3a	106	L106V		nonsyn	CtC	GtA	326	1	0.00306748	25708-25710
ORF3a	106	L106R		nonsyn	cTc	cGc	238	235	0.987395	25708-25710
ORF3a	106	L106R		nonsyn	cTC	cGA	238	3	0.012605	25708-25710
ORF3a	106	L106H		nonsyn	cTc	cAc	86	86	1	25708-25710
ORF3a	106	L106S		nonsyn	CTc	TCc	17	9	0.529412	25708-25710
ORF3a	106	L106S		nonsyn	CTC	TCT	17	7	0.411765	25708-25710
ORF3a	106	L106S		nonsyn	CTC	TCG	17	1	0.0588235	25708-25710
ORF3a	106	L106del2		del	CTc	--c	4	3	0.75	25708-25710
ORF3a	106	L106del1		del	Ctc	-tc	4	2	0.5	25708-25710
ORF3a	106	L106del1		del	CtC	-tT	4	2	0.5	25708-25710
ORF3a	106	L106del2		del	CTC	--A	4	1	0.25	25708-25710
ORF3a	106	L106C		nonsyn	CTc	TGc	3	3	1	25708-25710
ORF3a	106	L106X		nonsyn	CTC	TGA	2	2	1	25708-25710
ORF3a	106	L106G		nonsyn	CTc	GGc	2	1	0.5	25708-25710
ORF3a	106	L106G		nonsyn	CTC	GGA	2	1	0.5	25708-25710
ORF3a	106	L106Y		nonsyn	CTc	TAc	1	1	1	25708-25710

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	106	L106L	ctC	ctT	52777	53136	All	0.010094
ORF3a	106	L106L	ctC	ctA	214	53136	All	0.000041
ORF3a	106	L106L	ctC	ctG	133	53136	All	0.000025
ORF3a	106	L106L	CtC	TtG	10	53136	All	0.000002
ORF3a	106	L106L	CtC	TtA	2	53136	All	0
ORF3a	106	L106L	ctC	ctT	29776	29776	B.1.160	0.928643
ORF3a	106	L106F	Ctc	Ttc	12389	12426	All	0.00237
ORF3a	106	L106F	CtC	TtT	37	12426	All	0.000007
ORF3a	106	L106L	ctC	ctT	4951	4956	AY.3	0.049245
ORF3a	106	L106L	ctC	ctA	4	4956	AY.3	0.00004
ORF3a	106	L106L	ctC	ctG	1	4956	AY.3	0.00001
ORF3a	106	L106F	Ctc	Ttc	4227	4229	B.1.1.7	0.003784
ORF3a	106	L106F	CtC	TtT	2	4229	B.1.1.7	0.000002
ORF3a	106	L106L	ctC	ctT	2401	2584	B.1.1.7	0.002149
ORF3a	106	L106L	ctC	ctA	107	2584	B.1.1.7	0.000096
ORF3a	106	L106L	ctC	ctG	73	2584	B.1.1.7	0.000065
ORF3a	106	L106L	CtC	TtG	3	2584	B.1.1.7	0.000003
ORF3a	106	L106L	ctC	ctT	2449	2449	AY.63	0.947389
ORF3a	106	L106F	Ctc	Ttc	1664	1666	B.1.621	0.147296
ORF3a	106	L106F	CtC	TtT	2	1666	B.1.621	0.000177
ORF3a	106	L106L	ctC	ctT	1039	1039	B.1.160.16	0.965613
ORF3a	106	L106L	ctC	ctT	775	775	B.1.160.8	0.998711
ORF3a	106	L106L	ctC	ctT	718	730	AY.4	0.001118
ORF3a	106	L106L	ctC	ctA	8	730	AY.4	0.000012
ORF3a	106	L106L	ctC	ctG	4	730	AY.4	0.000006
ORF3a	106	L106F	Ctc	Ttc	647	647	AY.4	0.001007
ORF3a	106	L106L	ctC	ctT	585	585	B.1.160.17	0.994898
ORF3a	106	L106F	Ctc	Ttc	547	548	AY.25	0.00329
ORF3a	106	L106F	CtC	TtT	1	548	AY.25	0.000006
ORF3a	106	L106L	ctC	ctT	535	539	B.1	0.0049
ORF3a	106	L106L	ctC	ctA	2	539	B.1	0.000018
ORF3a	106	L106L	ctC	ctG	2	539	B.1	0.000018
ORF3a	106	L106F	Ctc	Ttc	493	493	AY.43	0.002184
ORF3a	106	L106L	ctC	ctT	479	479	B.1.160.7	0.995842
ORF3a	106	L106L	ctC	ctT	451	451	B.1.160.14	0.955508
ORF3a	106	L106F	Ctc	Ttc	435	435	P.1	0.006853
ORF3a	106	L106del	CTC	---	425	425	All	0.000081
ORF3a	106	L106L	ctC	ctT	409	409	B.1.160.26	0.990315
ORF3a	106	L106L	ctC	ctT	374	388	B.1.617.2	0.001408
ORF3a	106	L106L	ctC	ctG	8	388	B.1.617.2	0.00003
ORF3a	106	L106L	ctC	ctA	6	388	B.1.617.2	0.000023
ORF3a	106	L106I	Ctc	Atc	382	385	All	0.000073
ORF3a	106	L106I	CtC	AtT	2	385	All	0
ORF3a	106	L106I	CtC	AtA	1	385	All	0
ORF3a	106	L106L	ctC	ctT	338	338	B.1.160.28	0.988304
ORF3a	106	L106P	cTc	cCc	334	337	All	0.000064
ORF3a	106	L106P	cTC	cCT	2	337	All	0
ORF3a	106	L106P	cTC	cCG	1	337	All	0
ORF3a	106	L106V	Ctc	Gtc	324	326	All	0.000062
ORF3a	106	L106V	CtC	GtG	1	326	All	0
ORF3a	106	L106V	CtC	GtA	1	326	All	0
ORF3a	106	L106F	Ctc	Ttc	312	312	B.1.617.2	0.001175
ORF3a	106	L106F	Ctc	Ttc	289	289	B.1.351	0.008591
ORF3a	106	L106L	ctC	ctT	269	282	AY.43	0.001192
ORF3a	106	L106L	ctC	ctA	12	282	AY.43	0.000053
ORF3a	106	L106L	ctC	ctG	1	282	AY.43	0.000004
ORF3a	106	L106F	Ctc	Ttc	279	279	B.1.36	0.040706
ORF3a	106	L106L	ctC	ctT	275	275	AY.119	0.00971
ORF3a	106	L106F	Ctc	Ttc	263	264	AY.44	0.001601
ORF3a	106	L106F	CtC	TtT	1	264	AY.44	0.000006
ORF3a	106	L106L	ctC	ctT	243	246	B.1.2	0.00214
ORF3a	106	L106L	ctC	ctG	2	246	B.1.2	0.000018
ORF3a	106	L106L	ctC	ctA	1	246	B.1.2	0.000009
ORF3a	106	L106R	cTc	cGc	235	238	All	0.000045
ORF3a	106	L106R	cTC	cGA	3	238	All	0.000001
ORF3a	106	L106L	ctC	ctT	232	232	B.1.160.29	0.978903
ORF3a	106	L106F	Ctc	Ttc	227	228	B.1.2	0.001999
ORF3a	106	L106F	CtC	TtT	1	228	B.1.2	0.000009
ORF3a	106	L106I	Ctc	Atc	226	226	AY.99.2	0.020828
ORF3a	106	L106L	ctC	ctT	226	226	B.1.160.24	1
ORF3a	106	L106L	ctC	ctT	225	225	B.1.160.33	0.995575
ORF3a	106	L106L	ctC	ctT	198	215	AY.103	0.001229
ORF3a	106	L106L	ctC	ctG	17	215	AY.103	0.000106
ORF3a	106	L106L	ctC	ctT	205	205	B.1.160.23	0.990338
ORF3a	106	L106L	ctC	ctT	198	198	B.1.160.15	0.980198
ORF3a	106	L106L	ctC	ctT	197	197	B.1.160.30	0.58631
ORF3a	106	L106L	ctC	ctT	185	185	B.1.160.32	0.793991
ORF3a	106	L106F	Ctc	Ttc	176	177	B.1	0.001612
ORF3a	106	L106F	CtC	TtT	1	177	B.1	0.000009
ORF3a	106	L106L	ctC	ctT	174	174	B.1.160.11	0.994286
ORF3a	106	L106L	ctC	ctT	144	153	AY.44	0.000876
ORF3a	106	L106L	ctC	ctA	5	153	AY.44	0.00003
ORF3a	106	L106L	ctC	ctG	4	153	AY.44	0.000024
ORF3a	106	L106L	ctC	ctT	153	153	B.1.160.12	0.980769
ORF3a	106	L106L	ctC	ctT	146	146	B.1.160.22	0.986486
ORF3a	106	L106L	ctC	ctT	137	138	B.1.177	0.001804
ORF3a	106	L106L	ctC	ctA	1	138	B.1.177	0.000013
ORF3a	106	L106L	ctC	ctT	137	137	B.1.160.18	1
ORF3a	106	L106L	ctC	ctT	136	136	B.1.160.9	0.978417
ORF3a	106	L106V	Ctc	Gtc	133	133	AY.4.5	0.014296
ORF3a	106	L106F	Ctc	Ttc	122	123	AY.103	0.000758
ORF3a	106	L106F	CtC	TtT	1	123	AY.103	0.000006
ORF3a	106	L106F	Ctc	Ttc	123	123	C.35	0.095201
ORF3a	106	L106L	ctC	ctT	122	122	B.1.160.31	0.983871
ORF3a	106	L106L	ctC	ctT	121	121	AB.1	0.991803
ORF3a	106	L106L	ctC	ctT	120	120	AY.25	0.000722
ORF3a	106	L106L	ctC	ctT	115	119	B.1.1	0.002086
ORF3a	106	L106L	ctC	ctA	4	119	B.1.1	0.000073
ORF3a	106	L106L	ctC	ctT	117	117	B.1.160.10	0.943548
ORF3a	106	L106L	ctC	ctT	95	107	AY.39.1	0.003763
ORF3a	106	L106L	ctC	ctA	12	107	AY.39.1	0.000475
ORF3a	106	L106F	Ctc	Ttc	106	106	AY.47	0.003297
ORF3a	106	L106F	Ctc	Ttc	102	102	AY.3	0.001015
ORF3a	106	L106L	ctC	ctT	94	97	AY.34	0.009115
ORF3a	106	L106L	ctC	ctA	3	97	AY.34	0.000291
ORF3a	106	L106F	Ctc	Ttc	95	96	B.1.1	0.001723
ORF3a	106	L106F	CtC	TtT	1	96	B.1.1	0.000018
ORF3a	106	L106L	ctC	ctT	95	95	B.1.221	0.006748
ORF3a	106	L106L	ctC	ctT	92	94	AY.102	0.002439
ORF3a	106	L106L	ctC	ctA	2	94	AY.102	0.000053
ORF3a	106	L106P	cTc	cCc	94	94	B.1.1.7	0.000084
ORF3a	106	L106F	Ctc	Ttc	92	92	AY.20	0.003576
ORF3a	106	L106L	ctC	ctT	90	90	B.1.160.25	1
ORF3a	106	L106H	cTc	cAc	86	86	All	0.000016
ORF3a	106	L106F	Ctc	Ttc	86	86	B.1.1.519	0.003415
ORF3a	106	L106L	ctC	ctT	76	76	B.1.160.20	0.678571
ORF3a	106	L106F	Ctc	Ttc	75	75	B.1.429	0.001765
ORF3a	106	L106L	ctC	ctT	74	74	B.1.622	0.961039
ORF3a	106	L106L	ctC	ctT	72	72	AY.117	0.006085
ORF3a	106	L106P	cTc	cCc	72	72	B.1.258.17	0.007486
ORF3a	106	L106L	ctC	ctT	70	71	P.1	0.001103
ORF3a	106	L106L	CtC	TtG	1	71	P.1	0.000016
ORF3a	106	L106F	Ctc	Ttc	69	69	A.23.1	0.048592
ORF3a	106	L106del	CTC	---	69	69	B.1.1.7	0.000062
ORF3a	106	L106L	ctC	ctT	66	66	AY.100	0.003036
ORF3a	106	L106L	ctC	ctT	66	66	B.1.160.27	1
ORF3a	106	L106L	ctC	ctT	65	65	B.1.164	0.970149
ORF3a	106	L106F	Ctc	Ttc	63	63	AY.4.2	0.001366
ORF3a	106	L106F	Ctc	Ttc	62	62	AY.5.4	0.017156
ORF3a	106	L106F	Ctc	Ttc	62	62	B.1.526	0.001457
ORF3a	106	L106F	Ctc	Ttc	61	61	B.1.177.53	0.145933
ORF3a	106	L106V	Ctc	Gtc	61	61	B.1.617.2	0.00023
ORF3a	106	L106L	ctC	ctT	59	59	B.1.429	0.001388
ORF3a	106	L106L	ctC	ctT	53	57	B.1.258	0.003527
ORF3a	106	L106L	ctC	ctG	3	57	B.1.258	0.0002
ORF3a	106	L106L	ctC	ctA	1	57	B.1.258	0.000067
ORF3a	106	L106F	Ctc	Ttc	55	55	AY.113	0.007831
ORF3a	106	L106V	Ctc	Gtc	54	54	AY.4	0.000084
ORF3a	106	L106L	ctC	ctT	53	53	AY.20	0.00206
ORF3a	106	L106L	ctC	ctT	52	52	AY.47	0.001617
ORF3a	106	L106L	ctC	ctT	50	50	AY.6	0.002056
ORF3a	106	L106F	Ctc	Ttc	50	50	B.1.177	0.000658
ORF3a	106	L106L	ctC	ctT	49	49	AY.3.1	0.004178
ORF3a	106	L106del	CTC	---	49	49	AY.4	0.000076
ORF3a	106	L106F	Ctc	Ttc	49	49	AY.5	0.001012
ORF3a	106	L106L	ctC	ctT	49	49	B.1.160.21	1
ORF3a	106	L106F	Ctc	Ttc	48	48	B.1.311	0.01318
ORF3a	106	L106L	ctC	ctT	46	47	AY.29	0.000726
ORF3a	106	L106L	ctC	ctA	1	47	AY.29	0.000016
ORF3a	106	L106L	ctC	ctT	45	47	B.1.526	0.001058
ORF3a	106	L106L	ctC	ctA	1	47	B.1.526	0.000024
ORF3a	106	L106L	ctC	ctG	1	47	B.1.526	0.000024
ORF3a	106	L106F	Ctc	Ttc	46	46	P.1.14	0.002199
ORF3a	106	L106L	ctC	ctT	45	45	B.1.597	0.208333
ORF3a	106	L106del	CTC	---	42	42	AY.103	0.000261
ORF3a	106	L106F	Ctc	Ttc	41	41	AY.100	0.001886
ORF3a	106	L106R	cTc	cGc	41	41	AY.44	0.00025
ORF3a	106	L106L	ctC	ctT	39	40	AY.39	0.000964
ORF3a	106	L106L	ctC	ctA	1	40	AY.39	0.000025
ORF3a	106	L106F	Ctc	Ttc	40	40	B.1.1.222	0.00816
ORF3a	106	L106F	Ctc	Ttc	39	39	AY.102	0.001034
ORF3a	106	L106L	ctC	ctT	38	38	B.1.1.519	0.001509
ORF3a	106	L106L	ctC	ctT	38	38	B.1.177.31	0.436782
ORF3a	106	L106L	ctC	ctT	38	38	B.1.575	0.011529
ORF3a	106	L106F	Ctc	Ttc	37	37	B.1.279	0.019004
ORF3a	106	L106L	ctC	ctT	35	36	AY.5	0.000723
ORF3a	106	L106L	ctC	ctA	1	36	AY.5	0.000021
ORF3a	106	L106del	CTC	---	35	35	B.1	0.000321
ORF3a	106	L106L	ctC	ctT	35	35	B.1.160.13	0.972222
ORF3a	106	L106L	ctC	ctT	35	35	B.1.351.2	0.01059
ORF3a	106	L106F	Ctc	Ttc	34	34	AY.39.1	0.001347
ORF3a	106	L106F	Ctc	Ttc	34	34	AY.4.1	0.025074
ORF3a	106	L106R	cTc	cGc	34	34	B.1.1.7	0.00003
ORF3a	106	L106L	ctC	ctT	34	34	B.1.177.44	0.017644
ORF3a	106	L106F	Ctc	Ttc	33	33	AY.98	0.002607
ORF3a	106	L106L	ctC	ctT	32	33	B.1.1.216	0.028495
ORF3a	106	L106L	ctC	ctG	1	33	B.1.1.216	0.00089
ORF3a	106	L106L	ctC	ctT	28	33	B.1.621	0.002479
ORF3a	106	L106L	CtC	TtG	5	33	B.1.621	0.000443
ORF3a	106	L106F	Ctc	Ttc	31	31	AY.39	0.000766
ORF3a	106	L106F	Ctc	Ttc	31	31	B.1.349	0.022159
ORF3a	106	L106L	ctC	ctT	31	31	P.2	0.005786
ORF3a	106	L106del	CTC	---	30	30	AY.43	0.000133
ORF3a	106	L106F	Ctc	Ttc	30	30	P.2	0.005599
ORF3a	106	L106L	ctC	ctT	29	29	AY.41	0.008524
ORF3a	106	L106P	cTc	cCc	29	29	B.1.617.2	0.000109
ORF3a	106	L106L	ctC	ctT	28	28	B.1.160.19	1
ORF3a	106	L106L	ctC	ctT	27	27	B.1.1.214	0.001497
ORF3a	106	L106L	ctC	ctT	27	27	B.1.240	0.00582
ORF3a	106	L106L	ctC	ctT	26	26	AY.82	0.035278
ORF3a	106	L106L	ctC	ctT	25	25	B.1.1.445	0.925926
ORF3a	106	L106F	Ctc	Ttc	25	25	B.1.36.18	0.010504
ORF3a	106	L106I	Ctc	Atc	24	24	AY.67	0.011142
ORF3a	106	L106del	CTC	---	24	24	B.1.177	0.000316
ORF3a	106	L106F	Ctc	Ttc	23	23	B.1.1.153	0.025192
ORF3a	106	L106L	ctC	ctT	22	23	B.1.243	0.001531
ORF3a	106	L106L	ctC	ctG	1	23	B.1.243	0.00007
ORF3a	106	L106L	ctC	ctT	23	23	B.1.351	0.000684
ORF3a	106	L106L	ctC	ctT	23	23	B.1.618	0.092742
ORF3a	106	L106F	Ctc	Ttc	22	22	AY.119	0.000777
ORF3a	106	L106L	ctC	ctT	22	22	B.1.139	0.016129
ORF3a	106	L106P	cTc	cCc	22	22	B.1.2	0.000194
ORF3a	106	L106H	cTc	cAc	22	22	B.1.36.17	0.01087
ORF3a	106	L106I	Ctc	Atc	22	22	B.1.617.2	0.000083
ORF3a	106	L106L	ctC	ctT	21	21	AY.4.2	0.000455
ORF3a	106	L106L	ctC	ctT	21	21	B.1.1.291	0.01559
ORF3a	106	L106L	ctC	ctT	21	21	B.1.36	0.003064
ORF3a	106	L106R	cTc	cGc	21	21	Q.3	0.003046
ORF3a	106	L106H	cTc	cAc	20	20	B.1.1.519	0.000794
ORF3a	106	L106L	ctC	ctT	20	20	B.1.427	0.00101
ORF3a	106	L106L	ctC	ctT	20	20	C.36	0.018215
ORF3a	106	L106L	ctC	ctT	17	19	AY.120	0.000632
ORF3a	106	L106L	ctC	ctA	2	19	AY.120	0.000074
ORF3a	106	L106L	ctC	ctT	19	19	AY.23	0.001325
ORF3a	106	L106R	cTc	cGc	19	19	AY.25	0.000114
ORF3a	106	L106L	ctC	ctT	19	19	AY.4.1	0.014012
ORF3a	106	L106L	ctC	ctT	19	19	B.1.1.222	0.003876
ORF3a	106	L106F	CtC	TtT	18	19	B.1.160	0.000561
ORF3a	106	L106F	Ctc	Ttc	1	19	B.1.160	0.000031
ORF3a	106	L106L	ctC	ctT	19	19	B.1.258.11	0.007531
ORF3a	106	L106F	Ctc	Ttc	19	19	B.1.427	0.000959
ORF3a	106	L106R	cTc	cGc	19	19	P.1	0.000299
ORF3a	106	L106H	cTc	cAc	18	18	AY.111	0.003297
ORF3a	106	L106R	cTc	cGc	18	18	B.1.1.306	0.007891
ORF3a	106	L106F	Ctc	Ttc	18	18	B.1.1.372	0.012397
ORF3a	106	L106I	Ctc	Atc	18	18	B.1.1.7	0.000016
ORF3a	106	L106F	Ctc	Ttc	18	18	B.1.177.35	0.01244
ORF3a	106	L106S	CTc	TCc	9	17	All	0.000002
ORF3a	106	L106S	CTC	TCT	7	17	All	0.000001
ORF3a	106	L106S	CTC	TCG	1	17	All	0
ORF3a	106	L106F	Ctc	Ttc	17	17	AY.26	0.000481
ORF3a	106	L106L	ctC	ctT	17	17	B	0.002173
ORF3a	106	L106L	ctC	ctT	17	17	Q.4	0.007731
ORF3a	106	L106L	ctC	ctT	16	16	AY.45	0.001947
ORF3a	106	L106L	ctC	ctT	16	16	AY.46	0.001665
ORF3a	106	L106L	ctC	ctA	12	16	B.1.1.306	0.005261
ORF3a	106	L106L	ctC	ctT	4	16	B.1.1.306	0.001754
ORF3a	106	L106L	ctC	ctT	16	16	B.1.1.434	0.005577
ORF3a	106	L106L	ctC	ctT	16	16	B.1.111	0.018801
ORF3a	106	L106F	Ctc	Ttc	16	16	B.1.177.16	0.010631
ORF3a	106	L106L	ctC	ctT	15	15	A.2.5	0.007485
ORF3a	106	L106L	ctC	ctT	15	15	AY.35	0.003496
ORF3a	106	L106L	ctC	ctT	15	15	AY.98	0.001185
ORF3a	106	L106F	Ctc	Ttc	15	15	B.1.1.514	0.576923
ORF3a	106	L106F	Ctc	Ttc	14	14	AY.48	0.006512
ORF3a	106	L106F	Ctc	Ttc	14	14	AY.6	0.000576
ORF3a	106	L106L	ctC	ctT	14	14	AY.75	0.000784
ORF3a	106	L106F	Ctc	Ttc	14	14	B.1.1.1	0.004574
ORF3a	106	L106L	ctC	ctT	14	14	B.1.1.39	0.007136
ORF3a	106	L106F	Ctc	Ttc	14	14	B.1.1.50	0.009504
ORF3a	106	L106L	ctC	ctT	14	14	B.1.177.21	0.001071
ORF3a	106	L106F	Ctc	Ttc	14	14	B.1.391	0.015784
ORF3a	106	L106L	ctC	ctT	14	14	C.16	0.014846
ORF3a	106	L106V	Ctc	Gtc	13	13	AY.100	0.000598
ORF3a	106	L106F	Ctc	Ttc	13	13	AY.13	0.002093
ORF3a	106	L106del	CTC	---	13	13	AY.25	0.000078
ORF3a	106	L106F	Ctc	Ttc	13	13	AY.29	0.000205
ORF3a	106	L106del	CTC	---	13	13	AY.30	0.005144
ORF3a	106	L106L	ctC	ctT	9	13	AY.36	0.001334
ORF3a	106	L106L	ctC	ctA	4	13	AY.36	0.000593
ORF3a	106	L106I	Ctc	Atc	13	13	AY.4	0.00002
ORF3a	106	L106F	Ctc	Ttc	13	13	AY.45	0.001582
ORF3a	106	L106L	ctC	ctT	13	13	B.1.1.157	0.011872
ORF3a	106	L106L	ctC	ctT	13	13	B.1.1.433	0.018519
ORF3a	106	L106L	ctC	ctT	13	13	B.1.509	0.011255
ORF3a	106	L106L	ctC	ctT	12	13	B.23	0.035088
ORF3a	106	L106L	ctC	ctA	1	13	B.23	0.002924
ORF3a	106	L106L	ctC	ctT	12	13	P.1.14	0.000574
ORF3a	106	L106L	ctC	ctA	1	13	P.1.14	0.000048
ORF3a	106	L106L	ctC	ctT	12	12	AY.121	0.001624
ORF3a	106	L106L	ctC	ctT	12	12	AY.27	0.000777
ORF3a	106	L106L	ctC	ctT	10	12	AY.42	0.000402
ORF3a	106	L106L	ctC	ctA	2	12	AY.42	0.00008
ORF3a	106	L106V	Ctc	Gtc	12	12	AY.43	0.000053
ORF3a	106	L106I	Ctc	Atc	12	12	AY.44	0.000073
ORF3a	106	L106L	ctC	ctT	12	12	AY.46.6	0.000866
ORF3a	106	L106L	ctC	ctT	12	12	B.1.1.277	0.009105
ORF3a	106	L106L	ctC	ctT	12	12	B.1.177.43	0.017725
ORF3a	106	L106L	ctC	ctT	12	12	B.1.177.73	0.006795
ORF3a	106	L106F	Ctc	Ttc	12	12	B.1.177.82	0.005728
ORF3a	106	L106F	Ctc	Ttc	12	12	B.1.234	0.001583
ORF3a	106	L106L	ctC	ctT	11	12	B.1.311	0.00302
ORF3a	106	L106L	ctC	ctA	1	12	B.1.311	0.000275
ORF3a	106	L106F	Ctc	Ttc	12	12	B.1.351.3	0.010517
ORF3a	106	L106F	Ctc	Ttc	12	12	B.1.36.29	0.006208
ORF3a	106	L106L	ctC	ctT	12	12	B.1.596	0.001046
ORF3a	106	L106del	CTC	---	12	12	B.1.617.2	0.000045
ORF3a	106	L106F	Ctc	Ttc	12	12	P.1.17	0.001941
ORF3a	106	L106F	Ctc	Ttc	12	12	Q.1	0.001516
ORF3a	106	L106L	ctC	ctT	11	11	AY.118	0.000689
ORF3a	106	L106F	Ctc	Ttc	11	11	AY.36	0.00163
ORF3a	106	L106F	Ctc	Ttc	11	11	AY.42	0.000443
ORF3a	106	L106L	ctC	ctT	11	11	B.1.239	0.013431
ORF3a	106	L106L	ctC	ctT	11	11	B.1.258.17	0.001144
ORF3a	106	L106L	ctC	ctT	11	11	B.1.36.8	0.011
ORF3a	106	L106L	ctC	ctT	11	11	Q.1	0.00139
ORF3a	106	L106I	Ctc	Atc	10	10	AY.103	0.000062
ORF3a	106	L106L	ctC	ctT	6	10	AY.113	0.000854
ORF3a	106	L106L	ctC	ctG	4	10	AY.113	0.00057
ORF3a	106	L106F	Ctc	Ttc	10	10	AY.120	0.000372
ORF3a	106	L106L	ctC	ctT	10	10	AY.26	0.000283
ORF3a	106	L106del	CTC	---	10	10	AY.29	0.000158
ORF3a	106	L106F	Ctc	Ttc	10	10	AY.3.1	0.000853
ORF3a	106	L106F	Ctc	Ttc	10	10	AY.37	0.003161
ORF3a	106	L106P	cTc	cCc	10	10	AY.43	0.000044
ORF3a	106	L106L	ctC	ctT	9	10	AY.5.3	0.003036
ORF3a	106	L106L	ctC	ctA	1	10	AY.5.3	0.000337
ORF3a	106	L106L	ctC	ctT	9	10	AY.5.4	0.00249
ORF3a	106	L106L	ctC	ctA	1	10	AY.5.4	0.000277
ORF3a	106	L106L	ctC	ctT	10	10	AY.61	0.001048
ORF3a	106	L106F	Ctc	Ttc	10	10	AY.61	0.001048
ORF3a	106	L106L	ctC	ctT	10	10	AY.62	0.004357
ORF3a	106	L106F	Ctc	Ttc	10	10	AY.9.2	0.000367
ORF3a	106	L106L	ctC	ctT	7	10	AY.9.2	0.000257
ORF3a	106	L106L	ctC	ctA	3	10	AY.9.2	0.00011
ORF3a	106	L106F	Ctc	Ttc	10	10	AZ.1	0.008673
ORF3a	106	L106F	Ctc	Ttc	10	10	B.1.1.148	0.087719
ORF3a	106	L106L	ctC	ctT	10	10	B.1.1.284	0.001074
ORF3a	106	L106F	Ctc	Ttc	10	10	B.1.177.42	0.008945
ORF3a	106	L106L	ctC	ctT	10	10	B.1.36.29	0.005173
ORF3a	106	L106F	Ctc	Ttc	10	10	B.1.433	0.031949
ORF3a	106	L106L	ctC	ctT	10	10	B.1.76	0.113636
ORF3a	106	L106L	ctC	ctT	10	10	Q.8	0.001649
ORF3a	106	L106L	ctC	ctT	9	9	AY.116	0.002581
ORF3a	106	L106F	Ctc	Ttc	9	9	AY.117	0.000761
ORF3a	106	L106F	Ctc	Ttc	9	9	AY.120.2.1	0.004484
ORF3a	106	L106R	cTc	cGc	9	9	AY.41	0.002646
ORF3a	106	L106F	Ctc	Ttc	9	9	AY.46.4	0.001481
ORF3a	106	L106L	ctC	ctT	9	9	AY.51	0.008182
ORF3a	106	L106F	Ctc	Ttc	9	9	AY.74	0.001041
ORF3a	106	L106R	cTc	cGc	9	9	AY.75	0.000504
ORF3a	106	L106P	cTc	cCc	9	9	AY.9	0.000608
ORF3a	106	L106F	Ctc	Ttc	9	9	AY.9	0.000608
ORF3a	106	L106L	ctC	ctT	9	9	AY.98.1	0.000436
ORF3a	106	L106R	cTc	cGc	9	9	B.1	0.000082
ORF3a	106	L106L	ctC	ctT	9	9	B.1.1.50	0.00611
ORF3a	106	L106L	ctC	ctT	9	9	B.1.409	0.007031
ORF3a	106	L106L	ctC	ctT	9	9	B.1.637	0.000658
ORF3a	106	L106L	ctC	ctT	9	9	D.2	0.000675
ORF3a	106	L106F	Ctc	Ttc	8	8	AY.14	0.000704
ORF3a	106	L106del	CTC	---	8	8	AY.3	0.00008
ORF3a	106	L106F	Ctc	Ttc	8	8	AY.33	0.000534
ORF3a	106	L106F	Ctc	Ttc	7	8	AY.34	0.000679
ORF3a	106	L106F	CtC	TtT	1	8	AY.34	0.000097
ORF3a	106	L106F	Ctc	Ttc	8	8	AY.46	0.000833
ORF3a	106	L106L	ctC	ctT	7	8	AY.46.1	0.007187
ORF3a	106	L106L	ctC	ctA	1	8	AY.46.1	0.001027
ORF3a	106	L106L	ctC	ctT	8	8	AY.77	0.009019
ORF3a	106	L106F	Ctc	Ttc	8	8	AY.98.1	0.000387
ORF3a	106	L106F	Ctc	Ttc	8	8	B.1.1.216	0.007124
ORF3a	106	L106L	ctC	ctT	8	8	B.1.1.317	0.003294
ORF3a	106	L106F	Ctc	Ttc	8	8	B.1.1.37	0.001543
ORF3a	106	L106L	ctC	ctT	8	8	B.1.177.77	0.00581
ORF3a	106	L106F	Ctc	Ttc	8	8	B.1.232	0.004299
ORF3a	106	L106L	ctC	ctT	8	8	B.1.561	0.003176
ORF3a	106	L106F	Ctc	Ttc	8	8	C.37	0.000929
ORF3a	106	L106L	ctC	ctT	8	8	Q.7	0.008889
ORF3a	106	L106L	ctC	ctT	8	8	R.1	0.00072
ORF3a	106	L106F	Ctc	Ttc	6	7		0.333333
ORF3a	106	L106F	CtC	TtT	1	7		0.055556
ORF3a	106	L106R	cTc	cGc	7	7	AY.103	0.000043
ORF3a	106	L106L	ctC	ctT	7	7	AY.106	0.002344
ORF3a	106	L106F	Ctc	Ttc	7	7	AY.106	0.002344
ORF3a	106	L106F	Ctc	Ttc	7	7	AY.107	0.003262
ORF3a	106	L106F	Ctc	Ttc	7	7	AY.16	0.002658
ORF3a	106	L106F	Ctc	Ttc	7	7	AY.23	0.000488
ORF3a	106	L106P	cTc	cCc	7	7	AY.4	0.000011
ORF3a	106	L106L	ctC	ctT	7	7	AY.4.2.1	0.001043
ORF3a	106	L106F	Ctc	Ttc	7	7	AY.54	0.000667
ORF3a	106	L106L	ctC	ctT	7	7	AY.55	0.006422
ORF3a	106	L106L	ctC	ctT	7	7	AY.88	0.006189
ORF3a	106	L106L	ctC	ctT	7	7	AY.9	0.000473
ORF3a	106	L106F	Ctc	Ttc	7	7	AY.92	0.002011
ORF3a	106	L106F	Ctc	Ttc	7	7	AY.95	0.005327
ORF3a	106	L106F	Ctc	Ttc	7	7	B.1.1.322	0.061404
ORF3a	106	L106L	ctC	ctT	6	7	B.1.1.33	0.002525
ORF3a	106	L106L	ctC	ctG	1	7	B.1.1.33	0.000421
ORF3a	106	L106L	ctC	ctT	7	7	B.1.147	0.005291
ORF3a	106	L106del	CTC	---	7	7	B.1.2	0.000062
ORF3a	106	L106L	ctC	ctT	7	7	B.1.232	0.003761
ORF3a	106	L106F	Ctc	Ttc	7	7	B.1.243	0.000487
ORF3a	106	L106L	ctC	ctT	7	7	B.1.346	0.009174
ORF3a	106	L106F	Ctc	Ttc	7	7	B.1.517	0.002989
ORF3a	106	L106F	Ctc	Ttc	7	7	P.1.12	0.003388
ORF3a	106	L106L	ctC	ctT	7	7	P.1.17	0.001132
ORF3a	106	L106F	Ctc	Ttc	7	7	P.4	0.026616
ORF3a	106	L106F	Ctc	Ttc	6	6	AY.110	0.000676
ORF3a	106	L106L	ctC	ctT	6	6	AY.111	0.001099
ORF3a	106	L106I	Ctc	Atc	6	6	AY.113	0.000854
ORF3a	106	L106L	ctC	ctT	6	6	AY.33	0.000401
ORF3a	106	L106del	CTC	---	6	6	AY.39	0.000148
ORF3a	106	L106P	cTc	cCc	6	6	AY.39.1	0.000238
ORF3a	106	L106R	cTc	cGc	6	6	AY.4	0.000009
ORF3a	106	L106L	ctC	ctG	4	6	AY.52	0.003257
ORF3a	106	L106L	ctC	ctT	1	6	AY.52	0.000814
ORF3a	106	L106L	ctC	ctA	1	6	AY.52	0.000814
ORF3a	106	L106L	ctC	ctT	6	6	AY.75.1	0.001082
ORF3a	106	L106F	Ctc	Ttc	6	6	AY.79	0.007264
ORF3a	106	L106L	ctC	ctT	6	6	AY.84	0.002625
ORF3a	106	L106L	ctC	ctT	6	6	B.1.1.1	0.00196
ORF3a	106	L106V	Ctc	Gtc	6	6	B.1.1.214	0.000333
ORF3a	106	L106F	Ctc	Ttc	6	6	B.1.1.214	0.000333
ORF3a	106	L106L	ctC	ctT	5	6	B.1.1.25	0.002843
ORF3a	106	L106L	ctC	ctA	1	6	B.1.1.25	0.000569
ORF3a	106	L106F	Ctc	Ttc	6	6	B.1.1.28	0.001867
ORF3a	106	L106F	Ctc	Ttc	6	6	B.1.1.306	0.00263
ORF3a	106	L106L	ctC	ctT	6	6	B.1.177.20	0.009105
ORF3a	106	L106F	Ctc	Ttc	6	6	B.1.177.4	0.001266
ORF3a	106	L106F	Ctc	Ttc	5	6	B.1.221	0.000355
ORF3a	106	L106F	CtC	TtT	1	6	B.1.221	0.000071
ORF3a	106	L106F	Ctc	Ttc	6	6	B.1.258.17	0.000624
ORF3a	106	L106L	ctC	ctT	6	6	B.1.281	0.130435
ORF3a	106	L106L	ctC	ctT	6	6	B.1.416.1	0.009375
ORF3a	106	L106I	Ctc	Atc	6	6	B.1.438.1	0.000644
ORF3a	106	L106L	ctC	ctT	6	6	B.1.473	0.115385
ORF3a	106	L106F	Ctc	Ttc	6	6	B.1.564	0.002555
ORF3a	106	L106L	ctC	ctT	6	6	B.1.564	0.002555
ORF3a	106	L106H	cTc	cAc	6	6	B.1.617.2	0.000023
ORF3a	106	L106F	Ctc	Ttc	6	6	P.1.15	0.001394
ORF3a	106	L106L	ctC	ctT	6	6	P.1.15	0.001394
ORF3a	106	L106L	ctC	ctA	2	5		0.111111
ORF3a	106	L106L	CtC	TtA	2	5		0.111111
ORF3a	106	L106L	ctC	ctT	1	5		0.055556
ORF3a	106	L106F	Ctc	Ttc	5	5	AY.111	0.000916
ORF3a	106	L106F	Ctc	Ttc	5	5	AY.114	0.001156
ORF3a	106	L106F	Ctc	Ttc	5	5	AY.120.2	0.006427
ORF3a	106	L106L	ctC	ctT	5	5	AY.13	0.000805
ORF3a	106	L106F	Ctc	Ttc	5	5	AY.40	0.004822
ORF3a	106	L106L	ctC	ctT	5	5	AY.46.4	0.000823
ORF3a	106	L106F	Ctc	Ttc	5	5	AY.62	0.002179
ORF3a	106	L106F	Ctc	Ttc	5	5	AY.65	0.002665
ORF3a	106	L106F	Ctc	Ttc	5	5	AY.71	0.002375
ORF3a	106	L106V	Ctc	Gtc	5	5	AY.98	0.000395
ORF3a	106	L106F	Ctc	Ttc	5	5	B	0.000639
ORF3a	106	L106L	ctC	ctT	5	5	B.1.1.336	0.083333
ORF3a	106	L106F	Ctc	Ttc	5	5	B.1.1.358	0.172414
ORF3a	106	L106L	ctC	ctT	5	5	B.1.1.70	0.001705
ORF3a	106	L106del	CTC	---	5	5	B.1.160	0.000156
ORF3a	106	L106P	cTc	cCc	5	5	B.1.177	0.000066
ORF3a	106	L106F	Ctc	Ttc	5	5	B.1.177.12	0.000758
ORF3a	106	L106L	ctC	ctT	5	5	B.1.177.23	0.016181
ORF3a	106	L106F	Ctc	Ttc	5	5	B.1.237	0.024876
ORF3a	106	L106L	ctC	ctT	5	5	B.1.241	0.004058
ORF3a	106	L106F	Ctc	Ttc	5	5	B.1.36.16	0.007123
ORF3a	106	L106F	Ctc	Ttc	5	5	B.1.409	0.003906
ORF3a	106	L106R	cTc	cGc	5	5	B.1.411	0.018519
ORF3a	106	L106L	ctC	ctT	5	5	B.1.466.2	0.001956
ORF3a	106	L106del	CTC	---	5	5	B.1.525	0.000566
ORF3a	106	L106L	ctC	ctT	5	5	B.1.595	0.001305
ORF3a	106	L106R	cTc	cGc	5	5	B.1.617.2	0.000019
ORF3a	106	L106del	CTC	---	5	5	B.1.621	0.000443
ORF3a	106	L106del	CTC	---	5	5	D.2	0.000375
ORF3a	106	L106F	Ctc	Ttc	5	5	N.5	0.008834
ORF3a	106	L106F	Ctc	Ttc	5	5	Q.3	0.000725
ORF3a	106	L106P	cTc	cCc	3	4		0.166667
ORF3a	106	L106S	CTc	TCc	3	4		0.166667
ORF3a	106	L106R	cTc	cGc	2	4		0.111111
ORF3a	106	L106R	cTC	cGA	2	4		0.111111
ORF3a	106	L106S	CTC	TCT	1	4		0.055556
ORF3a	106	L106P	cTC	cCT	1	4		0.055556
ORF3a	106	L106del2	CTc	--c	3	4	All	0.000001
ORF3a	106	L106del1	Ctc	-tc	2	4	All	0
ORF3a	106	L106del1	CtC	-tT	2	4	All	0
ORF3a	106	L106del2	CTC	--A	1	4	All	0
ORF3a	106	L106V	Ctc	Gtc	4	4	AY.103	0.000025
ORF3a	106	L106L	ctC	ctT	4	4	AY.16	0.001519
ORF3a	106	L106F	Ctc	Ttc	4	4	AY.16.1	0.00188
ORF3a	106	L106L	ctC	ctG	2	4	AY.16.1	0.00094
ORF3a	106	L106L	ctC	ctT	2	4	AY.16.1	0.00094
ORF3a	106	L106F	Ctc	Ttc	4	4	AY.27	0.000259
ORF3a	106	L106H	cTc	cAc	4	4	AY.29	0.000063
ORF3a	106	L106P	cTc	cCc	4	4	AY.3.1	0.000341
ORF3a	106	L106del	CTC	---	4	4	AY.4.2	0.000087
ORF3a	106	L106L	ctC	ctT	4	4	AY.4.4	0.001637
ORF3a	106	L106I	Ctc	Atc	4	4	AY.43	0.000018
ORF3a	106	L106F	Ctc	Ttc	4	4	AY.46.6	0.000289
ORF3a	106	L106P	cTc	cCc	4	4	AY.47	0.000124
ORF3a	106	L106L	ctC	ctT	4	4	AY.50	0.003197
ORF3a	106	L106L	ctC	ctT	4	4	AY.53	0.00115
ORF3a	106	L106L	ctC	ctT	4	4	AY.54	0.000381
ORF3a	106	L106F	Ctc	Ttc	4	4	AY.68	0.001095
ORF3a	106	L106L	ctC	ctA	2	4	AY.7.1	0.000225
ORF3a	106	L106L	ctC	ctT	2	4	AY.7.1	0.000225
ORF3a	106	L106F	Ctc	Ttc	4	4	AY.75	0.000224
ORF3a	106	L106F	Ctc	Ttc	4	4	AY.85	0.001709
ORF3a	106	L106L	ctC	ctT	4	4	AY.86	0.00332
ORF3a	106	L106L	ctC	ctT	4	4	AY.95	0.003044
ORF3a	106	L106P	cTc	cCc	4	4	AY.99.2	0.000369
ORF3a	106	L106F	Ctc	Ttc	4	4	AY.99.2	0.000369
ORF3a	106	L106L	ctC	ctT	3	4	AY.99.2	0.000276
ORF3a	106	L106L	ctC	ctA	1	4	AY.99.2	0.000092
ORF3a	106	L106P	cTc	cCc	4	4	B.1	0.000037
ORF3a	106	L106I	Ctc	Atc	3	4	B.1	0.000027
ORF3a	106	L106I	CtC	AtA	1	4	B.1	0.000009
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.1.221	0.040404
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.1.284	0.00043
ORF3a	106	L106V	Ctc	Gtc	4	4	B.1.1.348	0.003185
ORF3a	106	L106V	Ctc	Gtc	4	4	B.1.1.7	0.000004
ORF3a	106	L106R	cTc	cGc	4	4	B.1.177	0.000053
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.177.54	0.002426
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.177.56	0.00267
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.177.73	0.002265
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.177.81	0.000757
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.177.86	0.000734
ORF3a	106	L106L	ctC	ctT	4	4	B.1.222	0.006768
ORF3a	106	L106L	ctC	ctT	4	4	B.1.234	0.000528
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.240	0.000862
ORF3a	106	L106L	ctC	ctT	4	4	B.1.260	0.013378
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.36.35	0.010417
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.369	0.001141
ORF3a	106	L106L	ctC	ctT	4	4	B.1.465	0.015209
ORF3a	106	L106R	cTc	cGc	4	4	B.1.525	0.000453
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.574	0.008602
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.596	0.000349
ORF3a	106	L106L	ctC	ctT	4	4	B.1.617.1	0.000516
ORF3a	106	L106I	Ctc	Atc	4	4	B.1.621	0.000354
ORF3a	106	L106F	Ctc	Ttc	4	4	B.1.623	0.002146
ORF3a	106	L106V	Ctc	Gtc	4	4	B.1.637	0.000292
ORF3a	106	L106L	ctC	ctT	4	4	C.37	0.000464
ORF3a	106	L106F	Ctc	Ttc	4	4	N.3	0.023256
ORF3a	106	L106del	CTC	---	4	4	P.1	0.000063
ORF3a	106	L106F	Ctc	Ttc	4	4	P.1.1	0.001271
ORF3a	106	L106F	Ctc	Ttc	3	3	A.2.4	0.010101
ORF3a	106	L106C	CTc	TGc	3	3	All	0.000001
ORF3a	106	L106I	Ctc	Atc	3	3	AY.100	0.000138
ORF3a	106	L106H	cTc	cAc	3	3	AY.103	0.000019
ORF3a	106	L106P	cTc	cCc	3	3	AY.103	0.000019
ORF3a	106	L106F	Ctc	Ttc	3	3	AY.109	0.002219
ORF3a	106	L106L	ctC	ctT	3	3	AY.110	0.000338
ORF3a	106	L106P	cTc	cCc	3	3	AY.119	0.000106
ORF3a	106	L106L	ctC	ctT	3	3	AY.2	0.001068
ORF3a	106	L106L	ctC	ctT	3	3	AY.34.1	0.00153
ORF3a	106	L106P	cTc	cCc	3	3	AY.4.5	0.000322
ORF3a	106	L106P	cTc	cCc	3	3	AY.42	0.000121
ORF3a	106	L106del	CTC	---	3	3	AY.44	0.000018
ORF3a	106	L106del	CTC	---	3	3	AY.47	0.000093
ORF3a	106	L106L	ctC	ctT	3	3	AY.48	0.001395
ORF3a	106	L106F	Ctc	Ttc	3	3	AY.55	0.002752
ORF3a	106	L106F	Ctc	Ttc	3	3	AY.7.1	0.000338
ORF3a	106	L106F	Ctc	Ttc	3	3	AY.75.1	0.000541
ORF3a	106	L106L	ctC	ctT	3	3	AY.79	0.003632
ORF3a	106	L106L	ctC	ctT	3	3	AY.87	0.002498
ORF3a	106	L106L	ctC	ctT	3	3	AY.9.1	0.000251
ORF3a	106	L106L	ctC	ctT	2	3	AY.92	0.000575
ORF3a	106	L106L	ctC	ctA	1	3	AY.92	0.000287
ORF3a	106	L106I	Ctc	Atc	3	3	AY.98.1	0.000145
ORF3a	106	L106F	Ctc	Ttc	3	3	AY.99	0.003148
ORF3a	106	L106S	CTC	TCT	2	3	B.1.1	0.000036
ORF3a	106	L106P	cTc	cCc	2	3	B.1.1	0.000036
ORF3a	106	L106P	cTC	cCT	1	3	B.1.1	0.000018
ORF3a	106	L106S	CTc	TCc	1	3	B.1.1	0.000018
ORF3a	106	L106L	ctC	ctT	3	3	B.1.1.174	0.010135
ORF3a	106	L106L	ctC	ctT	3	3	B.1.1.176	0.001318
ORF3a	106	L106L	ctC	ctT	3	3	B.1.1.180	0.032258
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.1.231	0.009288
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.1.25	0.001706
ORF3a	106	L106L	ctC	ctT	2	3	B.1.1.28	0.000622
ORF3a	106	L106L	ctC	ctA	1	3	B.1.1.28	0.000311
ORF3a	106	L106H	cTc	cAc	3	3	B.1.1.7	0.000003
ORF3a	106	L106del2	CTc	--c	3	3	B.1.177	0.00004
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.177.87	0.002183
ORF3a	106	L106P	cTc	cCc	3	3	B.1.221	0.000213
ORF3a	106	L106P	cTc	cCc	3	3	B.1.258	0.0002
ORF3a	106	L106L	ctC	ctT	2	3	B.1.301	0.011834
ORF3a	106	L106L	ctC	ctA	1	3	B.1.301	0.005917
ORF3a	106	L106L	ctC	ctT	3	3	B.1.36.1	0.003421
ORF3a	106	L106L	ctC	ctT	3	3	B.1.36.18	0.001261
ORF3a	106	L106L	ctC	ctT	3	3	B.1.36.22	0.003623
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.36.22	0.003623
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.396	0.002117
ORF3a	106	L106L	ctC	ctT	3	3	B.1.400	0.001287
ORF3a	106	L106L	ctC	ctT	3	3	B.1.470	0.004213
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.524	0.004219
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.525	0.000339
ORF3a	106	L106L	ctC	ctT	3	3	B.1.525	0.000339
ORF3a	106	L106L	ctC	ctT	3	3	B.1.555	0.066667
ORF3a	106	L106L	ctC	ctT	3	3	B.1.609	0.001438
ORF3a	106	L106F	Ctc	Ttc	3	3	B.1.637	0.000219
ORF3a	106	L106L	CtC	TtG	1	3	B.1.91	0.002075
ORF3a	106	L106L	ctC	ctG	1	3	B.1.91	0.002075
ORF3a	106	L106L	ctC	ctA	1	3	B.1.91	0.002075
ORF3a	106	L106F	Ctc	Ttc	3	3	C.1	0.007177
ORF3a	106	L106V	Ctc	Gtc	3	3	P.1	0.000047
ORF3a	106	L106del	CTC	---	3	3	P.1.15	0.000697
ORF3a	106	L106P	cTc	cCc	3	3	P.2	0.00056
ORF3a	106	L106F	Ctc	Ttc	3	3	Q.8	0.000495
ORF3a	106	L106R	cTc	cGc	3	3	R.1	0.00027
ORF3a	106	L106V	Ctc	Gtc	2	2		0.111111
ORF3a	106	L106X	CTC	TGA	2	2		0.111111
ORF3a	106	L106C	CTc	TGc	2	2		0.111111
ORF3a	106	L106del	CTC	---	2	2	AE.8	0.000978
ORF3a	106	L106X	CTC	TGA	2	2	All	0
ORF3a	106	L106G	CTc	GGc	1	2	All	0
ORF3a	106	L106G	CTC	GGA	1	2	All	0
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.10	0.00106
ORF3a	106	L106R	cTc	cGc	2	2	AY.102	0.000053
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.108	0.002205
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.118	0.000125
ORF3a	106	L106L	ctC	ctT	2	2	AY.120.2.1	0.000997
ORF3a	106	L106del	CTC	---	2	2	AY.121	0.000271
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.121	0.000271
ORF3a	106	L106L	ctC	ctT	2	2	AY.14	0.000176
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.19	0.002281
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.24	0.000862
ORF3a	106	L106I	Ctc	Atc	2	2	AY.3	0.00002
ORF3a	106	L106H	cTc	cAc	2	2	AY.3	0.00002
ORF3a	106	L106L	ctC	ctT	2	2	AY.30	0.000791
ORF3a	106	L106F	Ctc	Ttc	1	2	AY.30	0.000396
ORF3a	106	L106F	CtC	TtT	1	2	AY.30	0.000396
ORF3a	106	L106L	ctC	ctT	2	2	AY.32	0.001065
ORF3a	106	L106P	cTc	cCc	2	2	AY.36	0.000296
ORF3a	106	L106I	Ctc	Atc	2	2	AY.39	0.000049
ORF3a	106	L106del	CTC	---	2	2	AY.4.5	0.000215
ORF3a	106	L106I	Ctc	Atc	2	2	AY.42	0.00008
ORF3a	106	L106del	CTC	---	2	2	AY.46.6	0.000144
ORF3a	106	L106P	cTc	cCc	2	2	AY.5.4	0.000553
ORF3a	106	L106del	CTC	---	2	2	AY.5.4	0.000553
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.53	0.000575
ORF3a	106	L106R	cTc	cGc	2	2	AY.55	0.001835
ORF3a	106	L106L	ctC	ctT	2	2	AY.59	0.001059
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.72	0.002721
ORF3a	106	L106I	Ctc	Atc	2	2	AY.75	0.000112
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.84	0.000875
ORF3a	106	L106L	ctC	ctT	2	2	AY.85	0.000854
ORF3a	106	L106F	Ctc	Ttc	2	2	AY.9.1	0.000167
ORF3a	106	L106del	CTC	---	2	2	AY.9.1	0.000167
ORF3a	106	L106L	ctC	ctT	2	2	AY.93	0.000546
ORF3a	106	L106del	CTC	---	2	2	AY.98.1	0.000097
ORF3a	106	L106H	cTc	cAc	2	2	B.1	0.000018
ORF3a	106	L106R	cTc	cGc	2	2	B.1.1	0.000036
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.1.141	0.004024
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.1.161	0.007067
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.1.198	0.002937
ORF3a	106	L106L	ctC	ctT	2	2	B.1.1.220	0.003717
ORF3a	106	L106L	ctC	ctT	2	2	B.1.1.226	0.011628
ORF3a	106	L106L	ctC	ctT	2	2	B.1.1.249	0.142857
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.1.277	0.001517
ORF3a	106	L106del	CTC	---	2	2	B.1.1.298	0.001724
ORF3a	106	L106L	ctC	ctT	2	2	B.1.1.3	0.017391
ORF3a	106	L106V	CtC	GtG	1	2	B.1.1.33	0.000421
ORF3a	106	L106V	Ctc	Gtc	1	2	B.1.1.33	0.000421
ORF3a	106	L106L	ctC	ctT	2	2	B.1.1.332	0.0625
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.1.354	0.008772
ORF3a	106	L106L	ctC	ctT	2	2	B.1.1.37	0.000386
ORF3a	106	L106L	ctC	ctT	2	2	B.1.1.404	0.031746
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.1.63	0.000772
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.1.70	0.000682
ORF3a	106	L106F	CtC	TtT	2	2	B.1.14	0.035088
ORF3a	106	L106del1	CtC	-tT	2	2	B.1.160	0.000062
ORF3a	106	L106L	ctC	ctT	2	2	B.1.177.16	0.001329
ORF3a	106	L106L	ctC	ctT	2	2	B.1.177.26	0.013986
ORF3a	106	L106L	ctC	ctT	1	2	B.1.177.32	0.00135
ORF3a	106	L106L	ctC	ctG	1	2	B.1.177.32	0.00135
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.177.5	0.002484
ORF3a	106	L106L	ctC	ctT	2	2	B.1.177.50	0.00939
ORF3a	106	L106P	cTc	cCc	2	2	B.1.177.7	0.00033
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.177.7	0.00033
ORF3a	106	L106R	cTc	cGc	2	2	B.1.177.77	0.001452
ORF3a	106	L106L	ctC	ctT	2	2	B.1.177.81	0.000379
ORF3a	106	L106L	ctC	ctT	2	2	B.1.177.82	0.000955
ORF3a	106	L106V	Ctc	Gtc	2	2	B.1.2	0.000018
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.206	0.001631
ORF3a	106	L106L	ctC	ctT	2	2	B.1.221.2	0.008032
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.258	0.000133
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.258.2	0.009009
ORF3a	106	L106H	cTc	cAc	2	2	B.1.279	0.001027
ORF3a	106	L106del	CTC	---	2	2	B.1.351	0.000059
ORF3a	106	L106del	CTC	---	2	2	B.1.36	0.000292
ORF3a	106	L106R	cTc	cGc	2	2	B.1.36.18	0.00084
ORF3a	106	L106L	ctC	ctT	2	2	B.1.36.35	0.005208
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.36.8	0.002
ORF3a	106	L106L	ctC	ctT	2	2	B.1.367	0.001585
ORF3a	106	L106L	ctC	ctT	2	2	B.1.375	0.001639
ORF3a	106	L106L	ctC	ctT	2	2	B.1.395	0.014085
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.399	0.003868
ORF3a	106	L106L	ctC	ctT	2	2	B.1.417	0.057143
ORF3a	106	L106P	cTc	cCc	2	2	B.1.436	0.002058
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.456	0.006536
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.459	0.008163
ORF3a	106	L106L	ctC	ctT	2	2	B.1.459	0.008163
ORF3a	106	L106L	ctC	ctT	2	2	B.1.462	0.014493
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.470	0.002809
ORF3a	106	L106L	ctC	ctT	2	2	B.1.471	0.005464
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.497	0.00063
ORF3a	106	L106L	ctC	ctT	2	2	B.1.499	0.002101
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.499	0.002101
ORF3a	106	L106L	ctC	ctT	2	2	B.1.533	0.019231
ORF3a	106	L106I	Ctc	Atc	1	2	B.1.533	0.009615
ORF3a	106	L106I	CtC	AtT	1	2	B.1.533	0.009615
ORF3a	106	L106del	CTC	---	2	2	B.1.582	0.000981
ORF3a	106	L106P	cTc	cCc	2	2	B.1.617.1	0.000258
ORF3a	106	L106S	CTC	TCT	2	2	B.1.617.2	0.000008
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.617.3	0.00597
ORF3a	106	L106S	CTc	TCc	2	2	B.1.621	0.000177
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.621.1	0.001012
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.625	0.004706
ORF3a	106	L106L	ctC	ctT	2	2	B.1.628	0.000705
ORF3a	106	L106F	Ctc	Ttc	2	2	B.1.633	0.083333
ORF3a	106	L106G	CTc	GGc	1	2	B.1.91	0.002075
ORF3a	106	L106S	CTc	TCc	1	2	B.1.91	0.002075
ORF3a	106	L106V	Ctc	Gtc	1	2	B.1.91	0.002075
ORF3a	106	L106G	CTC	GGA	1	2	B.1.91	0.002075
ORF3a	106	L106R	cTc	cGc	1	2	B.1.91	0.002075
ORF3a	106	L106P	cTc	cCc	1	2	B.1.91	0.002075
ORF3a	106	L106V	CtC	GtA	1	2	B.1.91	0.002075
ORF3a	106	L106R	cTC	cGA	1	2	B.1.91	0.002075
ORF3a	106	L106P	cTC	cCG	1	2	B.1.91	0.002075
ORF3a	106	L106S	CTC	TCG	1	2	B.1.91	0.002075
ORF3a	106	L106F	Ctc	Ttc	2	2	B.3	0.001661
ORF3a	106	L106F	Ctc	Ttc	2	2	B.4.7	0.020202
ORF3a	106	L106L	ctC	ctG	1	2	B.6.6	0.000889
ORF3a	106	L106L	ctC	ctA	1	2	B.6.6	0.000889
ORF3a	106	L106F	Ctc	Ttc	2	2	C.36.3	0.001134
ORF3a	106	L106S	CTC	TCT	2	2	D.2	0.00015
ORF3a	106	L106P	cTc	cCc	2	2	P.1	0.000032
ORF3a	106	L106L	ctC	ctT	2	2	P.1.1	0.000635
ORF3a	106	L106P	cTc	cCc	2	2	P.1.7	0.000639
ORF3a	106	L106F	Ctc	Ttc	2	2	Q.2	0.001227
ORF3a	106	L106P	cTc	cCc	2	2	Q.8	0.00033
ORF3a	106	L106P	cTc	cCc	1	1	A	0.000387
ORF3a	106	L106del	CTC	---	1	1	A	0.000387
ORF3a	106	L106L	ctC	ctT	1	1	A	0.000387
ORF3a	106	L106F	Ctc	Ttc	1	1	A	0.000387
ORF3a	106	L106F	Ctc	Ttc	1	1	A.1	0.000282
ORF3a	106	L106F	Ctc	Ttc	1	1	A.11	0.058824
ORF3a	106	L106F	Ctc	Ttc	1	1	A.19	0.009434
ORF3a	106	L106L	ctC	ctT	1	1	A.23	0.010526
ORF3a	106	L106F	Ctc	Ttc	1	1	AD.2	0.000219
ORF3a	106	L106F	Ctc	Ttc	1	1	AE.8	0.000489
ORF3a	106	L106L	ctC	ctT	1	1	AF.1	0.037037
ORF3a	106	L106L	ctC	ctT	1	1	AH.3	0.003802
ORF3a	106	L106del	CTC	---	1	1	AH.3	0.003802
ORF3a	106	L106Y	CTc	TAc	1	1	All	0
ORF3a	106	L106L	ctC	ctT	1	1	AN.1	0.02
ORF3a	106	L106L	ctC	ctT	1	1	AP.1	0.001502
ORF3a	106	L106L	ctC	ctT	1	1	AQ.1	0.071429
ORF3a	106	L106F	Ctc	Ttc	1	1	AU.3	0.00211
ORF3a	106	L106del	CTC	---	1	1	AV.1	0.005051
ORF3a	106	L106del1	Ctc	-tc	1	1	AY.100	0.000046
ORF3a	106	L106del	CTC	---	1	1	AY.100	0.000046
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.102	0.000027
ORF3a	106	L106L	ctC	ctT	1	1	AY.105	0.000643
ORF3a	106	L106del	CTC	---	1	1	AY.106	0.000335
ORF3a	106	L106H	cTc	cAc	1	1	AY.107	0.000466
ORF3a	106	L106L	ctC	ctT	1	1	AY.108	0.001103
ORF3a	106	L106del	CTC	---	1	1	AY.108	0.001103
ORF3a	106	L106L	ctC	ctT	1	1	AY.109	0.00074
ORF3a	106	L106del	CTC	---	1	1	AY.111	0.000183
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.115	0.005208
ORF3a	106	L106I	Ctc	Atc	1	1	AY.116.1	0.000311
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.117	0.000085
ORF3a	106	L106P	cTc	cCc	1	1	AY.118	0.000063
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.119	0.000035
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.12	0.000316
ORF3a	106	L106L	ctC	ctT	1	1	AY.12	0.000316
ORF3a	106	L106del	CTC	---	1	1	AY.12	0.000316
ORF3a	106	L106L	ctC	ctT	1	1	AY.15	0.002222
ORF3a	106	L106L	ctC	ctT	1	1	AY.19	0.00114
ORF3a	106	L106P	cTc	cCc	1	1	AY.20	0.000039
ORF3a	106	L106R	cTc	cGc	1	1	AY.20	0.000039
ORF3a	106	L106del	CTC	---	1	1	AY.20	0.000039
ORF3a	106	L106del	CTC	---	1	1	AY.23	0.00007
ORF3a	106	L106I	Ctc	Atc	1	1	AY.25	0.000006
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.25	0.000006
ORF3a	106	L106P	cTc	cCc	1	1	AY.26	0.000028
ORF3a	106	L106del	CTC	---	1	1	AY.29.1	0.000221
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.3	0.00001
ORF3a	106	L106P	cTc	cCc	1	1	AY.3	0.00001
ORF3a	106	L106del	CTC	---	1	1	AY.3.1	0.000085
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.32	0.000532
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.33	0.000067
ORF3a	106	L106del	CTC	---	1	1	AY.33	0.000067
ORF3a	106	L106P	cTc	cCc	1	1	AY.34	0.000097
ORF3a	106	L106del	CTC	---	1	1	AY.34	0.000097
ORF3a	106	L106del	CTC	---	1	1	AY.34.1	0.00051
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.35	0.000233
ORF3a	106	L106L	ctC	ctT	1	1	AY.37	0.000316
ORF3a	106	L106L	ctC	ctT	1	1	AY.38	0.000499
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.39	0.000025
ORF3a	106	L106R	cTc	cGc	1	1	AY.39	0.000025
ORF3a	106	L106R	cTc	cGc	1	1	AY.4.2	0.000022
ORF3a	106	L106del	CTC	---	1	1	AY.4.2.1	0.000149
ORF3a	106	L106L	ctC	ctT	1	1	AY.4.3	0.000842
ORF3a	106	L106R	cTc	cGc	1	1	AY.4.4	0.000409
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.4.5	0.000107
ORF3a	106	L106L	ctC	ctT	1	1	AY.4.5	0.000107
ORF3a	106	L106L	ctC	ctT	1	1	AY.40	0.000964
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.42	0.00004
ORF3a	106	L106S	CTc	TCc	1	1	AY.43	0.000004
ORF3a	106	L106P	cTc	cCc	1	1	AY.44	0.000006
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.45	0.000122
ORF3a	106	L106P	cTc	cCc	1	1	AY.45	0.000122
ORF3a	106	L106P	cTc	cCc	1	1	AY.46	0.000104
ORF3a	106	L106L	ctC	ctT	1	1	AY.46.2	0.000635
ORF3a	106	L106I	Ctc	Atc	1	1	AY.46.6	0.000072
ORF3a	106	L106I	Ctc	Atc	1	1	AY.47	0.000031
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.49	0.003195
ORF3a	106	L106L	ctC	ctT	1	1	AY.49	0.003195
ORF3a	106	L106I	Ctc	Atc	1	1	AY.5	0.000021
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.52	0.000814
ORF3a	106	L106P	cTc	cCc	1	1	AY.53	0.000288
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.57	0.000656
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.58	0.000907
ORF3a	106	L106L	ctC	ctT	1	1	AY.58	0.000907
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.59	0.00053
ORF3a	106	L106V	Ctc	Gtc	1	1	AY.6	0.000041
ORF3a	106	L106L	ctC	ctT	1	1	AY.60	0.000938
ORF3a	106	L106del	CTC	---	1	1	AY.62	0.000436
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.67	0.000464
ORF3a	106	L106P	cTc	cCc	1	1	AY.67	0.000464
ORF3a	106	L106L	ctC	ctT	1	1	AY.68	0.000274
ORF3a	106	L106I	Ctc	Atc	1	1	AY.68	0.000274
ORF3a	106	L106del	CTC	---	1	1	AY.68	0.000274
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.69	0.000187
ORF3a	106	L106L	ctC	ctT	1	1	AY.70	0.000209
ORF3a	106	L106L	ctC	ctT	1	1	AY.71	0.000475
ORF3a	106	L106L	ctC	ctT	1	1	AY.72	0.001361
ORF3a	106	L106L	ctC	ctT	1	1	AY.73	0.000665
ORF3a	106	L106del	CTC	---	1	1	AY.73	0.000665
ORF3a	106	L106P	cTc	cCc	1	1	AY.75	0.000056
ORF3a	106	L106I	Ctc	Atc	1	1	AY.75.1	0.00018
ORF3a	106	L106L	ctC	ctT	1	1	AY.76	0.004831
ORF3a	106	L106L	ctC	ctT	1	1	AY.78	0.001541
ORF3a	106	L106L	ctC	ctT	1	1	AY.8	0.000606
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.80	0.001129
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.82	0.001357
ORF3a	106	L106R	cTc	cGc	1	1	AY.86	0.00083
ORF3a	106	L106F	Ctc	Ttc	1	1	AY.9.2.1	0.001976
ORF3a	106	L106L	ctC	ctT	1	1	AY.90	0.000684
ORF3a	106	L106I	Ctc	Atc	1	1	AY.91	0.00073
ORF3a	106	L106del	CTC	---	1	1	AY.91	0.00073
ORF3a	106	L106L	ctC	ctT	1	1	AY.96	0.002075
ORF3a	106	L106del	CTC	---	1	1	AY.99.2	0.000092
ORF3a	106	L106L	ctC	ctT	1	1	AZ.1	0.000867
ORF3a	106	L106F	Ctc	Ttc	1	1	AZ.5	0.003509
ORF3a	106	L106I	Ctc	Atc	1	1	B	0.000128
ORF3a	106	L106del	CTC	---	1	1	B	0.000128
ORF3a	106	L106S	CTc	TCc	1	1	B.1	0.000009
ORF3a	106	L106V	Ctc	Gtc	1	1	B.1	0.000009
ORF3a	106	L106del2	CTC	--A	1	1	B.1	0.000009
ORF3a	106	L106del	CTC	---	1	1	B.1.1	0.000018
ORF3a	106	L106Y	CTc	TAc	1	1	B.1.1	0.000018
ORF3a	106	L106del	CTC	---	1	1	B.1.1.117	0.009709
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.135	0.004695
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.141	0.002012
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.153	0.001095
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.157	0.000913
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.164	0.005155
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.176	0.000439
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.210	0.005714
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.219	0.005
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.227	0.004348
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.236	0.006897
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.263	0.001558
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.294	0.001266
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.297	0.002237
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.298	0.000862
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.304	0.002809
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.311	0.000358
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.312	0.001912
ORF3a	106	L106del	CTC	---	1	1	B.1.1.315	0.008475
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.317	0.000412
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.318	0.000302
ORF3a	106	L106C	CTc	TGc	1	1	B.1.1.33	0.000421
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.343	0.020833
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.348	0.000796
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.351	0.002793
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.369	0.000446
ORF3a	106	L106I	Ctc	Atc	1	1	B.1.1.369	0.000446
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.373	0.02381
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.377	0.001381
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.377	0.001381
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.389	0.006061
ORF3a	106	L106P	cTc	cCc	1	1	B.1.1.397	0.002252
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.398	0.003226
ORF3a	106	L106del	CTC	---	1	1	B.1.1.409	0.002833
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.409	0.002833
ORF3a	106	L106del	CTC	---	1	1	B.1.1.410	0.037037
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.411	0.014706
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.416	0.000905
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.416	0.000905
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.420	0.001006
ORF3a	106	L106del	CTC	---	1	1	B.1.1.420	0.001006
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.432	0.001266
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.433	0.001425
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.434	0.000349
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.448	0.002033
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.464	0.001473
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.47	0.005348
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.47	0.005348
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.507	0.008696
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.518	0.006329
ORF3a	106	L106del	CTC	---	1	1	B.1.1.519	0.00004
ORF3a	106	L106del	CTC	---	1	1	B.1.1.54	0.003021
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.77	0.041667
ORF3a	106	L106L	ctC	ctT	1	1	B.1.1.8	0.003584
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.83	0.00271
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.88	0.071429
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.1.89	0.006061
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.110.3	0.000718
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.111	0.001175
ORF3a	106	L106L	ctC	ctT	1	1	B.1.117	0.0125
ORF3a	106	L106L	ctC	ctT	1	1	B.1.124	0.007812
ORF3a	106	L106I	Ctc	Atc	1	1	B.1.126	0.001276
ORF3a	106	L106L	ctC	ctT	1	1	B.1.127	0.002198
ORF3a	106	L106V	Ctc	Gtc	1	1	B.1.128	0.000635
ORF3a	106	L106L	ctC	ctT	1	1	B.1.128	0.000635
ORF3a	106	L106del	CTC	---	1	1	B.1.140	0.018868
ORF3a	106	L106L	ctC	ctT	1	1	B.1.146	0.004237
ORF3a	106	L106del	CTC	---	1	1	B.1.157	0.002985
ORF3a	106	L106F	CtC	TtT	1	1	B.1.160.16	0.000929
ORF3a	106	L106F	CtC	TtT	1	1	B.1.160.20	0.008929
ORF3a	106	L106del	CTC	---	1	1	B.1.160.23	0.004831
ORF3a	106	L106I	Ctc	Atc	1	1	B.1.177	0.000013
ORF3a	106	L106del	CTC	---	1	1	B.1.177.16	0.000664
ORF3a	106	L106del	CTC	---	1	1	B.1.177.18	0.00116
ORF3a	106	L106L	ctC	ctT	1	1	B.1.177.19	0.001431
ORF3a	106	L106R	cTc	cGc	1	1	B.1.177.20	0.001517
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.177.21	0.000076
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.177.33	0.001645
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.177.43	0.001477
ORF3a	106	L106I	Ctc	Atc	1	1	B.1.177.44	0.000519
ORF3a	106	L106L	ctC	ctT	1	1	B.1.177.51	0.004566
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.177.57	0.000281
ORF3a	106	L106L	ctC	ctT	1	1	B.1.177.6	0.000977
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.177.60	0.000218
ORF3a	106	L106del	CTC	---	1	1	B.1.177.62	0.001192
ORF3a	106	L106P	cTc	cCc	1	1	B.1.177.69	0.001484
ORF3a	106	L106L	ctC	ctT	1	1	B.1.177.69	0.001484
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.177.77	0.000726
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.177.79	0.002342
ORF3a	106	L106L	ctC	ctT	1	1	B.1.177.8	0.000752
ORF3a	106	L106L	ctC	ctT	1	1	B.1.177.83	0.001481
ORF3a	106	L106L	ctC	ctT	1	1	B.1.192	0.009259
ORF3a	106	L106L	ctC	ctT	1	1	B.1.199	0.004132
ORF3a	106	L106R	cTc	cGc	1	1	B.1.2	0.000009
ORF3a	106	L106del	CTC	---	1	1	B.1.206	0.000816
ORF3a	106	L106P	cTc	cCc	1	1	B.1.206	0.000816
ORF3a	106	L106L	ctC	ctT	1	1	B.1.210	0.002132
ORF3a	106	L106L	ctC	ctT	1	1	B.1.214	0.003663
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.214.2	0.0006
ORF3a	106	L106L	ctC	ctT	1	1	B.1.214.2	0.0006
ORF3a	106	L106V	Ctc	Gtc	1	1	B.1.221	0.000071
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.221.3	0.000833
ORF3a	106	L106del	CTC	---	1	1	B.1.234	0.000132
ORF3a	106	L106L	ctC	ctT	1	1	B.1.235	0.002519
ORF3a	106	L106L	ctC	ctT	1	1	B.1.236	0.002053
ORF3a	106	L106L	ctC	ctT	1	1	B.1.237	0.004975
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.239	0.001221
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.241	0.000812
ORF3a	106	L106H	cTc	cAc	1	1	B.1.243	0.00007
ORF3a	106	L106del	CTC	---	1	1	B.1.243	0.00007
ORF3a	106	L106del1	Ctc	-tc	1	1	B.1.258.10	0.011364
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.260	0.003344
ORF3a	106	L106L	ctC	ctT	1	1	B.1.268	0.010417
ORF3a	106	L106L	ctC	ctT	1	1	B.1.279	0.000514
ORF3a	106	L106L	ctC	ctT	1	1	B.1.324	0.001605
ORF3a	106	L106L	ctC	ctT	1	1	B.1.333	0.010526
ORF3a	106	L106I	CtC	AtT	1	1	B.1.333	0.010526
ORF3a	106	L106F	CtC	TtT	1	1	B.1.333	0.010526
ORF3a	106	L106L	ctC	ctT	1	1	B.1.340	0.004292
ORF3a	106	L106P	cTc	cCc	1	1	B.1.349	0.000715
ORF3a	106	L106L	ctC	ctT	1	1	B.1.349	0.000715
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.351.2	0.000303
ORF3a	106	L106L	ctC	ctT	1	1	B.1.36.10	0.004785
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.36.25	0.002208
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.36.31	0.001751
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.36.39	0.002217
ORF3a	106	L106L	ctC	ctT	1	1	B.1.362	0.001541
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.362	0.001541
ORF3a	106	L106L	ctC	ctT	1	1	B.1.369	0.000285
ORF3a	106	L106del	CTC	---	1	1	B.1.375	0.00082
ORF3a	106	L106L	ctC	ctT	1	1	B.1.377	0.004566
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.380	0.006623
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.381	0.007812
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.398	0.002976
ORF3a	106	L106L	ctC	ctT	1	1	B.1.408	0.00369
ORF3a	106	L106L	ctC	ctT	1	1	B.1.416	0.001269
ORF3a	106	L106del	CTC	---	1	1	B.1.416.1	0.001563
ORF3a	106	L106L	ctC	ctT	1	1	B.1.423	0.010204
ORF3a	106	L106L	ctC	ctT	1	1	B.1.428	0.00102
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.428	0.00102
ORF3a	106	L106del	CTC	---	1	1	B.1.429	0.000024
ORF3a	106	L106I	Ctc	Atc	1	1	B.1.429	0.000024
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.432	0.011236
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.438.1	0.000107
ORF3a	106	L106L	ctC	ctT	1	1	B.1.438.1	0.000107
ORF3a	106	L106L	ctC	ctT	1	1	B.1.452	0.013699
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.462	0.007246
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.466	0.023256
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.466.2	0.000391
ORF3a	106	L106I	Ctc	Atc	1	1	B.1.466.2	0.000391
ORF3a	106	L106L	ctC	ctT	1	1	B.1.468	0.005714
ORF3a	106	L106L	ctC	ctT	1	1	B.1.474	0.001901
ORF3a	106	L106L	ctC	ctT	1	1	B.1.478	0.011765
ORF3a	106	L106L	ctC	ctT	1	1	B.1.485	0.014925
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.491	0.052632
ORF3a	106	L106L	ctC	ctT	1	1	B.1.497	0.000315
ORF3a	106	L106L	ctC	ctT	1	1	B.1.498	0.020408
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.503	0.002488
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.511	0.034483
ORF3a	106	L106L	ctC	ctT	1	1	B.1.517	0.000427
ORF3a	106	L106L	ctC	ctT	1	1	B.1.547	0.02439
ORF3a	106	L106L	ctC	ctT	1	1	B.1.560	0.00463
ORF3a	106	L106P	cTc	cCc	1	1	B.1.564	0.000426
ORF3a	106	L106L	ctC	ctT	1	1	B.1.567	0.003333
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.576	0.000907
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.577	0.000687
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.582	0.000491
ORF3a	106	L106L	ctC	ctT	1	1	B.1.582	0.000491
ORF3a	106	L106L	ctC	ctT	1	1	B.1.587	0.001898
ORF3a	106	L106L	ctC	ctT	1	1	B.1.589	0.007576
ORF3a	106	L106L	ctC	ctT	1	1	B.1.590	0.004545
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.595	0.000261
ORF3a	106	L106R	cTc	cGc	1	1	B.1.595	0.000261
ORF3a	106	L106del	CTC	---	1	1	B.1.596	0.000087
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.597	0.00463
ORF3a	106	L106L	ctC	ctT	1	1	B.1.600	0.005848
ORF3a	106	L106del	CTC	---	1	1	B.1.617.1	0.000129
ORF3a	106	L106R	cTc	cGc	1	1	B.1.617.1	0.000129
ORF3a	106	L106V	Ctc	Gtc	1	1	B.1.621	0.000089
ORF3a	106	L106P	cTc	cCc	1	1	B.1.621	0.000089
ORF3a	106	L106L	ctC	ctT	1	1	B.1.621.1	0.000506
ORF3a	106	L106L	ctC	ctA	1	1	B.1.623	0.000536
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.634	0.003425
ORF3a	106	L106H	cTc	cAc	1	1	B.1.637	0.000073
ORF3a	106	L106del	CTC	---	1	1	B.1.638	0.052632
ORF3a	106	L106L	ctC	ctT	1	1	B.1.78	0.008547
ORF3a	106	L106F	Ctc	Ttc	1	1	B.1.91	0.002075
ORF3a	106	L106L	ctC	ctT	1	1	B.3.1	0.001658
ORF3a	106	L106I	Ctc	Atc	1	1	B.3.1	0.001658
ORF3a	106	L106F	Ctc	Ttc	1	1	B.4	0.002208
ORF3a	106	L106F	Ctc	Ttc	1	1	B.40	0.000364
ORF3a	106	L106L	ctC	ctT	1	1	B.40	0.000364
ORF3a	106	L106L	ctC	ctT	1	1	B.55	0.00295
ORF3a	106	L106P	cTc	cCc	1	1	B.6.6	0.000889
ORF3a	106	L106L	ctC	ctT	1	1	B.6.8	0.008264
ORF3a	106	L106F	Ctc	Ttc	1	1	C.12	0.007194
ORF3a	106	L106L	ctC	ctT	1	1	C.34	0.037037
ORF3a	106	L106L	ctC	ctT	1	1	C.36.3.1	0.002717
ORF3a	106	L106P	cTc	cCc	1	1	C.37	0.000116
ORF3a	106	L106I	Ctc	Atc	1	1	C.37	0.000116
ORF3a	106	L106V	Ctc	Gtc	1	1	C.6	0.037037
ORF3a	106	L106F	Ctc	Ttc	1	1	N.2	0.038462
ORF3a	106	L106F	Ctc	Ttc	1	1	N.4	0.004255
ORF3a	106	L106I	Ctc	Atc	1	1	P.1	0.000016
ORF3a	106	L106H	cTc	cAc	1	1	P.1	0.000016
ORF3a	106	L106I	Ctc	Atc	1	1	P.1.1	0.000318
ORF3a	106	L106F	Ctc	Ttc	1	1	P.1.10	0.000269
ORF3a	106	L106L	ctC	ctT	1	1	P.1.12	0.000484
ORF3a	106	L106F	Ctc	Ttc	1	1	P.1.13	0.000898
ORF3a	106	L106P	cTc	cCc	1	1	P.1.14	0.000048
ORF3a	106	L106L	ctC	ctT	1	1	P.1.2	0.001156
ORF3a	106	L106F	Ctc	Ttc	1	1	P.1.7	0.000319
ORF3a	106	L106L	ctC	ctT	1	1	P.3	0.001595
ORF3a	106	L106L	ctC	ctG	1	1	P.6	0.003145
ORF3a	106	L106del	CTC	---	1	1	Q.1	0.000126
ORF3a	106	L106del	CTC	---	1	1	Q.4	0.000455
ORF3a	106	L106F	Ctc	Ttc	1	1	R.1	0.00009
ORF3a	106	L106del	CTC	---	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.