CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 34

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
ORF1ab/nsp4	34	S34F	S2797F	nonsyn	tCt	tTt	10307	10304	0.999709	8654-8656
ORF1ab/nsp4	34	S34F	S2797F	nonsyn	tCT	tTC	10307	3	0.000291064	8654-8656
ORF1ab/nsp4	34	S34S	S2797S	syn	tcT	tcC	3028	2974	0.982166	8654-8656
ORF1ab/nsp4	34	S34S	S2797S	syn	tcT	tcA	3028	43	0.0142008	8654-8656
ORF1ab/nsp4	34	S34S	S2797S	syn	tcT	tcG	3028	7	0.00231176	8654-8656
ORF1ab/nsp4	34	S34S	S2797S	syn	TCt	AGt	3028	4	0.001321	8654-8656
ORF1ab/nsp4	34	S34I	S2797I	nonsyn	TCT	ATA	268	135	0.503731	8654-8656
ORF1ab/nsp4	34	S34I	S2797I	nonsyn	TCt	ATt	268	123	0.458955	8654-8656
ORF1ab/nsp4	34	S34I	S2797I	nonsyn	TCT	ATC	268	10	0.0373134	8654-8656
ORF1ab/nsp4	34	S34Y	S2797Y	nonsyn	tCt	tAt	196	188	0.959184	8654-8656
ORF1ab/nsp4	34	S34Y	S2797Y	nonsyn	tCT	tAC	196	8	0.0408163	8654-8656
ORF1ab/nsp4	34	S34K	S2797K	nonsyn	TCT	AAA	168	168	1	8654-8656
ORF1ab/nsp4	34	S34N	S2797N	nonsyn	TCt	AAt	161	142	0.881988	8654-8656
ORF1ab/nsp4	34	S34N	S2797N	nonsyn	TCT	AAC	161	19	0.118012	8654-8656
ORF1ab/nsp4	34	S34X	S2797X	nonsyn	tCT	tAA	137	133	0.970803	8654-8656
ORF1ab/nsp4	34	S34X	S2797X	nonsyn	tCT	tGA	137	4	0.0291971	8654-8656
ORF1ab/nsp4	34	S34L	S2797L	nonsyn	tCT	tTA	128	115	0.898438	8654-8656
ORF1ab/nsp4	34	S34L	S2797L	nonsyn	TCT	CTA	128	7	0.0546875	8654-8656
ORF1ab/nsp4	34	S34L	S2797L	nonsyn	TCt	CTt	128	6	0.046875	8654-8656
ORF1ab/nsp4	34	S34del	S2797del	del	TCT	---	109	109	1	8654-8656
ORF1ab/nsp4	34	S34T	S2797T	nonsyn	Tct	Act	69	39	0.565217	8654-8656
ORF1ab/nsp4	34	S34T	S2797T	nonsyn	TcT	AcA	69	27	0.391304	8654-8656
ORF1ab/nsp4	34	S34T	S2797T	nonsyn	TcT	AcC	69	3	0.0434783	8654-8656
ORF1ab/nsp4	34	S34P	S2797P	nonsyn	Tct	Cct	35	31	0.885714	8654-8656
ORF1ab/nsp4	34	S34P	S2797P	nonsyn	TcT	CcA	35	4	0.114286	8654-8656
ORF1ab/nsp4	34	S34R	S2797R	nonsyn	TCT	CGA	20	9	0.45	8654-8656
ORF1ab/nsp4	34	S34R	S2797R	nonsyn	TCT	AGA	20	9	0.45	8654-8656
ORF1ab/nsp4	34	S34R	S2797R	nonsyn	TCt	CGt	20	2	0.1	8654-8656
ORF1ab/nsp4	34	S34Q	S2797Q	nonsyn	TCT	CAA	16	16	1	8654-8656
ORF1ab/nsp4	34	S34A	S2797A	nonsyn	Tct	Gct	10	10	1	8654-8656
ORF1ab/nsp4	34	S34del1	S2797del1	del	tcT	tc-	9	6	0.666667	8654-8656
ORF1ab/nsp4	34	S34del1	S2797del1	del	tCt	t-t	9	2	0.222222	8654-8656
ORF1ab/nsp4	34	S34del1	S2797del1	del	Tct	-ct	9	1	0.111111	8654-8656
ORF1ab/nsp4	34	S34H	S2797H	nonsyn	TCt	CAt	8	8	1	8654-8656
ORF1ab/nsp4	34	S34C	S2797C	nonsyn	tCt	tGt	6	6	1	8654-8656
ORF1ab/nsp4	34	S34V	S2797V	nonsyn	TCt	GTt	2	2	1	8654-8656
ORF1ab/nsp4	34	S34D	S2797D	nonsyn	TCt	GAt	1	1	1	8654-8656
ORF1ab/nsp4	34	S34del2	S2797del2	del	TCt	--t	1	1	1	8654-8656

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
ORF1ab/nsp4	34	S34F	tCt	tTt	10304	10307	All	0.001971
ORF1ab/nsp4	34	S34F	tCT	tTC	3	10307	All	0.000001
ORF1ab/nsp4	34	S34F	tCt	tTt	3402	3405	B.1.1.7	0.003046
ORF1ab/nsp4	34	S34F	tCT	tTC	3	3405	B.1.1.7	0.000003
ORF1ab/nsp4	34	S34S	tcT	tcC	2974	3028	All	0.000569
ORF1ab/nsp4	34	S34S	tcT	tcA	43	3028	All	0.000008
ORF1ab/nsp4	34	S34S	tcT	tcG	7	3028	All	0.000001
ORF1ab/nsp4	34	S34S	TCt	AGt	4	3028	All	0.000001
ORF1ab/nsp4	34	S34S	tcT	tcC	2093	2095	B.1.617.2	0.007881
ORF1ab/nsp4	34	S34S	tcT	tcG	1	2095	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34S	tcT	tcA	1	2095	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34F	tCt	tTt	1358	1358	AY.44	0.008266
ORF1ab/nsp4	34	S34F	tCt	tTt	1055	1055	AY.39	0.026071
ORF1ab/nsp4	34	S34F	tCt	tTt	573	573	AY.103	0.003558
ORF1ab/nsp4	34	S34S	tcT	tcC	442	442	AY.102	0.011719
ORF1ab/nsp4	34	S34F	tCt	tTt	346	346	AY.4	0.000539
ORF1ab/nsp4	34	S34F	tCt	tTt	340	340	B.1.617.2	0.00128
ORF1ab/nsp4	34	S34F	tCt	tTt	326	326	B.1	0.002986
ORF1ab/nsp4	34	S34I	TCT	ATA	135	268	All	0.000026
ORF1ab/nsp4	34	S34I	TCt	ATt	123	268	All	0.000024
ORF1ab/nsp4	34	S34I	TCT	ATC	10	268	All	0.000002
ORF1ab/nsp4	34	S34I	TCT	ATA	123	246	B.1.1.7	0.00011
ORF1ab/nsp4	34	S34I	TCt	ATt	113	246	B.1.1.7	0.000101
ORF1ab/nsp4	34	S34I	TCT	ATC	10	246	B.1.1.7	0.000009
ORF1ab/nsp4	34	S34Y	tCt	tAt	188	196	All	0.000036
ORF1ab/nsp4	34	S34Y	tCT	tAC	8	196	All	0.000002
ORF1ab/nsp4	34	S34Y	tCt	tAt	163	169	B.1.1.7	0.000146
ORF1ab/nsp4	34	S34Y	tCT	tAC	6	169	B.1.1.7	0.000005
ORF1ab/nsp4	34	S34K	TCT	AAA	168	168	All	0.000032
ORF1ab/nsp4	34	S34N	TCt	AAt	142	161	All	0.000027
ORF1ab/nsp4	34	S34N	TCT	AAC	19	161	All	0.000004
ORF1ab/nsp4	34	S34F	tCt	tTt	159	159	B.1.2	0.0014
ORF1ab/nsp4	34	S34K	TCT	AAA	154	154	B.1.1.7	0.000138
ORF1ab/nsp4	34	S34F	tCt	tTt	154	154	B.1.351	0.004578
ORF1ab/nsp4	34	S34N	TCt	AAt	131	150	B.1.1.7	0.000117
ORF1ab/nsp4	34	S34N	TCT	AAC	19	150	B.1.1.7	0.000017
ORF1ab/nsp4	34	S34X	tCT	tAA	133	137	All	0.000025
ORF1ab/nsp4	34	S34X	tCT	tGA	4	137	All	0.000001
ORF1ab/nsp4	34	S34F	tCt	tTt	131	131	AY.25	0.000788
ORF1ab/nsp4	34	S34F	tCt	tTt	129	129	B.1.565	0.104538
ORF1ab/nsp4	34	S34L	tCT	tTA	115	128	All	0.000022
ORF1ab/nsp4	34	S34L	TCT	CTA	7	128	All	0.000001
ORF1ab/nsp4	34	S34L	TCt	CTt	6	128	All	0.000001
ORF1ab/nsp4	34	S34X	tCT	tAA	123	127	B.1.1.7	0.00011
ORF1ab/nsp4	34	S34X	tCT	tGA	4	127	B.1.1.7	0.000004
ORF1ab/nsp4	34	S34F	tCt	tTt	119	119	B.1.429	0.0028
ORF1ab/nsp4	34	S34L	tCT	tTA	105	116	B.1.1.7	0.000094
ORF1ab/nsp4	34	S34L	TCT	CTA	6	116	B.1.1.7	0.000005
ORF1ab/nsp4	34	S34L	TCt	CTt	5	116	B.1.1.7	0.000004
ORF1ab/nsp4	34	S34F	tCt	tTt	110	110	AY.43	0.000487
ORF1ab/nsp4	34	S34del	TCT	---	109	109	All	0.000021
ORF1ab/nsp4	34	S34F	tCt	tTt	82	82	P.1	0.001292
ORF1ab/nsp4	34	S34F	tCt	tTt	76	76	B.1.177	0.001001
ORF1ab/nsp4	34	S34F	tCt	tTt	74	74	AY.3	0.000736
ORF1ab/nsp4	34	S34T	Tct	Act	39	69	All	0.000007
ORF1ab/nsp4	34	S34T	TcT	AcA	27	69	All	0.000005
ORF1ab/nsp4	34	S34T	TcT	AcC	3	69	All	0.000001
ORF1ab/nsp4	34	S34S	tcT	tcC	69	69	AY.34.1	0.035186
ORF1ab/nsp4	34	S34F	tCt	tTt	67	67	B.1.1.37	0.012922
ORF1ab/nsp4	34	S34T	Tct	Act	34	62	B.1.1.7	0.00003
ORF1ab/nsp4	34	S34T	TcT	AcA	25	62	B.1.1.7	0.000022
ORF1ab/nsp4	34	S34T	TcT	AcC	3	62	B.1.1.7	0.000003
ORF1ab/nsp4	34	S34F	tCt	tTt	60	60	AY.117	0.005071
ORF1ab/nsp4	34	S34F	tCt	tTt	59	59	B.1.596	0.005141
ORF1ab/nsp4	34	S34S	tcT	tcC	52	54	AY.43	0.00023
ORF1ab/nsp4	34	S34S	tcT	tcG	2	54	AY.43	0.000009
ORF1ab/nsp4	34	S34F	tCt	tTt	53	53	B.1.1	0.000961
ORF1ab/nsp4	34	S34F	tCt	tTt	51	51	B.1.36.37	0.141667
ORF1ab/nsp4	34	S34S	tcT	tcC	46	46	AY.39	0.001137
ORF1ab/nsp4	34	S34del	TCT	---	46	46	B.1.1.7	0.000041
ORF1ab/nsp4	34	S34S	tcT	tcA	34	45	B.1.1.7	0.00003
ORF1ab/nsp4	34	S34S	tcT	tcC	8	45	B.1.1.7	0.000007
ORF1ab/nsp4	34	S34S	TCt	AGt	2	45	B.1.1.7	0.000002
ORF1ab/nsp4	34	S34S	tcT	tcG	1	45	B.1.1.7	0.000001
ORF1ab/nsp4	34	S34F	tCt	tTt	43	43	B.1.160	0.001341
ORF1ab/nsp4	34	S34F	tCt	tTt	42	42	B.1.1.431	0.677419
ORF1ab/nsp4	34	S34S	tcT	tcC	41	41	AY.44	0.00025
ORF1ab/nsp4	34	S34F	tCt	tTt	41	41	B.1.1.434	0.014291
ORF1ab/nsp4	34	S34F	tCt	tTt	41	41	B.1.1.519	0.001628
ORF1ab/nsp4	34	S34F	tCt	tTt	37	37	AY.102	0.000981
ORF1ab/nsp4	34	S34F	tCt	tTt	37	37	AY.4.2	0.000802
ORF1ab/nsp4	34	S34F	tCt	tTt	36	36	B.1.1.328	0.610169
ORF1ab/nsp4	34	S34P	Tct	Cct	31	35	All	0.000006
ORF1ab/nsp4	34	S34P	TcT	CcA	4	35	All	0.000001
ORF1ab/nsp4	34	S34F	tCt	tTt	31	31	B.1.1.265	0.097792
ORF1ab/nsp4	34	S34F	tCt	tTt	29	29	B.1.139	0.021261
ORF1ab/nsp4	34	S34F	tCt	tTt	28	28	AY.20	0.001088
ORF1ab/nsp4	34	S34F	tCt	tTt	28	28	AY.46.6	0.002022
ORF1ab/nsp4	34	S34F	tCt	tTt	27	27	B.1.526	0.000635
ORF1ab/nsp4	34	S34F	tCt	tTt	26	26	B.1.1.8	0.09319
ORF1ab/nsp4	34	S34F	tCt	tTt	24	24	B.1.351.3	0.021034
ORF1ab/nsp4	34	S34S	tcT	tcC	20	21	B.1.177	0.000263
ORF1ab/nsp4	34	S34S	tcT	tcA	1	21	B.1.177	0.000013
ORF1ab/nsp4	34	S34F	tCt	tTt	21	21	B.1.617.1	0.002708
ORF1ab/nsp4	34	S34R	TCT	CGA	9	20	All	0.000002
ORF1ab/nsp4	34	S34R	TCT	AGA	9	20	All	0.000002
ORF1ab/nsp4	34	S34R	TCt	CGt	2	20	All	0
ORF1ab/nsp4	34	S34F	tCt	tTt	20	20	AY.5	0.000413
ORF1ab/nsp4	34	S34F	tCt	tTt	20	20	B.1.609	0.009588
ORF1ab/nsp4	34	S34R	TCT	CGA	9	19	B.1.1.7	0.000008
ORF1ab/nsp4	34	S34R	TCT	AGA	8	19	B.1.1.7	0.000007
ORF1ab/nsp4	34	S34R	TCt	CGt	2	19	B.1.1.7	0.000002
ORF1ab/nsp4	34	S34F	tCt	tTt	19	19	B.1.497	0.00598
ORF1ab/nsp4	34	S34F	tCt	tTt	19	19	Q.1	0.0024
ORF1ab/nsp4	34	S34F	tCt	tTt	18	18	AY.34	0.001745
ORF1ab/nsp4	34	S34F	tCt	tTt	18	18	AY.9.1	0.001507
ORF1ab/nsp4	34	S34F	tCt	tTt	18	18	B.1.234	0.002375
ORF1ab/nsp4	34	S34F	tCt	tTt	17	17	AY.118	0.001065
ORF1ab/nsp4	34	S34F	tCt	tTt	17	17	AY.33	0.001135
ORF1ab/nsp4	34	S34F	tCt	tTt	17	17	Q.8	0.002803
ORF1ab/nsp4	34	S34Q	TCT	CAA	16	16	All	0.000003
ORF1ab/nsp4	34	S34F	tCt	tTt	16	16	B.1.177.81	0.003029
ORF1ab/nsp4	34	S34F	tCt	tTt	16	16	C.36.3	0.009075
ORF1ab/nsp4	34	S34F	tCt	tTt	15	15	AY.100	0.00069
ORF1ab/nsp4	34	S34S	tcT	tcC	15	15	AY.120	0.000558
ORF1ab/nsp4	34	S34F	tCt	tTt	15	15	AY.99.2	0.001382
ORF1ab/nsp4	34	S34S	tcT	tcC	14	14	AY.91	0.010226
ORF1ab/nsp4	34	S34F	tCt	tTt	13	13	AY.26	0.000368
ORF1ab/nsp4	34	S34Q	TCT	CAA	13	13	B.1.1.7	0.000012
ORF1ab/nsp4	34	S34F	tCt	tTt	13	13	B.1.621	0.001151
ORF1ab/nsp4	34	S34F	tCt	tTt	12	12	AY.46.4	0.001974
ORF1ab/nsp4	34	S34P	Tct	Cct	9	12	B.1.1.7	0.000008
ORF1ab/nsp4	34	S34P	TcT	CcA	3	12	B.1.1.7	0.000003
ORF1ab/nsp4	34	S34F	tCt	tTt	12	12	B.1.160.16	0.011152
ORF1ab/nsp4	34	S34F	tCt	tTt	12	12	B.1.177.21	0.000918
ORF1ab/nsp4	34	S34I	TCt	ATt	6	12	P.1	0.000095
ORF1ab/nsp4	34	S34I	TCT	ATA	6	12	P.1	0.000095
ORF1ab/nsp4	34	S34F	tCt	tTt	11	11	AY.61	0.001153
ORF1ab/nsp4	34	S34F	tCt	tTt	11	11	B.1.1.63	0.004244
ORF1ab/nsp4	34	S34F	tCt	tTt	11	11	B.1.240	0.002371
ORF1ab/nsp4	34	S34F	tCt	tTt	11	11	B.1.258	0.000732
ORF1ab/nsp4	34	S34A	Tct	Gct	10	10	All	0.000002
ORF1ab/nsp4	34	S34F	tCt	tTt	10	10	AY.119	0.000353
ORF1ab/nsp4	34	S34F	tCt	tTt	10	10	AY.23	0.000697
ORF1ab/nsp4	34	S34S	tcT	tcC	10	10	AY.46.4	0.001645
ORF1ab/nsp4	34	S34F	tCt	tTt	10	10	AY.75	0.00056
ORF1ab/nsp4	34	S34F	tCt	tTt	10	10	B.1.1.306	0.004384
ORF1ab/nsp4	34	S34F	tCt	tTt	10	10	B.1.221	0.00071
ORF1ab/nsp4	34	S34F	tCt	tTt	10	10	B.1.243	0.000696
ORF1ab/nsp4	34	S34F	tCt	tTt	10	10	B.1.298	0.021142
ORF1ab/nsp4	34	S34del1	tcT	tc-	6	9	All	0.000001
ORF1ab/nsp4	34	S34del1	tCt	t-t	2	9	All	0
ORF1ab/nsp4	34	S34del1	Tct	-ct	1	9	All	0
ORF1ab/nsp4	34	S34F	tCt	tTt	9	9	AY.3.1	0.000767
ORF1ab/nsp4	34	S34S	tcT	tcC	7	9	AY.4	0.000011
ORF1ab/nsp4	34	S34S	tcT	tcA	2	9	AY.4	0.000003
ORF1ab/nsp4	34	S34F	tCt	tTt	9	9	AY.45	0.001095
ORF1ab/nsp4	34	S34S	tcT	tcC	9	9	AY.5.3	0.003036
ORF1ab/nsp4	34	S34F	tCt	tTt	9	9	AY.98.1	0.000436
ORF1ab/nsp4	34	S34F	tCt	tTt	9	9	B.1.396	0.006351
ORF1ab/nsp4	34	S34F	tCt	tTt	9	9	B.1.525	0.001018
ORF1ab/nsp4	34	S34F	tCt	tTt	9	9	B.1.637	0.000658
ORF1ab/nsp4	34	S34H	TCt	CAt	8	8	All	0.000002
ORF1ab/nsp4	34	S34S	tcT	tcC	8	8	AY.118	0.000501
ORF1ab/nsp4	34	S34F	tCt	tTt	8	8	AY.121	0.001083
ORF1ab/nsp4	34	S34S	tcT	tcC	8	8	AY.26	0.000226
ORF1ab/nsp4	34	S34F	tCt	tTt	8	8	AY.29	0.000126
ORF1ab/nsp4	34	S34F	tCt	tTt	8	8	B.1.1.317	0.003294
ORF1ab/nsp4	34	S34F	tCt	tTt	8	8	B.1.517	0.003416
ORF1ab/nsp4	34	S34F	tCt	tTt	8	8	B.1.568	0.008889
ORF1ab/nsp4	34	S34F	tCt	tTt	8	8	C.23	0.046512
ORF1ab/nsp4	34	S34F	tCt	tTt	8	8	P.2	0.001493
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	AY.113	0.000997
ORF1ab/nsp4	34	S34S	tcT	tcC	7	7	AY.19	0.007982
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	AY.4.5	0.000752
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	AY.47	0.000218
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	AY.69	0.001307
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	AY.9.2	0.000257
ORF1ab/nsp4	34	S34S	tcT	tcC	7	7	AY.98	0.000553
ORF1ab/nsp4	34	S34del	TCT	---	7	7	B.1	0.000064
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	B.1.1.222	0.001428
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	B.1.1.375	0.083333
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	B.1.177.11	0.011885
ORF1ab/nsp4	34	S34L	tCT	tTA	5	7	P.1	0.000079
ORF1ab/nsp4	34	S34L	TCt	CTt	1	7	P.1	0.000016
ORF1ab/nsp4	34	S34L	TCT	CTA	1	7	P.1	0.000016
ORF1ab/nsp4	34	S34F	tCt	tTt	7	7	Q.3	0.001015
ORF1ab/nsp4	34	S34C	tCt	tGt	6	6	All	0.000001
ORF1ab/nsp4	34	S34S	tcT	tcC	6	6	AY.103	0.000037
ORF1ab/nsp4	34	S34S	tcT	tcC	6	6	AY.117	0.000507
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	AY.120	0.000223
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	AY.42	0.000241
ORF1ab/nsp4	34	S34S	tcT	tcC	6	6	AY.5	0.000124
ORF1ab/nsp4	34	S34S	tcT	tcC	6	6	AY.75.1	0.001082
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	AY.98	0.000474
ORF1ab/nsp4	34	S34H	TCt	CAt	6	6	B.1.1.7	0.000005
ORF1ab/nsp4	34	S34del	TCT	---	6	6	B.1.177	0.000079
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	B.1.177.10	0.005268
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	B.1.595	0.001566
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	B.1.619.1	0.003849
ORF1ab/nsp4	34	S34K	TCT	AAA	6	6	P.1	0.000095
ORF1ab/nsp4	34	S34N	TCt	AAt	6	6	P.1	0.000095
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	P.1.14	0.000287
ORF1ab/nsp4	34	S34F	tCt	tTt	6	6	P.1.2	0.006936
ORF1ab/nsp4	34	S34S	tcT	tcC	5	5	AY.116	0.001434
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	AY.27	0.000324
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	AY.32	0.002662
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	AY.4.4	0.002046
ORF1ab/nsp4	34	S34S	tcT	tcC	5	5	AY.45	0.000608
ORF1ab/nsp4	34	S34S	tcT	tcC	5	5	B.1	0.000046
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	B.1.1.157	0.004566
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	B.1.1.214	0.000277
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	B.1.1.374	0.011876
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	B.1.466.2	0.001956
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	B.1.576	0.004533
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	B.1.582	0.002453
ORF1ab/nsp4	34	S34F	tCt	tTt	5	5	C.37	0.00058
ORF1ab/nsp4	34	S34X	tCT	tAA	5	5	P.1	0.000079
ORF1ab/nsp4	34	S34Y	tCt	tAt	5	5	P.1	0.000079
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	A.2.5	0.001996
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	AY.10	0.00212
ORF1ab/nsp4	34	S34S	tcT	tcC	4	4	AY.119	0.000141
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	AY.14	0.000352
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	AY.16	0.001519
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	AY.35	0.000932
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	AY.4.2.1	0.000596
ORF1ab/nsp4	34	S34S	tcT	tcC	3	4	AY.5.4	0.00083
ORF1ab/nsp4	34	S34S	tcT	tcG	1	4	AY.5.4	0.000277
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	AY.7	0.000784
ORF1ab/nsp4	34	S34S	tcT	tcC	4	4	AY.8	0.002424
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	AY.95	0.003044
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	B	0.000511
ORF1ab/nsp4	34	S34A	Tct	Gct	4	4	B.1	0.000037
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	B.1.1.25	0.002274
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	B.1.1.28	0.001245
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	B.1.1.33	0.001684
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	B.1.177.16	0.002658
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	B.1.232	0.002149
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	B.1.36	0.000584
ORF1ab/nsp4	34	S34del	TCT	---	4	4	B.1.621	0.000354
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	C.36	0.003643
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	P.1.1	0.001271
ORF1ab/nsp4	34	S34F	tCt	tTt	4	4	P.1.16	0.001496
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	A.23.1	0.002113
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.101	0.001471
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.110	0.000338
ORF1ab/nsp4	34	S34S	tcT	tcC	3	3	AY.23	0.000209
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.24	0.001293
ORF1ab/nsp4	34	S34S	tcT	tcC	3	3	AY.32	0.001597
ORF1ab/nsp4	34	S34S	tcT	tcC	2	3	AY.33	0.000134
ORF1ab/nsp4	34	S34S	tcT	tcG	1	3	AY.33	0.000067
ORF1ab/nsp4	34	S34Y	tCt	tAt	3	3	AY.36	0.000445
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.36	0.000445
ORF1ab/nsp4	34	S34del	TCT	---	3	3	AY.4	0.000005
ORF1ab/nsp4	34	S34del	TCT	---	3	3	AY.4.5	0.000322
ORF1ab/nsp4	34	S34Y	tCt	tAt	2	3	AY.44	0.000012
ORF1ab/nsp4	34	S34Y	tCT	tAC	1	3	AY.44	0.000006
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.46	0.000312
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.54	0.000286
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.6	0.000123
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.71	0.001425
ORF1ab/nsp4	34	S34S	tcT	tcC	3	3	AY.75	0.000168
ORF1ab/nsp4	34	S34S	tcT	tcC	3	3	AY.88	0.002653
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	AY.9	0.000203
ORF1ab/nsp4	34	S34del	TCT	---	3	3	B.1.1	0.000054
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.1.1	0.00098
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.1.163	0.022901
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.1.196	0.017143
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.1.284	0.000322
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.1.322	0.026316
ORF1ab/nsp4	34	S34S	tcT	tcC	3	3	B.1.1.432	0.003797
ORF1ab/nsp4	34	S34C	tCt	tGt	3	3	B.1.1.7	0.000003
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.128	0.001906
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.13	0.007126
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.177.23	0.009709
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.177.60	0.000655
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.177.7	0.000495
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.177.72	0.010169
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.177.77	0.002179
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.206	0.002447
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.241	0.002435
ORF1ab/nsp4	34	S34Y	tCt	tAt	3	3	B.1.258	0.0002
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.36.18	0.001261
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.369	0.000856
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.404	0.003906
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.427	0.000151
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	B.1.564	0.001278
ORF1ab/nsp4	34	S34del	TCT	---	3	3	B.1.617.2	0.000011
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	C.1	0.007177
ORF1ab/nsp4	34	S34F	tCt	tTt	3	3	C.7	0.103448
ORF1ab/nsp4	34	S34V	TCt	GTt	2	2		0.111111
ORF1ab/nsp4	34	S34del	TCT	---	2	2		0.111111
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	A	0.000774
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	A.2.4	0.006734
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	A.3	0.004193
ORF1ab/nsp4	34	S34V	TCt	GTt	2	2	All	0
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.1	0.000791
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.100	0.000092
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.106	0.00067
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.110	0.000225
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.111	0.000366
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.120.1	0.000642
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.13	0.000322
ORF1ab/nsp4	34	S34P	Tct	Cct	2	2	AY.23	0.000139
ORF1ab/nsp4	34	S34del	TCT	---	2	2	AY.25	0.000012
ORF1ab/nsp4	34	S34I	TCT	ATA	1	2	AY.25	0.000006
ORF1ab/nsp4	34	S34I	TCt	ATt	1	2	AY.25	0.000006
ORF1ab/nsp4	34	S34P	Tct	Cct	2	2	AY.27	0.000129
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.3	0.00002
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.38	0.000999
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.39.1	0.000079
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.4.1	0.001475
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.4.2	0.000043
ORF1ab/nsp4	34	S34del	TCT	---	2	2	AY.43	0.000009
ORF1ab/nsp4	34	S34P	Tct	Cct	2	2	AY.43	0.000009
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.46	0.000208
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.46.5	0.000397
ORF1ab/nsp4	34	S34Y	tCt	tAt	2	2	AY.5.3	0.000675
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.51	0.001818
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.59	0.001059
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.62	0.000871
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.62	0.000871
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.7.1	0.000225
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.75.1	0.000361
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.84	0.000875
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.85	0.000854
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.9.2	0.000073
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.92	0.000575
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	AY.92	0.000575
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	AY.95	0.001522
ORF1ab/nsp4	34	S34I	TCT	ATA	2	2	B.1	0.000018
ORF1ab/nsp4	34	S34del1	tcT	tc-	2	2	B.1	0.000018
ORF1ab/nsp4	34	S34K	TCT	AAA	2	2	B.1	0.000018
ORF1ab/nsp4	34	S34P	Tct	Cct	2	2	B.1.1	0.000036
ORF1ab/nsp4	34	S34I	TCT	ATA	1	2	B.1.1	0.000018
ORF1ab/nsp4	34	S34I	TCt	ATt	1	2	B.1.1	0.000018
ORF1ab/nsp4	34	S34S	tcT	tcC	1	2	B.1.1	0.000018
ORF1ab/nsp4	34	S34T	TcT	AcA	1	2	B.1.1	0.000018
ORF1ab/nsp4	34	S34T	Tct	Act	1	2	B.1.1	0.000018
ORF1ab/nsp4	34	S34S	tcT	tcA	1	2	B.1.1	0.000018
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.144	0.057143
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.204	0.006079
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.216	0.001781
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.27	0.011299
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.280	0.006173
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.291	0.001485
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.294	0.002532
ORF1ab/nsp4	34	S34del	TCT	---	2	2	B.1.1.315	0.016949
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.318	0.000604
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.333	0.002153
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.335	0.025974
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.397	0.004505
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.416	0.00181
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.432	0.002532
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.442	0.037037
ORF1ab/nsp4	34	S34A	Tct	Gct	2	2	B.1.1.7	0.000002
ORF1ab/nsp4	34	S34del1	tcT	tc-	2	2	B.1.1.7	0.000002
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.70	0.000682
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.1.89	0.012121
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.177.46	0.001837
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.177.63	0.005405
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.189	0.008584
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.195	0.01005
ORF1ab/nsp4	34	S34del	TCT	---	2	2	B.1.2	0.000018
ORF1ab/nsp4	34	S34Y	tCt	tAt	2	2	B.1.2	0.000018
ORF1ab/nsp4	34	S34P	Tct	Cct	2	2	B.1.2	0.000018
ORF1ab/nsp4	34	S34T	TcT	AcA	1	2	B.1.234	0.000132
ORF1ab/nsp4	34	S34T	Tct	Act	1	2	B.1.234	0.000132
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.258.11	0.000793
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	B.1.351	0.000059
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.36.17	0.000988
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	B.1.429	0.000047
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.524	0.002813
ORF1ab/nsp4	34	S34S	tcT	tcC	2	2	B.1.526	0.000047
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.530	0.014286
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.546	0.007407
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.558	0.009132
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.575	0.000607
ORF1ab/nsp4	34	S34I	TCT	ATA	1	2	B.1.576	0.000907
ORF1ab/nsp4	34	S34I	TCt	ATt	1	2	B.1.576	0.000907
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.1.606	0.012048
ORF1ab/nsp4	34	S34I	TCt	ATt	1	2	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34I	TCT	ATA	1	2	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34P	TcT	CcA	1	2	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34P	Tct	Cct	1	2	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.3	0.001661
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	B.6	0.00182
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	C.1.1	0.153846
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	C.35	0.001548
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	D.2	0.00015
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	P.1.15	0.000465
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	P.1.17	0.000324
ORF1ab/nsp4	34	S34F	tCt	tTt	2	2	P.1.7	0.000639
ORF1ab/nsp4	34	S34P	Tct	Cct	2	2	Q.8	0.00033
ORF1ab/nsp4	34	S34del	TCT	---	1	1	A.2.4	0.003367
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	A.2.5	0.000499
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	A.21	0.00277
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	A.23.1	0.000704
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	A.28	0.002646
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	A.3	0.002096
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	A.5	0.001923
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AA.1	0.007246
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AD.2	0.000219
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AE.8	0.000489
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AH.2	0.012048
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AH.3	0.003802
ORF1ab/nsp4	34	S34del2	TCt	--t	1	1	All	0
ORF1ab/nsp4	34	S34D	TCt	GAt	1	1	All	0
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AW.1	0.003049
ORF1ab/nsp4	34	S34del1	Tct	-ct	1	1	AY.102	0.000027
ORF1ab/nsp4	34	S34A	Tct	Gct	1	1	AY.103	0.000006
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.107	0.000466
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.114	0.000231
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.116	0.000287
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.116.1	0.000311
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	AY.12	0.000316
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.120.2.1	0.000498
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.22	0.002092
ORF1ab/nsp4	34	S34N	TCt	AAt	1	1	AY.25	0.000006
ORF1ab/nsp4	34	S34L	tCT	tTA	1	1	AY.25	0.000006
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	AY.25	0.000006
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.25	0.000006
ORF1ab/nsp4	34	S34A	Tct	Gct	1	1	AY.25	0.000006
ORF1ab/nsp4	34	S34K	TCT	AAA	1	1	AY.25	0.000006
ORF1ab/nsp4	34	S34X	tCT	tAA	1	1	AY.25	0.000006
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.29.1	0.000221
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	AY.3	0.00001
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.30	0.000396
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.34.1	0.00051
ORF1ab/nsp4	34	S34del	TCT	---	1	1	AY.34.1	0.00051
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	AY.4	0.000002
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.40	0.000964
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.41	0.000294
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.42	0.00004
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	AY.42	0.00004
ORF1ab/nsp4	34	S34del	TCT	---	1	1	AY.42	0.00004
ORF1ab/nsp4	34	S34A	Tct	Gct	1	1	AY.44	0.000006
ORF1ab/nsp4	34	S34del	TCT	---	1	1	AY.46	0.000104
ORF1ab/nsp4	34	S34del	TCT	---	1	1	AY.46.2	0.000635
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.47	0.000031
ORF1ab/nsp4	34	S34Y	tCT	tAC	1	1	AY.48	0.000465
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.5.3	0.000337
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.5.4	0.000277
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.53	0.000288
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	AY.54	0.000095
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.55	0.000917
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.56	0.001605
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.57	0.000656
ORF1ab/nsp4	34	S34del	TCT	---	1	1	AY.60	0.000938
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.63	0.000387
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.67	0.000464
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.67	0.000464
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.68	0.000274
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.68	0.000274
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.69	0.000187
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.70	0.000209
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.73	0.000665
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.81	0.001992
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.83	0.001724
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.84	0.000437
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.86	0.00083
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.86	0.00083
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.89	0.004902
ORF1ab/nsp4	34	S34del	TCT	---	1	1	AY.9	0.000068
ORF1ab/nsp4	34	S34C	tCt	tGt	1	1	AY.9.2	0.000037
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.9.2.1	0.001976
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.90	0.000684
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AY.91	0.00073
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.93	0.000273
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.96	0.002075
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	AY.98.1	0.000048
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	AZ.5	0.003509
ORF1ab/nsp4	34	S34X	tCT	tAA	1	1	B.1	0.000009
ORF1ab/nsp4	34	S34L	tCT	tTA	1	1	B.1	0.000009
ORF1ab/nsp4	34	S34K	TCT	AAA	1	1	B.1.1	0.000018
ORF1ab/nsp4	34	S34L	tCT	tTA	1	1	B.1.1	0.000018
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	B.1.1.132	0.014925
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.141	0.002012
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.186	0.003436
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.189	0.001513
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.198	0.001468
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.207	0.001182
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.210	0.005714
ORF1ab/nsp4	34	S34S	tcT	tcA	1	1	B.1.1.220	0.001859
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.274	0.005051
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.277	0.000759
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.279	0.001121
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.282	0.011628
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp4	34	S34T	Tct	Act	1	1	B.1.1.306	0.000438
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.329	0.003846
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.348	0.000796
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.355	0.015385
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.362	0.005618
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.383	0.0625
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.389	0.006061
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.412	0.007634
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.429	0.004608
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.448	0.002033
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.46	0.004367
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.5	0.008333
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.507	0.008696
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.51	0.001718
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.518	0.006329
ORF1ab/nsp4	34	S34S	tcT	tcG	1	1	B.1.1.519	0.00004
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.1.519	0.00004
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.521	0.005348
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	B.1.1.523	0.001563
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.54	0.003021
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.1.59	0.006494
ORF1ab/nsp4	34	S34del2	TCt	--t	1	1	B.1.1.7	0.000001
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.111	0.001175
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.140	0.018868
ORF1ab/nsp4	34	S34D	TCt	GAt	1	1	B.1.157	0.002985
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.160	0.000031
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.170	0.00431
ORF1ab/nsp4	34	S34C	tCt	tGt	1	1	B.1.177	0.000013
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.177.11	0.001698
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.177.17	0.000821
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.177.20	0.001517
ORF1ab/nsp4	34	S34T	Tct	Act	1	1	B.1.177.21	0.000076
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	B.1.177.25	0.014925
ORF1ab/nsp4	34	S34del1	tcT	tc-	1	1	B.1.177.33	0.001645
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.177.43	0.001477
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.177.54	0.000606
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.177.57	0.000281
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	B.1.177.60	0.000218
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.177.62	0.001192
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	B.1.177.65	0.000665
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	B.1.177.7	0.000165
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.177.82	0.000477
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.180	0.05
ORF1ab/nsp4	34	S34K	TCT	AAA	1	1	B.1.2	0.000009
ORF1ab/nsp4	34	S34S	tcT	tcA	1	1	B.1.2	0.000009
ORF1ab/nsp4	34	S34L	tCT	tTA	1	1	B.1.2	0.000009
ORF1ab/nsp4	34	S34S	TCt	AGt	1	1	B.1.234	0.000132
ORF1ab/nsp4	34	S34del1	tcT	tc-	1	1	B.1.234	0.000132
ORF1ab/nsp4	34	S34R	TCT	AGA	1	1	B.1.234	0.000132
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.237	0.004975
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.258.17	0.000104
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.258.2	0.004505
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.284	0.013158
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.305	0.002151
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.346	0.001311
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.349	0.000715
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.350	0.002933
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.351.2	0.000303
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	B.1.351.3	0.000876
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.351.5	0.0006
ORF1ab/nsp4	34	S34S	tcT	tcA	1	1	B.1.36	0.000146
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.36.18	0.00042
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.36.29	0.000517
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.36.31	0.001751
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.36.36	0.000602
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.366	0.004878
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.367	0.000792
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.381	0.007812
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.397	0.004854
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.400	0.000429
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.415	0.014286
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.416	0.001269
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	B.1.416.1	0.001563
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.416.1	0.001563
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.422	0.000812
ORF1ab/nsp4	34	S34S	tcT	tcC	1	1	B.1.427	0.00005
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.460	0.017857
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.465	0.003802
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.470	0.001404
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.474	0.001901
ORF1ab/nsp4	34	S34C	tCt	tGt	1	1	B.1.485	0.014925
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.501	0.007353
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.556	0.007519
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.564.1	0.001577
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.567	0.003333
ORF1ab/nsp4	34	S34N	TCt	AAt	1	1	B.1.574	0.002151
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.575.1	0.002439
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	B.1.576	0.000907
ORF1ab/nsp4	34	S34K	TCT	AAA	1	1	B.1.576	0.000907
ORF1ab/nsp4	34	S34X	tCT	tAA	1	1	B.1.576	0.000907
ORF1ab/nsp4	34	S34N	TCt	AAt	1	1	B.1.576	0.000907
ORF1ab/nsp4	34	S34L	tCT	tTA	1	1	B.1.576	0.000907
ORF1ab/nsp4	34	S34K	TCT	AAA	1	1	B.1.577	0.000687
ORF1ab/nsp4	34	S34X	tCT	tAA	1	1	B.1.577	0.000687
ORF1ab/nsp4	34	S34Q	TCT	CAA	1	1	B.1.577	0.000687
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.580	0.004065
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.581	0.009434
ORF1ab/nsp4	34	S34N	TCt	AAt	1	1	B.1.596	0.000087
ORF1ab/nsp4	34	S34del1	tCt	t-t	1	1	B.1.596	0.000087
ORF1ab/nsp4	34	S34del	TCT	---	1	1	B.1.596	0.000087
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.600	0.005848
ORF1ab/nsp4	34	S34T	Tct	Act	1	1	B.1.609	0.000479
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.612	0.002653
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.616	0.02439
ORF1ab/nsp4	34	S34del1	tCt	t-t	1	1	B.1.617.1	0.000129
ORF1ab/nsp4	34	S34K	TCT	AAA	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34X	tCT	tAA	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34Q	TCT	CAA	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34N	TCt	AAt	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34H	TCt	CAt	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.619	0.000871
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.620	0.000946
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.627	0.00202
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.630	0.005236
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.638	0.052632
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	B.1.70	0.02439
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.78	0.008547
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.1.88.1	0.004808
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.4	0.002208
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.4.6	0.016667
ORF1ab/nsp4	34	S34Y	tCt	tAt	1	1	B.6	0.00091
ORF1ab/nsp4	34	S34P	Tct	Cct	1	1	B.6.3	0.026316
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	B.6.8	0.008264
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	C.11	0.010638
ORF1ab/nsp4	34	S34S	TCt	AGt	1	1	C.35	0.000774
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	C.36.1	0.004149
ORF1ab/nsp4	34	S34del	TCT	---	1	1	C.37	0.000116
ORF1ab/nsp4	34	S34A	Tct	Gct	1	1	D.2	0.000075
ORF1ab/nsp4	34	S34S	tcT	tcA	1	1	D.3	0.005917
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	N.5	0.001767
ORF1ab/nsp4	34	S34Q	TCT	CAA	1	1	P.1	0.000016
ORF1ab/nsp4	34	S34H	TCt	CAt	1	1	P.1	0.000016
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	P.1.11	0.010204
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	P.1.12	0.000484
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	Q.2	0.000613
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	Q.6	0.006623
ORF1ab/nsp4	34	S34F	tCt	tTt	1	1	R.1	0.00009
ORF1ab/nsp4	34	S34del	TCT	---	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.