CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp13 : CodonNum = 301

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/nsp13	301	S301S	S5625S	syn	tcT	tcA	2364	2063	0.872673	17137-17139
ORF1ab/nsp13	301	S301S	S5625S	syn	tcT	tcC	2364	266	0.112521	17137-17139
ORF1ab/nsp13	301	S301S	S5625S	syn	tcT	tcG	2364	24	0.0101523	17137-17139
ORF1ab/nsp13	301	S301S	S5625S	syn	TCT	AGC	2364	6	0.00253807	17137-17139
ORF1ab/nsp13	301	S301S	S5625S	syn	TCt	AGt	2364	5	0.00211506	17137-17139
ORF1ab/nsp13	301	S301F	S5625F	nonsyn	tCt	tTt	465	458	0.984946	17137-17139
ORF1ab/nsp13	301	S301F	S5625F	nonsyn	tCT	tTC	465	7	0.0150538	17137-17139
ORF1ab/nsp13	301	S301P	S5625P	nonsyn	Tct	Cct	298	292	0.979866	17137-17139
ORF1ab/nsp13	301	S301P	S5625P	nonsyn	TcT	CcA	298	3	0.0100671	17137-17139
ORF1ab/nsp13	301	S301P	S5625P	nonsyn	TcT	CcC	298	3	0.0100671	17137-17139
ORF1ab/nsp13	301	S301T	S5625T	nonsyn	Tct	Act	91	46	0.505495	17137-17139
ORF1ab/nsp13	301	S301T	S5625T	nonsyn	TcT	AcA	91	24	0.263736	17137-17139
ORF1ab/nsp13	301	S301T	S5625T	nonsyn	TcT	AcC	91	19	0.208791	17137-17139
ORF1ab/nsp13	301	S301T	S5625T	nonsyn	TcT	AcG	91	2	0.021978	17137-17139
ORF1ab/nsp13	301	S301Y	S5625Y	nonsyn	tCt	tAt	42	27	0.642857	17137-17139
ORF1ab/nsp13	301	S301Y	S5625Y	nonsyn	tCT	tAC	42	15	0.357143	17137-17139
ORF1ab/nsp13	301	S301N	S5625N	nonsyn	TCT	AAC	41	26	0.634146	17137-17139
ORF1ab/nsp13	301	S301N	S5625N	nonsyn	TCt	AAt	41	15	0.365854	17137-17139
ORF1ab/nsp13	301	S301K	S5625K	nonsyn	TCT	AAA	40	37	0.925	17137-17139
ORF1ab/nsp13	301	S301K	S5625K	nonsyn	TCT	AAG	40	3	0.075	17137-17139
ORF1ab/nsp13	301	S301I	S5625I	nonsyn	TCT	ATA	34	17	0.5	17137-17139
ORF1ab/nsp13	301	S301I	S5625I	nonsyn	TCT	ATC	34	11	0.323529	17137-17139
ORF1ab/nsp13	301	S301I	S5625I	nonsyn	TCt	ATt	34	6	0.176471	17137-17139
ORF1ab/nsp13	301	S301A	S5625A	nonsyn	Tct	Gct	29	15	0.517241	17137-17139
ORF1ab/nsp13	301	S301A	S5625A	nonsyn	TcT	GcA	29	8	0.275862	17137-17139
ORF1ab/nsp13	301	S301A	S5625A	nonsyn	TcT	GcC	29	6	0.206897	17137-17139
ORF1ab/nsp13	301	S301X	S5625X	nonsyn	tCT	tAA	25	19	0.76	17137-17139
ORF1ab/nsp13	301	S301X	S5625X	nonsyn	tCT	tGA	25	4	0.16	17137-17139
ORF1ab/nsp13	301	S301X	S5625X	nonsyn	tCT	tAG	25	2	0.08	17137-17139
ORF1ab/nsp13	301	S301L	S5625L	nonsyn	tCT	tTA	21	10	0.47619	17137-17139
ORF1ab/nsp13	301	S301L	S5625L	nonsyn	TCT	CTA	21	5	0.238095	17137-17139
ORF1ab/nsp13	301	S301L	S5625L	nonsyn	TCT	CTC	21	4	0.190476	17137-17139
ORF1ab/nsp13	301	S301L	S5625L	nonsyn	TCt	CTt	21	1	0.047619	17137-17139
ORF1ab/nsp13	301	S301L	S5625L	nonsyn	TCT	CTG	21	1	0.047619	17137-17139
ORF1ab/nsp13	301	S301D	S5625D	nonsyn	TCT	GAC	17	10	0.588235	17137-17139
ORF1ab/nsp13	301	S301D	S5625D	nonsyn	TCt	GAt	17	7	0.411765	17137-17139
ORF1ab/nsp13	301	S301E	S5625E	nonsyn	TCT	GAA	15	15	1	17137-17139
ORF1ab/nsp13	301	S301V	S5625V	nonsyn	TCT	GTA	13	7	0.538462	17137-17139
ORF1ab/nsp13	301	S301V	S5625V	nonsyn	TCT	GTC	13	4	0.307692	17137-17139
ORF1ab/nsp13	301	S301V	S5625V	nonsyn	TCt	GTt	13	2	0.153846	17137-17139
ORF1ab/nsp13	301	S301R	S5625R	nonsyn	TCT	AGA	10	9	0.9	17137-17139
ORF1ab/nsp13	301	S301R	S5625R	nonsyn	TCT	CGA	10	1	0.1	17137-17139
ORF1ab/nsp13	301	S301Q	S5625Q	nonsyn	TCT	CAA	8	7	0.875	17137-17139
ORF1ab/nsp13	301	S301C	S5625C	nonsyn	tCT	tGC	8	5	0.625	17137-17139
ORF1ab/nsp13	301	S301C	S5625C	nonsyn	tCt	tGt	8	3	0.375	17137-17139
ORF1ab/nsp13	301	S301Q	S5625Q	nonsyn	TCT	CAG	8	1	0.125	17137-17139
ORF1ab/nsp13	301	S301H	S5625H	nonsyn	TCT	CAC	7	5	0.714286	17137-17139
ORF1ab/nsp13	301	S301H	S5625H	nonsyn	TCt	CAt	7	2	0.285714	17137-17139
ORF1ab/nsp13	301	S301del	S5625del	del	TCT	---	6	6	1	17137-17139
ORF1ab/nsp13	301	S301G	S5625G	nonsyn	TCT	GGC	4	2	0.5	17137-17139
ORF1ab/nsp13	301	S301G	S5625G	nonsyn	TCT	GGA	4	2	0.5	17137-17139
ORF1ab/nsp13	301	S301del2	S5625del2	del	TCt	--t	1	1	1	17137-17139
ORF1ab/nsp13	301	S301del1	S5625del1	del	tcT	tc-	1	1	1	17137-17139
ORF1ab/nsp13	301	S301M	S5625M	nonsyn	TCT	ATG	1	1	1	17137-17139

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/nsp13	301	S301S	tcT	tcA	2063	2364	All	0.000395
ORF1ab/nsp13	301	S301S	tcT	tcC	266	2364	All	0.000051
ORF1ab/nsp13	301	S301S	tcT	tcG	24	2364	All	0.000005
ORF1ab/nsp13	301	S301S	TCT	AGC	6	2364	All	0.000001
ORF1ab/nsp13	301	S301S	TCt	AGt	5	2364	All	0.000001
ORF1ab/nsp13	301	S301S	tcT	tcA	1774	1848	B.1.1.7	0.001588
ORF1ab/nsp13	301	S301S	tcT	tcC	53	1848	B.1.1.7	0.000047
ORF1ab/nsp13	301	S301S	tcT	tcG	10	1848	B.1.1.7	0.000009
ORF1ab/nsp13	301	S301S	TCT	AGC	6	1848	B.1.1.7	0.000005
ORF1ab/nsp13	301	S301S	TCt	AGt	5	1848	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301F	tCt	tTt	458	465	All	0.000088
ORF1ab/nsp13	301	S301F	tCT	tTC	7	465	All	0.000001
ORF1ab/nsp13	301	S301P	Tct	Cct	292	298	All	0.000056
ORF1ab/nsp13	301	S301P	TcT	CcA	3	298	All	0.000001
ORF1ab/nsp13	301	S301P	TcT	CcC	3	298	All	0.000001
ORF1ab/nsp13	301	S301F	tCt	tTt	279	286	B.1.1.7	0.00025
ORF1ab/nsp13	301	S301F	tCT	tTC	7	286	B.1.1.7	0.000006
ORF1ab/nsp13	301	S301P	Tct	Cct	110	110	B.1.595	0.028706
ORF1ab/nsp13	301	S301P	Tct	Cct	87	93	B.1.1.7	0.000078
ORF1ab/nsp13	301	S301P	TcT	CcA	3	93	B.1.1.7	0.000003
ORF1ab/nsp13	301	S301P	TcT	CcC	3	93	B.1.1.7	0.000003
ORF1ab/nsp13	301	S301T	Tct	Act	46	91	All	0.000009
ORF1ab/nsp13	301	S301T	TcT	AcA	24	91	All	0.000005
ORF1ab/nsp13	301	S301T	TcT	AcC	19	91	All	0.000004
ORF1ab/nsp13	301	S301T	TcT	AcG	2	91	All	0
ORF1ab/nsp13	301	S301S	tcT	tcA	48	79	AY.4	0.000075
ORF1ab/nsp13	301	S301S	tcT	tcC	31	79	AY.4	0.000048
ORF1ab/nsp13	301	S301T	TcT	AcA	22	56	B.1.1.7	0.00002
ORF1ab/nsp13	301	S301T	TcT	AcC	18	56	B.1.1.7	0.000016
ORF1ab/nsp13	301	S301T	Tct	Act	14	56	B.1.1.7	0.000013
ORF1ab/nsp13	301	S301T	TcT	AcG	2	56	B.1.1.7	0.000002
ORF1ab/nsp13	301	S301S	tcT	tcA	53	53	AU.3	0.111814
ORF1ab/nsp13	301	S301Y	tCt	tAt	27	42	All	0.000005
ORF1ab/nsp13	301	S301Y	tCT	tAC	15	42	All	0.000003
ORF1ab/nsp13	301	S301S	tcT	tcA	42	42	AY.14	0.003697
ORF1ab/nsp13	301	S301N	TCT	AAC	26	41	All	0.000005
ORF1ab/nsp13	301	S301N	TCt	AAt	15	41	All	0.000003
ORF1ab/nsp13	301	S301K	TCT	AAA	37	40	All	0.000007
ORF1ab/nsp13	301	S301K	TCT	AAG	3	40	All	0.000001
ORF1ab/nsp13	301	S301N	TCT	AAC	25	39	B.1.1.7	0.000022
ORF1ab/nsp13	301	S301N	TCt	AAt	14	39	B.1.1.7	0.000013
ORF1ab/nsp13	301	S301K	TCT	AAA	35	38	B.1.1.7	0.000031
ORF1ab/nsp13	301	S301K	TCT	AAG	3	38	B.1.1.7	0.000003
ORF1ab/nsp13	301	S301S	tcT	tcC	17	35	B.1.617.2	0.000064
ORF1ab/nsp13	301	S301S	tcT	tcA	15	35	B.1.617.2	0.000056
ORF1ab/nsp13	301	S301S	tcT	tcG	3	35	B.1.617.2	0.000011
ORF1ab/nsp13	301	S301I	TCT	ATA	17	34	All	0.000003
ORF1ab/nsp13	301	S301I	TCT	ATC	11	34	All	0.000002
ORF1ab/nsp13	301	S301I	TCt	ATt	6	34	All	0.000001
ORF1ab/nsp13	301	S301I	TCT	ATA	16	32	B.1.1.7	0.000014
ORF1ab/nsp13	301	S301I	TCT	ATC	11	32	B.1.1.7	0.00001
ORF1ab/nsp13	301	S301I	TCt	ATt	5	32	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301A	Tct	Gct	15	29	All	0.000003
ORF1ab/nsp13	301	S301A	TcT	GcA	8	29	All	0.000002
ORF1ab/nsp13	301	S301A	TcT	GcC	6	29	All	0.000001
ORF1ab/nsp13	301	S301Y	tCT	tAC	14	28	B.1.1.7	0.000013
ORF1ab/nsp13	301	S301Y	tCt	tAt	14	28	B.1.1.7	0.000013
ORF1ab/nsp13	301	S301S	tcT	tcC	27	27	B.1.1.50	0.01833
ORF1ab/nsp13	301	S301F	tCt	tTt	26	26	B.1.349	0.018585
ORF1ab/nsp13	301	S301X	tCT	tAA	19	25	All	0.000004
ORF1ab/nsp13	301	S301X	tCT	tGA	4	25	All	0.000001
ORF1ab/nsp13	301	S301X	tCT	tAG	2	25	All	0
ORF1ab/nsp13	301	S301X	tCT	tAA	18	24	B.1.1.7	0.000016
ORF1ab/nsp13	301	S301X	tCT	tGA	4	24	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301X	tCT	tAG	2	24	B.1.1.7	0.000002
ORF1ab/nsp13	301	S301S	tcT	tcC	23	23	AY.68	0.006296
ORF1ab/nsp13	301	S301F	tCt	tTt	22	22	B.1.177	0.00029
ORF1ab/nsp13	301	S301L	tCT	tTA	10	21	All	0.000002
ORF1ab/nsp13	301	S301L	TCT	CTA	5	21	All	0.000001
ORF1ab/nsp13	301	S301L	TCT	CTC	4	21	All	0.000001
ORF1ab/nsp13	301	S301L	TCT	CTG	1	21	All	0
ORF1ab/nsp13	301	S301L	TCt	CTt	1	21	All	0
ORF1ab/nsp13	301	S301L	tCT	tTA	10	21	B.1.1.7	0.000009
ORF1ab/nsp13	301	S301A	Tct	Gct	9	21	B.1.1.7	0.000008
ORF1ab/nsp13	301	S301A	TcT	GcA	7	21	B.1.1.7	0.000006
ORF1ab/nsp13	301	S301A	TcT	GcC	5	21	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301L	TCT	CTA	5	21	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301L	TCT	CTC	4	21	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301L	TCT	CTG	1	21	B.1.1.7	0.000001
ORF1ab/nsp13	301	S301L	TCt	CTt	1	21	B.1.1.7	0.000001
ORF1ab/nsp13	301	S301S	tcT	tcA	15	18	AY.39	0.000371
ORF1ab/nsp13	301	S301S	tcT	tcC	3	18	AY.39	0.000074
ORF1ab/nsp13	301	S301F	tCt	tTt	18	18	B.1.2	0.000158
ORF1ab/nsp13	301	S301D	TCT	GAC	10	17	All	0.000002
ORF1ab/nsp13	301	S301D	TCt	GAt	7	17	All	0.000001
ORF1ab/nsp13	301	S301D	TCT	GAC	10	16	B.1.1.7	0.000009
ORF1ab/nsp13	301	S301D	TCt	GAt	6	16	B.1.1.7	0.000005
ORF1ab/nsp13	301	S301E	TCT	GAA	15	15	All	0.000003
ORF1ab/nsp13	301	S301T	Tct	Act	15	15	AY.13	0.002415
ORF1ab/nsp13	301	S301P	Tct	Cct	15	15	B.1	0.000137
ORF1ab/nsp13	301	S301S	tcT	tcC	15	15	B.1.1.348	0.011943
ORF1ab/nsp13	301	S301S	tcT	tcA	11	15	R.1	0.00099
ORF1ab/nsp13	301	S301S	tcT	tcC	4	15	R.1	0.00036
ORF1ab/nsp13	301	S301E	TCT	GAA	14	14	B.1.1.7	0.000013
ORF1ab/nsp13	301	S301S	tcT	tcA	14	14	B.4.8	1
ORF1ab/nsp13	301	S301V	TCT	GTA	7	13	All	0.000001
ORF1ab/nsp13	301	S301V	TCT	GTC	4	13	All	0.000001
ORF1ab/nsp13	301	S301V	TCt	GTt	2	13	All	0
ORF1ab/nsp13	301	S301S	tcT	tcC	8	12	AY.43	0.000035
ORF1ab/nsp13	301	S301S	tcT	tcA	4	12	AY.43	0.000018
ORF1ab/nsp13	301	S301V	TCT	GTA	6	11	B.1.1.7	0.000005
ORF1ab/nsp13	301	S301V	TCT	GTC	4	11	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301V	TCt	GTt	1	11	B.1.1.7	0.000001
ORF1ab/nsp13	301	S301R	TCT	AGA	9	10	All	0.000002
ORF1ab/nsp13	301	S301R	TCT	CGA	1	10	All	0
ORF1ab/nsp13	301	S301S	tcT	tcC	7	10	AY.102	0.000186
ORF1ab/nsp13	301	S301S	tcT	tcG	2	10	AY.102	0.000053
ORF1ab/nsp13	301	S301S	tcT	tcA	1	10	AY.102	0.000027
ORF1ab/nsp13	301	S301S	tcT	tcC	6	10	AY.26	0.00017
ORF1ab/nsp13	301	S301S	tcT	tcA	4	10	AY.26	0.000113
ORF1ab/nsp13	301	S301S	tcT	tcA	9	10	B.1	0.000082
ORF1ab/nsp13	301	S301S	tcT	tcC	1	10	B.1	0.000009
ORF1ab/nsp13	301	S301R	TCT	AGA	9	10	B.1.1.7	0.000008
ORF1ab/nsp13	301	S301R	TCT	CGA	1	10	B.1.1.7	0.000001
ORF1ab/nsp13	301	S301F	tCt	tTt	10	10	C.30.1	0.067114
ORF1ab/nsp13	301	S301F	tCt	tTt	9	9	B.1.1.189	0.013616
ORF1ab/nsp13	301	S301Q	TCT	CAA	7	8	All	0.000001
ORF1ab/nsp13	301	S301C	tCT	tGC	5	8	All	0.000001
ORF1ab/nsp13	301	S301C	tCt	tGt	3	8	All	0.000001
ORF1ab/nsp13	301	S301Q	TCT	CAG	1	8	All	0
ORF1ab/nsp13	301	S301S	tcT	tcC	5	8	AY.3	0.00005
ORF1ab/nsp13	301	S301S	tcT	tcG	2	8	AY.3	0.00002
ORF1ab/nsp13	301	S301S	tcT	tcA	1	8	AY.3	0.00001
ORF1ab/nsp13	301	S301Q	TCT	CAA	7	8	B.1.1.7	0.000006
ORF1ab/nsp13	301	S301Q	TCT	CAG	1	8	B.1.1.7	0.000001
ORF1ab/nsp13	301	S301P	Tct	Cct	8	8	B.1.180	0.4
ORF1ab/nsp13	301	S301H	TCT	CAC	5	7	All	0.000001
ORF1ab/nsp13	301	S301H	TCt	CAt	2	7	All	0
ORF1ab/nsp13	301	S301F	tCt	tTt	7	7	B.1	0.000064
ORF1ab/nsp13	301	S301S	tcT	tcC	6	7	B.1.1	0.000109
ORF1ab/nsp13	301	S301S	tcT	tcA	1	7	B.1.1	0.000018
ORF1ab/nsp13	301	S301S	tcT	tcA	7	7	B.1.1.263	0.010903
ORF1ab/nsp13	301	S301H	TCT	CAC	5	7	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301C	tCT	tGC	4	7	B.1.1.7	0.000004
ORF1ab/nsp13	301	S301C	tCt	tGt	3	7	B.1.1.7	0.000003
ORF1ab/nsp13	301	S301H	TCt	CAt	2	7	B.1.1.7	0.000002
ORF1ab/nsp13	301	S301F	tCt	tTt	7	7	B.1.429	0.000165
ORF1ab/nsp13	301	S301F	tCt	tTt	7	7	B.1.526	0.000165
ORF1ab/nsp13	301	S301S	tcT	tcC	4	7	P.1	0.000063
ORF1ab/nsp13	301	S301S	tcT	tcA	3	7	P.1	0.000047
ORF1ab/nsp13	301	S301S	tcT	tcC	6	7	P.1.14	0.000287
ORF1ab/nsp13	301	S301S	tcT	tcA	1	7	P.1.14	0.000048
ORF1ab/nsp13	301	S301del	TCT	---	6	6	All	0.000001
ORF1ab/nsp13	301	S301S	tcT	tcC	4	6	B.1.2	0.000035
ORF1ab/nsp13	301	S301S	tcT	tcA	2	6	B.1.2	0.000018
ORF1ab/nsp13	301	S301S	tcT	tcG	5	6	B.1.429	0.000118
ORF1ab/nsp13	301	S301S	tcT	tcC	1	6	B.1.429	0.000024
ORF1ab/nsp13	301	S301P	Tct	Cct	6	6	B.1.460	0.107143
ORF1ab/nsp13	301	S301P	Tct	Cct	5	5	AY.102	0.000133
ORF1ab/nsp13	301	S301P	Tct	Cct	5	5	AY.44	0.00003
ORF1ab/nsp13	301	S301S	tcT	tcA	4	5	B.1.177	0.000053
ORF1ab/nsp13	301	S301S	tcT	tcC	1	5	B.1.177	0.000013
ORF1ab/nsp13	301	S301F	tCt	tTt	5	5	B.1.617.1	0.000645
ORF1ab/nsp13	301	S301G	TCT	GGC	2	4	All	0
ORF1ab/nsp13	301	S301G	TCT	GGA	2	4	All	0
ORF1ab/nsp13	301	S301S	tcT	tcA	4	4	AY.39.1	0.000158
ORF1ab/nsp13	301	S301P	Tct	Cct	4	4	AY.43	0.000018
ORF1ab/nsp13	301	S301T	Tct	Act	4	4	AY.6	0.000165
ORF1ab/nsp13	301	S301G	TCT	GGA	2	4	B.1.1.7	0.000002
ORF1ab/nsp13	301	S301G	TCT	GGC	2	4	B.1.1.7	0.000002
ORF1ab/nsp13	301	S301P	Tct	Cct	4	4	B.1.2	0.000035
ORF1ab/nsp13	301	S301S	tcT	tcC	3	4	B.1.526	0.000071
ORF1ab/nsp13	301	S301S	tcT	tcA	1	4	B.1.526	0.000024
ORF1ab/nsp13	301	S301S	tcT	tcA	3	3	AY.100	0.000138
ORF1ab/nsp13	301	S301P	Tct	Cct	3	3	AY.103	0.000019
ORF1ab/nsp13	301	S301P	Tct	Cct	3	3	AY.25	0.000018
ORF1ab/nsp13	301	S301P	Tct	Cct	3	3	AY.4	0.000005
ORF1ab/nsp13	301	S301S	tcT	tcA	3	3	AY.42	0.000121
ORF1ab/nsp13	301	S301T	Tct	Act	3	3	AY.44	0.000018
ORF1ab/nsp13	301	S301S	tcT	tcC	2	3	AY.44	0.000012
ORF1ab/nsp13	301	S301S	tcT	tcA	1	3	AY.44	0.000006
ORF1ab/nsp13	301	S301F	tCt	tTt	3	3	AY.9	0.000203
ORF1ab/nsp13	301	S301S	tcT	tcC	2	3	AY.98	0.000158
ORF1ab/nsp13	301	S301S	tcT	tcA	1	3	AY.98	0.000079
ORF1ab/nsp13	301	S301S	tcT	tcA	3	3	B	0.000383
ORF1ab/nsp13	301	S301T	Tct	Act	3	3	B.1	0.000027
ORF1ab/nsp13	301	S301S	tcT	tcA	3	3	B.1.1.519	0.000119
ORF1ab/nsp13	301	S301F	tCt	tTt	3	3	B.1.177.86	0.00055
ORF1ab/nsp13	301	S301S	tcT	tcC	3	3	B.1.221.3	0.0025
ORF1ab/nsp13	301	S301F	tCt	tTt	3	3	B.1.258	0.0002
ORF1ab/nsp13	301	S301Y	tCt	tAt	3	3	B.1.258	0.0002
ORF1ab/nsp13	301	S301P	Tct	Cct	3	3	B.1.429	0.000071
ORF1ab/nsp13	301	S301S	tcT	tcA	3	3	B.1.628	0.001057
ORF1ab/nsp13	301	S301S	tcT	tcC	3	3	C.36	0.002732
ORF1ab/nsp13	301	S301F	tCt	tTt	3	3	P.1	0.000047
ORF1ab/nsp13	301	S301F	tCt	tTt	3	3	Q.3	0.000435
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	AY.103	0.000012
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	AY.119	0.000071
ORF1ab/nsp13	301	S301A	Tct	Gct	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301I	TCT	ATA	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301I	TCt	ATt	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301A	TcT	GcA	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301V	TCt	GTt	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301T	Tct	Act	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301S	tcT	tcC	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301S	tcT	tcA	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301T	TcT	AcA	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301V	TCT	GTA	1	2	AY.25	0.000006
ORF1ab/nsp13	301	S301Y	tCt	tAt	2	2	AY.29	0.000032
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	AY.3	0.00002
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	AY.39	0.000049
ORF1ab/nsp13	301	S301T	Tct	Act	2	2	AY.4	0.000003
ORF1ab/nsp13	301	S301S	tcT	tcC	2	2	AY.4.2	0.000043
ORF1ab/nsp13	301	S301S	tcT	tcC	2	2	AY.5.4	0.000553
ORF1ab/nsp13	301	S301S	tcT	tcC	1	2	AY.54	0.000095
ORF1ab/nsp13	301	S301S	tcT	tcA	1	2	AY.54	0.000095
ORF1ab/nsp13	301	S301S	tcT	tcC	2	2	AY.75	0.000112
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	AY.98	0.000158
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	B.1.1	0.000036
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.1	0.000036
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.1.1	0.000653
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.1.222	0.000408
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.177.54	0.001213
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	B.1.221	0.000142
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.221	0.000142
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	B.1.258	0.000133
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.427	0.000101
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	B.1.470	0.002809
ORF1ab/nsp13	301	S301S	tcT	tcA	2	2	B.1.471	0.005464
ORF1ab/nsp13	301	S301S	tcT	tcC	2	2	B.1.595	0.000522
ORF1ab/nsp13	301	S301S	tcT	tcA	2	2	B.1.596	0.000174
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.617.2	0.000008
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	B.1.617.2	0.000008
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	B.1.620	0.001892
ORF1ab/nsp13	301	S301P	Tct	Cct	2	2	C.36.3	0.001134
ORF1ab/nsp13	301	S301F	tCt	tTt	2	2	D.2	0.00015
ORF1ab/nsp13	301	S301Y	tCT	tAC	1	2	P.1	0.000016
ORF1ab/nsp13	301	S301T	TcT	AcC	1	2	P.1	0.000016
ORF1ab/nsp13	301	S301T	TcT	AcA	1	2	P.1	0.000016
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	2	P.1	0.000016
ORF1ab/nsp13	301	S301S	tcT	tcA	2	2	Q.2	0.001227
ORF1ab/nsp13	301	S301C	tCT	tGC	1	1	A	0.000387
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	A	0.000387
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	A.2.5	0.000499
ORF1ab/nsp13	301	S301del1	tcT	tc-	1	1	All	0
ORF1ab/nsp13	301	S301M	TCT	ATG	1	1	All	0
ORF1ab/nsp13	301	S301del2	TCt	--t	1	1	All	0
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	AU.2	0.002421
ORF1ab/nsp13	301	S301T	Tct	Act	1	1	AY.100	0.000046
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.103	0.000006
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	AY.113	0.000142
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.117	0.000085
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.118	0.000063
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.119	0.000035
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.120	0.000037
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	AY.20	0.000039
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.23	0.00007
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	AY.23.1	0.000417
ORF1ab/nsp13	301	S301N	TCt	AAt	1	1	AY.25	0.000006
ORF1ab/nsp13	301	S301E	TCT	GAA	1	1	AY.25	0.000006
ORF1ab/nsp13	301	S301D	TCt	GAt	1	1	AY.25	0.000006
ORF1ab/nsp13	301	S301K	TCT	AAA	1	1	AY.25	0.000006
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	AY.27	0.000065
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	AY.29	0.000016
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	AY.3	0.00001
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	AY.33	0.000067
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.34	0.000097
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	AY.38	0.000499
ORF1ab/nsp13	301	S301T	Tct	Act	1	1	AY.39	0.000025
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	AY.39	0.000025
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	AY.39.1	0.00004
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	AY.4	0.000002
ORF1ab/nsp13	301	S301A	Tct	Gct	1	1	AY.4.2	0.000022
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.40	0.000964
ORF1ab/nsp13	301	S301del	TCT	---	1	1	AY.42	0.00004
ORF1ab/nsp13	301	S301T	Tct	Act	1	1	AY.43	0.000004
ORF1ab/nsp13	301	S301del	TCT	---	1	1	AY.43	0.000004
ORF1ab/nsp13	301	S301A	TcT	GcC	1	1	AY.44	0.000006
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	AY.45	0.000122
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.5	0.000021
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.6	0.000041
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.69	0.000187
ORF1ab/nsp13	301	S301S	tcT	tcG	1	1	AY.73	0.000665
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	AY.75	0.000056
ORF1ab/nsp13	301	S301del	TCT	---	1	1	AY.75.1	0.00018
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	AY.84	0.000437
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	AY.87	0.000833
ORF1ab/nsp13	301	S301A	Tct	Gct	1	1	AY.9	0.000068
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	AY.92	0.000287
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	AY.99	0.001049
ORF1ab/nsp13	301	S301del	TCT	---	1	1	B	0.000128
ORF1ab/nsp13	301	S301del	TCT	---	1	1	B.1	0.000009
ORF1ab/nsp13	301	S301del2	TCt	--t	1	1	B.1.1	0.000018
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	1	B.1.1	0.000018
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.1.189	0.001513
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.214	0.000055
ORF1ab/nsp13	301	S301A	Tct	Gct	1	1	B.1.1.214	0.000055
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.273	0.006757
ORF1ab/nsp13	301	S301S	tcT	tcG	1	1	B.1.1.277	0.000759
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.1.28	0.000311
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.28	0.000311
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.1.297	0.002237
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.1.298	0.000862
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.1.306	0.000438
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.306	0.000438
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.311	0.000358
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.317	0.000412
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	1	B.1.1.335	0.012987
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.370	0.012658
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.415	0.05
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.1.519	0.00004
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.1.519	0.00004
ORF1ab/nsp13	301	S301M	TCT	ATG	1	1	B.1.1.7	0.000001
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.157	0.002985
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.160	0.000031
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	1	B.1.177	0.000013
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.177.21	0.000076
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.177.4	0.000211
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.177.5	0.001242
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.177.5	0.001242
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.177.54	0.000606
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.177.77	0.000726
ORF1ab/nsp13	301	S301del1	tcT	tc-	1	1	B.1.2	0.000009
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.206	0.000816
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.214.2	0.0006
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.215	0.009615
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.223	0.002778
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.241	0.000812
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.243	0.00007
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.258	0.000067
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.258.5	0.008772
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.265	0.001271
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.311	0.000275
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.320	0.001245
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.340	0.004292
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.351	0.00003
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.351	0.00003
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.36.17	0.000494
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.361	0.001289
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.395	0.007042
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.398	0.002976
ORF1ab/nsp13	301	S301T	Tct	Act	1	1	B.1.416	0.001269
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	1	B.1.429	0.000024
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.438.1	0.000107
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.452	0.013699
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.466.2	0.000391
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	1	B.1.474	0.001901
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.520	0.021739
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.575	0.000303
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.587	0.001898
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.596	0.000087
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	1	B.1.596	0.000087
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	B.1.617.1	0.000129
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.1.617.1	0.000129
ORF1ab/nsp13	301	S301del	TCT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp13	301	S301A	Tct	Gct	1	1	B.1.621	0.000089
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.632	0.006711
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	B.1.637	0.000073
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.1.93	0.000934
ORF1ab/nsp13	301	S301A	Tct	Gct	1	1	B.3	0.000831
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.4	0.002208
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.4.7	0.010101
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	B.40	0.000364
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	B.58	0.010204
ORF1ab/nsp13	301	S301K	TCT	AAA	1	1	P.1	0.000016
ORF1ab/nsp13	301	S301X	tCT	tAA	1	1	P.1	0.000016
ORF1ab/nsp13	301	S301N	TCT	AAC	1	1	P.1	0.000016
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	P.1.14	0.000048
ORF1ab/nsp13	301	S301P	Tct	Cct	1	1	P.1.17	0.000162
ORF1ab/nsp13	301	S301S	tcT	tcC	1	1	P.1.2	0.001156
ORF1ab/nsp13	301	S301F	tCt	tTt	1	1	Q.1	0.000126
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	Q.1	0.000126
ORF1ab/nsp13	301	S301S	tcT	tcA	1	1	Q.8	0.000165
ORF1ab/nsp13	301	S301Y	tCt	tAt	1	1	Q.8	0.000165

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.