CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 140

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/nsp2	140	L140F	L320F	nonsyn	Ctc	Ttc	1252	1250	0.998403	1223-1225
ORF1ab/nsp2	140	L140F	L320F	nonsyn	CtC	TtT	1252	2	0.00159744	1223-1225
ORF1ab/nsp2	140	L140L	L320L	syn	ctC	ctT	780	764	0.979487	1223-1225
ORF1ab/nsp2	140	L140L	L320L	syn	ctC	ctA	780	13	0.0166667	1223-1225
ORF1ab/nsp2	140	L140L	L320L	syn	ctC	ctG	780	3	0.00384615	1223-1225
ORF1ab/nsp2	140	L140I	L320I	nonsyn	Ctc	Atc	147	147	1	1223-1225
ORF1ab/nsp2	140	L140R	L320R	nonsyn	cTc	cGc	43	43	1	1223-1225
ORF1ab/nsp2	140	L140del	L320del	del	CTC	---	30	30	1	1223-1225
ORF1ab/nsp2	140	L140H	L320H	nonsyn	cTc	cAc	24	21	0.875	1223-1225
ORF1ab/nsp2	140	L140H	L320H	nonsyn	cTC	cAT	24	3	0.125	1223-1225
ORF1ab/nsp2	140	L140P	L320P	nonsyn	cTc	cCc	16	12	0.75	1223-1225
ORF1ab/nsp2	140	L140P	L320P	nonsyn	cTC	cCG	16	2	0.125	1223-1225
ORF1ab/nsp2	140	L140P	L320P	nonsyn	cTC	cCA	16	2	0.125	1223-1225
ORF1ab/nsp2	140	L140V	L320V	nonsyn	Ctc	Gtc	6	6	1	1223-1225
ORF1ab/nsp2	140	L140S	L320S	nonsyn	CTC	TCG	6	3	0.5	1223-1225
ORF1ab/nsp2	140	L140S	L320S	nonsyn	CTC	TCA	6	2	0.333333	1223-1225
ORF1ab/nsp2	140	L140S	L320S	nonsyn	CTc	TCc	6	1	0.166667	1223-1225
ORF1ab/nsp2	140	L140Q	L320Q	nonsyn	cTC	cAA	5	3	0.6	1223-1225
ORF1ab/nsp2	140	L140Q	L320Q	nonsyn	cTC	cAG	5	2	0.4	1223-1225
ORF1ab/nsp2	140	L140X	L320X	nonsyn	CTC	TAG	4	2	0.5	1223-1225
ORF1ab/nsp2	140	L140X	L320X	nonsyn	CTC	TAA	4	2	0.5	1223-1225
ORF1ab/nsp2	140	L140A	L320A	nonsyn	CTc	GCc	2	2	1	1223-1225
ORF1ab/nsp2	140	L140del1	L320del1	del	ctC	ct-	1	1	1	1223-1225
ORF1ab/nsp2	140	L140C	L320C	nonsyn	CTc	TGc	1	1	1	1223-1225

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/nsp2	140	L140F	Ctc	Ttc	1250	1252	All	0.000239
ORF1ab/nsp2	140	L140F	CtC	TtT	2	1252	All	0
ORF1ab/nsp2	140	L140L	ctC	ctT	764	780	All	0.000146
ORF1ab/nsp2	140	L140L	ctC	ctA	13	780	All	0.000002
ORF1ab/nsp2	140	L140L	ctC	ctG	3	780	All	0.000001
ORF1ab/nsp2	140	L140F	Ctc	Ttc	453	453	B.1.1.7	0.000406
ORF1ab/nsp2	140	L140F	Ctc	Ttc	319	319	B.1.258.22	0.850667
ORF1ab/nsp2	140	L140L	ctC	ctT	231	232	B.1.1.7	0.000207
ORF1ab/nsp2	140	L140L	ctC	ctA	1	232	B.1.1.7	0.000001
ORF1ab/nsp2	140	L140I	Ctc	Atc	147	147	All	0.000028
ORF1ab/nsp2	140	L140L	ctC	ctT	121	121	B.1.36	0.017654
ORF1ab/nsp2	140	L140F	Ctc	Ttc	66	68	AY.4	0.000103
ORF1ab/nsp2	140	L140F	CtC	TtT	2	68	AY.4	0.000003
ORF1ab/nsp2	140	L140L	ctC	ctT	59	62	AY.4	0.000092
ORF1ab/nsp2	140	L140L	ctC	ctG	3	62	AY.4	0.000005
ORF1ab/nsp2	140	L140I	Ctc	Atc	60	60	B.1.1.263	0.093458
ORF1ab/nsp2	140	L140L	ctC	ctT	50	50	AY.5	0.001032
ORF1ab/nsp2	140	L140F	Ctc	Ttc	50	50	B.1.429	0.001176
ORF1ab/nsp2	140	L140R	cTc	cGc	43	43	All	0.000008
ORF1ab/nsp2	140	L140L	ctC	ctT	36	36	AY.3	0.000358
ORF1ab/nsp2	140	L140del	CTC	---	30	30	All	0.000006
ORF1ab/nsp2	140	L140L	ctC	ctT	27	27	AY.43	0.00012
ORF1ab/nsp2	140	L140L	ctC	ctT	24	25	B.1.617.2	0.00009
ORF1ab/nsp2	140	L140L	ctC	ctA	1	25	B.1.617.2	0.000004
ORF1ab/nsp2	140	L140H	cTc	cAc	21	24	All	0.000004
ORF1ab/nsp2	140	L140H	cTC	cAT	3	24	All	0.000001
ORF1ab/nsp2	140	L140F	Ctc	Ttc	23	23	B.1.617.2	0.000087
ORF1ab/nsp2	140	L140L	ctC	ctT	18	18	B.1.2	0.000158
ORF1ab/nsp2	140	L140F	Ctc	Ttc	17	17	AY.103	0.000106
ORF1ab/nsp2	140	L140F	Ctc	Ttc	17	17	AY.3	0.000169
ORF1ab/nsp2	140	L140P	cTc	cCc	12	16	All	0.000002
ORF1ab/nsp2	140	L140P	cTC	cCG	2	16	All	0
ORF1ab/nsp2	140	L140P	cTC	cCA	2	16	All	0
ORF1ab/nsp2	140	L140F	Ctc	Ttc	16	16	AY.47	0.000498
ORF1ab/nsp2	140	L140L	ctC	ctT	15	15	AY.25	0.00009
ORF1ab/nsp2	140	L140F	Ctc	Ttc	15	15	AY.25	0.00009
ORF1ab/nsp2	140	L140H	cTc	cAc	14	14	B.1.1.7	0.000013
ORF1ab/nsp2	140	L140F	Ctc	Ttc	13	13	B.1	0.000119
ORF1ab/nsp2	140	L140I	Ctc	Atc	13	13	B.1.126	0.016582
ORF1ab/nsp2	140	L140F	Ctc	Ttc	13	13	B.1.2	0.000114
ORF1ab/nsp2	140	L140F	Ctc	Ttc	12	12	B.1.592	0.48
ORF1ab/nsp2	140	L140F	Ctc	Ttc	11	11	AY.102	0.000292
ORF1ab/nsp2	140	L140I	Ctc	Atc	11	11	AY.4	0.000017
ORF1ab/nsp2	140	L140F	Ctc	Ttc	11	11	AY.43	0.000049
ORF1ab/nsp2	140	L140L	ctC	ctT	11	11	AY.44	0.000067
ORF1ab/nsp2	140	L140F	Ctc	Ttc	11	11	B.1.177.54	0.006671
ORF1ab/nsp2	140	L140F	Ctc	Ttc	11	11	B.1.596	0.000959
ORF1ab/nsp2	140	L140F	Ctc	Ttc	10	10	B.1.1	0.000181
ORF1ab/nsp2	140	L140L	ctC	ctT	10	10	B.1.596	0.000871
ORF1ab/nsp2	140	L140F	Ctc	Ttc	9	9	AY.119	0.000318
ORF1ab/nsp2	140	L140F	Ctc	Ttc	9	9	AY.27	0.000582
ORF1ab/nsp2	140	L140I	Ctc	Atc	9	9	AY.43	0.00004
ORF1ab/nsp2	140	L140F	Ctc	Ttc	9	9	AY.44	0.000055
ORF1ab/nsp2	140	L140R	cTc	cGc	8	8	AY.4	0.000012
ORF1ab/nsp2	140	L140F	Ctc	Ttc	8	8	B.1.36.26	0.022857
ORF1ab/nsp2	140	L140L	ctC	ctT	7	7	AY.102	0.000186
ORF1ab/nsp2	140	L140L	ctC	ctT	7	7	AY.121	0.000947
ORF1ab/nsp2	140	L140I	Ctc	Atc	7	7	AY.57	0.004593
ORF1ab/nsp2	140	L140L	ctC	ctT	7	7	B.1	0.000064
ORF1ab/nsp2	140	L140L	ctC	ctT	7	7	B.1.1.519	0.000278
ORF1ab/nsp2	140	L140F	Ctc	Ttc	7	7	B.1.526	0.000165
ORF1ab/nsp2	140	L140R	cTc	cGc	7	7	B.1.617.2	0.000026
ORF1ab/nsp2	140	L140F	Ctc	Ttc	7	7	P.1	0.00011
ORF1ab/nsp2	140	L140V	Ctc	Gtc	6	6	All	0.000001
ORF1ab/nsp2	140	L140S	CTC	TCG	3	6	All	0.000001
ORF1ab/nsp2	140	L140S	CTC	TCA	2	6	All	0
ORF1ab/nsp2	140	L140S	CTc	TCc	1	6	All	0
ORF1ab/nsp2	140	L140L	ctC	ctT	6	6	AY.117	0.000507
ORF1ab/nsp2	140	L140I	Ctc	Atc	6	6	B.1	0.000055
ORF1ab/nsp2	140	L140I	Ctc	Atc	6	6	B.1.1.7	0.000005
ORF1ab/nsp2	140	L140R	cTc	cGc	6	6	B.1.177.60	0.001311
ORF1ab/nsp2	140	L140L	ctC	ctT	6	6	B.1.36.27	0.00458
ORF1ab/nsp2	140	L140I	Ctc	Atc	6	6	B.1.525	0.000679
ORF1ab/nsp2	140	L140I	Ctc	Atc	5	5	AE.8	0.002445
ORF1ab/nsp2	140	L140Q	cTC	cAA	3	5	All	0.000001
ORF1ab/nsp2	140	L140Q	cTC	cAG	2	5	All	0
ORF1ab/nsp2	140	L140R	cTc	cGc	5	5	AY.102	0.000133
ORF1ab/nsp2	140	L140F	Ctc	Ttc	5	5	AY.108	0.005513
ORF1ab/nsp2	140	L140L	ctC	ctT	5	5	AY.111	0.000916
ORF1ab/nsp2	140	L140R	cTc	cGc	5	5	AY.46.6	0.000361
ORF1ab/nsp2	140	L140L	ctC	ctT	5	5	B.1.1	0.000091
ORF1ab/nsp2	140	L140L	ctC	ctT	5	5	B.1.1.222	0.00102
ORF1ab/nsp2	140	L140del	CTC	---	5	5	B.1.1.33	0.002104
ORF1ab/nsp2	140	L140F	Ctc	Ttc	5	5	B.1.1.374	0.011876
ORF1ab/nsp2	140	L140F	Ctc	Ttc	5	5	B.1.1.398	0.016129
ORF1ab/nsp2	140	L140F	Ctc	Ttc	5	5	B.1.177	0.000066
ORF1ab/nsp2	140	L140L	ctC	ctT	5	5	B.1.241	0.004058
ORF1ab/nsp2	140	L140F	Ctc	Ttc	5	5	B.1.36	0.00073
ORF1ab/nsp2	140	L140I	Ctc	Atc	5	5	B.1.617.2	0.000019
ORF1ab/nsp2	140	L140L	ctC	ctT	5	5	P.1	0.000079
ORF1ab/nsp2	140	L140F	Ctc	Ttc	5	5	P.1.10	0.001347
ORF1ab/nsp2	140	L140P	cTC	cCA	2	4		0.111111
ORF1ab/nsp2	140	L140S	CTC	TCG	2	4		0.111111
ORF1ab/nsp2	140	L140S	CTC	TCA	2	4		0.111111
ORF1ab/nsp2	140	L140Q	cTC	cAG	2	4		0.111111
ORF1ab/nsp2	140	L140Q	cTC	cAA	2	4		0.111111
ORF1ab/nsp2	140	L140X	CTC	TAA	2	4		0.111111
ORF1ab/nsp2	140	L140P	cTC	cCG	2	4		0.111111
ORF1ab/nsp2	140	L140X	CTC	TAG	2	4		0.111111
ORF1ab/nsp2	140	L140X	CTC	TAA	2	4	All	0
ORF1ab/nsp2	140	L140X	CTC	TAG	2	4	All	0
ORF1ab/nsp2	140	L140F	Ctc	Ttc	4	4	AY.26	0.000113
ORF1ab/nsp2	140	L140L	ctC	ctT	4	4	AY.39	0.000099
ORF1ab/nsp2	140	L140F	Ctc	Ttc	4	4	AY.46.6	0.000289
ORF1ab/nsp2	140	L140L	ctC	ctT	4	4	AZ.2	0.003284
ORF1ab/nsp2	140	L140del	CTC	---	4	4	B.1.1.7	0.000004
ORF1ab/nsp2	140	L140R	cTc	cGc	4	4	B.1.1.7	0.000004
ORF1ab/nsp2	140	L140L	ctC	ctT	4	4	B.1.177	0.000053
ORF1ab/nsp2	140	L140V	Ctc	Gtc	4	4	B.1.243	0.000278
ORF1ab/nsp2	140	L140F	Ctc	Ttc	4	4	B.1.258	0.000266
ORF1ab/nsp2	140	L140F	Ctc	Ttc	4	4	B.1.351	0.000119
ORF1ab/nsp2	140	L140L	ctC	ctA	2	4	B.1.526	0.000047
ORF1ab/nsp2	140	L140L	ctC	ctT	2	4	B.1.526	0.000047
ORF1ab/nsp2	140	L140F	Ctc	Ttc	4	4	Q.1	0.000505
ORF1ab/nsp2	140	L140H	cTC	cAT	2	3		0.111111
ORF1ab/nsp2	140	L140H	cTc	cAc	1	3		0.055556
ORF1ab/nsp2	140	L140L	ctC	ctT	2	3	AY.103	0.000012
ORF1ab/nsp2	140	L140L	ctC	ctA	1	3	AY.103	0.000006
ORF1ab/nsp2	140	L140L	ctC	ctT	3	3	AY.114	0.000693
ORF1ab/nsp2	140	L140L	ctC	ctT	3	3	AY.20	0.000117
ORF1ab/nsp2	140	L140F	Ctc	Ttc	3	3	AY.29	0.000047
ORF1ab/nsp2	140	L140F	Ctc	Ttc	3	3	AY.39	0.000074
ORF1ab/nsp2	140	L140H	cTc	cAc	2	3	AY.44	0.000012
ORF1ab/nsp2	140	L140H	cTC	cAT	1	3	AY.44	0.000006
ORF1ab/nsp2	140	L140L	ctC	ctT	3	3	AY.6	0.000123
ORF1ab/nsp2	140	L140F	Ctc	Ttc	3	3	AY.69	0.00056
ORF1ab/nsp2	140	L140del	CTC	---	3	3	B.1.1.348	0.002389
ORF1ab/nsp2	140	L140F	Ctc	Ttc	3	3	B.1.1.354	0.013158
ORF1ab/nsp2	140	L140L	ctC	ctT	3	3	B.1.243	0.000209
ORF1ab/nsp2	140	L140L	ctC	ctT	2	3	B.1.351	0.000059
ORF1ab/nsp2	140	L140L	ctC	ctA	1	3	B.1.351	0.00003
ORF1ab/nsp2	140	L140F	Ctc	Ttc	3	3	B.1.36.17	0.001482
ORF1ab/nsp2	140	L140del	CTC	---	3	3	B.1.617.2	0.000011
ORF1ab/nsp2	140	L140L	ctC	ctT	3	3	D.2	0.000225
ORF1ab/nsp2	140	L140F	Ctc	Ttc	3	3	P.1.14	0.000143
ORF1ab/nsp2	140	L140L	ctC	ctT	3	3	P.1.14	0.000143
ORF1ab/nsp2	140	L140del	CTC	---	2	2		0.111111
ORF1ab/nsp2	140	L140A	CTc	GCc	2	2	All	0
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	AY.100	0.000092
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	AY.116	0.000574
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	AY.119	0.000071
ORF1ab/nsp2	140	L140P	cTc	cCc	2	2	AY.119	0.000071
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	AY.34	0.000194
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	AY.4.2	0.000043
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	AY.4.2.1	0.000298
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	AY.41	0.000588
ORF1ab/nsp2	140	L140R	cTc	cGc	2	2	AY.43	0.000009
ORF1ab/nsp2	140	L140del	CTC	---	2	2	AY.43	0.000009
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	AY.6	0.000082
ORF1ab/nsp2	140	L140L	ctC	ctT	1	2	AY.61	0.000105
ORF1ab/nsp2	140	L140L	ctC	ctA	1	2	AY.61	0.000105
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	AY.75.1	0.000361
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	AY.92	0.000575
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	AY.98	0.000158
ORF1ab/nsp2	140	L140R	cTc	cGc	2	2	AY.98.1	0.000097
ORF1ab/nsp2	140	L140I	Ctc	Atc	2	2	B.1.1	0.000036
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	B.1.1.28	0.000622
ORF1ab/nsp2	140	L140I	Ctc	Atc	2	2	B.1.1.63	0.000772
ORF1ab/nsp2	140	L140P	cTc	cCc	2	2	B.1.1.7	0.000002
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	B.1.160	0.000062
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	B.1.221	0.000142
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	B.1.234	0.000264
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	B.1.293	0.025
ORF1ab/nsp2	140	L140del	CTC	---	2	2	B.1.429	0.000047
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	B.1.429	0.000047
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	B.1.497	0.00063
ORF1ab/nsp2	140	L140P	cTc	cCc	2	2	B.1.596	0.000174
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	B.1.620	0.001892
ORF1ab/nsp2	140	L140del	CTC	---	2	2	N.6	0.014184
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	P.1.12	0.000968
ORF1ab/nsp2	140	L140I	Ctc	Atc	2	2	P.1.4	0.001953
ORF1ab/nsp2	140	L140F	Ctc	Ttc	2	2	P.1.7	0.000639
ORF1ab/nsp2	140	L140del	CTC	---	2	2	P.2	0.000373
ORF1ab/nsp2	140	L140L	ctC	ctT	2	2	Q.4	0.00091
ORF1ab/nsp2	140	L140R	cTc	cGc	1	1		0.055556
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1		0.055556
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1		0.055556
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	A.2	0.000662
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	A.23.1	0.000704
ORF1ab/nsp2	140	L140C	CTc	TGc	1	1	All	0
ORF1ab/nsp2	140	L140del1	ctC	ct-	1	1	All	0
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AU.1	0.001266
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.100	0.000046
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.101	0.00049
ORF1ab/nsp2	140	L140del1	ctC	ct-	1	1	AY.103	0.000006
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	AY.103	0.000006
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.113	0.000142
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.113	0.000142
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.116.1	0.000311
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.120	0.000037
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.16	0.00038
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.16.1	0.00047
ORF1ab/nsp2	140	L140H	cTc	cAc	1	1	AY.2	0.000356
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.20	0.000039
ORF1ab/nsp2	140	L140del	CTC	---	1	1	AY.25	0.000006
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.29	0.000016
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.3.1	0.000085
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	AY.33	0.000067
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.33	0.000067
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	AY.36	0.000148
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.39.1	0.00004
ORF1ab/nsp2	140	L140del	CTC	---	1	1	AY.4	0.000002
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.4.2	0.000022
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.40	0.000964
ORF1ab/nsp2	140	L140S	CTc	TCc	1	1	AY.44	0.000006
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.45	0.000122
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.45	0.000122
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.46.5	0.000198
ORF1ab/nsp2	140	L140L	ctC	ctA	1	1	AY.46.6	0.000072
ORF1ab/nsp2	140	L140L	ctC	ctA	1	1	AY.47	0.000031
ORF1ab/nsp2	140	L140P	cTc	cCc	1	1	AY.47	0.000031
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	AY.47	0.000031
ORF1ab/nsp2	140	L140Q	cTC	cAA	1	1	AY.47	0.000031
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.5	0.000021
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.54	0.000095
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.54	0.000095
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.57	0.000656
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.59	0.00053
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	AY.61	0.000105
ORF1ab/nsp2	140	L140P	cTc	cCc	1	1	AY.64	0.000595
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.68	0.000274
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	AY.7	0.000196
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.70	0.000209
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.71	0.000475
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.74	0.000116
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.75	0.000056
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.75	0.000056
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.75.1	0.00018
ORF1ab/nsp2	140	L140del	CTC	---	1	1	AY.84	0.000437
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	AY.9	0.000068
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.9.2	0.000037
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	AY.94	0.000443
ORF1ab/nsp2	140	L140S	CTC	TCG	1	1	AY.99	0.001049
ORF1ab/nsp2	140	L140L	ctC	ctA	1	1	AY.99.2	0.000092
ORF1ab/nsp2	140	L140H	cTc	cAc	1	1	B.1	0.000009
ORF1ab/nsp2	140	L140P	cTc	cCc	1	1	B.1.1	0.000018
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.1.1	0.000327
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.1.10	0.001115
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.1.10	0.001115
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.1.214	0.000055
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.1.243	0.004082
ORF1ab/nsp2	140	L140H	cTc	cAc	1	1	B.1.1.25	0.000569
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	B.1.1.275	0.011236
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.1.318	0.000302
ORF1ab/nsp2	140	L140L	ctC	ctA	1	1	B.1.1.318	0.000302
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.1.33	0.000421
ORF1ab/nsp2	140	L140V	Ctc	Gtc	1	1	B.1.1.37	0.000193
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.1.376	0.005952
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.1.409	0.002833
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.1.416	0.000905
ORF1ab/nsp2	140	L140R	cTc	cGc	1	1	B.1.1.519	0.00004
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.1.61	0.008772
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.1.63	0.000386
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.160.27	0.015152
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.177.54	0.000606
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.177.6	0.000977
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.177.81	0.000189
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.177.86	0.000183
ORF1ab/nsp2	140	L140C	CTc	TGc	1	1	B.1.2	0.000009
ORF1ab/nsp2	140	L140del	CTC	---	1	1	B.1.2	0.000009
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	B.1.2	0.000009
ORF1ab/nsp2	140	L140H	cTc	cAc	1	1	B.1.2	0.000009
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.234	0.000132
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	B.1.240	0.000216
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.241	0.000812
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.258	0.000067
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.258.17	0.000104
ORF1ab/nsp2	140	L140V	Ctc	Gtc	1	1	B.1.36	0.000146
ORF1ab/nsp2	140	L140P	cTc	cCc	1	1	B.1.36	0.000146
ORF1ab/nsp2	140	L140A	CTc	GCc	1	1	B.1.36	0.000146
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.36.18	0.00042
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.36.29	0.000517
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.36.8	0.001
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.36.8	0.001
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.400	0.000429
ORF1ab/nsp2	140	L140A	CTc	GCc	1	1	B.1.416	0.001269
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	B.1.416	0.001269
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.456	0.003268
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.466.2	0.000391
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.466.2	0.000391
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.468	0.005714
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.471	0.002732
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	B.1.541	0.004425
ORF1ab/nsp2	140	L140P	cTc	cCc	1	1	B.1.576	0.000907
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.587	0.001898
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.595	0.000261
ORF1ab/nsp2	140	L140R	cTc	cGc	1	1	B.1.617.1	0.000129
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.623	0.000536
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	B.1.93	0.000934
ORF1ab/nsp2	140	L140L	ctC	ctA	1	1	B.4	0.002208
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	B.55	0.00295
ORF1ab/nsp2	140	L140L	ctC	ctA	1	1	B.6	0.00091
ORF1ab/nsp2	140	L140I	Ctc	Atc	1	1	B.6	0.00091
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	C.16	0.00106
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	C.36	0.000911
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	C.36.3	0.000567
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	C.37	0.000116
ORF1ab/nsp2	140	L140F	Ctc	Ttc	1	1	C.37	0.000116
ORF1ab/nsp2	140	L140R	cTc	cGc	1	1	D.2	0.000075
ORF1ab/nsp2	140	L140P	cTc	cCc	1	1	D.2	0.000075
ORF1ab/nsp2	140	L140del	CTC	---	1	1	N.4	0.004255
ORF1ab/nsp2	140	L140L	ctC	ctT	1	1	Z.1	0.00289

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.