CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 96

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	96	L96L		syn	ctC	ctT	2711	2214	0.816673	25678-25680
ORF3a	96	L96L		syn	ctC	ctG	2711	285	0.105127	25678-25680
ORF3a	96	L96L		syn	ctC	ctA	2711	210	0.0774622	25678-25680
ORF3a	96	L96L		syn	CtC	TtA	2711	1	0.000368868	25678-25680
ORF3a	96	L96L		syn	CtC	TtG	2711	1	0.000368868	25678-25680
ORF3a	96	L96F		nonsyn	Ctc	Ttc	1316	1301	0.988602	25678-25680
ORF3a	96	L96F		nonsyn	CtC	TtT	1316	15	0.0113982	25678-25680
ORF3a	96	L96P		nonsyn	cTc	cCc	934	914	0.978587	25678-25680
ORF3a	96	L96P		nonsyn	cTC	cCT	934	20	0.0214133	25678-25680
ORF3a	96	L96I		nonsyn	Ctc	Atc	792	791	0.998737	25678-25680
ORF3a	96	L96I		nonsyn	CtC	AtA	792	1	0.00126263	25678-25680
ORF3a	96	L96del		del	CTC	---	128	128	1	25678-25680
ORF3a	96	L96R		nonsyn	cTc	cGc	55	48	0.872727	25678-25680
ORF3a	96	L96R		nonsyn	cTC	cGA	55	3	0.0545455	25678-25680
ORF3a	96	L96R		nonsyn	CTC	AGA	55	2	0.0363636	25678-25680
ORF3a	96	L96R		nonsyn	cTC	cGG	55	1	0.0181818	25678-25680
ORF3a	96	L96R		nonsyn	cTC	cGT	55	1	0.0181818	25678-25680
ORF3a	96	L96H		nonsyn	cTc	cAc	39	39	1	25678-25680
ORF3a	96	L96Q		nonsyn	cTC	cAA	6	6	1	25678-25680
ORF3a	96	L96V		nonsyn	Ctc	Gtc	5	4	0.8	25678-25680
ORF3a	96	L96del1		del	ctC	ct-	5	2	0.4	25678-25680
ORF3a	96	L96del1		del	Ctc	-tc	5	1	0.2	25678-25680
ORF3a	96	L96del1		del	CtC	-tG	5	1	0.2	25678-25680
ORF3a	96	L96V		nonsyn	CtC	GtT	5	1	0.2	25678-25680
ORF3a	96	L96del1		del	CTC	-NN	5	1	0.2	25678-25680
ORF3a	96	L96N		nonsyn	CTc	AAc	3	3	1	25678-25680
ORF3a	96	L96S		nonsyn	CTc	AGc	3	3	1	25678-25680
ORF3a	96	L96K		nonsyn	CTC	AAA	2	2	1	25678-25680
ORF3a	96	L96A		nonsyn	CTC	GCT	1	1	1	25678-25680
ORF3a	96	L96Y		nonsyn	CTc	TAc	1	1	1	25678-25680
ORF3a	96	L96T		nonsyn	CTC	ACA	1	1	1	25678-25680
ORF3a	96	L96G		nonsyn	CTC	GGA	1	1	1	25678-25680
ORF3a	96	L96E		nonsyn	CTC	GAA	1	1	1	25678-25680
ORF3a	96	L96X		nonsyn	CTC	TAA	1	1	1	25678-25680
ORF3a	96	L96del2		del	cTC	c--	1	1	1	25678-25680

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	96	L96L	ctC	ctT	2214	2711	All	0.000423
ORF3a	96	L96L	ctC	ctG	285	2711	All	0.000055
ORF3a	96	L96L	ctC	ctA	210	2711	All	0.00004
ORF3a	96	L96L	CtC	TtA	1	2711	All	0
ORF3a	96	L96L	CtC	TtG	1	2711	All	0
ORF3a	96	L96F	Ctc	Ttc	1301	1316	All	0.000249
ORF3a	96	L96F	CtC	TtT	15	1316	All	0.000003
ORF3a	96	L96P	cTc	cCc	914	934	All	0.000175
ORF3a	96	L96P	cTC	cCT	20	934	All	0.000004
ORF3a	96	L96I	Ctc	Atc	791	792	All	0.000151
ORF3a	96	L96I	CtC	AtA	1	792	All	0
ORF3a	96	L96I	Ctc	Atc	711	711	AY.39.1	0.028165
ORF3a	96	L96L	ctC	ctT	586	588	B.1.617.2	0.002207
ORF3a	96	L96L	ctC	ctA	2	588	B.1.617.2	0.000008
ORF3a	96	L96P	cTc	cCc	561	561	AY.4	0.000873
ORF3a	96	L96F	Ctc	Ttc	403	415	AY.39	0.009959
ORF3a	96	L96F	CtC	TtT	12	415	AY.39	0.000297
ORF3a	96	L96L	ctC	ctT	201	325	B.1.1.7	0.00018
ORF3a	96	L96L	ctC	ctA	121	325	B.1.1.7	0.000108
ORF3a	96	L96L	ctC	ctG	3	325	B.1.1.7	0.000003
ORF3a	96	L96L	ctC	ctG	262	263	AY.39.1	0.010379
ORF3a	96	L96L	ctC	ctT	1	263	AY.39.1	0.00004
ORF3a	96	L96L	ctC	ctT	222	222	B.1.541	0.982301
ORF3a	96	L96L	ctC	ctT	220	220	B.1.427	0.011109
ORF3a	96	L96del	CTC	---	128	128	All	0.000024
ORF3a	96	L96F	Ctc	Ttc	114	114	B.1.1.7	0.000102
ORF3a	96	L96L	ctC	ctT	113	113	AY.98	0.008926
ORF3a	96	L96F	Ctc	Ttc	106	106	B.1.177	0.001396
ORF3a	96	L96F	Ctc	Ttc	93	93	AY.23	0.006487
ORF3a	96	L96L	ctC	ctT	77	83	AY.4	0.00012
ORF3a	96	L96L	ctC	ctA	5	83	AY.4	0.000008
ORF3a	96	L96L	ctC	ctG	1	83	AY.4	0.000002
ORF3a	96	L96L	ctC	ctT	82	82	B.1.429	0.001929
ORF3a	96	L96P	cTc	cCc	75	81	B.1.1.7	0.000067
ORF3a	96	L96P	cTC	cCT	6	81	B.1.1.7	0.000005
ORF3a	96	L96F	Ctc	Ttc	71	71	AY.44	0.000432
ORF3a	96	L96L	ctC	ctT	70	70	AY.3	0.000696
ORF3a	96	L96L	ctC	ctT	63	63	B.1.443	0.294393
ORF3a	96	L96F	Ctc	Ttc	57	57	B.1.243	0.003966
ORF3a	96	L96R	cTc	cGc	48	55	All	0.000009
ORF3a	96	L96R	cTC	cGA	3	55	All	0.000001
ORF3a	96	L96R	CTC	AGA	2	55	All	0
ORF3a	96	L96R	cTC	cGG	1	55	All	0
ORF3a	96	L96R	cTC	cGT	1	55	All	0
ORF3a	96	L96P	cTc	cCc	54	54	AY.3.1	0.004604
ORF3a	96	L96F	Ctc	Ttc	51	51	AY.4	0.000079
ORF3a	96	L96F	Ctc	Ttc	47	48	B.1.617.2	0.000177
ORF3a	96	L96F	CtC	TtT	1	48	B.1.617.2	0.000004
ORF3a	96	L96F	Ctc	Ttc	46	47	AY.43	0.000204
ORF3a	96	L96F	CtC	TtT	1	47	AY.43	0.000004
ORF3a	96	L96L	ctC	ctT	47	47	B.1.1.70	0.01603
ORF3a	96	L96L	ctC	ctT	42	42	B.1.160	0.00131
ORF3a	96	L96P	cTc	cCc	41	42	B.1.617.2	0.000154
ORF3a	96	L96P	cTC	cCT	1	42	B.1.617.2	0.000004
ORF3a	96	L96L	ctC	ctT	26	40	B.1	0.000238
ORF3a	96	L96L	ctC	ctA	7	40	B.1	0.000064
ORF3a	96	L96L	ctC	ctG	5	40	B.1	0.000046
ORF3a	96	L96L	CtC	TtG	1	40	B.1	0.000009
ORF3a	96	L96L	CtC	TtA	1	40	B.1	0.000009
ORF3a	96	L96H	cTc	cAc	39	39	All	0.000007
ORF3a	96	L96P	cTc	cCc	39	39	AY.5	0.000805
ORF3a	96	L96L	ctC	ctT	35	37	AY.103	0.000217
ORF3a	96	L96L	ctC	ctA	1	37	AY.103	0.000006
ORF3a	96	L96L	ctC	ctG	1	37	AY.103	0.000006
ORF3a	96	L96del	CTC	---	32	32	B.1.1.7	0.000029
ORF3a	96	L96F	Ctc	Ttc	27	27	AY.102	0.000716
ORF3a	96	L96L	ctC	ctT	27	27	AY.119	0.000953
ORF3a	96	L96L	ctC	ctT	22	26	AY.44	0.000134
ORF3a	96	L96L	ctC	ctA	3	26	AY.44	0.000018
ORF3a	96	L96L	ctC	ctG	1	26	AY.44	0.000006
ORF3a	96	L96L	ctC	ctT	25	25	AY.4.5	0.002687
ORF3a	96	L96F	Ctc	Ttc	24	24	AY.46	0.002498
ORF3a	96	L96L	ctC	ctT	24	24	B.1.621	0.002124
ORF3a	96	L96F	Ctc	Ttc	23	23	B.1.351	0.000684
ORF3a	96	L96L	ctC	ctT	21	23	B.1.526	0.000494
ORF3a	96	L96L	ctC	ctG	2	23	B.1.526	0.000047
ORF3a	96	L96L	ctC	ctT	17	22	B.1.2	0.00015
ORF3a	96	L96L	ctC	ctA	3	22	B.1.2	0.000026
ORF3a	96	L96L	ctC	ctG	2	22	B.1.2	0.000018
ORF3a	96	L96L	ctC	ctA	20	20	B.6	0.018198
ORF3a	96	L96L	ctC	ctT	17	18	AY.43	0.000075
ORF3a	96	L96L	ctC	ctA	1	18	AY.43	0.000004
ORF3a	96	L96F	Ctc	Ttc	18	18	B.1.2	0.000158
ORF3a	96	L96F	Ctc	Ttc	17	17	AY.3	0.000169
ORF3a	96	L96L	ctC	ctT	17	17	AY.9.1	0.001423
ORF3a	96	L96F	Ctc	Ttc	16	16	AW.1	0.04878
ORF3a	96	L96F	Ctc	Ttc	16	16	AY.103	0.000099
ORF3a	96	L96L	ctC	ctT	16	16	AY.27	0.001036
ORF3a	96	L96P	cTc	cCc	16	16	B.1.177	0.000211
ORF3a	96	L96P	cTc	cCc	13	13	AY.103	0.000081
ORF3a	96	L96L	ctC	ctT	13	13	B.1.1	0.000236
ORF3a	96	L96P	cTc	cCc	13	13	B.1.1.222	0.002652
ORF3a	96	L96I	Ctc	Atc	13	13	B.1.617.2	0.000049
ORF3a	96	L96F	Ctc	Ttc	12	12	AY.100	0.000552
ORF3a	96	L96del	CTC	---	12	12	B.1	0.00011
ORF3a	96	L96P	cTc	cCc	7	12	B.1	0.000064
ORF3a	96	L96P	cTC	cCT	5	12	B.1	0.000046
ORF3a	96	L96P	cTc	cCc	12	12	B.1.1	0.000218
ORF3a	96	L96L	ctC	ctT	12	12	C.37	0.001393
ORF3a	96	L96L	ctC	ctT	10	11	AY.39	0.000247
ORF3a	96	L96L	ctC	ctA	1	11	AY.39	0.000025
ORF3a	96	L96R	cTc	cGc	9	9	AY.4	0.000014
ORF3a	96	L96P	cTc	cCc	9	9	AY.59	0.004767
ORF3a	96	L96F	Ctc	Ttc	9	9	B.1.1	0.000163
ORF3a	96	L96L	ctC	ctT	9	9	B.1.1.180	0.096774
ORF3a	96	L96L	ctC	ctT	9	9	B.1.596.1	0.084112
ORF3a	96	L96L	ctC	ctA	9	9	C.30.1	0.060403
ORF3a	96	L96L	ctC	ctT	8	8	AY.117	0.000676
ORF3a	96	L96L	ctC	ctT	8	8	AY.20	0.000311
ORF3a	96	L96L	ctC	ctT	7	8	AY.25	0.000042
ORF3a	96	L96L	ctC	ctG	1	8	AY.25	0.000006
ORF3a	96	L96P	cTc	cCc	8	8	AY.3	0.00008
ORF3a	96	L96H	cTc	cAc	8	8	B.1	0.000073
ORF3a	96	L96F	Ctc	Ttc	7	8	B.1	0.000064
ORF3a	96	L96F	CtC	TtT	1	8	B.1	0.000009
ORF3a	96	L96I	Ctc	Atc	8	8	B.1.1.7	0.000007
ORF3a	96	L96del	CTC	---	8	8	B.1.177	0.000105
ORF3a	96	L96F	Ctc	Ttc	8	8	B.1.429	0.000188
ORF3a	96	L96L	ctC	ctT	8	8	B.1.595	0.002088
ORF3a	96	L96F	Ctc	Ttc	8	8	P.1	0.000126
ORF3a	96	L96L	ctC	ctT	7	7	AY.102	0.000186
ORF3a	96	L96L	ctC	ctT	7	7	AY.106	0.002344
ORF3a	96	L96F	Ctc	Ttc	7	7	AY.25	0.000042
ORF3a	96	L96F	Ctc	Ttc	7	7	AY.29	0.00011
ORF3a	96	L96L	ctC	ctT	7	7	AY.29	0.00011
ORF3a	96	L96L	ctC	ctT	7	7	B.1.561	0.002779
ORF3a	96	L96L	ctC	ctT	6	7	P.1.14	0.000287
ORF3a	96	L96L	ctC	ctA	1	7	P.1.14	0.000048
ORF3a	96	L96Q	cTC	cAA	6	6	All	0.000001
ORF3a	96	L96P	cTc	cCc	6	6	AY.119	0.000212
ORF3a	96	L96L	ctC	ctT	4	6	AY.26	0.000113
ORF3a	96	L96L	ctC	ctA	2	6	AY.26	0.000057
ORF3a	96	L96I	Ctc	Atc	6	6	AY.39	0.000148
ORF3a	96	L96del	CTC	---	6	6	AY.43	0.000027
ORF3a	96	L96F	Ctc	Ttc	6	6	AY.45	0.00073
ORF3a	96	L96R	cTc	cGc	6	6	AY.9.1	0.000502
ORF3a	96	L96P	cTc	cCc	6	6	B.1.1.519	0.000238
ORF3a	96	L96R	cTc	cGc	6	6	B.1.1.7	0.000005
ORF3a	96	L96F	Ctc	Ttc	6	6	B.1.160	0.000187
ORF3a	96	L96F	Ctc	Ttc	6	6	B.1.221	0.000426
ORF3a	96	L96L	ctC	ctT	5	6	B.1.596	0.000436
ORF3a	96	L96L	ctC	ctA	1	6	B.1.596	0.000087
ORF3a	96	L96R	cTc	cGc	2	6	B.1.91	0.004149
ORF3a	96	L96R	cTC	cGA	2	6	B.1.91	0.004149
ORF3a	96	L96R	CTC	AGA	2	6	B.1.91	0.004149
ORF3a	96	L96L	ctC	ctA	6	6	B.6.6	0.005333
ORF3a	96	L96del	CTC	---	6	6	P.1	0.000095
ORF3a	96	L96L	ctC	ctT	6	6	P.1	0.000095
ORF3a	96	L96L	ctC	ctT	6	6	P.1.7	0.001916
ORF3a	96	L96V	Ctc	Gtc	4	5	All	0.000001
ORF3a	96	L96del1	ctC	ct-	2	5	All	0
ORF3a	96	L96del1	Ctc	-tc	1	5	All	0
ORF3a	96	L96del1	CTC	-NN	1	5	All	0
ORF3a	96	L96del1	CtC	-tG	1	5	All	0
ORF3a	96	L96V	CtC	GtT	1	5	All	0
ORF3a	96	L96F	Ctc	Ttc	5	5	AY.118	0.000313
ORF3a	96	L96H	cTc	cAc	5	5	AY.4	0.000008
ORF3a	96	L96P	cTc	cCc	5	5	AY.43	0.000022
ORF3a	96	L96H	cTc	cAc	5	5	AY.44	0.00003
ORF3a	96	L96P	cTc	cCc	5	5	AY.44	0.00003
ORF3a	96	L96P	cTc	cCc	5	5	B.1.1.207	0.00591
ORF3a	96	L96F	Ctc	Ttc	5	5	B.1.13	0.011876
ORF3a	96	L96del	CTC	---	5	5	B.1.525	0.000566
ORF3a	96	L96L	ctC	ctA	5	5	Q.8	0.000825
ORF3a	96	L96L	ctC	ctT	4	4	AY.111	0.000733
ORF3a	96	L96F	Ctc	Ttc	4	4	AY.117	0.000338
ORF3a	96	L96F	Ctc	Ttc	4	4	AY.20	0.000155
ORF3a	96	L96P	cTc	cCc	4	4	AY.20	0.000155
ORF3a	96	L96F	Ctc	Ttc	4	4	AY.26	0.000113
ORF3a	96	L96L	ctC	ctA	4	4	AY.3.1	0.000341
ORF3a	96	L96L	ctC	ctT	4	4	AY.4.2	0.000087
ORF3a	96	L96del	CTC	---	4	4	AY.4.5	0.00043
ORF3a	96	L96R	cTc	cGc	3	4	AY.43	0.000013
ORF3a	96	L96R	cTC	cGG	1	4	AY.43	0.000004
ORF3a	96	L96I	Ctc	Atc	4	4	AY.44	0.000024
ORF3a	96	L96L	ctC	ctT	4	4	AY.52	0.003257
ORF3a	96	L96H	cTc	cAc	4	4	B.1.1.7	0.000004
ORF3a	96	L96L	ctC	ctA	3	4	B.1.466.2	0.001174
ORF3a	96	L96L	ctC	ctT	1	4	B.1.466.2	0.000391
ORF3a	96	L96del	CTC	---	4	4	P.1.15	0.000929
ORF3a	96	L96N	CTc	AAc	3	3	All	0.000001
ORF3a	96	L96S	CTc	AGc	3	3	All	0.000001
ORF3a	96	L96L	ctC	ctT	3	3	AY.100	0.000138
ORF3a	96	L96I	Ctc	Atc	3	3	AY.103	0.000019
ORF3a	96	L96P	cTc	cCc	3	3	AY.16.1	0.00141
ORF3a	96	L96I	Ctc	Atc	3	3	AY.20	0.000117
ORF3a	96	L96del	CTC	---	3	3	AY.23	0.000209
ORF3a	96	L96R	cTc	cGc	3	3	AY.25	0.000018
ORF3a	96	L96del	CTC	---	3	3	AY.25	0.000018
ORF3a	96	L96I	Ctc	Atc	3	3	AY.26	0.000085
ORF3a	96	L96I	Ctc	Atc	3	3	AY.37	0.000948
ORF3a	96	L96P	cTc	cCc	3	3	AY.39	0.000074
ORF3a	96	L96I	Ctc	Atc	3	3	AY.43	0.000013
ORF3a	96	L96F	Ctc	Ttc	3	3	AY.53	0.000863
ORF3a	96	L96I	Ctc	Atc	3	3	AY.65	0.001599
ORF3a	96	L96F	Ctc	Ttc	3	3	AY.9.2	0.00011
ORF3a	96	L96Q	cTC	cAA	3	3	B.1	0.000027
ORF3a	96	L96I	Ctc	Atc	3	3	B.1	0.000027
ORF3a	96	L96R	cTc	cGc	3	3	B.1.1.15	0.040541
ORF3a	96	L96F	Ctc	Ttc	3	3	B.1.1.214	0.000166
ORF3a	96	L96I	Ctc	Atc	3	3	B.1.1.428	0.028302
ORF3a	96	L96del1	ctC	ct-	2	3	B.1.1.7	0.000002
ORF3a	96	L96del1	Ctc	-tc	1	3	B.1.1.7	0.000001
ORF3a	96	L96I	Ctc	Atc	3	3	B.1.177	0.00004
ORF3a	96	L96P	cTc	cCc	3	3	B.1.2	0.000026
ORF3a	96	L96L	ctC	ctT	3	3	B.1.258	0.0002
ORF3a	96	L96L	ctC	ctA	2	3	B.1.351	0.000059
ORF3a	96	L96L	ctC	ctT	1	3	B.1.351	0.00003
ORF3a	96	L96F	Ctc	Ttc	3	3	B.1.438.1	0.000322
ORF3a	96	L96L	ctC	ctT	3	3	B.1.438.1	0.000322
ORF3a	96	L96del	CTC	---	3	3	B.1.621	0.000266
ORF3a	96	L96L	ctC	ctT	2	3	B.1.623	0.001073
ORF3a	96	L96L	ctC	ctA	1	3	B.1.623	0.000536
ORF3a	96	L96L	ctC	ctT	3	3	D.2	0.000225
ORF3a	96	L96F	Ctc	Ttc	3	3	P.1.7	0.000958
ORF3a	96	L96del	CTC	---	2	2		0.111111
ORF3a	96	L96V	Ctc	Gtc	2	2		0.111111
ORF3a	96	L96L	ctC	ctG	2	2		0.111111
ORF3a	96	L96K	CTC	AAA	2	2	All	0
ORF3a	96	L96I	Ctc	Atc	2	2	AY.102	0.000053
ORF3a	96	L96R	cTc	cGc	2	2	AY.103	0.000012
ORF3a	96	L96F	Ctc	Ttc	2	2	AY.16	0.000759
ORF3a	96	L96L	ctC	ctA	1	2	AY.23	0.00007
ORF3a	96	L96L	ctC	ctT	1	2	AY.23	0.00007
ORF3a	96	L96I	Ctc	Atc	2	2	AY.25	0.000012
ORF3a	96	L96I	Ctc	Atc	2	2	AY.3	0.00002
ORF3a	96	L96F	Ctc	Ttc	2	2	AY.33	0.000134
ORF3a	96	L96L	ctC	ctT	2	2	AY.35	0.000466
ORF3a	96	L96del	CTC	---	2	2	AY.44	0.000012
ORF3a	96	L96L	ctC	ctT	2	2	AY.5	0.000041
ORF3a	96	L96F	Ctc	Ttc	2	2	AY.57	0.001312
ORF3a	96	L96F	Ctc	Ttc	2	2	AY.72	0.002721
ORF3a	96	L96P	cTC	cCT	1	2	AY.75	0.000056
ORF3a	96	L96P	cTc	cCc	1	2	AY.75	0.000056
ORF3a	96	L96L	ctC	ctT	2	2	AY.9.2	0.000073
ORF3a	96	L96P	cTC	cCT	1	2	AY.9.2	0.000037
ORF3a	96	L96P	cTc	cCc	1	2	AY.9.2	0.000037
ORF3a	96	L96F	Ctc	Ttc	2	2	AY.90	0.001369
ORF3a	96	L96P	cTc	cCc	2	2	AY.98.1	0.000097
ORF3a	96	L96F	Ctc	Ttc	2	2	AY.99.2	0.000184
ORF3a	96	L96R	cTc	cGc	1	2	B.1	0.000009
ORF3a	96	L96R	cTC	cGA	1	2	B.1	0.000009
ORF3a	96	L96L	ctC	ctT	2	2	B.1.1.306	0.000877
ORF3a	96	L96L	ctC	ctT	2	2	B.1.1.371	0.020833
ORF3a	96	L96F	Ctc	Ttc	2	2	B.1.1.519	0.000079
ORF3a	96	L96L	ctC	ctT	2	2	B.1.110.3	0.001437
ORF3a	96	L96F	Ctc	Ttc	2	2	B.1.14	0.035088
ORF3a	96	L96H	cTc	cAc	2	2	B.1.160	0.000062
ORF3a	96	L96L	ctC	ctT	2	2	B.1.177	0.000026
ORF3a	96	L96L	ctC	ctT	2	2	B.1.177.7	0.00033
ORF3a	96	L96L	ctC	ctT	2	2	B.1.243	0.000139
ORF3a	96	L96L	ctC	ctT	2	2	B.1.258.14	0.001961
ORF3a	96	L96F	Ctc	Ttc	2	2	B.1.311	0.000549
ORF3a	96	L96P	cTc	cCc	2	2	B.1.311	0.000549
ORF3a	96	L96L	ctC	ctT	2	2	B.1.349	0.00143
ORF3a	96	L96L	ctC	ctT	1	2	B.1.36	0.000146
ORF3a	96	L96L	ctC	ctG	1	2	B.1.36	0.000146
ORF3a	96	L96L	ctC	ctA	2	2	B.1.465	0.007605
ORF3a	96	L96L	ctC	ctA	2	2	B.1.540	0.019417
ORF3a	96	L96P	cTC	cCT	2	2	B.1.617.1	0.000258
ORF3a	96	L96del	CTC	---	2	2	B.1.617.2	0.000008
ORF3a	96	L96F	Ctc	Ttc	2	2	B.1.628	0.000705
ORF3a	96	L96L	ctC	ctT	2	2	B.1.637	0.000146
ORF3a	96	L96K	CTC	AAA	2	2	B.1.91	0.004149
ORF3a	96	L96N	CTc	AAc	2	2	B.1.91	0.004149
ORF3a	96	L96S	CTc	AGc	2	2	B.1.91	0.004149
ORF3a	96	L96Q	cTC	cAA	2	2	B.1.91	0.004149
ORF3a	96	L96H	cTc	cAc	2	2	B.1.91	0.004149
ORF3a	96	L96L	ctC	ctT	2	2	C.16	0.002121
ORF3a	96	L96del	CTC	---	2	2	C.37	0.000232
ORF3a	96	L96F	Ctc	Ttc	2	2	P.1.14	0.000096
ORF3a	96	L96H	cTc	cAc	2	2	P.6	0.006289
ORF3a	96	L96L	ctC	ctT	2	2	R.1	0.00018
ORF3a	96	L96L	ctC	ctA	1	1	A	0.000387
ORF3a	96	L96del	CTC	---	1	1	A	0.000387
ORF3a	96	L96P	cTc	cCc	1	1	A	0.000387
ORF3a	96	L96del	CTC	---	1	1	AD.2	0.000219
ORF3a	96	L96del	CTC	---	1	1	AH.3	0.003802
ORF3a	96	L96T	CTC	ACA	1	1	All	0
ORF3a	96	L96G	CTC	GGA	1	1	All	0
ORF3a	96	L96E	CTC	GAA	1	1	All	0
ORF3a	96	L96del2	cTC	c--	1	1	All	0
ORF3a	96	L96Y	CTc	TAc	1	1	All	0
ORF3a	96	L96X	CTC	TAA	1	1	All	0
ORF3a	96	L96A	CTC	GCT	1	1	All	0
ORF3a	96	L96del	CTC	---	1	1	AV.1	0.005051
ORF3a	96	L96L	ctC	ctA	1	1	AY.1	0.000396
ORF3a	96	L96I	Ctc	Atc	1	1	AY.100	0.000046
ORF3a	96	L96del	CTC	---	1	1	AY.100	0.000046
ORF3a	96	L96H	cTc	cAc	1	1	AY.103	0.000006
ORF3a	96	L96I	Ctc	Atc	1	1	AY.106	0.000335
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.106	0.000335
ORF3a	96	L96P	cTc	cCc	1	1	AY.108	0.001103
ORF3a	96	L96del	CTC	---	1	1	AY.108	0.001103
ORF3a	96	L96del	CTC	---	1	1	AY.110	0.000113
ORF3a	96	L96del	CTC	---	1	1	AY.111	0.000183
ORF3a	96	L96R	cTc	cGc	1	1	AY.111	0.000183
ORF3a	96	L96del	CTC	---	1	1	AY.113	0.000142
ORF3a	96	L96L	ctC	ctT	1	1	AY.115	0.005208
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.119	0.000035
ORF3a	96	L96H	cTc	cAc	1	1	AY.119	0.000035
ORF3a	96	L96I	Ctc	Atc	1	1	AY.12	0.000316
ORF3a	96	L96L	ctC	ctT	1	1	AY.120	0.000037
ORF3a	96	L96L	ctC	ctT	1	1	AY.121	0.000135
ORF3a	96	L96P	cTc	cCc	1	1	AY.14	0.000088
ORF3a	96	L96L	ctC	ctT	1	1	AY.14	0.000088
ORF3a	96	L96R	cTc	cGc	1	1	AY.16	0.00038
ORF3a	96	L96L	ctC	ctT	1	1	AY.16	0.00038
ORF3a	96	L96L	ctC	ctT	1	1	AY.16.1	0.00047
ORF3a	96	L96del	CTC	---	1	1	AY.20	0.000039
ORF3a	96	L96H	cTc	cAc	1	1	AY.20	0.000039
ORF3a	96	L96P	cTc	cCc	1	1	AY.23	0.00007
ORF3a	96	L96H	cTc	cAc	1	1	AY.25	0.000006
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.27	0.000065
ORF3a	96	L96del	CTC	---	1	1	AY.29	0.000016
ORF3a	96	L96I	Ctc	Atc	1	1	AY.29	0.000016
ORF3a	96	L96H	cTc	cAc	1	1	AY.3	0.00001
ORF3a	96	L96H	cTc	cAc	1	1	AY.3.1	0.000085
ORF3a	96	L96N	CTc	AAc	1	1	AY.30	0.000396
ORF3a	96	L96S	CTc	AGc	1	1	AY.30	0.000396
ORF3a	96	L96H	cTc	cAc	1	1	AY.30	0.000396
ORF3a	96	L96R	cTc	cGc	1	1	AY.30	0.000396
ORF3a	96	L96L	ctC	ctA	1	1	AY.33	0.000067
ORF3a	96	L96P	cTc	cCc	1	1	AY.34	0.000097
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.34	0.000097
ORF3a	96	L96R	cTc	cGc	1	1	AY.34	0.000097
ORF3a	96	L96del	CTC	---	1	1	AY.34.1	0.00051
ORF3a	96	L96del	CTC	---	1	1	AY.35	0.000233
ORF3a	96	L96del	CTC	---	1	1	AY.36	0.000148
ORF3a	96	L96del	CTC	---	1	1	AY.39	0.000025
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.39.2	0.001541
ORF3a	96	L96I	Ctc	Atc	1	1	AY.4	0.000002
ORF3a	96	L96V	Ctc	Gtc	1	1	AY.4	0.000002
ORF3a	96	L96del	CTC	---	1	1	AY.4.2	0.000022
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.4.2	0.000022
ORF3a	96	L96P	cTc	cCc	1	1	AY.4.2.1	0.000149
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.4.3	0.000842
ORF3a	96	L96L	ctC	ctT	1	1	AY.41	0.000294
ORF3a	96	L96P	cTc	cCc	1	1	AY.42	0.00004
ORF3a	96	L96R	cTc	cGc	1	1	AY.42	0.00004
ORF3a	96	L96L	ctC	ctT	1	1	AY.46	0.000104
ORF3a	96	L96L	ctC	ctT	1	1	AY.46.1	0.001027
ORF3a	96	L96L	ctC	ctG	1	1	AY.46.6	0.000072
ORF3a	96	L96L	ctC	ctT	1	1	AY.47	0.000031
ORF3a	96	L96P	cTc	cCc	1	1	AY.47	0.000031
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.47	0.000031
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.5	0.000021
ORF3a	96	L96R	cTc	cGc	1	1	AY.52	0.000814
ORF3a	96	L96del	CTC	---	1	1	AY.52	0.000814
ORF3a	96	L96P	cTc	cCc	1	1	AY.53	0.000288
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.54	0.000095
ORF3a	96	L96L	ctC	ctT	1	1	AY.57	0.000656
ORF3a	96	L96L	ctC	ctT	1	1	AY.6	0.000041
ORF3a	96	L96L	ctC	ctT	1	1	AY.61	0.000105
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.62	0.000436
ORF3a	96	L96del	CTC	---	1	1	AY.68	0.000274
ORF3a	96	L96P	cTc	cCc	1	1	AY.68	0.000274
ORF3a	96	L96R	cTc	cGc	1	1	AY.69	0.000187
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.7.1	0.000113
ORF3a	96	L96L	ctC	ctT	1	1	AY.74	0.000116
ORF3a	96	L96I	Ctc	Atc	1	1	AY.75	0.000056
ORF3a	96	L96L	ctC	ctT	1	1	AY.75.1	0.00018
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.77	0.001127
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.88	0.000884
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.9	0.000068
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.9.1	0.000084
ORF3a	96	L96R	cTc	cGc	1	1	AY.9.2	0.000037
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.98	0.000079
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.98.1	0.000048
ORF3a	96	L96F	Ctc	Ttc	1	1	AY.99	0.001049
ORF3a	96	L96P	cTc	cCc	1	1	AY.99.2	0.000092
ORF3a	96	L96L	ctC	ctT	1	1	B	0.000128
ORF3a	96	L96del	CTC	---	1	1	B	0.000128
ORF3a	96	L96I	Ctc	Atc	1	1	B	0.000128
ORF3a	96	L96F	Ctc	Ttc	1	1	B	0.000128
ORF3a	96	L96E	CTC	GAA	1	1	B.1	0.000009
ORF3a	96	L96Y	CTc	TAc	1	1	B.1	0.000009
ORF3a	96	L96X	CTC	TAA	1	1	B.1	0.000009
ORF3a	96	L96G	CTC	GGA	1	1	B.1	0.000009
ORF3a	96	L96R	cTc	cGc	1	1	B.1.1	0.000018
ORF3a	96	L96del1	CtC	-tG	1	1	B.1.1.101	0.01
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.216	0.00089
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.218	0.007692
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.221	0.010101
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.1.25	0.000569
ORF3a	96	L96L	ctC	ctG	1	1	B.1.1.25	0.000569
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.299	0.012195
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.1.306	0.000438
ORF3a	96	L96R	cTC	cGT	1	1	B.1.1.306	0.000438
ORF3a	96	L96del1	CTC	-NN	1	1	B.1.1.315	0.008475
ORF3a	96	L96del	CTC	---	1	1	B.1.1.315	0.008475
ORF3a	96	L96L	ctC	ctG	1	1	B.1.1.326	0.001761
ORF3a	96	L96H	cTc	cAc	1	1	B.1.1.33	0.000421
ORF3a	96	L96R	cTc	cGc	1	1	B.1.1.33	0.000421
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.1.344	0.010753
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.1.351	0.002793
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.357	0.125
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.37	0.000193
ORF3a	96	L96del	CTC	---	1	1	B.1.1.409	0.002833
ORF3a	96	L96del	CTC	---	1	1	B.1.1.420	0.001006
ORF3a	96	L96L	ctC	ctA	1	1	B.1.1.44	0.00241
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.47	0.005348
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.51	0.001718
ORF3a	96	L96I	Ctc	Atc	1	1	B.1.1.519	0.00004
ORF3a	96	L96L	ctC	ctT	1	1	B.1.1.519	0.00004
ORF3a	96	L96V	CtC	GtT	1	1	B.1.1.7	0.000001
ORF3a	96	L96del2	cTC	c--	1	1	B.1.1.7	0.000001
ORF3a	96	L96del	CTC	---	1	1	B.1.140	0.018868
ORF3a	96	L96H	cTc	cAc	1	1	B.1.157	0.002985
ORF3a	96	L96del	CTC	---	1	1	B.1.160	0.000031
ORF3a	96	L96H	cTc	cAc	1	1	B.1.177	0.000013
ORF3a	96	L96L	ctC	ctT	1	1	B.1.177.12	0.000152
ORF3a	96	L96L	ctC	ctT	1	1	B.1.177.21	0.000076
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.177.21	0.000076
ORF3a	96	L96P	cTc	cCc	1	1	B.1.177.21	0.000076
ORF3a	96	L96I	Ctc	Atc	1	1	B.1.177.44	0.000519
ORF3a	96	L96del	CTC	---	1	1	B.1.177.51	0.004566
ORF3a	96	L96del	CTC	---	1	1	B.1.177.62	0.001192
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.177.81	0.000189
ORF3a	96	L96L	ctC	ctT	1	1	B.1.177.81	0.000189
ORF3a	96	L96P	cTC	cCT	1	1	B.1.179	0.003759
ORF3a	96	L96L	ctC	ctA	1	1	B.1.182	0.007246
ORF3a	96	L96del	CTC	---	1	1	B.1.2	0.000009
ORF3a	96	L96I	CtC	AtA	1	1	B.1.2	0.000009
ORF3a	96	L96Q	cTC	cAA	1	1	B.1.2	0.000009
ORF3a	96	L96R	cTc	cGc	1	1	B.1.2	0.000009
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.210	0.002132
ORF3a	96	L96P	cTc	cCc	1	1	B.1.221	0.000071
ORF3a	96	L96L	ctC	ctT	1	1	B.1.234	0.000132
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.258	0.000067
ORF3a	96	L96P	cTC	cCT	1	1	B.1.260	0.003344
ORF3a	96	L96L	ctC	ctT	1	1	B.1.311	0.000275
ORF3a	96	L96L	ctC	ctT	1	1	B.1.313	0.006579
ORF3a	96	L96A	CTC	GCT	1	1	B.1.351	0.00003
ORF3a	96	L96V	Ctc	Gtc	1	1	B.1.36	0.000146
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.36.1	0.00114
ORF3a	96	L96L	ctC	ctT	1	1	B.1.36.19	0.009259
ORF3a	96	L96P	cTC	cCT	1	1	B.1.36.8	0.001
ORF3a	96	L96L	ctC	ctT	1	1	B.1.36.8	0.001
ORF3a	96	L96del	CTC	---	1	1	B.1.362	0.001541
ORF3a	96	L96L	ctC	ctT	1	1	B.1.367	0.000792
ORF3a	96	L96del	CTC	---	1	1	B.1.416.1	0.001563
ORF3a	96	L96L	ctC	ctT	1	1	B.1.436	0.001029
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.462	0.007246
ORF3a	96	L96L	ctC	ctT	1	1	B.1.503	0.002488
ORF3a	96	L96L	ctC	ctT	1	1	B.1.509	0.000866
ORF3a	96	L96L	ctC	ctA	1	1	B.1.524	0.001406
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.526	0.000024
ORF3a	96	L96R	cTc	cGc	1	1	B.1.526	0.000024
ORF3a	96	L96I	Ctc	Atc	1	1	B.1.526	0.000024
ORF3a	96	L96P	cTC	cCT	1	1	B.1.537	0.02
ORF3a	96	L96I	Ctc	Atc	1	1	B.1.561	0.000397
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.561	0.000397
ORF3a	96	L96L	ctC	ctT	1	1	B.1.564	0.000426
ORF3a	96	L96L	ctC	ctT	1	1	B.1.575	0.000303
ORF3a	96	L96I	Ctc	Atc	1	1	B.1.595	0.000261
ORF3a	96	L96del	CTC	---	1	1	B.1.596	0.000087
ORF3a	96	L96H	cTc	cAc	1	1	B.1.596	0.000087
ORF3a	96	L96del	CTC	---	1	1	B.1.617.1	0.000129
ORF3a	96	L96L	ctC	ctG	1	1	B.1.617.1	0.000129
ORF3a	96	L96T	CTC	ACA	1	1	B.1.617.2	0.000004
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.619.1	0.000641
ORF3a	96	L96P	cTc	cCc	1	1	B.1.621	0.000089
ORF3a	96	L96F	Ctc	Ttc	1	1	B.1.621	0.000089
ORF3a	96	L96del	CTC	---	1	1	B.1.638	0.052632
ORF3a	96	L96F	Ctc	Ttc	1	1	B.4.7	0.010101
ORF3a	96	L96P	cTc	cCc	1	1	B.6.6	0.000889
ORF3a	96	L96L	ctC	ctA	1	1	B.6.8	0.008264
ORF3a	96	L96L	ctC	ctT	1	1	C.14	0.004329
ORF3a	96	L96P	cTc	cCc	1	1	C.37	0.000116
ORF3a	96	L96I	Ctc	Atc	1	1	C.37	0.000116
ORF3a	96	L96I	Ctc	Atc	1	1	P.1	0.000016
ORF3a	96	L96R	cTc	cGc	1	1	P.1.1	0.000318
ORF3a	96	L96L	ctC	ctT	1	1	P.1.12	0.000484
ORF3a	96	L96P	cTc	cCc	1	1	P.1.14	0.000048
ORF3a	96	L96F	Ctc	Ttc	1	1	P.1.15	0.000232
ORF3a	96	L96L	ctC	ctT	1	1	P.1.16	0.000374
ORF3a	96	L96L	ctC	ctT	1	1	P.1.17	0.000162
ORF3a	96	L96I	Ctc	Atc	1	1	P.1.17	0.000162
ORF3a	96	L96F	Ctc	Ttc	1	1	P.1.17	0.000162
ORF3a	96	L96L	ctC	ctT	1	1	P.3	0.001595
ORF3a	96	L96L	ctC	ctT	1	1	P.6	0.003145
ORF3a	96	L96L	ctC	ctT	1	1	P.7	0.004367
ORF3a	96	L96del	CTC	---	1	1	Q.4	0.000455
ORF3a	96	L96P	cTc	cCc	1	1	Q.7	0.001111
ORF3a	96	L96P	cTc	cCc	1	1	Q.8	0.000165
ORF3a	96	L96I	Ctc	Atc	1	1	R.1	0.00009
ORF3a	96	L96P	cTc	cCc	1	1	R.1	0.00009
ORF3a	96	L96del	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.