CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = E : CodonNum = 75

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
E	75	V75V		syn	gtC	gtT	2054	1654	0.805258	26467-26469
E	75	V75V		syn	gtC	gtA	2054	276	0.134372	26467-26469
E	75	V75V		syn	gtC	gtG	2054	124	0.06037	26467-26469
E	75	V75L		nonsyn	Gtc	Ctc	1612	1607	0.996898	26467-26469
E	75	V75L		nonsyn	GtC	CtT	1612	4	0.00248139	26467-26469
E	75	V75L		nonsyn	GtC	CtG	1612	1	0.000620347	26467-26469
E	75	V75del		del	GTC	---	218	218	1	26467-26469
E	75	V75I		nonsyn	Gtc	Atc	140	137	0.978571	26467-26469
E	75	V75I		nonsyn	GtC	AtT	140	3	0.0214286	26467-26469
E	75	V75F		nonsyn	Gtc	Ttc	91	88	0.967033	26467-26469
E	75	V75F		nonsyn	GtC	TtT	91	3	0.032967	26467-26469
E	75	V75A		nonsyn	gTc	gCc	49	47	0.959184	26467-26469
E	75	V75A		nonsyn	gTC	gCT	49	2	0.0408163	26467-26469
E	75	V75del1		del	gTc	g-c	17	9	0.529412	26467-26469
E	75	V75del1		del	Gtc	-tc	17	7	0.411765	26467-26469
E	75	V75del1		del	gtC	gt-	17	1	0.0588235	26467-26469
E	75	V75D		nonsyn	gTc	gAc	5	4	0.8	26467-26469
E	75	V75D		nonsyn	gTC	gAT	5	1	0.2	26467-26469
E	75	V75G		nonsyn	gTc	gGc	4	3	0.75	26467-26469
E	75	V75G		nonsyn	gTC	gGT	4	1	0.25	26467-26469
E	75	V75S		nonsyn	GTc	TCc	3	1	0.333333	26467-26469
E	75	V75S		nonsyn	GTC	TCT	3	1	0.333333	26467-26469
E	75	V75S		nonsyn	GTC	AGT	3	1	0.333333	26467-26469
E	75	V75C		nonsyn	GTC	TGT	2	1	0.5	26467-26469
E	75	V75T		nonsyn	GTC	ACT	2	1	0.5	26467-26469
E	75	V75T		nonsyn	GTc	ACc	2	1	0.5	26467-26469
E	75	V75C		nonsyn	GTc	TGc	2	1	0.5	26467-26469
E	75	V75P		nonsyn	GTc	CCc	1	1	1	26467-26469

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
E	75	V75V	gtC	gtT	1654	2054	All	0.000316
E	75	V75V	gtC	gtA	276	2054	All	0.000053
E	75	V75V	gtC	gtG	124	2054	All	0.000024
E	75	V75L	Gtc	Ctc	1607	1612	All	0.000307
E	75	V75L	GtC	CtT	4	1612	All	0.000001
E	75	V75L	GtC	CtG	1	1612	All	0
E	75	V75V	gtC	gtT	885	885	B.1.214.2	0.530576
E	75	V75L	Gtc	Ctc	399	401	B.1.1.7	0.000357
E	75	V75L	GtC	CtT	2	401	B.1.1.7	0.000002
E	75	V75L	Gtc	Ctc	220	220	B.1	0.002015
E	75	V75del	GTC	---	218	218	All	0.000042
E	75	V75V	gtC	gtT	169	175	B.1.1.7	0.000151
E	75	V75V	gtC	gtA	5	175	B.1.1.7	0.000004
E	75	V75V	gtC	gtG	1	175	B.1.1.7	0.000001
E	75	V75V	gtC	gtT	147	147	B.1.177.4	0.031026
E	75	V75I	Gtc	Atc	137	140	All	0.000026
E	75	V75I	GtC	AtT	3	140	All	0.000001
E	75	V75L	Gtc	Ctc	106	106	B.1.2	0.000933
E	75	V75V	gtC	gtG	106	106	B.1.501	0.779412
E	75	V75F	Gtc	Ttc	88	91	All	0.000017
E	75	V75F	GtC	TtT	3	91	All	0.000001
E	75	V75V	gtC	gtA	86	86	B.1.1.216	0.076581
E	75	V75V	gtC	gtT	42	71	AY.4	0.000065
E	75	V75V	gtC	gtA	29	71	AY.4	0.000045
E	75	V75V	gtC	gtA	31	63	B.1	0.000284
E	75	V75V	gtC	gtT	27	63	B.1	0.000247
E	75	V75V	gtC	gtG	5	63	B.1	0.000046
E	75	V75L	Gtc	Ctc	56	56	AY.103	0.000348
E	75	V75A	gTc	gCc	47	49	All	0.000009
E	75	V75A	gTC	gCT	2	49	All	0
E	75	V75L	Gtc	Ctc	49	49	AY.44	0.000298
E	75	V75del	GTC	---	46	46	AY.4	0.000072
E	75	V75V	gtC	gtT	41	45	B.1.617.2	0.000154
E	75	V75V	gtC	gtG	3	45	B.1.617.2	0.000011
E	75	V75V	gtC	gtA	1	45	B.1.617.2	0.000004
E	75	V75I	Gtc	Atc	44	44	AY.4	0.000068
E	75	V75L	Gtc	Ctc	39	39	B.1.596	0.003398
E	75	V75V	gtC	gtT	38	38	B.1.1.198	0.0558
E	75	V75L	Gtc	Ctc	36	36	AY.43	0.000159
E	75	V75del	GTC	---	35	35	B.1.1.7	0.000031
E	75	V75L	Gtc	Ctc	31	31	AY.25	0.000186
E	75	V75L	Gtc	Ctc	31	31	B.1.1	0.000562
E	75	V75V	gtC	gtA	22	30	B.1.1	0.000399
E	75	V75V	gtC	gtT	7	30	B.1.1	0.000127
E	75	V75V	gtC	gtG	1	30	B.1.1	0.000018
E	75	V75F	Gtc	Ttc	29	29	B.1.1.7	0.000026
E	75	V75I	Gtc	Atc	27	27	AY.25	0.000162
E	75	V75L	Gtc	Ctc	27	27	B.1.617.2	0.000102
E	75	V75L	Gtc	Ctc	24	24	B.1.160	0.000749
E	75	V75L	Gtc	Ctc	23	23	AY.39	0.000568
E	75	V75L	Gtc	Ctc	23	23	P.1	0.000362
E	75	V75V	gtC	gtA	22	22	B.1.505	0.096491
E	75	V75L	Gtc	Ctc	21	21	AY.4	0.000033
E	75	V75L	Gtc	Ctc	21	21	B	0.002684
E	75	V75V	gtC	gtA	13	21	B.1.258	0.000865
E	75	V75V	gtC	gtT	8	21	B.1.258	0.000532
E	75	V75V	gtC	gtT	21	21	P.1	0.000331
E	75	V75L	Gtc	Ctc	18	20	B.1.351	0.000535
E	75	V75L	GtC	CtG	1	20	B.1.351	0.00003
E	75	V75L	GtC	CtT	1	20	B.1.351	0.00003
E	75	V75L	Gtc	Ctc	19	19	AY.3	0.000189
E	75	V75V	gtC	gtT	17	18	B.1.2	0.00015
E	75	V75V	gtC	gtA	1	18	B.1.2	0.000009
E	75	V75del1	gTc	g-c	9	17	All	0.000002
E	75	V75del1	Gtc	-tc	7	17	All	0.000001
E	75	V75del1	gtC	gt-	1	17	All	0
E	75	V75L	Gtc	Ctc	17	17	B.1.1.519	0.000675
E	75	V75I	Gtc	Atc	16	17	B.1.1.7	0.000014
E	75	V75I	GtC	AtT	1	17	B.1.1.7	0.000001
E	75	V75L	Gtc	Ctc	17	17	B.1.526	0.0004
E	75	V75L	Gtc	Ctc	17	17	D.2	0.001276
E	75	V75L	Gtc	Ctc	16	16	B.1.177	0.000211
E	75	V75V	gtC	gtT	16	16	B.1.214.3	0.114286
E	75	V75V	gtC	gtT	12	15	AY.43	0.000053
E	75	V75V	gtC	gtG	3	15	AY.43	0.000013
E	75	V75V	gtC	gtA	15	15	B.1.1.306	0.006576
E	75	V75V	gtC	gtT	12	15	B.1.177	0.000158
E	75	V75V	gtC	gtA	3	15	B.1.177	0.00004
E	75	V75V	gtC	gtA	13	14	AY.4.5	0.001397
E	75	V75V	gtC	gtT	1	14	AY.4.5	0.000107
E	75	V75A	gTc	gCc	14	14	B.1.1.7	0.000013
E	75	V75V	gtC	gtT	14	14	P.1.12	0.006776
E	75	V75L	Gtc	Ctc	12	12	AY.100	0.000552
E	75	V75V	gtC	gtT	12	12	AY.44	0.000073
E	75	V75L	Gtc	Ctc	11	11	AY.26	0.000311
E	75	V75del	GTC	---	11	11	B.1.2	0.000097
E	75	V75L	Gtc	Ctc	10	10	AY.42	0.000402
E	75	V75del	GTC	---	10	10	B.1	0.000092
E	75	V75V	gtC	gtT	9	9	B.1.427	0.000454
E	75	V75F	Gtc	Ttc	9	9	B.6	0.008189
E	75	V75V	gtC	gtT	9	9	D.2	0.000675
E	75	V75del	GTC	---	8	8	AY.103	0.00005
E	75	V75del	GTC	---	8	8	AY.44	0.000049
E	75	V75V	gtC	gtA	6	8	AY.9	0.000406
E	75	V75V	gtC	gtT	2	8	AY.9	0.000135
E	75	V75L	Gtc	Ctc	8	8	B.1.1.433	0.011396
E	75	V75L	Gtc	Ctc	8	8	B.1.429	0.000188
E	75	V75del	GTC	---	7	7	AY.108	0.007718
E	75	V75V	gtC	gtT	7	7	AY.99.2	0.000645
E	75	V75L	Gtc	Ctc	7	7	B.1.329	0.004253
E	75	V75del	GTC	---	7	7	P.1	0.00011
E	75	V75L	Gtc	Ctc	7	7	P.2	0.001306
E	75	V75L	Gtc	Ctc	7	7	Q.3	0.001015
E	75	V75L	Gtc	Ctc	6	6	A.23.1	0.004225
E	75	V75L	Gtc	Ctc	6	6	AY.119	0.000212
E	75	V75V	gtC	gtT	6	6	AY.25	0.000036
E	75	V75del	GTC	---	6	6	AY.25	0.000036
E	75	V75V	gtC	gtT	6	6	AY.26	0.00017
E	75	V75A	gTc	gCc	6	6	AY.4	0.000009
E	75	V75del	GTC	---	6	6	AY.43	0.000027
E	75	V75L	Gtc	Ctc	6	6	AY.46	0.000624
E	75	V75L	Gtc	Ctc	6	6	AY.5	0.000124
E	75	V75V	gtC	gtA	4	6	AY.98.1	0.000194
E	75	V75V	gtC	gtT	2	6	AY.98.1	0.000097
E	75	V75del1	gTc	g-c	6	6	B.1.1	0.000109
E	75	V75I	Gtc	Atc	6	6	B.1.177.4	0.001266
E	75	V75L	Gtc	Ctc	6	6	B.1.221	0.000426
E	75	V75L	Gtc	Ctc	6	6	B.1.427	0.000303
E	75	V75A	gTc	gCc	6	6	B.1.429	0.000141
E	75	V75L	Gtc	Ctc	6	6	B.1.580	0.02439
E	75	V75L	Gtc	Ctc	6	6	P.1.15	0.001394
E	75	V75D	gTc	gAc	4	5	All	0.000001
E	75	V75D	gTC	gAT	1	5	All	0
E	75	V75L	Gtc	Ctc	5	5	AY.3.1	0.000426
E	75	V75L	Gtc	Ctc	5	5	AY.47	0.000156
E	75	V75V	gtC	gtA	3	5	AY.8	0.001818
E	75	V75V	gtC	gtT	2	5	AY.8	0.001212
E	75	V75L	Gtc	Ctc	5	5	AY.98.1	0.000242
E	75	V75F	Gtc	Ttc	5	5	B.1	0.000046
E	75	V75F	Gtc	Ttc	4	5	B.1.1	0.000073
E	75	V75F	GtC	TtT	1	5	B.1.1	0.000018
E	75	V75F	Gtc	Ttc	5	5	B.1.2	0.000044
E	75	V75L	Gtc	Ctc	5	5	B.1.243	0.000348
E	75	V75L	Gtc	Ctc	5	5	B.1.258	0.000333
E	75	V75del	GTC	---	5	5	B.1.258	0.000333
E	75	V75V	gtC	gtT	5	5	B.1.429	0.000118
E	75	V75L	Gtc	Ctc	5	5	B.1.525	0.000566
E	75	V75V	gtC	gtA	5	5	B.1.525	0.000566
E	75	V75L	Gtc	Ctc	5	5	B.1.595	0.001305
E	75	V75L	Gtc	Ctc	3	4		0.166667
E	75	V75I	Gtc	Atc	2	4		0.111111
E	75	V75I	GtC	AtT	2	4		0.111111
E	75	V75L	GtC	CtT	1	4		0.055556
E	75	V75G	gTc	gGc	3	4	All	0.000001
E	75	V75G	gTC	gGT	1	4	All	0
E	75	V75V	gtC	gtT	4	4	AY.102	0.000106
E	75	V75V	gtC	gtT	4	4	AY.114	0.000924
E	75	V75L	Gtc	Ctc	4	4	AY.118	0.000251
E	75	V75L	Gtc	Ctc	4	4	AY.23	0.000279
E	75	V75I	Gtc	Atc	4	4	AY.39	0.000099
E	75	V75L	Gtc	Ctc	4	4	AY.61	0.000419
E	75	V75L	Gtc	Ctc	4	4	AY.75.1	0.000721
E	75	V75L	Gtc	Ctc	4	4	B.1.1.25	0.002274
E	75	V75V	gtC	gtT	4	4	B.1.160	0.000125
E	75	V75A	gTc	gCc	4	4	B.1.2	0.000035
E	75	V75V	gtC	gtT	4	4	B.1.214.1	0.08
E	75	V75V	gtC	gtT	4	4	B.1.258.17	0.000416
E	75	V75V	gtC	gtT	4	4	B.1.338	0.034483
E	75	V75del	GTC	---	4	4	B.1.351	0.000119
E	75	V75L	Gtc	Ctc	4	4	B.1.375	0.003279
E	75	V75L	Gtc	Ctc	4	4	B.1.438.1	0.000429
E	75	V75V	gtC	gtT	4	4	B.1.596	0.000349
E	75	V75V	gtC	gtT	3	3		0.166667
E	75	V75V	gtC	gtT	3	3	A.28	0.007937
E	75	V75S	GTC	TCT	1	3	All	0
E	75	V75S	GTC	AGT	1	3	All	0
E	75	V75S	GTc	TCc	1	3	All	0
E	75	V75del	GTC	---	3	3	AY.1	0.001187
E	75	V75V	gtC	gtT	3	3	AY.103	0.000019
E	75	V75L	Gtc	Ctc	3	3	AY.117	0.000254
E	75	V75L	Gtc	Ctc	3	3	AY.16	0.001139
E	75	V75L	Gtc	Ctc	3	3	AY.16.1	0.00141
E	75	V75L	Gtc	Ctc	3	3	AY.20	0.000117
E	75	V75V	gtC	gtT	3	3	AY.29	0.000047
E	75	V75L	Gtc	Ctc	3	3	AY.29	0.000047
E	75	V75del	GTC	---	3	3	AY.3	0.00003
E	75	V75I	Gtc	Atc	3	3	AY.3	0.00003
E	75	V75L	Gtc	Ctc	3	3	AY.33	0.0002
E	75	V75L	Gtc	Ctc	3	3	AY.35	0.000699
E	75	V75V	gtC	gtT	3	3	AY.39	0.000074
E	75	V75L	Gtc	Ctc	3	3	AY.62	0.001307
E	75	V75L	Gtc	Ctc	3	3	AY.7.1	0.000338
E	75	V75L	Gtc	Ctc	3	3	AY.75	0.000168
E	75	V75del1	Gtc	-tc	2	3	B.1	0.000018
E	75	V75del1	gTc	g-c	1	3	B.1	0.000009
E	75	V75A	gTc	gCc	3	3	B.1.1	0.000054
E	75	V75I	Gtc	Atc	3	3	B.1.2	0.000026
E	75	V75V	gtC	gtT	3	3	B.1.265	0.003812
E	75	V75V	gtC	gtT	3	3	B.1.335	0.030928
E	75	V75V	gtC	gtT	2	3	B.1.351	0.000059
E	75	V75V	gtC	gtG	1	3	B.1.351	0.00003
E	75	V75L	Gtc	Ctc	3	3	B.1.609	0.001438
E	75	V75L	Gtc	Ctc	3	3	B.1.621	0.000266
E	75	V75del	GTC	---	3	3	P.1.15	0.000697
E	75	V75V	gtC	gtT	3	3	P.1.17	0.000485
E	75	V75del	GTC	---	3	3	P.1.7	0.000958
E	75	V75V	gtC	gtT	3	3	P.3	0.004785
E	75	V75V	gtC	gtT	3	3	Q.1	0.000379
E	75	V75L	Gtc	Ctc	3	3	Q.1	0.000379
E	75	V75del	GTC	---	2	2		0.111111
E	75	V75F	Gtc	Ttc	2	2		0.111111
E	75	V75A	gTC	gCT	1	2		0.055556
E	75	V75T	GTC	ACT	1	2		0.055556
E	75	V75T	GTc	ACc	1	2		0.055556
E	75	V75A	gTc	gCc	1	2		0.055556
E	75	V75L	Gtc	Ctc	2	2	A	0.000774
E	75	V75C	GTC	TGT	1	2	All	0
E	75	V75C	GTc	TGc	1	2	All	0
E	75	V75T	GTC	ACT	1	2	All	0
E	75	V75T	GTc	ACc	1	2	All	0
E	75	V75L	Gtc	Ctc	2	2	AU.1	0.002532
E	75	V75I	Gtc	Atc	2	2	AY.102	0.000053
E	75	V75I	Gtc	Atc	2	2	AY.103	0.000012
E	75	V75L	Gtc	Ctc	2	2	AY.116.1	0.000623
E	75	V75L	Gtc	Ctc	2	2	AY.120	0.000074
E	75	V75del	GTC	---	2	2	AY.120	0.000074
E	75	V75L	Gtc	Ctc	2	2	AY.121	0.000271
E	75	V75del	GTC	---	2	2	AY.14	0.000176
E	75	V75L	Gtc	Ctc	2	2	AY.14	0.000176
E	75	V75V	gtC	gtT	2	2	AY.20	0.000078
E	75	V75F	Gtc	Ttc	2	2	AY.25	0.000012
E	75	V75del	GTC	---	2	2	AY.26	0.000057
E	75	V75del	GTC	---	2	2	AY.29	0.000032
E	75	V75V	gtC	gtA	1	2	AY.3	0.00001
E	75	V75V	gtC	gtG	1	2	AY.3	0.00001
E	75	V75I	Gtc	Atc	2	2	AY.38	0.000999
E	75	V75V	gtC	gtT	2	2	AY.4.2	0.000043
E	75	V75V	gtC	gtT	2	2	AY.4.4	0.000818
E	75	V75I	Gtc	Atc	2	2	AY.44	0.000012
E	75	V75V	gtC	gtT	2	2	AY.46.6	0.000144
E	75	V75L	Gtc	Ctc	2	2	AY.46.6	0.000144
E	75	V75A	gTc	gCc	2	2	AY.47	0.000062
E	75	V75L	Gtc	Ctc	2	2	AY.52	0.001629
E	75	V75L	Gtc	Ctc	2	2	AY.6	0.000082
E	75	V75V	gtC	gtT	2	2	AY.61	0.00021
E	75	V75L	Gtc	Ctc	2	2	AY.65	0.001066
E	75	V75V	gtC	gtT	2	2	AY.72	0.002721
E	75	V75L	Gtc	Ctc	2	2	AY.9.1	0.000167
E	75	V75L	Gtc	Ctc	2	2	AY.9.2	0.000073
E	75	V75L	Gtc	Ctc	2	2	AY.91	0.001461
E	75	V75V	gtC	gtA	1	2	B	0.000128
E	75	V75V	gtC	gtT	1	2	B	0.000128
E	75	V75A	gTc	gCc	2	2	B.1	0.000018
E	75	V75V	gtC	gtT	2	2	B.1.1.160	0.047619
E	75	V75V	gtC	gtA	2	2	B.1.1.305	0.007722
E	75	V75I	Gtc	Atc	2	2	B.1.1.306	0.000877
E	75	V75V	gtC	gtT	2	2	B.1.1.318	0.000604
E	75	V75L	Gtc	Ctc	2	2	B.1.1.335	0.025974
E	75	V75L	Gtc	Ctc	2	2	B.1.1.409	0.005666
E	75	V75L	Gtc	Ctc	2	2	B.1.1.507	0.017391
E	75	V75V	gtC	gtT	2	2	B.1.1.519	0.000079
E	75	V75G	gTc	gGc	2	2	B.1.1.7	0.000002
E	75	V75del	GTC	---	2	2	B.1.110.3	0.001437
E	75	V75F	Gtc	Ttc	2	2	B.1.160	0.000062
E	75	V75del	GTC	---	2	2	B.1.160	0.000062
E	75	V75A	gTc	gCc	2	2	B.1.177	0.000026
E	75	V75L	Gtc	Ctc	2	2	B.1.177.23	0.006472
E	75	V75V	gtC	gtA	1	2	B.1.177.35	0.000691
E	75	V75V	gtC	gtT	1	2	B.1.177.35	0.000691
E	75	V75L	Gtc	Ctc	2	2	B.1.177.43	0.002954
E	75	V75L	Gtc	Ctc	2	2	B.1.177.44	0.001038
E	75	V75L	Gtc	Ctc	2	2	B.1.177.7	0.00033
E	75	V75L	Gtc	Ctc	2	2	B.1.206	0.001631
E	75	V75V	gtC	gtT	2	2	B.1.221	0.000142
E	75	V75A	gTc	gCc	1	2	B.1.221	0.000071
E	75	V75C	GTc	TGc	1	2	B.1.221	0.000071
E	75	V75S	GTc	TCc	1	2	B.1.221	0.000071
E	75	V75C	GTC	TGT	1	2	B.1.221	0.000071
E	75	V75G	gTC	gGT	1	2	B.1.221	0.000071
E	75	V75F	Gtc	Ttc	1	2	B.1.221	0.000071
E	75	V75G	gTc	gGc	1	2	B.1.221	0.000071
E	75	V75F	GtC	TtT	1	2	B.1.221	0.000071
E	75	V75A	gTC	gCT	1	2	B.1.221	0.000071
E	75	V75S	GTC	TCT	1	2	B.1.221	0.000071
E	75	V75L	Gtc	Ctc	2	2	B.1.232	0.001075
E	75	V75V	gtC	gtT	2	2	B.1.234	0.000264
E	75	V75L	Gtc	Ctc	2	2	B.1.240	0.000431
E	75	V75V	gtC	gtT	2	2	B.1.243	0.000139
E	75	V75L	Gtc	Ctc	2	2	B.1.289	0.005319
E	75	V75L	Gtc	Ctc	2	2	B.1.311	0.000549
E	75	V75L	Gtc	Ctc	2	2	B.1.351.2	0.000605
E	75	V75V	gtC	gtT	2	2	B.1.36	0.000292
E	75	V75V	gtC	gtT	2	2	B.1.397	0.009709
E	75	V75V	gtC	gtT	2	2	B.1.416	0.002538
E	75	V75del	GTC	---	2	2	B.1.429	0.000047
E	75	V75F	Gtc	Ttc	2	2	B.1.466.2	0.000782
E	75	V75L	Gtc	Ctc	2	2	B.1.517	0.000854
E	75	V75V	gtC	gtT	2	2	B.1.575	0.000607
E	75	V75V	gtC	gtT	1	2	B.1.582	0.000491
E	75	V75V	gtC	gtG	1	2	B.1.582	0.000491
E	75	V75L	Gtc	Ctc	2	2	B.1.617.1	0.000258
E	75	V75V	gtC	gtT	2	2	B.1.617.1	0.000258
E	75	V75I	Gtc	Atc	2	2	B.1.617.2	0.000008
E	75	V75del	GTC	---	2	2	B.1.617.2	0.000008
E	75	V75V	gtC	gtT	2	2	B.1.621	0.000177
E	75	V75L	Gtc	Ctc	2	2	B.1.623	0.001073
E	75	V75L	Gtc	Ctc	2	2	B.1.637	0.000146
E	75	V75V	gtC	gtA	2	2	B.6	0.00182
E	75	V75F	Gtc	Ttc	2	2	C.36	0.001821
E	75	V75L	Gtc	Ctc	2	2	C.36.3	0.001134
E	75	V75L	Gtc	Ctc	2	2	C.37	0.000232
E	75	V75del1	Gtc	-tc	2	2	P.1	0.000032
E	75	V75I	Gtc	Atc	2	2	P.1	0.000032
E	75	V75L	Gtc	Ctc	2	2	P.1.1	0.000635
E	75	V75L	Gtc	Ctc	2	2	P.1.10	0.000539
E	75	V75del	GTC	---	2	2	P.2	0.000373
E	75	V75L	Gtc	Ctc	2	2	P.3	0.00319
E	75	V75L	Gtc	Ctc	2	2	Q.7	0.002222
E	75	V75V	gtC	gtT	1	1	A	0.000387
E	75	V75A	gTc	gCc	1	1	A.2.4	0.003367
E	75	V75L	Gtc	Ctc	1	1	A.2.5	0.000499
E	75	V75L	Gtc	Ctc	1	1	A.21	0.00277
E	75	V75L	Gtc	Ctc	1	1	A.27	0.001656
E	75	V75I	Gtc	Atc	1	1	AE.8	0.000489
E	75	V75P	GTc	CCc	1	1	All	0
E	75	V75L	Gtc	Ctc	1	1	AM.4	0.003571
E	75	V75L	Gtc	Ctc	1	1	AP.1	0.001502
E	75	V75L	Gtc	Ctc	1	1	AU.2	0.002421
E	75	V75L	Gtc	Ctc	1	1	AU.3	0.00211
E	75	V75I	Gtc	Atc	1	1	AY.10	0.00053
E	75	V75del	GTC	---	1	1	AY.100	0.000046
E	75	V75del	GTC	---	1	1	AY.102	0.000027
E	75	V75A	gTc	gCc	1	1	AY.103	0.000006
E	75	V75L	Gtc	Ctc	1	1	AY.105	0.000643
E	75	V75L	Gtc	Ctc	1	1	AY.110	0.000113
E	75	V75I	Gtc	Atc	1	1	AY.111	0.000183
E	75	V75L	Gtc	Ctc	1	1	AY.111	0.000183
E	75	V75L	Gtc	Ctc	1	1	AY.113	0.000142
E	75	V75L	Gtc	Ctc	1	1	AY.116	0.000287
E	75	V75del	GTC	---	1	1	AY.118	0.000063
E	75	V75I	Gtc	Atc	1	1	AY.120	0.000037
E	75	V75V	gtC	gtA	1	1	AY.120	0.000037
E	75	V75L	Gtc	Ctc	1	1	AY.120.1	0.000321
E	75	V75L	Gtc	Ctc	1	1	AY.13	0.000161
E	75	V75V	gtC	gtT	1	1	AY.16.1	0.00047
E	75	V75V	gtC	gtT	1	1	AY.23	0.00007
E	75	V75A	gTc	gCc	1	1	AY.23	0.00007
E	75	V75L	Gtc	Ctc	1	1	AY.24	0.000431
E	75	V75V	gtC	gtT	1	1	AY.24	0.000431
E	75	V75I	Gtc	Atc	1	1	AY.29	0.000016
E	75	V75F	Gtc	Ttc	1	1	AY.3	0.00001
E	75	V75del	GTC	---	1	1	AY.3.1	0.000085
E	75	V75F	Gtc	Ttc	1	1	AY.30	0.000396
E	75	V75V	gtC	gtT	1	1	AY.33	0.000067
E	75	V75V	gtC	gtT	1	1	AY.34	0.000097
E	75	V75L	Gtc	Ctc	1	1	AY.36	0.000148
E	75	V75del	GTC	---	1	1	AY.39	0.000025
E	75	V75L	Gtc	Ctc	1	1	AY.39.1	0.00004
E	75	V75F	Gtc	Ttc	1	1	AY.4	0.000002
E	75	V75V	gtC	gtT	1	1	AY.4.1	0.000737
E	75	V75L	Gtc	Ctc	1	1	AY.4.2	0.000022
E	75	V75F	Gtc	Ttc	1	1	AY.4.2.1	0.000149
E	75	V75F	Gtc	Ttc	1	1	AY.42	0.00004
E	75	V75I	Gtc	Atc	1	1	AY.43	0.000004
E	75	V75F	Gtc	Ttc	1	1	AY.44	0.000006
E	75	V75L	Gtc	Ctc	1	1	AY.45	0.000122
E	75	V75del	GTC	---	1	1	AY.45	0.000122
E	75	V75V	gtC	gtG	1	1	AY.46	0.000104
E	75	V75L	Gtc	Ctc	1	1	AY.46.2	0.000635
E	75	V75del	GTC	---	1	1	AY.46.4	0.000165
E	75	V75L	Gtc	Ctc	1	1	AY.46.4	0.000165
E	75	V75I	Gtc	Atc	1	1	AY.47	0.000031
E	75	V75V	gtC	gtT	1	1	AY.5	0.000021
E	75	V75del	GTC	---	1	1	AY.5	0.000021
E	75	V75I	Gtc	Atc	1	1	AY.5	0.000021
E	75	V75L	Gtc	Ctc	1	1	AY.54	0.000095
E	75	V75V	gtC	gtA	1	1	AY.58	0.000907
E	75	V75L	Gtc	Ctc	1	1	AY.58	0.000907
E	75	V75F	GtC	TtT	1	1	AY.62	0.000436
E	75	V75L	Gtc	Ctc	1	1	AY.68	0.000274
E	75	V75del	GTC	---	1	1	AY.68	0.000274
E	75	V75D	gTc	gAc	1	1	AY.7	0.000196
E	75	V75V	gtC	gtT	1	1	AY.7	0.000196
E	75	V75L	Gtc	Ctc	1	1	AY.7.2	0.000559
E	75	V75V	gtC	gtT	1	1	AY.70	0.000209
E	75	V75L	Gtc	Ctc	1	1	AY.74	0.000116
E	75	V75V	gtC	gtA	1	1	AY.75	0.000056
E	75	V75del	GTC	---	1	1	AY.75.1	0.00018
E	75	V75L	Gtc	Ctc	1	1	AY.83	0.001724
E	75	V75V	gtC	gtT	1	1	AY.84	0.000437
E	75	V75L	Gtc	Ctc	1	1	AY.85	0.000427
E	75	V75V	gtC	gtA	1	1	AY.87	0.000833
E	75	V75del	GTC	---	1	1	AY.9	0.000068
E	75	V75V	gtC	gtT	1	1	AY.9.2	0.000037
E	75	V75L	Gtc	Ctc	1	1	AY.92	0.000287
E	75	V75del1	Gtc	-tc	1	1	AY.95	0.000761
E	75	V75L	Gtc	Ctc	1	1	AY.96	0.002075
E	75	V75V	gtC	gtT	1	1	AY.98	0.000079
E	75	V75L	Gtc	Ctc	1	1	AY.98	0.000079
E	75	V75F	Gtc	Ttc	1	1	AY.98.1	0.000048
E	75	V75F	Gtc	Ttc	1	1	AY.99.2	0.000092
E	75	V75V	gtC	gtT	1	1	AZ.1	0.000867
E	75	V75V	gtC	gtT	1	1	AZ.2	0.000821
E	75	V75F	Gtc	Ttc	1	1	B	0.000128
E	75	V75D	gTc	gAc	1	1	B.1	0.000009
E	75	V75P	GTc	CCc	1	1	B.1	0.000009
E	75	V75I	Gtc	Atc	1	1	B.1	0.000009
E	75	V75I	Gtc	Atc	1	1	B.1.1	0.000018
E	75	V75L	Gtc	Ctc	1	1	B.1.1.153	0.001095
E	75	V75L	Gtc	Ctc	1	1	B.1.1.164	0.005155
E	75	V75L	Gtc	Ctc	1	1	B.1.1.174	0.003378
E	75	V75F	Gtc	Ttc	1	1	B.1.1.174	0.003378
E	75	V75L	Gtc	Ctc	1	1	B.1.1.176	0.000439
E	75	V75L	Gtc	Ctc	1	1	B.1.1.192	0.002309
E	75	V75V	gtC	gtT	1	1	B.1.1.210	0.005714
E	75	V75V	gtC	gtT	1	1	B.1.1.214	0.000055
E	75	V75I	Gtc	Atc	1	1	B.1.1.219	0.005
E	75	V75L	Gtc	Ctc	1	1	B.1.1.220	0.001859
E	75	V75V	gtC	gtA	1	1	B.1.1.220	0.001859
E	75	V75L	Gtc	Ctc	1	1	B.1.1.225	0.007194
E	75	V75del	GTC	---	1	1	B.1.1.232	0.001815
E	75	V75V	gtC	gtT	1	1	B.1.1.25	0.000569
E	75	V75V	gtC	gtT	1	1	B.1.1.261	0.008621
E	75	V75L	Gtc	Ctc	1	1	B.1.1.263	0.001558
E	75	V75del1	gTc	g-c	1	1	B.1.1.271	0.055556
E	75	V75V	gtC	gtT	1	1	B.1.1.279	0.001121
E	75	V75L	Gtc	Ctc	1	1	B.1.1.28	0.000311
E	75	V75I	Gtc	Atc	1	1	B.1.1.284	0.000107
E	75	V75del	GTC	---	1	1	B.1.1.284	0.000107
E	75	V75V	gtC	gtT	1	1	B.1.1.284	0.000107
E	75	V75del1	gtC	gt-	1	1	B.1.1.306	0.000438
E	75	V75L	Gtc	Ctc	1	1	B.1.1.306	0.000438
E	75	V75L	Gtc	Ctc	1	1	B.1.1.317	0.000412
E	75	V75del	GTC	---	1	1	B.1.1.37	0.000193
E	75	V75L	Gtc	Ctc	1	1	B.1.1.389	0.006061
E	75	V75L	Gtc	Ctc	1	1	B.1.1.413	0.006897
E	75	V75L	Gtc	Ctc	1	1	B.1.1.420	0.001006
E	75	V75L	Gtc	Ctc	1	1	B.1.1.434	0.000349
E	75	V75del1	gTc	g-c	1	1	B.1.1.449	0.022727
E	75	V75V	gtC	gtT	1	1	B.1.1.46	0.004367
E	75	V75del	GTC	---	1	1	B.1.1.519	0.00004
E	75	V75L	Gtc	Ctc	1	1	B.1.1.526	0.003546
E	75	V75F	Gtc	Ttc	1	1	B.1.1.58	0.005376
E	75	V75L	Gtc	Ctc	1	1	B.1.1.63	0.000386
E	75	V75I	Gtc	Atc	1	1	B.1.1.63	0.000386
E	75	V75S	GTC	AGT	1	1	B.1.1.7	0.000001
E	75	V75V	gtC	gtT	1	1	B.1.110	0.004525
E	75	V75del	GTC	---	1	1	B.1.12	0.008
E	75	V75L	Gtc	Ctc	1	1	B.1.139	0.000733
E	75	V75V	gtC	gtT	1	1	B.1.140	0.018868
E	75	V75L	Gtc	Ctc	1	1	B.1.143	0.021277
E	75	V75F	Gtc	Ttc	1	1	B.1.157	0.002985
E	75	V75L	Gtc	Ctc	1	1	B.1.160.15	0.00495
E	75	V75L	Gtc	Ctc	1	1	B.1.160.25	0.011111
E	75	V75L	Gtc	Ctc	1	1	B.1.160.32	0.004292
E	75	V75del	GTC	---	1	1	B.1.161	0.017241
E	75	V75F	Gtc	Ttc	1	1	B.1.177	0.000013
E	75	V75I	Gtc	Atc	1	1	B.1.177	0.000013
E	75	V75L	Gtc	Ctc	1	1	B.1.177.17	0.000821
E	75	V75del	GTC	---	1	1	B.1.177.4	0.000211
E	75	V75F	Gtc	Ttc	1	1	B.1.177.4	0.000211
E	75	V75V	gtC	gtT	1	1	B.1.177.42	0.000894
E	75	V75V	gtC	gtT	1	1	B.1.177.54	0.000606
E	75	V75L	Gtc	Ctc	1	1	B.1.177.57	0.000281
E	75	V75del	GTC	---	1	1	B.1.177.58	0.001332
E	75	V75del	GTC	---	1	1	B.1.177.62	0.001192
E	75	V75L	Gtc	Ctc	1	1	B.1.177.65	0.000665
E	75	V75L	Gtc	Ctc	1	1	B.1.177.73	0.000566
E	75	V75L	Gtc	Ctc	1	1	B.1.177.81	0.000189
E	75	V75A	gTc	gCc	1	1	B.1.177.81	0.000189
E	75	V75D	gTC	gAT	1	1	B.1.177.83	0.001481
E	75	V75L	Gtc	Ctc	1	1	B.1.177.86	0.000183
E	75	V75V	gtC	gtT	1	1	B.1.177.86	0.000183
E	75	V75L	Gtc	Ctc	1	1	B.1.179	0.003759
E	75	V75D	gTc	gAc	1	1	B.1.2	0.000009
E	75	V75del1	Gtc	-tc	1	1	B.1.2	0.000009
E	75	V75L	Gtc	Ctc	1	1	B.1.210	0.002132
E	75	V75F	Gtc	Ttc	1	1	B.1.210	0.002132
E	75	V75L	Gtc	Ctc	1	1	B.1.222	0.001692
E	75	V75L	Gtc	Ctc	1	1	B.1.223	0.002778
E	75	V75V	gtC	gtT	1	1	B.1.232	0.000537
E	75	V75L	Gtc	Ctc	1	1	B.1.234	0.000132
E	75	V75del	GTC	---	1	1	B.1.234	0.000132
E	75	V75L	Gtc	Ctc	1	1	B.1.239	0.001221
E	75	V75V	gtC	gtT	1	1	B.1.240	0.000216
E	75	V75del	GTC	---	1	1	B.1.243	0.00007
E	75	V75del	GTC	---	1	1	B.1.249	0.0625
E	75	V75L	Gtc	Ctc	1	1	B.1.258.17	0.000104
E	75	V75L	Gtc	Ctc	1	1	B.1.258.3	0.001675
E	75	V75V	gtC	gtA	1	1	B.1.301	0.005917
E	75	V75L	Gtc	Ctc	1	1	B.1.330	0.028571
E	75	V75F	Gtc	Ttc	1	1	B.1.351	0.00003
E	75	V75L	Gtc	Ctc	1	1	B.1.351.5	0.0006
E	75	V75del1	Gtc	-tc	1	1	B.1.36	0.000146
E	75	V75L	Gtc	Ctc	1	1	B.1.36.1	0.00114
E	75	V75F	Gtc	Ttc	1	1	B.1.36.29	0.000517
E	75	V75L	Gtc	Ctc	1	1	B.1.36.8	0.001
E	75	V75del	GTC	---	1	1	B.1.366	0.004878
E	75	V75V	gtC	gtG	1	1	B.1.369	0.000285
E	75	V75L	Gtc	Ctc	1	1	B.1.369	0.000285
E	75	V75V	gtC	gtT	1	1	B.1.389	0.001002
E	75	V75L	Gtc	Ctc	1	1	B.1.396	0.000706
E	75	V75L	Gtc	Ctc	1	1	B.1.399	0.001934
E	75	V75L	Gtc	Ctc	1	1	B.1.400	0.000429
E	75	V75L	Gtc	Ctc	1	1	B.1.413	0.004255
E	75	V75F	Gtc	Ttc	1	1	B.1.416	0.001269
E	75	V75L	Gtc	Ctc	1	1	B.1.416.1	0.001563
E	75	V75L	Gtc	Ctc	1	1	B.1.422	0.000812
E	75	V75L	Gtc	Ctc	1	1	B.1.432	0.011236
E	75	V75L	Gtc	Ctc	1	1	B.1.445	0.011765
E	75	V75L	Gtc	Ctc	1	1	B.1.456	0.003268
E	75	V75L	Gtc	Ctc	1	1	B.1.462	0.007246
E	75	V75I	Gtc	Atc	1	1	B.1.499	0.00105
E	75	V75V	gtC	gtA	1	1	B.1.510	0.026316
E	75	V75L	Gtc	Ctc	1	1	B.1.511	0.034483
E	75	V75L	Gtc	Ctc	1	1	B.1.521	0.004975
E	75	V75L	Gtc	Ctc	1	1	B.1.523	0.002451
E	75	V75del	GTC	---	1	1	B.1.525	0.000113
E	75	V75V	gtC	gtT	1	1	B.1.526	0.000024
E	75	V75I	Gtc	Atc	1	1	B.1.526	0.000024
E	75	V75F	Gtc	Ttc	1	1	B.1.538	0.008065
E	75	V75V	gtC	gtT	1	1	B.1.541	0.004425
E	75	V75V	gtC	gtT	1	1	B.1.552	0.015152
E	75	V75L	Gtc	Ctc	1	1	B.1.558	0.004566
E	75	V75V	gtC	gtT	1	1	B.1.560	0.00463
E	75	V75V	gtC	gtT	1	1	B.1.564	0.000426
E	75	V75L	Gtc	Ctc	1	1	B.1.576	0.000907
E	75	V75F	Gtc	Ttc	1	1	B.1.596	0.000087
E	75	V75V	gtC	gtA	1	1	B.1.599	0.00365
E	75	V75del	GTC	---	1	1	B.1.609	0.000479
E	75	V75V	gtC	gtA	1	1	B.1.609	0.000479
E	75	V75del	GTC	---	1	1	B.1.617.1	0.000129
E	75	V75F	Gtc	Ttc	1	1	B.1.617.2	0.000004
E	75	V75D	gTc	gAc	1	1	B.1.619	0.000871
E	75	V75L	Gtc	Ctc	1	1	B.1.619	0.000871
E	75	V75F	Gtc	Ttc	1	1	B.1.619	0.000871
E	75	V75del	GTC	---	1	1	B.1.627	0.00202
E	75	V75L	Gtc	Ctc	1	1	B.1.627	0.00202
E	75	V75V	gtC	gtT	1	1	B.1.637	0.000073
E	75	V75del	GTC	---	1	1	B.1.638	0.052632
E	75	V75L	Gtc	Ctc	1	1	B.1.78	0.008547
E	75	V75L	Gtc	Ctc	1	1	B.1.9.5	0.005682
E	75	V75V	gtC	gtA	1	1	B.1.93	0.000934
E	75	V75L	Gtc	Ctc	1	1	B.35	0.007812
E	75	V75del	GTC	---	1	1	B.39	0.002331
E	75	V75L	Gtc	Ctc	1	1	B.40	0.000364
E	75	V75L	Gtc	Ctc	1	1	C.32	0.023256
E	75	V75L	Gtc	Ctc	1	1	C.35	0.000774
E	75	V75F	Gtc	Ttc	1	1	C.37	0.000116
E	75	V75L	Gtc	Ctc	1	1	C.6	0.037037
E	75	V75A	gTc	gCc	1	1	D.2	0.000075
E	75	V75L	Gtc	Ctc	1	1	D.3	0.005917
E	75	V75A	gTc	gCc	1	1	P.1	0.000016
E	75	V75del	GTC	---	1	1	P.1.13	0.000898
E	75	V75L	Gtc	Ctc	1	1	P.1.14	0.000048
E	75	V75del	GTC	---	1	1	P.1.14	0.000048
E	75	V75I	Gtc	Atc	1	1	P.1.15	0.000232
E	75	V75V	gtC	gtT	1	1	P.1.15	0.000232
E	75	V75L	Gtc	Ctc	1	1	P.1.17	0.000162
E	75	V75L	Gtc	Ctc	1	1	P.1.2	0.001156
E	75	V75I	Gtc	Atc	1	1	P.3	0.001595
E	75	V75del	GTC	---	1	1	Q.3	0.000145
E	75	V75L	Gtc	Ctc	1	1	Q.4	0.000455
E	75	V75F	Gtc	Ttc	1	1	Q.4	0.000455
E	75	V75L	Gtc	Ctc	1	1	Q.6	0.006623
E	75	V75V	gtC	gtT	1	1	Q.8	0.000165
E	75	V75F	Gtc	Ttc	1	1	R.1	0.00009

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.