CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 66

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
N	66	F66F		syn	ttC	ttT	712	712	1	28469-28471
N	66	F66V		nonsyn	Ttc	Gtc	80	76	0.95	28469-28471
N	66	F66V		nonsyn	TtC	GtG	80	3	0.0375	28469-28471
N	66	F66V		nonsyn	TtC	GtA	80	1	0.0125	28469-28471
N	66	F66del		del	TTC	---	23	23	1	28469-28471
N	66	F66S		nonsyn	tTc	tCc	20	12	0.6	28469-28471
N	66	F66S		nonsyn	TTc	AGc	20	6	0.3	28469-28471
N	66	F66S		nonsyn	tTC	tCT	20	1	0.05	28469-28471
N	66	F66S		nonsyn	tTC	tCG	20	1	0.05	28469-28471
N	66	F66L		nonsyn	Ttc	Ctc	18	9	0.5	28469-28471
N	66	F66L		nonsyn	ttC	ttA	18	5	0.277778	28469-28471
N	66	F66L		nonsyn	ttC	ttG	18	3	0.166667	28469-28471
N	66	F66L		nonsyn	TtC	CtG	18	1	0.0555556	28469-28471
N	66	F66C		nonsyn	tTc	tGc	13	11	0.846154	28469-28471
N	66	F66C		nonsyn	tTC	tGT	13	2	0.153846	28469-28471
N	66	F66I		nonsyn	Ttc	Atc	10	6	0.6	28469-28471
N	66	F66I		nonsyn	TtC	AtA	10	4	0.4	28469-28471
N	66	F66del1		del	ttC	tt-	8	7	0.875	28469-28471
N	66	F66del1		del	Ttc	-tc	8	1	0.125	28469-28471
N	66	F66A		nonsyn	TTC	GCT	5	5	1	28469-28471
N	66	F66T		nonsyn	TTc	ACc	5	4	0.8	28469-28471
N	66	F66T		nonsyn	TTC	ACA	5	1	0.2	28469-28471
N	66	F66G		nonsyn	TTc	GGc	4	2	0.5	28469-28471
N	66	F66G		nonsyn	TTC	GGG	4	1	0.25	28469-28471
N	66	F66G		nonsyn	TTC	GGA	4	1	0.25	28469-28471
N	66	F66X		nonsyn	tTC	tGA	3	3	1	28469-28471
N	66	F66R		nonsyn	TTC	AGA	3	3	1	28469-28471
N	66	F66Y		nonsyn	tTc	tAc	2	2	1	28469-28471
N	66	F66N		nonsyn	TTc	AAc	1	1	1	28469-28471
N	66	F66D		nonsyn	TTc	GAc	1	1	1	28469-28471
N	66	F66W		nonsyn	tTC	tGG	1	1	1	28469-28471
N	66	F66K		nonsyn	TTC	AAA	1	1	1	28469-28471

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
N	66	F66F	ttC	ttT	712	712	All	0.000136
N	66	F66F	ttC	ttT	98	98	B.1.1.7	0.000088
N	66	F66F	ttC	ttT	96	96	B.1.36.33	0.727273
N	66	F66F	ttC	ttT	84	84	AY.4	0.000131
N	66	F66V	Ttc	Gtc	76	80	All	0.000015
N	66	F66V	TtC	GtG	3	80	All	0.000001
N	66	F66V	TtC	GtA	1	80	All	0
N	66	F66F	ttC	ttT	73	73	B.1.526	0.001716
N	66	F66V	Ttc	Gtc	37	37	B.1.1.7	0.000033
N	66	F66F	ttC	ttT	35	35	AY.25	0.000211
N	66	F66F	ttC	ttT	33	33	B.1.351	0.000981
N	66	F66F	ttC	ttT	26	26	P.1	0.00041
N	66	F66F	ttC	ttT	24	24	B.1.1.307	0.060759
N	66	F66del	TTC	---	23	23	All	0.000004
N	66	F66F	ttC	ttT	22	22	B.1.2	0.000194
N	66	F66F	ttC	ttT	21	21	AY.43	0.000093
N	66	F66S	tTc	tCc	12	20	All	0.000002
N	66	F66S	TTc	AGc	6	20	All	0.000001
N	66	F66S	tTC	tCT	1	20	All	0
N	66	F66S	tTC	tCG	1	20	All	0
N	66	F66L	Ttc	Ctc	9	18	All	0.000002
N	66	F66L	ttC	ttA	5	18	All	0.000001
N	66	F66L	ttC	ttG	3	18	All	0.000001
N	66	F66L	TtC	CtG	1	18	All	0
N	66	F66F	ttC	ttT	15	15	AY.3	0.000149
N	66	F66F	ttC	ttT	14	14	C.37	0.001625
N	66	F66C	tTc	tGc	11	13	All	0.000002
N	66	F66C	tTC	tGT	2	13	All	0
N	66	F66F	ttC	ttT	13	13	B.1.617.2	0.000049
N	66	F66F	ttC	ttT	12	12	AY.103	0.000075
N	66	F66F	ttC	ttT	12	12	B.1.177.7	0.001978
N	66	F66I	Ttc	Atc	6	10	All	0.000001
N	66	F66I	TtC	AtA	4	10	All	0.000001
N	66	F66F	ttC	ttT	10	10	AY.44	0.000061
N	66	F66F	ttC	ttT	10	10	B.1	0.000092
N	66	F66F	ttC	ttT	9	9	AY.119	0.000318
N	66	F66V	Ttc	Gtc	9	9	AY.43	0.00004
N	66	F66F	ttC	ttT	9	9	B.1.438.1	0.000965
N	66	F66del1	ttC	tt-	7	8	All	0.000001
N	66	F66del1	Ttc	-tc	1	8	All	0
N	66	F66F	ttC	ttT	8	8	AY.39	0.000198
N	66	F66F	ttC	ttT	8	8	B.1.1.157	0.007306
N	66	F66A	TTC	GCT	5	5	All	0.000001
N	66	F66T	TTc	ACc	4	5	All	0.000001
N	66	F66T	TTC	ACA	1	5	All	0
N	66	F66S	tTc	tCc	5	5	B.1	0.000046
N	66	F66G	TTc	GGc	2	4	All	0
N	66	F66G	TTC	GGG	1	4	All	0
N	66	F66G	TTC	GGA	1	4	All	0
N	66	F66V	Ttc	Gtc	4	4	AY.42	0.000161
N	66	F66V	Ttc	Gtc	4	4	AY.98.1	0.000194
N	66	F66F	ttC	ttT	4	4	B.1.177.4	0.000844
N	66	F66F	ttC	ttT	4	4	B.1.429	0.000094
N	66	F66V	Ttc	Gtc	4	4	B.1.617.2	0.000015
N	66	F66C	tTc	tGc	4	4	P.1	0.000063
N	66	F66S	TTc	AGc	4	4	P.1	0.000063
N	66	F66I	Ttc	Atc	3	4	P.1	0.000047
N	66	F66I	TtC	AtA	1	4	P.1	0.000016
N	66	F66X	tTC	tGA	3	3	All	0.000001
N	66	F66R	TTC	AGA	3	3	All	0.000001
N	66	F66F	ttC	ttT	3	3	AT.1	0.015385
N	66	F66F	ttC	ttT	3	3	AY.102	0.00008
N	66	F66F	ttC	ttT	3	3	AY.26	0.000085
N	66	F66F	ttC	ttT	3	3	AY.29	0.000047
N	66	F66V	Ttc	Gtc	3	3	AY.46	0.000312
N	66	F66A	TTC	GCT	3	3	B.1.1.7	0.000003
N	66	F66F	ttC	ttT	3	3	B.1.378	0.020548
N	66	F66F	ttC	ttT	3	3	B.1.427	0.000151
N	66	F66F	ttC	ttT	3	3	B.1.610	0.010638
N	66	F66F	ttC	ttT	3	3	D.2	0.000225
N	66	F66A	TTC	GCT	2	2		0.111111
N	66	F66T	TTc	ACc	2	2		0.111111
N	66	F66V	TtC	GtG	2	2		0.111111
N	66	F66C	tTc	tGc	2	2		0.111111
N	66	F66Y	tTc	tAc	2	2	All	0
N	66	F66V	Ttc	Gtc	2	2	AY.103	0.000012
N	66	F66F	ttC	ttT	2	2	AY.118	0.000125
N	66	F66F	ttC	ttT	2	2	AY.20	0.000078
N	66	F66L	Ttc	Ctc	2	2	AY.4	0.000003
N	66	F66V	Ttc	Gtc	2	2	AY.4	0.000003
N	66	F66del	TTC	---	2	2	AY.43	0.000009
N	66	F66I	TtC	AtA	1	2	AY.43	0.000004
N	66	F66I	Ttc	Atc	1	2	AY.43	0.000004
N	66	F66L	ttC	ttG	1	2	AY.43	0.000004
N	66	F66T	TTc	ACc	1	2	AY.43	0.000004
N	66	F66T	TTC	ACA	1	2	AY.43	0.000004
N	66	F66L	Ttc	Ctc	1	2	AY.43	0.000004
N	66	F66del1	ttC	tt-	2	2	AY.44	0.000012
N	66	F66V	Ttc	Gtc	2	2	AY.46.6	0.000144
N	66	F66G	TTc	GGc	1	2	B.1	0.000009
N	66	F66V	TtC	GtG	1	2	B.1	0.000009
N	66	F66G	TTC	GGG	1	2	B.1	0.000009
N	66	F66V	Ttc	Gtc	1	2	B.1	0.000009
N	66	F66L	TtC	CtG	1	2	B.1.1	0.000018
N	66	F66L	ttC	ttA	1	2	B.1.1	0.000018
N	66	F66V	TtC	GtA	1	2	B.1.1.28	0.000311
N	66	F66G	TTc	GGc	1	2	B.1.1.28	0.000311
N	66	F66I	TtC	AtA	1	2	B.1.1.28	0.000311
N	66	F66I	Ttc	Atc	1	2	B.1.1.28	0.000311
N	66	F66V	Ttc	Gtc	1	2	B.1.1.28	0.000311
N	66	F66G	TTC	GGA	1	2	B.1.1.28	0.000311
N	66	F66del	TTC	---	2	2	B.1.1.7	0.000002
N	66	F66del1	ttC	tt-	2	2	B.1.1.7	0.000002
N	66	F66F	ttC	ttT	2	2	B.1.177	0.000026
N	66	F66V	Ttc	Gtc	2	2	B.1.258.17	0.000208
N	66	F66F	ttC	ttT	2	2	B.1.258.17	0.000208
N	66	F66F	ttC	ttT	2	2	B.1.351.3	0.001753
N	66	F66F	ttC	ttT	2	2	B.1.409	0.001563
N	66	F66F	ttC	ttT	2	2	B.1.517	0.000854
N	66	F66F	ttC	ttT	2	2	B.1.575.1	0.004878
N	66	F66S	tTc	tCc	1	2	B.1.617.2	0.000004
N	66	F66S	tTC	tCT	1	2	B.1.617.2	0.000004
N	66	F66I	TtC	AtA	1	2	P.2	0.000187
N	66	F66I	Ttc	Atc	1	2	P.2	0.000187
N	66	F66F	ttC	ttT	2	2	Q.8	0.00033
N	66	F66D	TTc	GAc	1	1	All	0
N	66	F66K	TTC	AAA	1	1	All	0
N	66	F66W	tTC	tGG	1	1	All	0
N	66	F66N	TTc	AAc	1	1	All	0
N	66	F66F	ttC	ttT	1	1	AY.100	0.000046
N	66	F66S	tTc	tCc	1	1	AY.16	0.00038
N	66	F66F	ttC	ttT	1	1	AY.16.1	0.00047
N	66	F66del	TTC	---	1	1	AY.18	0.010101
N	66	F66F	ttC	ttT	1	1	AY.18	0.010101
N	66	F66F	ttC	ttT	1	1	AY.23	0.00007
N	66	F66del1	Ttc	-tc	1	1	AY.3	0.00001
N	66	F66F	ttC	ttT	1	1	AY.3.1	0.000085
N	66	F66F	ttC	ttT	1	1	AY.39.1	0.00004
N	66	F66S	tTc	tCc	1	1	AY.4	0.000002
N	66	F66del	TTC	---	1	1	AY.4	0.000002
N	66	F66V	Ttc	Gtc	1	1	AY.41	0.000294
N	66	F66K	TTC	AAA	1	1	AY.43	0.000004
N	66	F66N	TTc	AAc	1	1	AY.43	0.000004
N	66	F66C	tTc	tGc	1	1	AY.44	0.000006
N	66	F66L	Ttc	Ctc	1	1	AY.44	0.000006
N	66	F66F	ttC	ttT	1	1	AY.5.3	0.000337
N	66	F66F	ttC	ttT	1	1	AY.56	0.001605
N	66	F66F	ttC	ttT	1	1	AY.58	0.000907
N	66	F66F	ttC	ttT	1	1	AY.61	0.000105
N	66	F66del	TTC	---	1	1	AY.67	0.000464
N	66	F66F	ttC	ttT	1	1	AY.7.1	0.000113
N	66	F66V	Ttc	Gtc	1	1	AY.7.2	0.000559
N	66	F66V	Ttc	Gtc	1	1	AY.70	0.000209
N	66	F66del1	ttC	tt-	1	1	AY.79	0.001211
N	66	F66F	ttC	ttT	1	1	AY.84	0.000437
N	66	F66del	TTC	---	1	1	AY.9.2	0.000037
N	66	F66del	TTC	---	1	1	AY.98	0.000079
N	66	F66F	ttC	ttT	1	1	AY.98	0.000079
N	66	F66del	TTC	---	1	1	AY.99	0.001049
N	66	F66del	TTC	---	1	1	AZ.2	0.000821
N	66	F66C	tTc	tGc	1	1	B.1	0.000009
N	66	F66del	TTC	---	1	1	B.1	0.000009
N	66	F66L	ttC	ttG	1	1	B.1	0.000009
N	66	F66W	tTC	tGG	1	1	B.1	0.000009
N	66	F66del1	ttC	tt-	1	1	B.1.1	0.000018
N	66	F66del	TTC	---	1	1	B.1.1	0.000018
N	66	F66F	ttC	ttT	1	1	B.1.1	0.000018
N	66	F66S	tTC	tCG	1	1	B.1.1	0.000018
N	66	F66del	TTC	---	1	1	B.1.1.139	0.022727
N	66	F66F	ttC	ttT	1	1	B.1.1.176	0.000439
N	66	F66L	Ttc	Ctc	1	1	B.1.1.214	0.000055
N	66	F66del	TTC	---	1	1	B.1.1.216	0.00089
N	66	F66F	ttC	ttT	1	1	B.1.1.218	0.007692
N	66	F66F	ttC	ttT	1	1	B.1.1.220	0.001859
N	66	F66F	ttC	ttT	1	1	B.1.1.222	0.000204
N	66	F66L	ttC	ttG	1	1	B.1.1.25	0.000569
N	66	F66C	tTc	tGc	1	1	B.1.1.28	0.000311
N	66	F66L	ttC	ttA	1	1	B.1.1.28	0.000311
N	66	F66X	tTC	tGA	1	1	B.1.1.28	0.000311
N	66	F66R	TTC	AGA	1	1	B.1.1.28	0.000311
N	66	F66S	TTc	AGc	1	1	B.1.1.28	0.000311
N	66	F66F	ttC	ttT	1	1	B.1.1.519	0.00004
N	66	F66del	TTC	---	1	1	B.1.1.63	0.000386
N	66	F66C	tTC	tGT	1	1	B.1.1.7	0.000001
N	66	F66L	Ttc	Ctc	1	1	B.1.1.7	0.000001
N	66	F66Y	tTc	tAc	1	1	B.1.157	0.002985
N	66	F66V	Ttc	Gtc	1	1	B.1.157	0.002985
N	66	F66D	TTc	GAc	1	1	B.1.157	0.002985
N	66	F66C	tTC	tGT	1	1	B.1.177	0.000013
N	66	F66L	Ttc	Ctc	1	1	B.1.177	0.000013
N	66	F66S	tTc	tCc	1	1	B.1.177.60	0.000218
N	66	F66del	TTC	---	1	1	B.1.177.63	0.002703
N	66	F66T	TTc	ACc	1	1	B.1.177.82	0.000477
N	66	F66S	tTc	tCc	1	1	B.1.2	0.000009
N	66	F66F	ttC	ttT	1	1	B.1.221	0.000071
N	66	F66F	ttC	ttT	1	1	B.1.234	0.000132
N	66	F66F	ttC	ttT	1	1	B.1.241	0.000812
N	66	F66F	ttC	ttT	1	1	B.1.258	0.000067
N	66	F66del	TTC	---	1	1	B.1.258.11	0.000396
N	66	F66S	tTc	tCc	1	1	B.1.338	0.008621
N	66	F66F	ttC	ttT	1	1	B.1.36	0.000146
N	66	F66F	ttC	ttT	1	1	B.1.36.17	0.000494
N	66	F66del	TTC	---	1	1	B.1.415	0.014286
N	66	F66del	TTC	---	1	1	B.1.429	0.000024
N	66	F66del	TTC	---	1	1	B.1.439	0.005917
N	66	F66Y	tTc	tAc	1	1	B.1.497	0.000315
N	66	F66F	ttC	ttT	1	1	B.1.525	0.000113
N	66	F66del1	ttC	tt-	1	1	B.1.560	0.00463
N	66	F66F	ttC	ttT	1	1	B.1.561	0.000397
N	66	F66F	ttC	ttT	1	1	B.1.575	0.000303
N	66	F66C	tTc	tGc	1	1	B.1.596	0.000087
N	66	F66del	TTC	---	1	1	B.1.617.2	0.000004
N	66	F66L	Ttc	Ctc	1	1	B.1.617.2	0.000004
N	66	F66L	Ttc	Ctc	1	1	B.1.637	0.000073
N	66	F66V	Ttc	Gtc	1	1	B.1.91	0.002075
N	66	F66L	ttC	ttA	1	1	D.2	0.000075
N	66	F66S	tTc	tCc	1	1	D.2	0.000075
N	66	F66del	TTC	---	1	1	P.1	0.000016
N	66	F66L	ttC	ttA	1	1	P.1	0.000016
N	66	F66X	tTC	tGA	1	1	P.1	0.000016
N	66	F66R	TTC	AGA	1	1	P.1	0.000016
N	66	F66F	ttC	ttT	1	1	P.1.15	0.000232
N	66	F66C	tTc	tGc	1	1	P.2	0.000187
N	66	F66L	ttC	ttA	1	1	P.2	0.000187
N	66	F66X	tTC	tGA	1	1	P.2	0.000187
N	66	F66R	TTC	AGA	1	1	P.2	0.000187
N	66	F66S	TTc	AGc	1	1	P.2	0.000187
N	66	F66F	ttC	ttT	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.