CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1052

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
S	1052	F1052F		syn	ttC	ttT	1087	1087	1	24716-24718
S	1052	F1052L		nonsyn	ttC	ttA	634	399	0.629338	24716-24718
S	1052	F1052L		nonsyn	Ttc	Ctc	634	231	0.364353	24716-24718
S	1052	F1052L		nonsyn	TtC	CtT	634	4	0.00630915	24716-24718
S	1052	F1052Y		nonsyn	tTc	tAc	441	439	0.995465	24716-24718
S	1052	F1052Y		nonsyn	tTC	tAT	441	2	0.00453515	24716-24718
S	1052	F1052del		del	TTC	---	35	35	1	24716-24718
S	1052	F1052I		nonsyn	Ttc	Atc	33	31	0.939394	24716-24718
S	1052	F1052I		nonsyn	TtC	AtA	33	1	0.030303	24716-24718
S	1052	F1052I		nonsyn	TtC	AtT	33	1	0.030303	24716-24718
S	1052	F1052V		nonsyn	Ttc	Gtc	24	23	0.958333	24716-24718
S	1052	F1052V		nonsyn	TtC	GtT	24	1	0.0416667	24716-24718
S	1052	F1052del1		del	ttC	tt-	8	7	0.875	24716-24718
S	1052	F1052del1		del	TtC	Ct-	8	1	0.125	24716-24718
S	1052	F1052S		nonsyn	tTc	tCc	5	4	0.8	24716-24718
S	1052	F1052S		nonsyn	TTc	AGc	5	1	0.2	24716-24718
S	1052	F1052D		nonsyn	TTC	GAT	2	1	0.5	24716-24718
S	1052	F1052D		nonsyn	TTc	GAc	2	1	0.5	24716-24718
S	1052	F1052H		nonsyn	TTC	CAT	2	1	0.5	24716-24718
S	1052	F1052H		nonsyn	TTc	CAc	2	1	0.5	24716-24718
S	1052	F1052K		nonsyn	TTC	AAA	1	1	1	24716-24718
S	1052	F1052N		nonsyn	TTc	AAc	1	1	1	24716-24718
S	1052	F1052X		nonsyn	tTC	tAA	1	1	1	24716-24718

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
S	1052	F1052F	ttC	ttT	1087	1087	All	0.000208
S	1052	F1052L	ttC	ttA	399	634	All	0.000076
S	1052	F1052L	Ttc	Ctc	231	634	All	0.000044
S	1052	F1052L	TtC	CtT	4	634	All	0.000001
S	1052	F1052Y	tTc	tAc	439	441	All	0.000084
S	1052	F1052Y	tTC	tAT	2	441	All	0
S	1052	F1052Y	tTc	tAc	421	421	B.1.627	0.850505
S	1052	F1052L	ttC	ttA	363	372	B.1	0.003325
S	1052	F1052L	Ttc	Ctc	8	372	B.1	0.000073
S	1052	F1052L	TtC	CtT	1	372	B.1	0.000009
S	1052	F1052F	ttC	ttT	226	226	B.1.637	0.016514
S	1052	F1052F	ttC	ttT	97	97	B.1.617.2	0.000365
S	1052	F1052F	ttC	ttT	95	95	B.1.1.7	0.000085
S	1052	F1052F	ttC	ttT	83	83	AY.4	0.000129
S	1052	F1052L	Ttc	Ctc	74	78	AY.4	0.000115
S	1052	F1052L	ttC	ttA	4	78	AY.4	0.000006
S	1052	F1052F	ttC	ttT	77	77	AY.3	0.000766
S	1052	F1052F	ttC	ttT	58	58	B.1	0.000531
S	1052	F1052F	ttC	ttT	47	47	AY.25	0.000283
S	1052	F1052F	ttC	ttT	46	46	B.1.427	0.002323
S	1052	F1052F	ttC	ttT	39	39	B.1.2	0.000343
S	1052	F1052del	TTC	---	35	35	All	0.000007
S	1052	F1052L	Ttc	Ctc	31	34	B.1.2	0.000273
S	1052	F1052L	ttC	ttA	3	34	B.1.2	0.000026
S	1052	F1052I	Ttc	Atc	31	33	All	0.000006
S	1052	F1052I	TtC	AtT	1	33	All	0
S	1052	F1052I	TtC	AtA	1	33	All	0
S	1052	F1052V	Ttc	Gtc	23	24	All	0.000004
S	1052	F1052V	TtC	GtT	1	24	All	0
S	1052	F1052F	ttC	ttT	22	22	AY.44	0.000134
S	1052	F1052F	ttC	ttT	19	19	AY.61	0.001991
S	1052	F1052L	Ttc	Ctc	17	17	AY.3	0.000169
S	1052	F1052F	ttC	ttT	17	17	AY.54	0.001621
S	1052	F1052L	Ttc	Ctc	16	16	C.37	0.001857
S	1052	F1052F	ttC	ttT	15	15	AY.103	0.000093
S	1052	F1052F	ttC	ttT	15	15	AY.20	0.000583
S	1052	F1052F	ttC	ttT	14	14	AY.100	0.000644
S	1052	F1052F	ttC	ttT	14	14	AY.43	0.000062
S	1052	F1052L	Ttc	Ctc	14	14	B.1.351.2	0.004236
S	1052	F1052F	ttC	ttT	12	12	B.1.351	0.000357
S	1052	F1052del	TTC	---	11	11	B.1.1.7	0.00001
S	1052	F1052V	Ttc	Gtc	11	11	B.1.177.79	0.025761
S	1052	F1052F	ttC	ttT	10	10	AY.102	0.000265
S	1052	F1052F	ttC	ttT	10	10	AY.92	0.002873
S	1052	F1052I	Ttc	Atc	10	10	B.1.177.86	0.001835
S	1052	F1052F	ttC	ttT	9	9	B.1.1.222	0.001836
S	1052	F1052del1	ttC	tt-	7	8	All	0.000001
S	1052	F1052del1	TtC	Ct-	1	8	All	0
S	1052	F1052L	Ttc	Ctc	8	8	AY.42	0.000322
S	1052	F1052L	Ttc	Ctc	6	8	B.1.1.7	0.000005
S	1052	F1052L	ttC	ttA	2	8	B.1.1.7	0.000002
S	1052	F1052F	ttC	ttT	7	7	AY.9	0.000473
S	1052	F1052I	Ttc	Atc	6	6	AY.100	0.000276
S	1052	F1052F	ttC	ttT	6	6	AY.47	0.000187
S	1052	F1052F	ttC	ttT	6	6	AY.52	0.004886
S	1052	F1052F	ttC	ttT	6	6	B.1.1.33	0.002525
S	1052	F1052L	Ttc	Ctc	6	6	B.1.160	0.000187
S	1052	F1052F	ttC	ttT	6	6	B.1.177	0.000079
S	1052	F1052F	ttC	ttT	6	6	B.1.235	0.015113
S	1052	F1052F	ttC	ttT	6	6	B.1.416.1	0.009375
S	1052	F1052L	Ttc	Ctc	6	6	B.1.617.2	0.000023
S	1052	F1052Y	tTc	tAc	3	5		0.166667
S	1052	F1052Y	tTC	tAT	2	5		0.111111
S	1052	F1052S	tTc	tCc	4	5	All	0.000001
S	1052	F1052S	TTc	AGc	1	5	All	0
S	1052	F1052L	Ttc	Ctc	4	5	AY.44	0.000024
S	1052	F1052L	ttC	ttA	1	5	AY.44	0.000006
S	1052	F1052Y	tTc	tAc	5	5	B.1	0.000046
S	1052	F1052V	Ttc	Gtc	5	5	B.1.1.7	0.000004
S	1052	F1052I	Ttc	Atc	5	5	B.1.617.2	0.000019
S	1052	F1052F	ttC	ttT	5	5	P.1	0.000079
S	1052	F1052F	ttC	ttT	5	5	R.1	0.00045
S	1052	F1052L	Ttc	Ctc	3	4	AY.103	0.000019
S	1052	F1052L	ttC	ttA	1	4	AY.103	0.000006
S	1052	F1052F	ttC	ttT	4	4	AY.3.1	0.000341
S	1052	F1052F	ttC	ttT	4	4	AY.35	0.000932
S	1052	F1052L	Ttc	Ctc	4	4	AY.51	0.003636
S	1052	F1052F	ttC	ttT	4	4	AY.98	0.000316
S	1052	F1052F	ttC	ttT	4	4	B.1.1.284	0.00043
S	1052	F1052L	Ttc	Ctc	4	4	B.1.1.519	0.000159
S	1052	F1052F	ttC	ttT	4	4	B.1.243	0.000278
S	1052	F1052F	ttC	ttT	3	3		0.166667
S	1052	F1052L	ttC	ttA	1	3		0.055556
S	1052	F1052L	TtC	CtT	1	3		0.055556
S	1052	F1052L	Ttc	Ctc	1	3		0.055556
S	1052	F1052I	Ttc	Atc	3	3	AY.117	0.000254
S	1052	F1052F	ttC	ttT	3	3	AY.120	0.000112
S	1052	F1052L	Ttc	Ctc	2	3	AY.25	0.000012
S	1052	F1052L	ttC	ttA	1	3	AY.25	0.000006
S	1052	F1052I	Ttc	Atc	3	3	AY.3.1	0.000256
S	1052	F1052F	ttC	ttT	3	3	AY.30	0.001187
S	1052	F1052F	ttC	ttT	3	3	AY.39	0.000074
S	1052	F1052del	TTC	---	3	3	AY.4	0.000005
S	1052	F1052Y	tTc	tAc	3	3	AY.4	0.000005
S	1052	F1052F	ttC	ttT	3	3	AY.4.2	0.000065
S	1052	F1052F	ttC	ttT	3	3	AY.46.4	0.000494
S	1052	F1052F	ttC	ttT	3	3	AY.5	0.000062
S	1052	F1052F	ttC	ttT	3	3	AY.75.1	0.000541
S	1052	F1052L	Ttc	Ctc	3	3	B	0.000383
S	1052	F1052L	ttC	ttA	3	3	B.1.1	0.000054
S	1052	F1052L	ttC	ttA	3	3	B.1.177.7	0.000495
S	1052	F1052F	ttC	ttT	3	3	B.1.177.72	0.010169
S	1052	F1052D	TTc	GAc	1	2		0.055556
S	1052	F1052D	TTC	GAT	1	2		0.055556
S	1052	F1052H	TTC	CAT	1	2		0.055556
S	1052	F1052V	TtC	GtT	1	2		0.055556
S	1052	F1052I	Ttc	Atc	1	2		0.055556
S	1052	F1052H	TTc	CAc	1	2		0.055556
S	1052	F1052I	TtC	AtA	1	2		0.055556
S	1052	F1052V	Ttc	Gtc	1	2		0.055556
S	1052	F1052D	TTc	GAc	1	2	All	0
S	1052	F1052D	TTC	GAT	1	2	All	0
S	1052	F1052H	TTC	CAT	1	2	All	0
S	1052	F1052H	TTc	CAc	1	2	All	0
S	1052	F1052F	ttC	ttT	2	2	AY.109	0.001479
S	1052	F1052F	ttC	ttT	2	2	AY.117	0.000169
S	1052	F1052V	Ttc	Gtc	2	2	AY.118	0.000125
S	1052	F1052F	ttC	ttT	2	2	AY.23	0.000139
S	1052	F1052L	Ttc	Ctc	2	2	AY.39	0.000049
S	1052	F1052I	Ttc	Atc	2	2	AY.4	0.000003
S	1052	F1052del	TTC	---	2	2	AY.43	0.000009
S	1052	F1052Y	tTc	tAc	2	2	AY.43	0.000009
S	1052	F1052L	Ttc	Ctc	2	2	AY.43	0.000009
S	1052	F1052F	ttC	ttT	2	2	AY.6	0.000082
S	1052	F1052F	ttC	ttT	2	2	AY.84	0.000875
S	1052	F1052S	tTc	tCc	2	2	B	0.000256
S	1052	F1052F	ttC	ttT	2	2	B.1.1	0.000036
S	1052	F1052L	Ttc	Ctc	2	2	B.1.1.214	0.000111
S	1052	F1052F	ttC	ttT	2	2	B.1.1.316	0.00185
S	1052	F1052del	TTC	---	2	2	B.1.177	0.000026
S	1052	F1052F	ttC	ttT	2	2	B.1.221	0.000142
S	1052	F1052L	Ttc	Ctc	1	2	B.1.221	0.000071
S	1052	F1052L	TtC	CtT	1	2	B.1.221	0.000071
S	1052	F1052F	ttC	ttT	2	2	B.1.36.29	0.001035
S	1052	F1052F	ttC	ttT	2	2	B.1.389	0.002004
S	1052	F1052F	ttC	ttT	2	2	B.1.396	0.001411
S	1052	F1052F	ttC	ttT	2	2	B.1.526	0.000047
S	1052	F1052L	Ttc	Ctc	2	2	B.1.595	0.000522
S	1052	F1052F	ttC	ttT	2	2	B.1.596	0.000174
S	1052	F1052F	ttC	ttT	2	2	B.1.617.1	0.000258
S	1052	F1052L	Ttc	Ctc	2	2	B.1.621	0.000177
S	1052	F1052L	Ttc	Ctc	2	2	P.1	0.000032
S	1052	F1052F	ttC	ttT	2	2	P.1.17	0.000324
S	1052	F1052F	ttC	ttT	2	2	S.1	0.009901
S	1052	F1052N	TTc	AAc	1	1		0.055556
S	1052	F1052X	tTC	tAA	1	1		0.055556
S	1052	F1052K	TTC	AAA	1	1		0.055556
S	1052	F1052F	ttC	ttT	1	1	A.2.5	0.000499
S	1052	F1052X	tTC	tAA	1	1	All	0
S	1052	F1052N	TTc	AAc	1	1	All	0
S	1052	F1052K	TTC	AAA	1	1	All	0
S	1052	F1052F	ttC	ttT	1	1	AY.1	0.000396
S	1052	F1052V	Ttc	Gtc	1	1	AY.103	0.000006
S	1052	F1052F	ttC	ttT	1	1	AY.105	0.000643
S	1052	F1052F	ttC	ttT	1	1	AY.106	0.000335
S	1052	F1052del	TTC	---	1	1	AY.111	0.000183
S	1052	F1052L	ttC	ttA	1	1	AY.119	0.000035
S	1052	F1052del	TTC	---	1	1	AY.120	0.000037
S	1052	F1052L	Ttc	Ctc	1	1	AY.120.2.1	0.000498
S	1052	F1052del1	ttC	tt-	1	1	AY.23	0.00007
S	1052	F1052L	Ttc	Ctc	1	1	AY.26	0.000028
S	1052	F1052Y	tTc	tAc	1	1	AY.29	0.000016
S	1052	F1052F	ttC	ttT	1	1	AY.29.1	0.000221
S	1052	F1052F	ttC	ttT	1	1	AY.33	0.000067
S	1052	F1052F	ttC	ttT	1	1	AY.34.1	0.00051
S	1052	F1052L	Ttc	Ctc	1	1	AY.4.2	0.000022
S	1052	F1052L	Ttc	Ctc	1	1	AY.4.4	0.000409
S	1052	F1052L	Ttc	Ctc	1	1	AY.4.5	0.000107
S	1052	F1052del	TTC	---	1	1	AY.4.5	0.000107
S	1052	F1052F	ttC	ttT	1	1	AY.42	0.00004
S	1052	F1052L	ttC	ttA	1	1	AY.45	0.000122
S	1052	F1052F	ttC	ttT	1	1	AY.45	0.000122
S	1052	F1052F	ttC	ttT	1	1	AY.46	0.000104
S	1052	F1052del	TTC	---	1	1	AY.46.2	0.000635
S	1052	F1052del1	ttC	tt-	1	1	AY.48	0.000465
S	1052	F1052F	ttC	ttT	1	1	AY.48	0.000465
S	1052	F1052I	Ttc	Atc	1	1	AY.55	0.000917
S	1052	F1052F	ttC	ttT	1	1	AY.71	0.000475
S	1052	F1052del	TTC	---	1	1	AY.75	0.000056
S	1052	F1052F	ttC	ttT	1	1	AY.87	0.000833
S	1052	F1052F	ttC	ttT	1	1	AY.9.2	0.000037
S	1052	F1052del	TTC	---	1	1	AY.93	0.000273
S	1052	F1052Y	tTc	tAc	1	1	B	0.000128
S	1052	F1052del	TTC	---	1	1	B.1	0.000009
S	1052	F1052S	tTc	tCc	1	1	B.1	0.000009
S	1052	F1052V	Ttc	Gtc	1	1	B.1	0.000009
S	1052	F1052Y	tTc	tAc	1	1	B.1.1	0.000018
S	1052	F1052F	ttC	ttT	1	1	B.1.1.139	0.022727
S	1052	F1052F	ttC	ttT	1	1	B.1.1.170	0.001247
S	1052	F1052del	TTC	---	1	1	B.1.1.236	0.006897
S	1052	F1052F	ttC	ttT	1	1	B.1.1.25	0.000569
S	1052	F1052del1	ttC	tt-	1	1	B.1.1.28	0.000311
S	1052	F1052F	ttC	ttT	1	1	B.1.1.317	0.000412
S	1052	F1052del	TTC	---	1	1	B.1.1.37	0.000193
S	1052	F1052L	TtC	CtT	1	1	B.1.1.37	0.000193
S	1052	F1052V	Ttc	Gtc	1	1	B.1.1.385	0.004464
S	1052	F1052L	ttC	ttA	1	1	B.1.1.387	0.058824
S	1052	F1052L	Ttc	Ctc	1	1	B.1.1.485	0.016667
S	1052	F1052F	ttC	ttT	1	1	B.1.1.519	0.00004
S	1052	F1052Y	tTc	tAc	1	1	B.1.1.7	0.000001
S	1052	F1052del1	ttC	tt-	1	1	B.1.1.7	0.000001
S	1052	F1052F	ttC	ttT	1	1	B.1.111	0.001175
S	1052	F1052L	Ttc	Ctc	1	1	B.1.151	0.011111
S	1052	F1052F	ttC	ttT	1	1	B.1.160	0.000031
S	1052	F1052S	tTc	tCc	1	1	B.1.177	0.000013
S	1052	F1052del	TTC	---	1	1	B.1.177.18	0.00116
S	1052	F1052del	TTC	---	1	1	B.1.177.5	0.001242
S	1052	F1052I	TtC	AtT	1	1	B.1.177.65	0.000665
S	1052	F1052L	ttC	ttA	1	1	B.1.190	0.01
S	1052	F1052del1	ttC	tt-	1	1	B.1.2	0.000009
S	1052	F1052L	ttC	ttA	1	1	B.1.258.17	0.000104
S	1052	F1052L	ttC	ttA	1	1	B.1.311	0.000275
S	1052	F1052L	ttC	ttA	1	1	B.1.326	0.007576
S	1052	F1052F	ttC	ttT	1	1	B.1.340	0.004292
S	1052	F1052L	ttC	ttA	1	1	B.1.340	0.004292
S	1052	F1052L	Ttc	Ctc	1	1	B.1.351	0.00003
S	1052	F1052del	TTC	---	1	1	B.1.351	0.00003
S	1052	F1052F	ttC	ttT	1	1	B.1.351.3	0.000876
S	1052	F1052F	ttC	ttT	1	1	B.1.36	0.000146
S	1052	F1052L	Ttc	Ctc	1	1	B.1.36.36	0.000602
S	1052	F1052L	ttC	ttA	1	1	B.1.391	0.001127
S	1052	F1052del	TTC	---	1	1	B.1.415	0.014286
S	1052	F1052L	ttC	ttA	1	1	B.1.429	0.000024
S	1052	F1052del1	ttC	tt-	1	1	B.1.429	0.000024
S	1052	F1052L	ttC	ttA	1	1	B.1.432	0.011236
S	1052	F1052V	Ttc	Gtc	1	1	B.1.459	0.004082
S	1052	F1052L	ttC	ttA	1	1	B.1.462	0.007246
S	1052	F1052L	ttC	ttA	1	1	B.1.521	0.004975
S	1052	F1052L	Ttc	Ctc	1	1	B.1.526	0.000024
S	1052	F1052F	ttC	ttT	1	1	B.1.537	0.02
S	1052	F1052L	ttC	ttA	1	1	B.1.564	0.000426
S	1052	F1052L	ttC	ttA	1	1	B.1.596	0.000087
S	1052	F1052L	Ttc	Ctc	1	1	B.1.601	0.030303
S	1052	F1052del1	ttC	tt-	1	1	B.1.617.2	0.000004
S	1052	F1052S	TTc	AGc	1	1	B.1.617.2	0.000004
S	1052	F1052del	TTC	---	1	1	B.1.617.2	0.000004
S	1052	F1052F	ttC	ttT	1	1	B.1.633	0.041667
S	1052	F1052F	ttC	ttT	1	1	B.1.9.4	0.006135
S	1052	F1052Y	tTc	tAc	1	1	B.55	0.00295
S	1052	F1052L	ttC	ttA	1	1	B.6.6	0.000889
S	1052	F1052F	ttC	ttT	1	1	C.35	0.000774
S	1052	F1052del	TTC	---	1	1	C.37	0.000116
S	1052	F1052F	ttC	ttT	1	1	D.2	0.000075
S	1052	F1052del	TTC	---	1	1	P.1.15	0.000232
S	1052	F1052del1	TtC	Ct-	1	1	Q.1	0.000126
S	1052	F1052F	ttC	ttT	1	1	Q.8	0.000165
S	1052	F1052del	TTC	---	1	1	Q.8	0.000165
S	1052	F1052L	ttC	ttA	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.