CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1023

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	1023	N1023N		syn	aaT	aaC	405	405	1	24629-24631
S	1023	N1023S		nonsyn	aAt	aGt	192	192	1	24629-24631
S	1023	N1023D		nonsyn	Aat	Gat	70	70	1	24629-24631
S	1023	N1023del		del	AAT	---	38	38	1	24629-24631
S	1023	N1023Y		nonsyn	Aat	Tat	30	30	1	24629-24631
S	1023	N1023T		nonsyn	aAt	aCt	27	27	1	24629-24631
S	1023	N1023K		nonsyn	aaT	aaG	20	16	0.8	24629-24631
S	1023	N1023K		nonsyn	aaT	aaA	20	4	0.2	24629-24631
S	1023	N1023I		nonsyn	aAt	aTt	11	11	1	24629-24631
S	1023	N1023H		nonsyn	Aat	Cat	3	3	1	24629-24631
S	1023	N1023del1		del	Aat	-at	3	2	0.666667	24629-24631
S	1023	N1023del1		del	aaT	aa-	3	1	0.333333	24629-24631
S	1023	N1023G		nonsyn	AAt	GGt	2	2	1	24629-24631
S	1023	N1023P		nonsyn	AAt	CCt	1	1	1	24629-24631
S	1023	N1023V		nonsyn	AAt	GTt	1	1	1	24629-24631

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	1023	N1023N	aaT	aaC	405	405	All	0.000077
S	1023	N1023S	aAt	aGt	192	192	All	0.000037
S	1023	N1023S	aAt	aGt	105	105	B.1.2	0.000925
S	1023	N1023D	Aat	Gat	70	70	All	0.000013
S	1023	N1023N	aaT	aaC	66	66	AY.44	0.000402
S	1023	N1023N	aaT	aaC	56	56	B.1.617.2	0.000211
S	1023	N1023N	aaT	aaC	41	41	B.1.1.7	0.000037
S	1023	N1023del	AAT	---	38	38	All	0.000007
S	1023	N1023Y	Aat	Tat	30	30	All	0.000006
S	1023	N1023T	aAt	aCt	27	27	All	0.000005
S	1023	N1023N	aaT	aaC	25	25	AY.4	0.000039
S	1023	N1023N	aaT	aaC	25	25	B.1.2	0.00022
S	1023	N1023D	Aat	Gat	23	23	AY.119	0.000812
S	1023	N1023S	aAt	aGt	22	22	AY.4	0.000034
S	1023	N1023K	aaT	aaG	16	20	All	0.000003
S	1023	N1023K	aaT	aaA	4	20	All	0.000001
S	1023	N1023N	aaT	aaC	20	20	B.1.1.391	0.17094
S	1023	N1023N	aaT	aaC	17	17	B.1	0.000156
S	1023	N1023N	aaT	aaC	16	16	AY.61	0.001676
S	1023	N1023T	aAt	aCt	14	14	AY.43	0.000062
S	1023	N1023N	aaT	aaC	14	14	B.1.1.464	0.020619
S	1023	N1023N	aaT	aaC	12	12	AY.120	0.000446
S	1023	N1023del	AAT	---	12	12	B.1.1.7	0.000011
S	1023	N1023I	aAt	aTt	11	11	All	0.000002
S	1023	N1023K	aaT	aaG	10	10	AY.25	0.00006
S	1023	N1023D	Aat	Gat	10	10	AY.5	0.000206
S	1023	N1023N	aaT	aaC	10	10	B.1.1.90	1
S	1023	N1023S	aAt	aGt	10	10	P.1	0.000158
S	1023	N1023N	aaT	aaC	9	9	AY.103	0.000056
S	1023	N1023S	aAt	aGt	9	9	AY.4.2	0.000195
S	1023	N1023S	aAt	aGt	9	9	B.1	0.000082
S	1023	N1023N	aaT	aaC	9	9	B.1.160.14	0.019068
S	1023	N1023N	aaT	aaC	8	8	AY.3	0.00008
S	1023	N1023D	Aat	Gat	7	7	AY.43	0.000031
S	1023	N1023Y	Aat	Tat	7	7	Q.3	0.001015
S	1023	N1023N	aaT	aaC	5	5	AY.43	0.000022
S	1023	N1023Y	Aat	Tat	5	5	B.1.177.81	0.000947
S	1023	N1023S	aAt	aGt	4	4	AY.117	0.000338
S	1023	N1023del	AAT	---	4	4	AY.4	0.000006
S	1023	N1023N	aaT	aaC	4	4	B.1.1	0.000073
S	1023	N1023del	AAT	---	4	4	B.1.177	0.000053
S	1023	N1023H	Aat	Cat	3	3	All	0.000001
S	1023	N1023del1	Aat	-at	2	3	All	0
S	1023	N1023del1	aaT	aa-	1	3	All	0
S	1023	N1023D	Aat	Gat	3	3	AY.100	0.000138
S	1023	N1023D	Aat	Gat	3	3	AY.120	0.000112
S	1023	N1023N	aaT	aaC	3	3	AY.20	0.000117
S	1023	N1023I	aAt	aTt	3	3	AY.21	0.005693
S	1023	N1023D	Aat	Gat	3	3	AY.25	0.000018
S	1023	N1023S	aAt	aGt	3	3	AY.25	0.000018
S	1023	N1023N	aaT	aaC	3	3	AY.29	0.000047
S	1023	N1023N	aaT	aaC	3	3	AY.38	0.001498
S	1023	N1023N	aaT	aaC	3	3	AY.39	0.000074
S	1023	N1023Y	Aat	Tat	3	3	AY.4	0.000005
S	1023	N1023D	Aat	Gat	3	3	AY.4.2.1	0.000447
S	1023	N1023S	aAt	aGt	3	3	B.1.1.189	0.004539
S	1023	N1023N	aaT	aaC	3	3	B.1.1.486	0.004732
S	1023	N1023S	aAt	aGt	3	3	B.1.1.7	0.000003
S	1023	N1023Y	Aat	Tat	3	3	B.1.177	0.00004
S	1023	N1023N	aaT	aaC	3	3	B.1.427	0.000151
S	1023	N1023K	aaT	aaA	3	3	B.1.617.1	0.000387
S	1023	N1023S	aAt	aGt	3	3	B.1.617.2	0.000011
S	1023	N1023T	aAt	aCt	3	3	P.1	0.000047
S	1023	N1023G	AAt	GGt	2	2	All	0
S	1023	N1023D	Aat	Gat	2	2	AY.102	0.000053
S	1023	N1023N	aaT	aaC	2	2	AY.117	0.000169
S	1023	N1023D	Aat	Gat	2	2	AY.29	0.000032
S	1023	N1023N	aaT	aaC	2	2	AY.29.1	0.000441
S	1023	N1023N	aaT	aaC	2	2	AY.39.1	0.000079
S	1023	N1023I	aAt	aTt	2	2	AY.42	0.00008
S	1023	N1023S	aAt	aGt	2	2	AY.43	0.000009
S	1023	N1023del	AAT	---	2	2	AY.43	0.000009
S	1023	N1023H	Aat	Cat	2	2	AY.43	0.000009
S	1023	N1023K	aaT	aaG	2	2	AY.43	0.000009
S	1023	N1023S	aAt	aGt	2	2	AY.6	0.000082
S	1023	N1023N	aaT	aaC	2	2	AY.71	0.00095
S	1023	N1023N	aaT	aaC	2	2	AY.98	0.000158
S	1023	N1023del	AAT	---	2	2	B.1	0.000018
S	1023	N1023N	aaT	aaC	2	2	B.1.1.214	0.000111
S	1023	N1023K	aaT	aaG	2	2	B.1.1.359	0.055556
S	1023	N1023N	aaT	aaC	2	2	B.1.160	0.000062
S	1023	N1023S	aAt	aGt	2	2	B.1.177	0.000026
S	1023	N1023N	aaT	aaC	2	2	B.1.177.4	0.000422
S	1023	N1023N	aaT	aaC	2	2	B.1.177.7	0.00033
S	1023	N1023N	aaT	aaC	2	2	B.1.36.10	0.009569
S	1023	N1023T	aAt	aCt	2	2	B.1.617.2	0.000008
S	1023	N1023N	aaT	aaC	2	2	P.1	0.000032
S	1023	N1023P	AAt	CCt	1	1	All	0
S	1023	N1023V	AAt	GTt	1	1	All	0
S	1023	N1023I	aAt	aTt	1	1	AY.102	0.000027
S	1023	N1023T	aAt	aCt	1	1	AY.103	0.000006
S	1023	N1023S	aAt	aGt	1	1	AY.103	0.000006
S	1023	N1023N	aaT	aaC	1	1	AY.110	0.000113
S	1023	N1023D	Aat	Gat	1	1	AY.113	0.000142
S	1023	N1023del	AAT	---	1	1	AY.120	0.000037
S	1023	N1023N	aaT	aaC	1	1	AY.121	0.000135
S	1023	N1023N	aaT	aaC	1	1	AY.16.1	0.00047
S	1023	N1023S	aAt	aGt	1	1	AY.23	0.00007
S	1023	N1023I	aAt	aTt	1	1	AY.25	0.000006
S	1023	N1023T	aAt	aCt	1	1	AY.25	0.000006
S	1023	N1023H	Aat	Cat	1	1	AY.25	0.000006
S	1023	N1023N	aaT	aaC	1	1	AY.25	0.000006
S	1023	N1023Y	Aat	Tat	1	1	AY.3	0.00001
S	1023	N1023T	aAt	aCt	1	1	AY.3	0.00001
S	1023	N1023D	Aat	Gat	1	1	AY.35	0.000233
S	1023	N1023N	aaT	aaC	1	1	AY.35	0.000233
S	1023	N1023D	Aat	Gat	1	1	AY.38	0.000499
S	1023	N1023V	AAt	GTt	1	1	AY.39	0.000025
S	1023	N1023G	AAt	GGt	1	1	AY.39	0.000025
S	1023	N1023D	Aat	Gat	1	1	AY.39	0.000025
S	1023	N1023del1	aaT	aa-	1	1	AY.4	0.000002
S	1023	N1023D	Aat	Gat	1	1	AY.4	0.000002
S	1023	N1023P	AAt	CCt	1	1	AY.4	0.000002
S	1023	N1023del1	Aat	-at	1	1	AY.4.5	0.000107
S	1023	N1023Y	Aat	Tat	1	1	AY.4.5	0.000107
S	1023	N1023del	AAT	---	1	1	AY.4.5	0.000107
S	1023	N1023Y	Aat	Tat	1	1	AY.42	0.00004
S	1023	N1023I	aAt	aTt	1	1	AY.43	0.000004
S	1023	N1023K	aaT	aaA	1	1	AY.44	0.000006
S	1023	N1023N	aaT	aaC	1	1	AY.45	0.000122
S	1023	N1023S	aAt	aGt	1	1	AY.46	0.000104
S	1023	N1023N	aaT	aaC	1	1	AY.47	0.000031
S	1023	N1023S	aAt	aGt	1	1	AY.5	0.000021
S	1023	N1023Y	Aat	Tat	1	1	AY.5	0.000021
S	1023	N1023N	aaT	aaC	1	1	AY.5.4	0.000277
S	1023	N1023N	aaT	aaC	1	1	AY.53	0.000288
S	1023	N1023T	aAt	aCt	1	1	AY.6	0.000041
S	1023	N1023N	aaT	aaC	1	1	AY.62	0.000436
S	1023	N1023del	AAT	---	1	1	AY.68	0.000274
S	1023	N1023Y	Aat	Tat	1	1	AY.75	0.000056
S	1023	N1023S	aAt	aGt	1	1	AY.79	0.001211
S	1023	N1023del	AAT	---	1	1	AY.81	0.001992
S	1023	N1023N	aaT	aaC	1	1	AY.84	0.000437
S	1023	N1023N	aaT	aaC	1	1	AY.9.1	0.000084
S	1023	N1023N	aaT	aaC	1	1	AY.90	0.000684
S	1023	N1023N	aaT	aaC	1	1	AY.99	0.001049
S	1023	N1023Y	Aat	Tat	1	1	AY.99.2	0.000092
S	1023	N1023S	aAt	aGt	1	1	B	0.000128
S	1023	N1023S	aAt	aGt	1	1	B.1.1	0.000018
S	1023	N1023Y	Aat	Tat	1	1	B.1.1	0.000018
S	1023	N1023del	AAT	---	1	1	B.1.1.236	0.006897
S	1023	N1023N	aaT	aaC	1	1	B.1.1.25	0.000569
S	1023	N1023S	aAt	aGt	1	1	B.1.1.263	0.001558
S	1023	N1023N	aaT	aaC	1	1	B.1.1.277	0.000759
S	1023	N1023Y	Aat	Tat	1	1	B.1.1.372	0.000689
S	1023	N1023N	aaT	aaC	1	1	B.1.1.416	0.000905
S	1023	N1023D	Aat	Gat	1	1	B.1.1.434	0.000349
S	1023	N1023K	aaT	aaG	1	1	B.1.1.434	0.000349
S	1023	N1023S	aAt	aGt	1	1	B.1.1.448	0.002033
S	1023	N1023S	aAt	aGt	1	1	B.1.1.519	0.00004
S	1023	N1023D	Aat	Gat	1	1	B.1.1.523	0.001563
S	1023	N1023Y	Aat	Tat	1	1	B.1.1.7	0.000001
S	1023	N1023G	AAt	GGt	1	1	B.1.1.7	0.000001
S	1023	N1023I	aAt	aTt	1	1	B.1.1.7	0.000001
S	1023	N1023S	aAt	aGt	1	1	B.1.110.3	0.000718
S	1023	N1023del	AAT	---	1	1	B.1.140	0.018868
S	1023	N1023Y	Aat	Tat	1	1	B.1.160	0.000031
S	1023	N1023I	aAt	aTt	1	1	B.1.160.32	0.004292
S	1023	N1023N	aaT	aaC	1	1	B.1.177	0.000013
S	1023	N1023del	AAT	---	1	1	B.1.177.4	0.000211
S	1023	N1023del	AAT	---	1	1	B.1.177.62	0.001192
S	1023	N1023del	AAT	---	1	1	B.1.177.63	0.002703
S	1023	N1023N	aaT	aaC	1	1	B.1.177.81	0.000189
S	1023	N1023T	aAt	aCt	1	1	B.1.2	0.000009
S	1023	N1023del	AAT	---	1	1	B.1.2	0.000009
S	1023	N1023D	Aat	Gat	1	1	B.1.2	0.000009
S	1023	N1023S	aAt	aGt	1	1	B.1.243	0.00007
S	1023	N1023D	Aat	Gat	1	1	B.1.351	0.00003
S	1023	N1023T	aAt	aCt	1	1	B.1.351	0.00003
S	1023	N1023N	aaT	aaC	1	1	B.1.351	0.00003
S	1023	N1023S	aAt	aGt	1	1	B.1.36	0.000146
S	1023	N1023N	aaT	aaC	1	1	B.1.36.22	0.001208
S	1023	N1023N	aaT	aaC	1	1	B.1.389	0.001002
S	1023	N1023Y	Aat	Tat	1	1	B.1.399	0.001934
S	1023	N1023D	Aat	Gat	1	1	B.1.399	0.001934
S	1023	N1023del	AAT	---	1	1	B.1.415	0.014286
S	1023	N1023del1	Aat	-at	1	1	B.1.445	0.011765
S	1023	N1023N	aaT	aaC	1	1	B.1.517	0.000427
S	1023	N1023T	aAt	aCt	1	1	B.1.525	0.000113
S	1023	N1023I	aAt	aTt	1	1	B.1.526	0.000024
S	1023	N1023N	aaT	aaC	1	1	B.1.526	0.000024
S	1023	N1023D	Aat	Gat	1	1	B.1.617.2	0.000004
S	1023	N1023Y	Aat	Tat	1	1	B.1.617.2	0.000004
S	1023	N1023del	AAT	---	1	1	B.1.617.2	0.000004
S	1023	N1023N	aaT	aaC	1	1	B.1.637	0.000073
S	1023	N1023D	Aat	Gat	1	1	B.4	0.002208
S	1023	N1023S	aAt	aGt	1	1	C.16	0.00106
S	1023	N1023D	Aat	Gat	1	1	C.17	0.055556
S	1023	N1023S	aAt	aGt	1	1	C.36	0.000911
S	1023	N1023N	aaT	aaC	1	1	C.36.2	0.034483
S	1023	N1023D	Aat	Gat	1	1	C.37	0.000116
S	1023	N1023del	AAT	---	1	1	C.37	0.000116
S	1023	N1023del	AAT	---	1	1	P.1	0.000016
S	1023	N1023N	aaT	aaC	1	1	P.1.10	0.000269
S	1023	N1023N	aaT	aaC	1	1	P.1.2	0.001156
S	1023	N1023K	aaT	aaG	1	1	P.1.7	0.000319
S	1023	N1023T	aAt	aCt	1	1	P.2	0.000187

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.