CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 989

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	989	A989A		syn	gcT	gcC	252	231	0.916667	24527-24529
S	989	A989A		syn	gcT	gcG	252	11	0.0436508	24527-24529
S	989	A989A		syn	gcT	gcA	252	10	0.0396825	24527-24529
S	989	A989del		del	GCT	---	37	37	1	24527-24529
S	989	A989S		nonsyn	Gct	Tct	27	26	0.962963	24527-24529
S	989	A989S		nonsyn	GcT	TcA	27	1	0.037037	24527-24529
S	989	A989T		nonsyn	Gct	Act	15	14	0.933333	24527-24529
S	989	A989T		nonsyn	GcT	AcA	15	1	0.0666667	24527-24529
S	989	A989V		nonsyn	gCt	gTt	9	9	1	24527-24529
S	989	A989F		nonsyn	GCt	TTt	7	7	1	24527-24529
S	989	A989P		nonsyn	Gct	Cct	6	6	1	24527-24529
S	989	A989D		nonsyn	gCt	gAt	5	5	1	24527-24529
S	989	A989I		nonsyn	GCt	ATt	5	4	0.8	24527-24529
S	989	A989I		nonsyn	GCT	ATA	5	1	0.2	24527-24529
S	989	A989N		nonsyn	GCt	AAt	3	3	1	24527-24529
S	989	A989Y		nonsyn	GCt	TAt	3	3	1	24527-24529
S	989	A989G		nonsyn	gCt	gGt	2	2	1	24527-24529
S	989	A989L		nonsyn	GCT	TTA	1	1	1	24527-24529
S	989	A989K		nonsyn	GCT	AAA	1	1	1	24527-24529
S	989	A989del1		del	gcT	gc-	1	1	1	24527-24529
S	989	A989X		nonsyn	GCT	TAA	1	1	1	24527-24529
S	989	A989H		nonsyn	GCt	CAt	1	1	1	24527-24529
S	989	A989del2		del	GCt	--t	1	1	1	24527-24529

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	989	A989A	gcT	gcC	231	252	All	0.000044
S	989	A989A	gcT	gcG	11	252	All	0.000002
S	989	A989A	gcT	gcA	10	252	All	0.000002
S	989	A989A	gcT	gcC	35	38	AY.25	0.000211
S	989	A989A	gcT	gcG	3	38	AY.25	0.000018
S	989	A989del	GCT	---	37	37	All	0.000007
S	989	A989S	Gct	Tct	26	27	All	0.000005
S	989	A989S	GcT	TcA	1	27	All	0
S	989	A989A	gcT	gcC	22	22	B.1.146	0.09322
S	989	A989A	gcT	gcC	13	18	B.1.1.7	0.000012
S	989	A989A	gcT	gcA	4	18	B.1.1.7	0.000004
S	989	A989A	gcT	gcG	1	18	B.1.1.7	0.000001
S	989	A989A	gcT	gcC	17	17	B.1.1.216	0.015138
S	989	A989T	Gct	Act	14	15	All	0.000003
S	989	A989T	GcT	AcA	1	15	All	0
S	989	A989A	gcT	gcC	14	14	B.1.617.2	0.000053
S	989	A989A	gcT	gcC	13	13	AY.3	0.000129
S	989	A989A	gcT	gcC	10	12	AY.4	0.000016
S	989	A989A	gcT	gcG	1	12	AY.4	0.000002
S	989	A989A	gcT	gcA	1	12	AY.4	0.000002
S	989	A989A	gcT	gcC	10	10	P.1.4	0.009766
S	989	A989V	gCt	gTt	9	9	All	0.000002
S	989	A989A	gcT	gcC	9	9	AY.39.1	0.000357
S	989	A989S	Gct	Tct	7	8	AY.25	0.000042
S	989	A989S	GcT	TcA	1	8	AY.25	0.000006
S	989	A989del	GCT	---	8	8	B.1.1.7	0.000007
S	989	A989F	GCt	TTt	7	7	All	0.000001
S	989	A989F	GCt	TTt	7	7	AY.25	0.000042
S	989	A989T	Gct	Act	6	7	AY.25	0.000036
S	989	A989T	GcT	AcA	1	7	AY.25	0.000006
S	989	A989A	gcT	gcC	7	7	B.1	0.000064
S	989	A989A	gcT	gcC	7	7	B.1.177	0.000092
S	989	A989A	gcT	gcC	7	7	B.1.350.1	1
S	989	A989P	Gct	Cct	6	6	All	0.000001
S	989	A989A	gcT	gcC	5	5	AE.8	0.002445
S	989	A989D	gCt	gAt	5	5	All	0.000001
S	989	A989I	GCt	ATt	4	5	All	0.000001
S	989	A989I	GCT	ATA	1	5	All	0
S	989	A989I	GCt	ATt	4	5	AY.25	0.000024
S	989	A989I	GCT	ATA	1	5	AY.25	0.000006
S	989	A989A	gcT	gcC	5	5	B.1.1.318	0.001509
S	989	A989A	gcT	gcC	5	5	B.1.2	0.000044
S	989	A989A	gcT	gcC	4	4	AY.43	0.000018
S	989	A989A	gcT	gcC	4	4	B.1.351	0.000119
S	989	A989N	GCt	AAt	3	3	All	0.000001
S	989	A989Y	GCt	TAt	3	3	All	0.000001
S	989	A989A	gcT	gcG	2	3	AY.103	0.000012
S	989	A989A	gcT	gcC	1	3	AY.103	0.000006
S	989	A989Y	GCt	TAt	3	3	AY.25	0.000018
S	989	A989N	GCt	AAt	3	3	AY.25	0.000018
S	989	A989A	gcT	gcC	3	3	AY.33	0.0002
S	989	A989A	gcT	gcC	3	3	AY.39	0.000074
S	989	A989S	Gct	Tct	3	3	AY.4	0.000005
S	989	A989del	GCT	---	3	3	B.1	0.000027
S	989	A989A	gcT	gcC	2	3	B.1.1	0.000036
S	989	A989A	gcT	gcA	1	3	B.1.1	0.000018
S	989	A989S	Gct	Tct	3	3	B.1.1.7	0.000003
S	989	A989T	Gct	Act	3	3	B.1.617.2	0.000011
S	989	A989A	gcT	gcC	3	3	P.1.14	0.000143
S	989	A989S	Gct	Tct	3	3	Q.1	0.000379
S	989	A989G	gCt	gGt	2	2	All	0
S	989	A989A	gcT	gcC	2	2	AY.106	0.00067
S	989	A989A	gcT	gcC	2	2	AY.20	0.000078
S	989	A989V	gCt	gTt	2	2	AY.25	0.000012
S	989	A989A	gcT	gcC	2	2	AY.4.2	0.000043
S	989	A989S	Gct	Tct	2	2	AY.44	0.000012
S	989	A989A	gcT	gcC	2	2	AY.5	0.000041
S	989	A989del	GCT	---	2	2	AY.5	0.000041
S	989	A989A	gcT	gcC	2	2	AY.61	0.00021
S	989	A989A	gcT	gcA	1	2	B	0.000128
S	989	A989A	gcT	gcG	1	2	B	0.000128
S	989	A989D	gCt	gAt	2	2	B.1	0.000018
S	989	A989A	gcT	gcG	1	2	B.1.1.519	0.00004
S	989	A989A	gcT	gcC	1	2	B.1.1.519	0.00004
S	989	A989del	GCT	---	2	2	B.1.177	0.000026
S	989	A989S	Gct	Tct	2	2	B.1.177.70	0.011834
S	989	A989A	gcT	gcC	2	2	B.1.427	0.000101
S	989	A989del	GCT	---	2	2	B.1.617.2	0.000008
S	989	A989P	Gct	Cct	2	2	B.1.617.2	0.000008
S	989	A989V	gCt	gTt	2	2	D.2	0.00015
S	989	A989del1	gcT	gc-	1	1	All	0
S	989	A989K	GCT	AAA	1	1	All	0
S	989	A989X	GCT	TAA	1	1	All	0
S	989	A989del2	GCt	--t	1	1	All	0
S	989	A989H	GCt	CAt	1	1	All	0
S	989	A989L	GCT	TTA	1	1	All	0
S	989	A989A	gcT	gcA	1	1	AY.104	0.001984
S	989	A989A	gcT	gcG	1	1	AY.117	0.000085
S	989	A989A	gcT	gcC	1	1	AY.120	0.000037
S	989	A989del	GCT	---	1	1	AY.120	0.000037
S	989	A989A	gcT	gcC	1	1	AY.121	0.000135
S	989	A989A	gcT	gcC	1	1	AY.24	0.000431
S	989	A989del	GCT	---	1	1	AY.25	0.000006
S	989	A989D	gCt	gAt	1	1	AY.25	0.000006
S	989	A989L	GCT	TTA	1	1	AY.25	0.000006
S	989	A989X	GCT	TAA	1	1	AY.25	0.000006
S	989	A989G	gCt	gGt	1	1	AY.25	0.000006
S	989	A989K	GCT	AAA	1	1	AY.25	0.000006
S	989	A989A	gcT	gcC	1	1	AY.26	0.000028
S	989	A989T	Gct	Act	1	1	AY.27	0.000065
S	989	A989A	gcT	gcC	1	1	AY.3.1	0.000085
S	989	A989P	Gct	Cct	1	1	AY.4	0.000002
S	989	A989del	GCT	---	1	1	AY.4.5	0.000107
S	989	A989G	gCt	gGt	1	1	AY.42	0.00004
S	989	A989del	GCT	---	1	1	AY.43	0.000004
S	989	A989A	gcT	gcC	1	1	AY.44	0.000006
S	989	A989A	gcT	gcC	1	1	AY.46	0.000104
S	989	A989A	gcT	gcC	1	1	AY.54	0.000095
S	989	A989A	gcT	gcC	1	1	AY.55	0.000917
S	989	A989A	gcT	gcC	1	1	AY.6	0.000041
S	989	A989V	gCt	gTt	1	1	AY.65	0.000533
S	989	A989del	GCT	---	1	1	AY.68	0.000274
S	989	A989A	gcT	gcC	1	1	AY.73	0.000665
S	989	A989A	gcT	gcA	1	1	AY.75	0.000056
S	989	A989A	gcT	gcC	1	1	AY.75.1	0.00018
S	989	A989del	GCT	---	1	1	AY.81	0.001992
S	989	A989S	Gct	Tct	1	1	AY.83	0.001724
S	989	A989V	gCt	gTt	1	1	AY.9.2	0.000037
S	989	A989V	gCt	gTt	1	1	AY.98	0.000079
S	989	A989T	Gct	Act	1	1	AY.99.2	0.000092
S	989	A989V	gCt	gTt	1	1	B.1	0.000009
S	989	A989S	Gct	Tct	1	1	B.1	0.000009
S	989	A989S	Gct	Tct	1	1	B.1.1	0.000018
S	989	A989A	gcT	gcG	1	1	B.1.1.153	0.001095
S	989	A989del	GCT	---	1	1	B.1.1.236	0.006897
S	989	A989del	GCT	---	1	1	B.1.1.312	0.001912
S	989	A989del	GCT	---	1	1	B.1.1.315	0.008475
S	989	A989A	gcT	gcC	1	1	B.1.1.39	0.00051
S	989	A989V	gCt	gTt	1	1	B.1.1.7	0.000001
S	989	A989del2	GCt	--t	1	1	B.1.1.7	0.000001
S	989	A989P	Gct	Cct	1	1	B.1.13	0.002375
S	989	A989del	GCT	---	1	1	B.1.140	0.018868
S	989	A989del	GCT	---	1	1	B.1.177.17	0.000821
S	989	A989del	GCT	---	1	1	B.1.177.4	0.000211
S	989	A989del	GCT	---	1	1	B.1.177.5	0.001242
S	989	A989del	GCT	---	1	1	B.1.177.62	0.001192
S	989	A989del	GCT	---	1	1	B.1.177.63	0.002703
S	989	A989D	gCt	gAt	1	1	B.1.2	0.000009
S	989	A989T	Gct	Act	1	1	B.1.2	0.000009
S	989	A989del1	gcT	gc-	1	1	B.1.2	0.000009
S	989	A989P	Gct	Cct	1	1	B.1.2	0.000009
S	989	A989del	GCT	---	1	1	B.1.2	0.000009
S	989	A989A	gcT	gcC	1	1	B.1.320	0.001245
S	989	A989del	GCT	---	1	1	B.1.36.17	0.000494
S	989	A989T	Gct	Act	1	1	B.1.438.1	0.000107
S	989	A989A	gcT	gcC	1	1	B.1.561	0.000397
S	989	A989A	gcT	gcC	1	1	B.1.575	0.000303
S	989	A989A	gcT	gcC	1	1	B.1.595	0.000261
S	989	A989P	Gct	Cct	1	1	B.1.596	0.000087
S	989	A989S	Gct	Tct	1	1	B.1.596	0.000087
S	989	A989S	Gct	Tct	1	1	B.1.617.2	0.000004
S	989	A989H	GCt	CAt	1	1	B.1.617.2	0.000004
S	989	A989D	gCt	gAt	1	1	B.1.617.2	0.000004
S	989	A989S	Gct	Tct	1	1	B.29	0.003509
S	989	A989del	GCT	---	1	1	C.37	0.000116
S	989	A989A	gcT	gcC	1	1	D.2	0.000075
S	989	A989del	GCT	---	1	1	P.1	0.000016
S	989	A989A	gcT	gcA	1	1	P.1.12	0.000484
S	989	A989T	Gct	Act	1	1	P.1.14	0.000048
S	989	A989A	gcT	gcC	1	1	P.1.7	0.000319
S	989	A989del	GCT	---	1	1	Q.1	0.000126

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.