CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = P1140P

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	1140	P1140P		syn	ccT	ccC	1665	1349	0.81021	24980-24982
S	1140	P1140P		syn	ccT	ccG	1665	276	0.165766	24980-24982
S	1140	P1140P		syn	ccT	ccA	1665	40	0.024024	24980-24982

Details of the mutation P1140P 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	1140	P1140P	ccT	ccC	1349	1665	All	0.000258
S	1140	P1140P	ccT	ccG	276	1665	All	0.000053
S	1140	P1140P	ccT	ccA	40	1665	All	0.000008
S	1140	P1140P	ccT	ccC	988	988	B.1	0.00905
S	1140	P1140P	ccT	ccG	203	215	B.1.617.2	0.000764
S	1140	P1140P	ccT	ccC	9	215	B.1.617.2	0.000034
S	1140	P1140P	ccT	ccA	3	215	B.1.617.2	0.000011
S	1140	P1140P	ccT	ccC	63	63	B.1.569	0.913043
S	1140	P1140P	ccT	ccC	61	61	B.1.521	0.303483
S	1140	P1140P	ccT	ccG	43	43	AY.98	0.003397
S	1140	P1140P	ccT	ccC	28	31	AY.4	0.000044
S	1140	P1140P	ccT	ccA	2	31	AY.4	0.000003
S	1140	P1140P	ccT	ccG	1	31	AY.4	0.000002
S	1140	P1140P	ccT	ccC	20	26	B.1.1.7	0.000018
S	1140	P1140P	ccT	ccG	4	26	B.1.1.7	0.000004
S	1140	P1140P	ccT	ccA	2	26	B.1.1.7	0.000002
S	1140	P1140P	ccT	ccC	19	19	B.1.2	0.000167
S	1140	P1140P	ccT	ccC	12	19	B.1.526	0.000282
S	1140	P1140P	ccT	ccA	7	19	B.1.526	0.000165
S	1140	P1140P	ccT	ccA	11	11	AY.4.2	0.000239
S	1140	P1140P	ccT	ccC	9	10	AY.103	0.000056
S	1140	P1140P	ccT	ccA	1	10	AY.103	0.000006
S	1140	P1140P	ccT	ccC	10	10	AY.26	0.000283
S	1140	P1140P	ccT	ccG	7	10	AY.3	0.00007
S	1140	P1140P	ccT	ccC	3	10	AY.3	0.00003
S	1140	P1140P	ccT	ccC	8	10	AY.44	0.000049
S	1140	P1140P	ccT	ccG	2	10	AY.44	0.000012
S	1140	P1140P	ccT	ccC	9	9	B.1.76	0.102273
S	1140	P1140P	ccT	ccC	8	8	AY.27	0.000518
S	1140	P1140P	ccT	ccC	6	6	AE.8	0.002934
S	1140	P1140P	ccT	ccA	3	6	AY.102	0.00008
S	1140	P1140P	ccT	ccC	3	6	AY.102	0.00008
S	1140	P1140P	ccT	ccC	5	6	B.1.1	0.000091
S	1140	P1140P	ccT	ccG	1	6	B.1.1	0.000018
S	1140	P1140P	ccT	ccG	5	5	B.1.36	0.00073
S	1140	P1140P	ccT	ccC	5	5	B.1.438.1	0.000536
S	1140	P1140P	ccT	ccC	4	4	AY.25	0.000024
S	1140	P1140P	ccT	ccG	3	4	AY.32	0.001597
S	1140	P1140P	ccT	ccA	1	4	AY.32	0.000532
S	1140	P1140P	ccT	ccC	4	4	B.1.177	0.000053
S	1140	P1140P	ccT	ccC	4	4	B.1.429	0.000094
S	1140	P1140P	ccT	ccC	4	4	B.1.9.5	0.022727
S	1140	P1140P	ccT	ccA	3	3		0.166667
S	1140	P1140P	ccT	ccC	2	3	AY.43	0.000009
S	1140	P1140P	ccT	ccA	1	3	AY.43	0.000004
S	1140	P1140P	ccT	ccC	3	3	AY.54	0.000286
S	1140	P1140P	ccT	ccC	3	3	B.1.284	0.039474
S	1140	P1140P	ccT	ccC	3	3	B.1.621	0.000266
S	1140	P1140P	ccT	ccC	2	2	AY.100	0.000092
S	1140	P1140P	ccT	ccA	2	2	AY.118	0.000125
S	1140	P1140P	ccT	ccC	2	2	AY.45	0.000243
S	1140	P1140P	ccT	ccC	1	2	AY.5	0.000021
S	1140	P1140P	ccT	ccG	1	2	AY.5	0.000021
S	1140	P1140P	ccT	ccC	2	2	AY.99.2	0.000184
S	1140	P1140P	ccT	ccG	2	2	B.1.1.174	0.006757
S	1140	P1140P	ccT	ccA	2	2	B.1.1.306	0.000877
S	1140	P1140P	ccT	ccG	2	2	B.1.177.81	0.000379
S	1140	P1140P	ccT	ccC	2	2	B.1.243	0.000139
S	1140	P1140P	ccT	ccC	2	2	B.1.36.8	0.002
S	1140	P1140P	ccT	ccC	2	2	B.1.396	0.001411
S	1140	P1140P	ccT	ccG	1	2	B.3	0.000831
S	1140	P1140P	ccT	ccC	1	2	B.3	0.000831
S	1140	P1140P	ccT	ccC	2	2	D.2	0.00015
S	1140	P1140P	ccT	ccC	2	2	P.1	0.000032
S	1140	P1140P	ccT	ccC	1	1	A.2	0.000662
S	1140	P1140P	ccT	ccC	1	1	AY.105	0.000643
S	1140	P1140P	ccT	ccC	1	1	AY.117	0.000085
S	1140	P1140P	ccT	ccC	1	1	AY.119	0.000035
S	1140	P1140P	ccT	ccC	1	1	AY.12	0.000316
S	1140	P1140P	ccT	ccC	1	1	AY.120	0.000037
S	1140	P1140P	ccT	ccC	1	1	AY.20	0.000039
S	1140	P1140P	ccT	ccA	1	1	AY.23	0.00007
S	1140	P1140P	ccT	ccC	1	1	AY.29	0.000016
S	1140	P1140P	ccT	ccG	1	1	AY.39	0.000025
S	1140	P1140P	ccT	ccC	1	1	AY.39.1	0.00004
S	1140	P1140P	ccT	ccC	1	1	AY.39.1.1	0.000725
S	1140	P1140P	ccT	ccC	1	1	AY.74	0.000116
S	1140	P1140P	ccT	ccC	1	1	AY.9.1	0.000084
S	1140	P1140P	ccT	ccC	1	1	B	0.000128
S	1140	P1140P	ccT	ccC	1	1	B.1.1.1	0.000327
S	1140	P1140P	ccT	ccC	1	1	B.1.1.123	0.017857
S	1140	P1140P	ccT	ccC	1	1	B.1.1.194	0.00495
S	1140	P1140P	ccT	ccC	1	1	B.1.1.222	0.000204
S	1140	P1140P	ccT	ccA	1	1	B.1.160	0.000031
S	1140	P1140P	ccT	ccC	1	1	B.1.177.56	0.000668
S	1140	P1140P	ccT	ccC	1	1	B.1.206	0.000816
S	1140	P1140P	ccT	ccC	1	1	B.1.221	0.000071
S	1140	P1140P	ccT	ccC	1	1	B.1.298	0.002114
S	1140	P1140P	ccT	ccC	1	1	B.1.311	0.000275
S	1140	P1140P	ccT	ccC	1	1	B.1.324	0.001605
S	1140	P1140P	ccT	ccC	1	1	B.1.361	0.001289
S	1140	P1140P	ccT	ccC	1	1	B.1.367	0.000792
S	1140	P1140P	ccT	ccC	1	1	B.1.370	0.008
S	1140	P1140P	ccT	ccC	1	1	B.1.377	0.004566
S	1140	P1140P	ccT	ccC	1	1	B.1.413	0.004255
S	1140	P1140P	ccT	ccC	1	1	B.1.438	0.006536
S	1140	P1140P	ccT	ccC	1	1	B.1.452	0.013699
S	1140	P1140P	ccT	ccC	1	1	B.1.459	0.004082
S	1140	P1140P	ccT	ccC	1	1	B.1.501	0.007353
S	1140	P1140P	ccT	ccC	1	1	B.1.575	0.000303
S	1140	P1140P	ccT	ccC	1	1	B.1.577	0.000687
S	1140	P1140P	ccT	ccC	1	1	B.1.88.1	0.004808
S	1140	P1140P	ccT	ccC	1	1	B.1.94	0.027027
S	1140	P1140P	ccT	ccC	1	1	N.4	0.004255
S	1140	P1140P	ccT	ccC	1	1	P.1.16	0.000374

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.