CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : Mut = L5L

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
ORF7a	5	L5L		syn	ctT	ctC	778	370	0.475578	27406-27408
ORF7a	5	L5L		syn	ctT	ctA	778	271	0.348329	27406-27408
ORF7a	5	L5L		syn	ctT	ctG	778	137	0.176093	27406-27408

Details of the mutation L5L 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
ORF7a	5	L5L	ctT	ctC	370	778	All	0.000071
ORF7a	5	L5L	ctT	ctA	271	778	All	0.000052
ORF7a	5	L5L	ctT	ctG	137	778	All	0.000026
ORF7a	5	L5L	ctT	ctC	144	187	B.1.1.7	0.000129
ORF7a	5	L5L	ctT	ctA	30	187	B.1.1.7	0.000027
ORF7a	5	L5L	ctT	ctG	13	187	B.1.1.7	0.000012
ORF7a	5	L5L	ctT	ctA	132	138	AY.5	0.002726
ORF7a	5	L5L	ctT	ctG	5	138	AY.5	0.000103
ORF7a	5	L5L	ctT	ctC	1	138	AY.5	0.000021
ORF7a	5	L5L	ctT	ctC	57	60	AY.4	0.000089
ORF7a	5	L5L	ctT	ctA	3	60	AY.4	0.000005
ORF7a	5	L5L	ctT	ctC	29	44	B.1.617.2	0.000109
ORF7a	5	L5L	ctT	ctG	13	44	B.1.617.2	0.000049
ORF7a	5	L5L	ctT	ctA	2	44	B.1.617.2	0.000008
ORF7a	5	L5L	ctT	ctA	40	41	AY.103	0.000248
ORF7a	5	L5L	ctT	ctC	1	41	AY.103	0.000006
ORF7a	5	L5L	ctT	ctG	28	28	AY.85	0.011961
ORF7a	5	L5L	ctT	ctA	20	28	B.1.429	0.000471
ORF7a	5	L5L	ctT	ctC	8	28	B.1.429	0.000188
ORF7a	5	L5L	ctT	ctA	25	25	AY.33	0.001669
ORF7a	5	L5L	ctT	ctG	19	19	B.1.565	0.015397
ORF7a	5	L5L	ctT	ctC	17	18	B.1.596	0.001481
ORF7a	5	L5L	ctT	ctA	1	18	B.1.596	0.000087
ORF7a	5	L5L	ctT	ctG	14	18	P.1	0.000221
ORF7a	5	L5L	ctT	ctC	4	18	P.1	0.000063
ORF7a	5	L5L	ctT	ctC	10	13	AY.44	0.000061
ORF7a	5	L5L	ctT	ctG	2	13	AY.44	0.000012
ORF7a	5	L5L	ctT	ctA	1	13	AY.44	0.000006
ORF7a	5	L5L	ctT	ctC	8	12	AY.25	0.000048
ORF7a	5	L5L	ctT	ctA	4	12	AY.25	0.000024
ORF7a	5	L5L	ctT	ctC	10	12	B.1.2	0.000088
ORF7a	5	L5L	ctT	ctG	2	12	B.1.2	0.000018
ORF7a	5	L5L	ctT	ctG	9	11	AY.43	0.00004
ORF7a	5	L5L	ctT	ctA	1	11	AY.43	0.000004
ORF7a	5	L5L	ctT	ctC	1	11	AY.43	0.000004
ORF7a	5	L5L	ctT	ctC	10	10	C.37	0.001161
ORF7a	5	L5L	ctT	ctC	9	9	AY.120	0.000335
ORF7a	5	L5L	ctT	ctG	4	4	AY.30	0.001583
ORF7a	5	L5L	ctT	ctA	3	4	AY.6	0.000123
ORF7a	5	L5L	ctT	ctC	1	4	AY.6	0.000041
ORF7a	5	L5L	ctT	ctC	3	4	AY.99.2	0.000276
ORF7a	5	L5L	ctT	ctG	1	4	AY.99.2	0.000092
ORF7a	5	L5L	ctT	ctC	3	4	B.1.177	0.00004
ORF7a	5	L5L	ctT	ctG	1	4	B.1.177	0.000013
ORF7a	5	L5L	ctT	ctG	3	3	AY.101	0.001471
ORF7a	5	L5L	ctT	ctA	2	3	AY.102	0.000053
ORF7a	5	L5L	ctT	ctG	1	3	AY.102	0.000027
ORF7a	5	L5L	ctT	ctC	3	3	AY.27	0.000194
ORF7a	5	L5L	ctT	ctC	2	3	AY.39	0.000049
ORF7a	5	L5L	ctT	ctG	1	3	AY.39	0.000025
ORF7a	5	L5L	ctT	ctG	3	3	AY.94	0.001328
ORF7a	5	L5L	ctT	ctC	3	3	B.1.1.189	0.004539
ORF7a	5	L5L	ctT	ctC	3	3	B.1.258.14	0.002941
ORF7a	5	L5L	ctT	ctC	3	3	B.1.621	0.000266
ORF7a	5	L5L	ctT	ctC	2	2	AY.3	0.00002
ORF7a	5	L5L	ctT	ctG	2	2	AY.39.1	0.000079
ORF7a	5	L5L	ctT	ctG	2	2	AY.62	0.000871
ORF7a	5	L5L	ctT	ctG	2	2	AY.67	0.000929
ORF7a	5	L5L	ctT	ctA	2	2	AY.84	0.000875
ORF7a	5	L5L	ctT	ctC	2	2	B.1.1	0.000036
ORF7a	5	L5L	ctT	ctG	2	2	B.1.1.207	0.002364
ORF7a	5	L5L	ctT	ctG	2	2	B.1.258.3	0.00335
ORF7a	5	L5L	ctT	ctC	2	2	B.1.351	0.000059
ORF7a	5	L5L	ctT	ctG	1	2	B.1.427	0.00005
ORF7a	5	L5L	ctT	ctC	1	2	B.1.427	0.00005
ORF7a	5	L5L	ctT	ctC	2	2	B.1.617.1	0.000258
ORF7a	5	L5L	ctT	ctC	2	2	B.15	0.035088
ORF7a	5	L5L	ctT	ctG	1	2	P.1.12	0.000484
ORF7a	5	L5L	ctT	ctC	1	2	P.1.12	0.000484
ORF7a	5	L5L	ctT	ctC	2	2	P.1.14	0.000096
ORF7a	5	L5L	ctT	ctC	1	2	P.1.2	0.001156
ORF7a	5	L5L	ctT	ctG	1	2	P.1.2	0.001156
ORF7a	5	L5L	ctT	ctC	1	1	A.1	0.000282
ORF7a	5	L5L	ctT	ctC	1	1	AY.107	0.000466
ORF7a	5	L5L	ctT	ctA	1	1	AY.111	0.000183
ORF7a	5	L5L	ctT	ctC	1	1	AY.114	0.000231
ORF7a	5	L5L	ctT	ctC	1	1	AY.115	0.005208
ORF7a	5	L5L	ctT	ctC	1	1	AY.117	0.000085
ORF7a	5	L5L	ctT	ctC	1	1	AY.120.2.1	0.000498
ORF7a	5	L5L	ctT	ctC	1	1	AY.23	0.00007
ORF7a	5	L5L	ctT	ctG	1	1	AY.26	0.000028
ORF7a	5	L5L	ctT	ctC	1	1	AY.34	0.000097
ORF7a	5	L5L	ctT	ctC	1	1	AY.4.2	0.000022
ORF7a	5	L5L	ctT	ctC	1	1	AY.47	0.000031
ORF7a	5	L5L	ctT	ctA	1	1	AY.58	0.000907
ORF7a	5	L5L	ctT	ctC	1	1	AY.75.1	0.00018
ORF7a	5	L5L	ctT	ctC	1	1	AY.98	0.000079
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.1	0.000327
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.216	0.00089
ORF7a	5	L5L	ctT	ctA	1	1	B.1.1.33	0.000421
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.378	0.007299
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.519	0.00004
ORF7a	5	L5L	ctT	ctG	1	1	B.1.1.521	0.005348
ORF7a	5	L5L	ctT	ctC	1	1	B.1.160	0.000031
ORF7a	5	L5L	ctT	ctA	1	1	B.1.214.2	0.0006
ORF7a	5	L5L	ctT	ctC	1	1	B.1.234	0.000132
ORF7a	5	L5L	ctT	ctC	1	1	B.1.36.29	0.000517
ORF7a	5	L5L	ctT	ctC	1	1	B.1.404	0.001302
ORF7a	5	L5L	ctT	ctG	1	1	B.1.462	0.007246
ORF7a	5	L5L	ctT	ctC	1	1	B.1.582	0.000491
ORF7a	5	L5L	ctT	ctC	1	1	B.1.595	0.000261
ORF7a	5	L5L	ctT	ctC	1	1	B.51	0.047619
ORF7a	5	L5L	ctT	ctA	1	1	C.18	0.002591
ORF7a	5	L5L	ctT	ctC	1	1	D.2	0.000075
ORF7a	5	L5L	ctT	ctG	1	1	P.2	0.000187
ORF7a	5	L5L	ctT	ctG	1	1	P.7	0.004367
ORF7a	5	L5L	ctT	ctC	1	1	Q.8	0.000165

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.