CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = S312S

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
N	312	S312S		syn	tcA	tcG	859	471	0.548312	29207-29209
N	312	S312S		syn	tcA	tcT	859	329	0.383004	29207-29209
N	312	S312S		syn	tcA	tcC	859	59	0.0686845	29207-29209

Details of the mutation S312S 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
N	312	S312S	tcA	tcG	471	859	All	0.00009
N	312	S312S	tcA	tcT	329	859	All	0.000063
N	312	S312S	tcA	tcC	59	859	All	0.000011
N	312	S312S	tcA	tcT	171	251	B.1.1.7	0.000153
N	312	S312S	tcA	tcG	80	251	B.1.1.7	0.000072
N	312	S312S	tcA	tcG	81	81	B.1.1.461	0.975904
N	312	S312S	tcA	tcG	41	74	AY.4	0.000064
N	312	S312S	tcA	tcT	25	74	AY.4	0.000039
N	312	S312S	tcA	tcC	8	74	AY.4	0.000012
N	312	S312S	tcA	tcG	65	73	B.1.160	0.002027
N	312	S312S	tcA	tcT	8	73	B.1.160	0.00025
N	312	S312S	tcA	tcG	35	35	B.1.526	0.000823
N	312	S312S	tcA	tcC	17	31	AY.44	0.000103
N	312	S312S	tcA	tcG	12	31	AY.44	0.000073
N	312	S312S	tcA	tcT	2	31	AY.44	0.000012
N	312	S312S	tcA	tcC	16	29	AY.103	0.000099
N	312	S312S	tcA	tcT	7	29	AY.103	0.000043
N	312	S312S	tcA	tcG	6	29	AY.103	0.000037
N	312	S312S	tcA	tcG	24	25	B.1	0.00022
N	312	S312S	tcA	tcT	1	25	B.1	0.000009
N	312	S312S	tcA	tcG	11	23	B.1.617.2	0.000041
N	312	S312S	tcA	tcT	11	23	B.1.617.2	0.000041
N	312	S312S	tcA	tcC	1	23	B.1.617.2	0.000004
N	312	S312S	tcA	tcT	19	22	AY.102	0.000504
N	312	S312S	tcA	tcG	3	22	AY.102	0.00008
N	312	S312S	tcA	tcT	13	17	AY.25	0.000078
N	312	S312S	tcA	tcG	4	17	AY.25	0.000024
N	312	S312S	tcA	tcG	13	13	AY.118	0.000814
N	312	S312S	tcA	tcT	13	13	AY.39	0.000321
N	312	S312S	tcA	tcG	10	12	P.1	0.000158
N	312	S312S	tcA	tcT	2	12	P.1	0.000032
N	312	S312S	tcA	tcT	11	11	AY.98.1	0.000533
N	312	S312S	tcA	tcC	7	9	B.1.2	0.000062
N	312	S312S	tcA	tcG	2	9	B.1.2	0.000018
N	312	S312S	tcA	tcG	6	7	AY.3	0.00006
N	312	S312S	tcA	tcT	1	7	AY.3	0.00001
N	312	S312S	tcA	tcG	4	6	B.1.1	0.000073
N	312	S312S	tcA	tcT	2	6	B.1.1	0.000036
N	312	S312S	tcA	tcG	5	5	AD.2	0.001095
N	312	S312S	tcA	tcG	4	5	AY.43	0.000018
N	312	S312S	tcA	tcT	1	5	AY.43	0.000004
N	312	S312S	tcA	tcG	5	5	B.1.177.77	0.003631
N	312	S312S	tcA	tcC	4	4	AY.100	0.000184
N	312	S312S	tcA	tcG	4	4	AY.20	0.000155
N	312	S312S	tcA	tcG	4	4	AY.4.2	0.000087
N	312	S312S	tcA	tcG	4	4	B.1.243	0.000278
N	312	S312S	tcA	tcT	3	3	AY.113	0.000427
N	312	S312S	tcA	tcT	2	3	AY.14	0.000176
N	312	S312S	tcA	tcG	1	3	AY.14	0.000088
N	312	S312S	tcA	tcG	3	3	AY.23	0.000209
N	312	S312S	tcA	tcG	3	3	AY.27	0.000194
N	312	S312S	tcA	tcG	2	3	AY.46	0.000208
N	312	S312S	tcA	tcT	1	3	AY.46	0.000104
N	312	S312S	tcA	tcG	3	3	AY.70	0.000626
N	312	S312S	tcA	tcG	3	3	AY.75	0.000168
N	312	S312S	tcA	tcT	3	3	B.1.1.369	0.001339
N	312	S312S	tcA	tcT	3	3	B.1.177.4	0.000633
N	312	S312S	tcA	tcT	3	3	B.1.206	0.002447
N	312	S312S	tcA	tcG	1	2	AY.119	0.000035
N	312	S312S	tcA	tcT	1	2	AY.119	0.000035
N	312	S312S	tcA	tcG	2	2	AY.13	0.000322
N	312	S312S	tcA	tcG	2	2	AY.36	0.000296
N	312	S312S	tcA	tcG	2	2	AY.4.4	0.000818
N	312	S312S	tcA	tcT	2	2	AY.66	0.002139
N	312	S312S	tcA	tcT	2	2	AY.7.2	0.001119
N	312	S312S	tcA	tcT	2	2	AY.9.1	0.000167
N	312	S312S	tcA	tcG	2	2	AY.99.2	0.000184
N	312	S312S	tcA	tcT	2	2	B.1.375	0.001639
N	312	S312S	tcA	tcT	2	2	B.1.415.1	0.015152
N	312	S312S	tcA	tcG	1	2	B.1.621	0.000089
N	312	S312S	tcA	tcC	1	2	B.1.621	0.000089
N	312	S312S	tcA	tcT	1	2	P.1.14	0.000048
N	312	S312S	tcA	tcG	1	2	P.1.14	0.000048
N	312	S312S	tcA	tcT	2	2	P.1.7	0.000639
N	312	S312S	tcA	tcT	1	1	A.2.4	0.003367
N	312	S312S	tcA	tcG	1	1	A.21	0.00277
N	312	S312S	tcA	tcT	1	1	AY.2	0.000356
N	312	S312S	tcA	tcG	1	1	AY.26	0.000028
N	312	S312S	tcA	tcT	1	1	AY.33	0.000067
N	312	S312S	tcA	tcG	1	1	AY.37	0.000316
N	312	S312S	tcA	tcT	1	1	AY.4.1	0.000737
N	312	S312S	tcA	tcT	1	1	AY.46.4	0.000165
N	312	S312S	tcA	tcG	1	1	AY.54	0.000095
N	312	S312S	tcA	tcT	1	1	AY.69	0.000187
N	312	S312S	tcA	tcC	1	1	AY.85	0.000427
N	312	S312S	tcA	tcG	1	1	AY.9	0.000068
N	312	S312S	tcA	tcG	1	1	AY.9.2	0.000037
N	312	S312S	tcA	tcG	1	1	B	0.000128
N	312	S312S	tcA	tcG	1	1	B.1.1.139	0.022727
N	312	S312S	tcA	tcG	1	1	B.1.1.153	0.001095
N	312	S312S	tcA	tcT	1	1	B.1.1.180	0.010753
N	312	S312S	tcA	tcG	1	1	B.1.1.200	0.007463
N	312	S312S	tcA	tcT	1	1	B.1.1.25	0.000569
N	312	S312S	tcA	tcT	1	1	B.1.1.277	0.000759
N	312	S312S	tcA	tcC	1	1	B.1.1.33	0.000421
N	312	S312S	tcA	tcT	1	1	B.1.1.374	0.002375
N	312	S312S	tcA	tcC	1	1	B.1.1.39	0.00051
N	312	S312S	tcA	tcG	1	1	B.1.1.409	0.002833
N	312	S312S	tcA	tcG	1	1	B.1.1.434	0.000349
N	312	S312S	tcA	tcG	1	1	B.1.1.519	0.00004
N	312	S312S	tcA	tcT	1	1	B.1.177	0.000013
N	312	S312S	tcA	tcG	1	1	B.1.177.7	0.000165
N	312	S312S	tcA	tcG	1	1	B.1.351	0.00003
N	312	S312S	tcA	tcT	1	1	B.1.351.3	0.000876
N	312	S312S	tcA	tcG	1	1	B.1.36	0.000146
N	312	S312S	tcA	tcC	1	1	B.1.400	0.000429
N	312	S312S	tcA	tcC	1	1	B.1.548	0.035714
N	312	S312S	tcA	tcG	1	1	B.1.561	0.000397
N	312	S312S	tcA	tcG	1	1	B.1.617.1	0.000129
N	312	S312S	tcA	tcG	1	1	B.1.625	0.002353
N	312	S312S	tcA	tcG	1	1	D.2	0.000075
N	312	S312S	tcA	tcG	1	1	P.1.15	0.000232
N	312	S312S	tcA	tcG	1	1	Q.3	0.000145
N	312	S312S	tcA	tcT	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.