CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = S416S

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	416	S416S		syn	tcA	tcT	1305	718	0.550192	29519-29521
N	416	S416S		syn	tcA	tcG	1305	568	0.435249	29519-29521
N	416	S416S		syn	tcA	tcC	1305	19	0.0145594	29519-29521

Details of the mutation S416S 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	416	S416S	tcA	tcT	718	1305	All	0.000137
N	416	S416S	tcA	tcG	568	1305	All	0.000109
N	416	S416S	tcA	tcC	19	1305	All	0.000004
N	416	S416S	tcA	tcG	411	423	AY.4	0.00064
N	416	S416S	tcA	tcT	9	423	AY.4	0.000014
N	416	S416S	tcA	tcC	3	423	AY.4	0.000005
N	416	S416S	tcA	tcT	223	225	AY.39	0.005511
N	416	S416S	tcA	tcG	2	225	AY.39	0.000049
N	416	S416S	tcA	tcT	213	213	B.1.1.240	1
N	416	S416S	tcA	tcG	60	100	B.1.1.7	0.000054
N	416	S416S	tcA	tcT	38	100	B.1.1.7	0.000034
N	416	S416S	tcA	tcC	2	100	B.1.1.7	0.000002
N	416	S416S	tcA	tcT	35	36	B.1.526	0.000823
N	416	S416S	tcA	tcG	1	36	B.1.526	0.000024
N	416	S416S	tcA	tcT	24	34	B.1	0.00022
N	416	S416S	tcA	tcG	10	34	B.1	0.000092
N	416	S416S	tcA	tcT	33	33	AY.71	0.015677
N	416	S416S	tcA	tcT	16	29	B.1.617.2	0.00006
N	416	S416S	tcA	tcG	12	29	B.1.617.2	0.000045
N	416	S416S	tcA	tcC	1	29	B.1.617.2	0.000004
N	416	S416S	tcA	tcT	22	22	AJ.1	1
N	416	S416S	tcA	tcG	8	11	AY.103	0.00005
N	416	S416S	tcA	tcT	3	11	AY.103	0.000019
N	416	S416S	tcA	tcG	6	11	AY.25	0.000036
N	416	S416S	tcA	tcT	5	11	AY.25	0.00003
N	416	S416S	tcA	tcG	5	10	B.1.1	0.000091
N	416	S416S	tcA	tcT	5	10	B.1.1	0.000091
N	416	S416S	tcA	tcG	6	8	AY.43	0.000027
N	416	S416S	tcA	tcT	2	8	AY.43	0.000009
N	416	S416S	tcA	tcT	5	8	AY.44	0.00003
N	416	S416S	tcA	tcG	3	8	AY.44	0.000018
N	416	S416S	tcA	tcT	8	8	B.1.596	0.000697
N	416	S416S	tcA	tcG	7	7	AY.46	0.000729
N	416	S416S	tcA	tcC	7	7	B.1.362	0.010786
N	416	S416S	tcA	tcT	4	6	AY.3	0.00004
N	416	S416S	tcA	tcG	2	6	AY.3	0.00002
N	416	S416S	tcA	tcT	5	6	B.1.2	0.000044
N	416	S416S	tcA	tcC	1	6	B.1.2	0.000009
N	416	S416S	tcA	tcG	4	5	B.1.351	0.000119
N	416	S416S	tcA	tcT	1	5	B.1.351	0.00003
N	416	S416S	tcA	tcT	3	4	AY.16	0.001139
N	416	S416S	tcA	tcG	1	4	AY.16	0.00038
N	416	S416S	tcA	tcT	4	4	AY.34	0.000388
N	416	S416S	tcA	tcT	3	4	AY.5	0.000062
N	416	S416S	tcA	tcG	1	4	AY.5	0.000021
N	416	S416S	tcA	tcC	4	4	B.1.1.214	0.000222
N	416	S416S	tcA	tcG	3	4	B.1.427	0.000151
N	416	S416S	tcA	tcT	1	4	B.1.427	0.00005
N	416	S416S	tcA	tcT	3	3	AY.119	0.000106
N	416	S416S	tcA	tcT	2	3	AY.14	0.000176
N	416	S416S	tcA	tcG	1	3	AY.14	0.000088
N	416	S416S	tcA	tcT	3	3	AY.26	0.000085
N	416	S416S	tcA	tcT	2	3	AY.39.1	0.000079
N	416	S416S	tcA	tcG	1	3	AY.39.1	0.00004
N	416	S416S	tcA	tcT	3	3	AY.4.2	0.000065
N	416	S416S	tcA	tcT	3	3	B.1.177	0.00004
N	416	S416S	tcA	tcG	3	3	B.1.497	0.000944
N	416	S416S	tcA	tcG	2	3	P.1	0.000032
N	416	S416S	tcA	tcT	1	3	P.1	0.000016
N	416	S416S	tcA	tcT	3	3	Q.1	0.000379
N	416	S416S	tcA	tcT	2	2	AY.20	0.000078
N	416	S416S	tcA	tcT	2	2	AY.33	0.000134
N	416	S416S	tcA	tcT	2	2	AY.4.5	0.000215
N	416	S416S	tcA	tcG	1	2	AY.42	0.00004
N	416	S416S	tcA	tcT	1	2	AY.42	0.00004
N	416	S416S	tcA	tcG	2	2	AY.5.4	0.000553
N	416	S416S	tcA	tcT	2	2	AY.98	0.000158
N	416	S416S	tcA	tcC	1	2	B.1.1.33	0.000421
N	416	S416S	tcA	tcT	1	2	B.1.1.33	0.000421
N	416	S416S	tcA	tcT	2	2	B.1.160.16	0.001859
N	416	S416S	tcA	tcG	2	2	B.1.177.60	0.000437
N	416	S416S	tcA	tcT	2	2	B.1.221	0.000142
N	416	S416S	tcA	tcT	1	1	A	0.000387
N	416	S416S	tcA	tcG	1	1	A.29	0.005319
N	416	S416S	tcA	tcG	1	1	AY.100	0.000046
N	416	S416S	tcA	tcT	1	1	AY.106	0.000335
N	416	S416S	tcA	tcT	1	1	AY.113	0.000142
N	416	S416S	tcA	tcT	1	1	AY.116	0.000287
N	416	S416S	tcA	tcT	1	1	AY.117	0.000085
N	416	S416S	tcA	tcG	1	1	AY.12	0.000316
N	416	S416S	tcA	tcT	1	1	AY.120	0.000037
N	416	S416S	tcA	tcT	1	1	AY.121	0.000135
N	416	S416S	tcA	tcT	1	1	AY.13	0.000161
N	416	S416S	tcA	tcT	1	1	AY.24	0.000431
N	416	S416S	tcA	tcT	1	1	AY.46.6	0.000072
N	416	S416S	tcA	tcG	1	1	AY.47	0.000031
N	416	S416S	tcA	tcT	1	1	AY.74	0.000116
N	416	S416S	tcA	tcT	1	1	AY.87	0.000833
N	416	S416S	tcA	tcG	1	1	AY.9.1	0.000084
N	416	S416S	tcA	tcT	1	1	AY.99.2	0.000092
N	416	S416S	tcA	tcG	1	1	B.1.1.1	0.000327
N	416	S416S	tcA	tcT	1	1	B.1.1.166	0.033333
N	416	S416S	tcA	tcT	1	1	B.1.1.270	0.010309
N	416	S416S	tcA	tcT	1	1	B.1.1.307	0.002532
N	416	S416S	tcA	tcT	1	1	B.1.1.416	0.000905
N	416	S416S	tcA	tcG	1	1	B.1.1.50	0.000679
N	416	S416S	tcA	tcT	1	1	B.1.160	0.000031
N	416	S416S	tcA	tcT	1	1	B.1.177.83	0.001481
N	416	S416S	tcA	tcG	1	1	B.1.256	0.017241
N	416	S416S	tcA	tcT	1	1	B.1.258	0.000067
N	416	S416S	tcA	tcG	1	1	B.1.471	0.002732
N	416	S416S	tcA	tcG	1	1	B.1.509	0.000866
N	416	S416S	tcA	tcG	1	1	B.1.577	0.000687
N	416	S416S	tcA	tcG	1	1	B.1.617.1	0.000129
N	416	S416S	tcA	tcG	1	1	B.1.631	0.003367
N	416	S416S	tcA	tcT	1	1	P.1.1	0.000318
N	416	S416S	tcA	tcT	1	1	P.1.11	0.010204
N	416	S416S	tcA	tcG	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.