CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 188

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	188	S188L		nonsyn	tCa	tTa	1272	1271	0.999214	28835-28837
N	188	S188L		nonsyn	tCA	tTG	1272	1	0.000786163	28835-28837
N	188	S188S		syn	tcA	tcG	215	154	0.716279	28835-28837
N	188	S188S		syn	tcA	tcT	215	54	0.251163	28835-28837
N	188	S188S		syn	tcA	tcC	215	7	0.0325581	28835-28837
N	188	S188P		nonsyn	Tca	Cca	168	167	0.994048	28835-28837
N	188	S188P		nonsyn	TcA	CcG	168	1	0.00595238	28835-28837
N	188	S188del		del	TCA	---	52	52	1	28835-28837
N	188	S188A		nonsyn	Tca	Gca	9	8	0.888889	28835-28837
N	188	S188A		nonsyn	TcA	GcG	9	1	0.111111	28835-28837
N	188	S188X		nonsyn	tCa	tAa	6	5	0.833333	28835-28837
N	188	S188X		nonsyn	tCa	tGa	6	1	0.166667	28835-28837
N	188	S188T		nonsyn	Tca	Aca	3	3	1	28835-28837
N	188	S188V		nonsyn	TCA	GTG	2	1	0.5	28835-28837
N	188	S188V		nonsyn	TCa	GTa	2	1	0.5	28835-28837
N	188	S188G		nonsyn	TCA	GGG	2	1	0.5	28835-28837
N	188	S188G		nonsyn	TCa	GGa	2	1	0.5	28835-28837
N	188	S188del1		del	tCa	t-a	2	1	0.5	28835-28837
N	188	S188del1		del	tcA	tc-	2	1	0.5	28835-28837
N	188	S188W		nonsyn	tCA	tGG	1	1	1	28835-28837
N	188	S188F		nonsyn	tCA	tTC	1	1	1	28835-28837
N	188	S188Q		nonsyn	TCa	CAa	1	1	1	28835-28837

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
N	188	S188L	tCa	tTa	1271	1272	All	0.000243
N	188	S188L	tCA	tTG	1	1272	All	0
N	188	S188L	tCa	tTa	1061	1061	B.1.93	0.990663
N	188	S188S	tcA	tcG	154	215	All	0.000029
N	188	S188S	tcA	tcT	54	215	All	0.00001
N	188	S188S	tcA	tcC	7	215	All	0.000001
N	188	S188P	Tca	Cca	167	168	All	0.000032
N	188	S188P	TcA	CcG	1	168	All	0
N	188	S188L	tCa	tTa	75	75	AY.54	0.007151
N	188	S188S	tcA	tcG	29	55	B.1.1.7	0.000026
N	188	S188S	tcA	tcT	24	55	B.1.1.7	0.000021
N	188	S188S	tcA	tcC	2	55	B.1.1.7	0.000002
N	188	S188P	Tca	Cca	53	53	B.4	0.116998
N	188	S188del	TCA	---	52	52	All	0.00001
N	188	S188L	tCa	tTa	41	41	B.1	0.000376
N	188	S188P	Tca	Cca	36	36	B.1.258.17	0.003743
N	188	S188S	tcA	tcG	28	28	AY.25	0.000168
N	188	S188del	TCA	---	13	13	B.1	0.000119
N	188	S188S	tcA	tcG	11	12	AY.45	0.001339
N	188	S188S	tcA	tcC	1	12	AY.45	0.000122
N	188	S188S	tcA	tcG	12	12	B.1.139	0.008798
N	188	S188S	tcA	tcT	11	11	AY.4	0.000017
N	188	S188S	tcA	tcG	10	10	AY.102	0.000265
N	188	S188P	Tca	Cca	10	10	B.1.1.7	0.000009
N	188	S188A	Tca	Gca	8	9	All	0.000002
N	188	S188A	TcA	GcG	1	9	All	0
N	188	S188del	TCA	---	9	9	B.1.1.7	0.000008
N	188	S188L	tCa	tTa	9	9	B.1.1.7	0.000008
N	188	S188P	Tca	Cca	8	8	AY.4	0.000012
N	188	S188S	tcA	tcG	5	8	AY.43	0.000022
N	188	S188S	tcA	tcT	3	8	AY.43	0.000013
N	188	S188L	tCa	tTa	7	7	B.1.128	0.004447
N	188	S188P	Tca	Cca	7	7	B.1.210	0.014925
N	188	S188X	tCa	tAa	5	6	All	0.000001
N	188	S188X	tCa	tGa	1	6	All	0
N	188	S188S	tcA	tcG	6	6	B.1.1.163	0.045802
N	188	S188L	tCa	tTa	6	6	B.1.617.2	0.000023
N	188	S188S	tcA	tcT	3	5	B.1	0.000027
N	188	S188S	tcA	tcG	2	5	B.1	0.000018
N	188	S188S	tcA	tcG	5	5	B.1.1	0.000091
N	188	S188L	tCa	tTa	5	5	B.1.1.214	0.000277
N	188	S188S	tcA	tcG	5	5	B.1.564	0.002129
N	188	S188S	tcA	tcG	4	5	B.1.617.2	0.000015
N	188	S188S	tcA	tcT	1	5	B.1.617.2	0.000004
N	188	S188L	tCa	tTa	4	4	AY.103	0.000025
N	188	S188L	tCa	tTa	4	4	AY.4	0.000006
N	188	S188L	tCa	tTa	4	4	AY.43	0.000018
N	188	S188T	Tca	Aca	3	3	All	0.000001
N	188	S188S	tcA	tcG	3	3	AY.103	0.000019
N	188	S188L	tCa	tTa	3	3	AY.25	0.000018
N	188	S188S	tcA	tcG	3	3	AY.44	0.000018
N	188	S188P	Tca	Cca	3	3	AY.44	0.000018
N	188	S188L	tCa	tTa	3	3	AY.44	0.000018
N	188	S188L	tCa	tTa	3	3	AY.47	0.000093
N	188	S188L	tCa	tTa	3	3	AY.59	0.001589
N	188	S188L	tCa	tTa	3	3	AY.74	0.000347
N	188	S188P	Tca	Cca	3	3	B.1	0.000027
N	188	S188S	tcA	tcG	3	3	B.1.1.519	0.000119
N	188	S188P	Tca	Cca	3	3	B.1.177	0.00004
N	188	S188L	tCa	tTa	3	3	B.1.178	0.071429
N	188	S188P	Tca	Cca	3	3	B.1.258.11	0.001189
N	188	S188L	tCa	tTa	3	3	B.1.258.11	0.001189
N	188	S188L	tCa	tTa	3	3	B.1.258.3	0.005025
N	188	S188S	tcA	tcG	3	3	B.1.375	0.002459
N	188	S188P	Tca	Cca	3	3	B.1.495	0.027273
N	188	S188P	Tca	Cca	2	2		0.111111
N	188	S188V	TCA	GTG	1	2		0.055556
N	188	S188A	Tca	Gca	1	2		0.055556
N	188	S188L	tCA	tTG	1	2		0.055556
N	188	S188L	tCa	tTa	1	2		0.055556
N	188	S188V	TCa	GTa	1	2		0.055556
N	188	S188G	TCA	GGG	1	2		0.055556
N	188	S188G	TCa	GGa	1	2		0.055556
N	188	S188A	TcA	GcG	1	2		0.055556
N	188	S188V	TCa	GTa	1	2	All	0
N	188	S188del1	tcA	tc-	1	2	All	0
N	188	S188G	TCa	GGa	1	2	All	0
N	188	S188G	TCA	GGG	1	2	All	0
N	188	S188V	TCA	GTG	1	2	All	0
N	188	S188del1	tCa	t-a	1	2	All	0
N	188	S188L	tCa	tTa	2	2	AY.121	0.000271
N	188	S188P	Tca	Cca	2	2	AY.14	0.000176
N	188	S188S	tcA	tcG	2	2	AY.23	0.000139
N	188	S188del	TCA	---	2	2	AY.40	0.001929
N	188	S188del	TCA	---	2	2	AY.43	0.000009
N	188	S188del	TCA	---	2	2	AY.50	0.001599
N	188	S188del	TCA	---	2	2	AY.75	0.000112
N	188	S188del	TCA	---	2	2	AY.9.2	0.000073
N	188	S188S	tcA	tcG	2	2	AY.99.2	0.000184
N	188	S188P	Tca	Cca	2	2	B	0.000256
N	188	S188P	Tca	Cca	2	2	B.1.160	0.000062
N	188	S188del	TCA	---	2	2	B.1.177	0.000026
N	188	S188S	tcA	tcG	1	2	B.1.177	0.000013
N	188	S188S	tcA	tcC	1	2	B.1.177	0.000013
N	188	S188P	Tca	Cca	1	2	B.1.221	0.000071
N	188	S188P	TcA	CcG	1	2	B.1.221	0.000071
N	188	S188S	tcA	tcG	2	2	B.1.258.17	0.000208
N	188	S188S	tcA	tcT	2	2	B.1.466.2	0.000782
N	188	S188L	tCa	tTa	2	2	C.37	0.000232
N	188	S188L	tCa	tTa	2	2	D.2	0.00015
N	188	S188S	tcA	tcC	2	2	P.1.14	0.000096
N	188	S188S	tcA	tcT	2	2	P.1.15	0.000465
N	188	S188S	tcA	tcG	1	1		0.055556
N	188	S188X	tCa	tGa	1	1		0.055556
N	188	S188W	tCA	tGG	1	1		0.055556
N	188	S188X	tCa	tAa	1	1	A	0.000387
N	188	S188W	tCA	tGG	1	1	All	0
N	188	S188F	tCA	tTC	1	1	All	0
N	188	S188Q	TCa	CAa	1	1	All	0
N	188	S188P	Tca	Cca	1	1	AY.103	0.000006
N	188	S188P	Tca	Cca	1	1	AY.108	0.001103
N	188	S188S	tcA	tcG	1	1	AY.110	0.000113
N	188	S188P	Tca	Cca	1	1	AY.114	0.000231
N	188	S188P	Tca	Cca	1	1	AY.119	0.000035
N	188	S188S	tcA	tcG	1	1	AY.119	0.000035
N	188	S188S	tcA	tcG	1	1	AY.121	0.000135
N	188	S188A	Tca	Gca	1	1	AY.16.1	0.00047
N	188	S188P	Tca	Cca	1	1	AY.25	0.000006
N	188	S188L	tCa	tTa	1	1	AY.26	0.000028
N	188	S188P	Tca	Cca	1	1	AY.26	0.000028
N	188	S188S	tcA	tcT	1	1	AY.27	0.000065
N	188	S188S	tcA	tcG	1	1	AY.29	0.000016
N	188	S188del	TCA	---	1	1	AY.3	0.00001
N	188	S188P	Tca	Cca	1	1	AY.3	0.00001
N	188	S188L	tCa	tTa	1	1	AY.3	0.00001
N	188	S188S	tcA	tcT	1	1	AY.30	0.000396
N	188	S188P	Tca	Cca	1	1	AY.34	0.000097
N	188	S188S	tcA	tcT	1	1	AY.34	0.000097
N	188	S188A	Tca	Gca	1	1	AY.4	0.000002
N	188	S188L	tCa	tTa	1	1	AY.4.2	0.000022
N	188	S188P	Tca	Cca	1	1	AY.4.3	0.000842
N	188	S188L	tCa	tTa	1	1	AY.4.5	0.000107
N	188	S188X	tCa	tAa	1	1	AY.43	0.000004
N	188	S188S	tcA	tcG	1	1	AY.46	0.000104
N	188	S188del	TCA	---	1	1	AY.46	0.000104
N	188	S188S	tcA	tcG	1	1	AY.46.3	0.000934
N	188	S188P	Tca	Cca	1	1	AY.47	0.000031
N	188	S188P	Tca	Cca	1	1	AY.5	0.000021
N	188	S188S	tcA	tcT	1	1	AY.5	0.000021
N	188	S188del	TCA	---	1	1	AY.5	0.000021
N	188	S188S	tcA	tcG	1	1	AY.55	0.000917
N	188	S188L	tCa	tTa	1	1	AY.75	0.000056
N	188	S188P	Tca	Cca	1	1	AY.75	0.000056
N	188	S188L	tCa	tTa	1	1	AY.9	0.000068
N	188	S188del1	tcA	tc-	1	1	AY.9.1	0.000084
N	188	S188S	tcA	tcG	1	1	AY.95	0.000761
N	188	S188S	tcA	tcG	1	1	AY.98	0.000079
N	188	S188X	tCa	tAa	1	1	B	0.000128
N	188	S188L	tCa	tTa	1	1	B	0.000128
N	188	S188P	Tca	Cca	1	1	B.1.1	0.000018
N	188	S188L	tCa	tTa	1	1	B.1.1	0.000018
N	188	S188S	tcA	tcG	1	1	B.1.1.192	0.002309
N	188	S188P	Tca	Cca	1	1	B.1.1.214	0.000055
N	188	S188T	Tca	Aca	1	1	B.1.1.216	0.00089
N	188	S188P	Tca	Cca	1	1	B.1.1.316	0.000925
N	188	S188P	Tca	Cca	1	1	B.1.1.323	0.014085
N	188	S188S	tcA	tcG	1	1	B.1.1.413	0.006897
N	188	S188P	Tca	Cca	1	1	B.1.1.519	0.00004
N	188	S188A	Tca	Gca	1	1	B.1.1.7	0.000001
N	188	S188T	Tca	Aca	1	1	B.1.1.70	0.000341
N	188	S188P	Tca	Cca	1	1	B.1.157	0.002985
N	188	S188L	tCa	tTa	1	1	B.1.157	0.002985
N	188	S188S	tcA	tcT	1	1	B.1.160	0.000031
N	188	S188L	tCa	tTa	1	1	B.1.177	0.000013
N	188	S188F	tCA	tTC	1	1	B.1.177	0.000013
N	188	S188L	tCa	tTa	1	1	B.1.177.62	0.001192
N	188	S188P	Tca	Cca	1	1	B.1.177.63	0.002703
N	188	S188del	TCA	---	1	1	B.1.177.68	0.015152
N	188	S188X	tCa	tAa	1	1	B.1.2	0.000009
N	188	S188del	TCA	---	1	1	B.1.2	0.000009
N	188	S188S	tcA	tcG	1	1	B.1.2	0.000009
N	188	S188L	tCa	tTa	1	1	B.1.2	0.000009
N	188	S188L	tCa	tTa	1	1	B.1.206	0.000816
N	188	S188A	Tca	Gca	1	1	B.1.221	0.000071
N	188	S188S	tcA	tcG	1	1	B.1.221	0.000071
N	188	S188L	tCa	tTa	1	1	B.1.222	0.001692
N	188	S188L	tCa	tTa	1	1	B.1.243	0.00007
N	188	S188P	Tca	Cca	1	1	B.1.243	0.00007
N	188	S188S	tcA	tcT	1	1	B.1.258.11	0.000396
N	188	S188A	Tca	Gca	1	1	B.1.258.17	0.000104
N	188	S188S	tcA	tcG	1	1	B.1.265	0.001271
N	188	S188del	TCA	---	1	1	B.1.351	0.00003
N	188	S188del1	tCa	t-a	1	1	B.1.391	0.001127
N	188	S188T	Tca	Aca	1	1	B.1.404	0.001302
N	188	S188del	TCA	---	1	1	B.1.416.1	0.001563
N	188	S188P	Tca	Cca	1	1	B.1.422	0.000812
N	188	S188del	TCA	---	1	1	B.1.427	0.00005
N	188	S188L	tCa	tTa	1	1	B.1.429	0.000024
N	188	S188S	tcA	tcC	1	1	B.1.429	0.000024
N	188	S188P	Tca	Cca	1	1	B.1.438.1	0.000107
N	188	S188L	tCa	tTa	1	1	B.1.456	0.003268
N	188	S188del	TCA	---	1	1	B.1.465	0.003802
N	188	S188L	tCa	tTa	1	1	B.1.485	0.014925
N	188	S188X	tCa	tAa	1	1	B.1.525	0.000113
N	188	S188del	TCA	---	1	1	B.1.525	0.000113
N	188	S188A	Tca	Gca	1	1	B.1.526	0.000024
N	188	S188P	Tca	Cca	1	1	B.1.526	0.000024
N	188	S188L	tCa	tTa	1	1	B.1.526	0.000024
N	188	S188del	TCA	---	1	1	B.1.560	0.00463
N	188	S188A	Tca	Gca	1	1	B.1.564	0.000426
N	188	S188del	TCA	---	1	1	B.1.576	0.000907
N	188	S188del	TCA	---	1	1	B.1.596	0.000087
N	188	S188L	tCa	tTa	1	1	B.1.617.1	0.000129
N	188	S188del	TCA	---	1	1	B.1.617.1	0.000129
N	188	S188P	Tca	Cca	1	1	B.1.617.1	0.000129
N	188	S188P	Tca	Cca	1	1	B.1.617.2	0.000004
N	188	S188del	TCA	---	1	1	B.1.617.2	0.000004
N	188	S188S	tcA	tcG	1	1	B.1.623	0.000536
N	188	S188S	tcA	tcT	1	1	B.1.631	0.003367
N	188	S188L	tCa	tTa	1	1	B.13	0.045455
N	188	S188L	tCa	tTa	1	1	B.26	0.014706
N	188	S188P	Tca	Cca	1	1	B.3	0.000831
N	188	S188P	Tca	Cca	1	1	B.39	0.002331
N	188	S188L	tCa	tTa	1	1	B.40	0.000364
N	188	S188P	Tca	Cca	1	1	B.40	0.000364
N	188	S188L	tCa	tTa	1	1	C.30	0.001727
N	188	S188Q	TCa	CAa	1	1	C.35	0.000774
N	188	S188del	TCA	---	1	1	C.37.1	0.002618
N	188	S188P	Tca	Cca	1	1	D.2	0.000075
N	188	S188del	TCA	---	1	1	P.1	0.000016
N	188	S188S	tcA	tcG	1	1	P.1	0.000016
N	188	S188del	TCA	---	1	1	P.1.15	0.000232
N	188	S188S	tcA	tcT	1	1	Q.8	0.000165
N	188	S188S	tcA	tcG	1	1	R.1	0.00009

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.