CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 258

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	258	P258P		syn	ccT	ccC	683	563	0.824305	29045-29047
N	258	P258P		syn	ccT	ccG	683	67	0.0980966	29045-29047
N	258	P258P		syn	ccT	ccA	683	53	0.0775988	29045-29047
N	258	P258L		nonsyn	cCt	cTt	497	495	0.995976	29045-29047
N	258	P258L		nonsyn	cCT	cTC	497	2	0.00402414	29045-29047
N	258	P258S		nonsyn	Cct	Tct	175	174	0.994286	29045-29047
N	258	P258S		nonsyn	CcT	TcC	175	1	0.00571429	29045-29047
N	258	P258H		nonsyn	cCt	cAt	70	69	0.985714	29045-29047
N	258	P258H		nonsyn	cCT	cAC	70	1	0.0142857	29045-29047
N	258	P258T		nonsyn	Cct	Act	25	23	0.92	29045-29047
N	258	P258T		nonsyn	CcT	AcA	25	1	0.04	29045-29047
N	258	P258T		nonsyn	CcT	AcG	25	1	0.04	29045-29047
N	258	P258R		nonsyn	cCt	cGt	19	19	1	29045-29047
N	258	P258del		del	CCT	---	15	15	1	29045-29047
N	258	P258del1		del	ccT	cc-	10	5	0.5	29045-29047
N	258	P258del1		del	Cct	-ct	10	4	0.4	29045-29047
N	258	P258del1		del	CCt	-Tt	10	1	0.1	29045-29047
N	258	P258A		nonsyn	Cct	Gct	9	8	0.888889	29045-29047
N	258	P258A		nonsyn	CcT	GcC	9	1	0.111111	29045-29047
N	258	P258del2		del	cCT	c--	2	2	1	29045-29047
N	258	P258Q		nonsyn	cCT	cAA	1	1	1	29045-29047
N	258	P258V		nonsyn	CCt	GTt	1	1	1	29045-29047
N	258	P258F		nonsyn	CCT	TTC	1	1	1	29045-29047
N	258	P258G		nonsyn	CCt	GGt	1	1	1	29045-29047

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	258	P258P	ccT	ccC	563	683	All	0.000108
N	258	P258P	ccT	ccG	67	683	All	0.000013
N	258	P258P	ccT	ccA	53	683	All	0.00001
N	258	P258L	cCt	cTt	495	497	All	0.000095
N	258	P258L	cCT	cTC	2	497	All	0
N	258	P258L	cCt	cTt	299	299	B.1.526	0.007028
N	258	P258S	Cct	Tct	174	175	All	0.000033
N	258	P258S	CcT	TcC	1	175	All	0
N	258	P258P	ccT	ccC	168	174	B.1.429	0.003953
N	258	P258P	ccT	ccA	6	174	B.1.429	0.000141
N	258	P258P	ccT	ccC	120	120	B.1.1.294	0.151899
N	258	P258H	cCt	cAt	69	70	All	0.000013
N	258	P258H	cCT	cAC	1	70	All	0
N	258	P258S	Cct	Tct	58	58	AY.4	0.00009
N	258	P258P	ccT	ccC	44	45	AY.44	0.000268
N	258	P258P	ccT	ccG	1	45	AY.44	0.000006
N	258	P258P	ccT	ccC	28	45	B.1.1.7	0.000025
N	258	P258P	ccT	ccA	14	45	B.1.1.7	0.000013
N	258	P258P	ccT	ccG	3	45	B.1.1.7	0.000003
N	258	P258P	ccT	ccC	43	43	M.1	1
N	258	P258L	cCt	cTt	38	38	AY.4	0.000059
N	258	P258T	Cct	Act	23	25	All	0.000004
N	258	P258T	CcT	AcG	1	25	All	0
N	258	P258T	CcT	AcA	1	25	All	0
N	258	P258R	cCt	cGt	19	19	All	0.000004
N	258	P258S	Cct	Tct	18	18	B.1.1.274	0.090909
N	258	P258P	ccT	ccG	17	17	AY.3	0.000169
N	258	P258H	cCt	cAt	17	17	B.1.1.7	0.000015
N	258	P258del	CCT	---	15	15	All	0.000003
N	258	P258L	cCt	cTt	14	14	AY.120.1	0.004494
N	258	P258P	ccT	ccG	14	14	B.1.351	0.000416
N	258	P258P	ccT	ccC	12	14	B.1.617.2	0.000045
N	258	P258P	ccT	ccA	2	14	B.1.617.2	0.000008
N	258	P258H	cCt	cAt	13	13	AY.4	0.00002
N	258	P258P	ccT	ccC	11	13	B.1	0.000101
N	258	P258P	ccT	ccG	2	13	B.1	0.000018
N	258	P258P	ccT	ccC	13	13	B.1.632	0.087248
N	258	P258P	ccT	ccG	12	12	AY.26	0.00034
N	258	P258P	ccT	ccC	6	12	AY.4	0.000009
N	258	P258P	ccT	ccG	5	12	AY.4	0.000008
N	258	P258P	ccT	ccA	1	12	AY.4	0.000002
N	258	P258L	cCt	cTt	12	12	B.1.1.7	0.000011
N	258	P258L	cCt	cTt	12	12	B.1.452	0.164384
N	258	P258P	ccT	ccC	10	11	AY.43	0.000044
N	258	P258P	ccT	ccG	1	11	AY.43	0.000004
N	258	P258S	Cct	Tct	11	11	AY.44	0.000067
N	258	P258L	cCt	cTt	11	11	AY.44	0.000067
N	258	P258del1	ccT	cc-	5	10	All	0.000001
N	258	P258del1	Cct	-ct	4	10	All	0.000001
N	258	P258del1	CCt	-Tt	1	10	All	0
N	258	P258A	Cct	Gct	8	9	All	0.000002
N	258	P258A	CcT	GcC	1	9	All	0
N	258	P258R	cCt	cGt	9	9	B.1.1.7	0.000008
N	258	P258R	cCt	cGt	9	9	B.1.525	0.001018
N	258	P258S	Cct	Tct	8	8	AY.25	0.000048
N	258	P258P	ccT	ccA	6	8	AY.5	0.000124
N	258	P258P	ccT	ccC	2	8	AY.5	0.000041
N	258	P258L	cCt	cTt	8	8	B.1.221	0.000568
N	258	P258P	ccT	ccC	8	8	B.1.400	0.003432
N	258	P258P	ccT	ccC	8	8	B.1.480	0.0199
N	258	P258S	Cct	Tct	8	8	B.1.617.2	0.00003
N	258	P258L	cCt	cTt	7	7	AY.37	0.002212
N	258	P258L	cCt	cTt	7	7	AY.43	0.000031
N	258	P258L	cCt	cTt	7	7	AY.69	0.001307
N	258	P258L	cCt	cTt	7	7	B.1.2	0.000062
N	258	P258S	Cct	Tct	7	7	B.1.351	0.000208
N	258	P258P	ccT	ccC	3	6	AY.20	0.000117
N	258	P258P	ccT	ccG	3	6	AY.20	0.000117
N	258	P258L	cCt	cTt	6	6	AY.25	0.000036
N	258	P258S	Cct	Tct	5	6	B.1.1.7	0.000004
N	258	P258S	CcT	TcC	1	6	B.1.1.7	0.000001
N	258	P258P	ccT	ccA	3	6	B.1.2	0.000026
N	258	P258P	ccT	ccG	2	6	B.1.2	0.000018
N	258	P258P	ccT	ccC	1	6	B.1.2	0.000009
N	258	P258P	ccT	ccC	6	6	B.1.427	0.000303
N	258	P258L	cCt	cTt	6	6	B.1.617.2	0.000023
N	258	P258P	ccT	ccA	6	6	P.1	0.000095
N	258	P258H	cCt	cAt	5	5	AY.25	0.00003
N	258	P258P	ccT	ccC	5	5	AY.29	0.000079
N	258	P258P	ccT	ccC	5	5	AY.29.1	0.001103
N	258	P258L	cCt	cTt	5	5	AY.39	0.000124
N	258	P258P	ccT	ccA	2	5	AY.39	0.000049
N	258	P258P	ccT	ccC	2	5	AY.39	0.000049
N	258	P258P	ccT	ccG	1	5	AY.39	0.000025
N	258	P258S	Cct	Tct	5	5	B.1	0.000046
N	258	P258L	cCt	cTt	5	5	B.1.1.222	0.00102
N	258	P258H	cCt	cAt	5	5	B.1.2	0.000044
N	258	P258P	ccT	ccC	3	5	B.1.36.29	0.001552
N	258	P258P	ccT	ccG	2	5	B.1.36.29	0.001035
N	258	P258T	Cct	Act	5	5	B.1.438.1	0.000536
N	258	P258P	ccT	ccC	5	5	B.1.469	0.018051
N	258	P258S	Cct	Tct	5	5	P.1	0.000079
N	258	P258P	ccT	ccC	4	4	AY.102	0.000106
N	258	P258H	cCt	cAt	4	4	AY.118	0.000251
N	258	P258L	cCt	cTt	4	4	AY.6	0.000165
N	258	P258S	Cct	Tct	4	4	AY.79	0.004843
N	258	P258L	cCt	cTt	3	4	B.1	0.000027
N	258	P258L	cCT	cTC	1	4	B.1	0.000009
N	258	P258L	cCt	cTt	4	4	B.1.1.153	0.004381
N	258	P258S	Cct	Tct	4	4	B.1.2	0.000035
N	258	P258L	cCt	cTt	4	4	B.1.239	0.004884
N	258	P258P	ccT	ccA	4	4	B.1.258.17	0.000416
N	258	P258P	ccT	ccC	3	3	AY.103	0.000019
N	258	P258P	ccT	ccC	3	3	AY.25	0.000018
N	258	P258T	Cct	Act	3	3	AY.30	0.001187
N	258	P258P	ccT	ccA	3	3	AY.98.1	0.000145
N	258	P258P	ccT	ccC	3	3	B.1.177.57	0.000843
N	258	P258S	Cct	Tct	3	3	B.1.243	0.000209
N	258	P258P	ccT	ccC	3	3	B.1.369	0.000856
N	258	P258L	cCt	cTt	3	3	B.1.429	0.000071
N	258	P258H	cCt	cAt	3	3	B.1.617.2	0.000011
N	258	P258A	Cct	Gct	2	2		0.111111
N	258	P258del2	cCT	c--	2	2	All	0
N	258	P258S	Cct	Tct	2	2	AY.100	0.000092
N	258	P258L	cCt	cTt	2	2	AY.103	0.000012
N	258	P258H	cCt	cAt	2	2	AY.103	0.000012
N	258	P258L	cCt	cTt	2	2	AY.119	0.000071
N	258	P258del	CCT	---	2	2	AY.25	0.000012
N	258	P258S	Cct	Tct	2	2	AY.33	0.000134
N	258	P258L	cCt	cTt	1	2	AY.40	0.000964
N	258	P258L	cCT	cTC	1	2	AY.40	0.000964
N	258	P258H	cCt	cAt	2	2	AY.43	0.000009
N	258	P258T	Cct	Act	2	2	AY.44	0.000012
N	258	P258H	cCt	cAt	2	2	AY.44	0.000012
N	258	P258P	ccT	ccC	2	2	AY.47	0.000062
N	258	P258S	Cct	Tct	2	2	AY.5	0.000041
N	258	P258H	cCt	cAt	2	2	AY.9	0.000135
N	258	P258L	cCt	cTt	2	2	AY.9	0.000135
N	258	P258S	Cct	Tct	2	2	AY.9.2	0.000073
N	258	P258P	ccT	ccC	2	2	AY.93	0.000546
N	258	P258T	Cct	Act	2	2	B.1	0.000018
N	258	P258del	CCT	---	2	2	B.1	0.000018
N	258	P258H	cCT	cAC	1	2	B.1	0.000009
N	258	P258H	cCt	cAt	1	2	B.1	0.000009
N	258	P258P	ccT	ccC	2	2	B.1.1	0.000036
N	258	P258L	cCt	cTt	2	2	B.1.1.10	0.00223
N	258	P258P	ccT	ccA	2	2	B.1.1.70	0.000682
N	258	P258S	Cct	Tct	2	2	B.1.177	0.000026
N	258	P258P	ccT	ccC	2	2	B.1.177	0.000026
N	258	P258P	ccT	ccC	2	2	B.1.177.86	0.000367
N	258	P258P	ccT	ccC	2	2	B.1.258	0.000133
N	258	P258P	ccT	ccA	2	2	B.1.564.1	0.003155
N	258	P258P	ccT	ccC	2	2	B.1.621	0.000177
N	258	P258P	ccT	ccC	2	2	C.1	0.004785
N	258	P258L	cCt	cTt	2	2	P.1	0.000032
N	258	P258G	CCt	GGt	1	1	All	0
N	258	P258F	CCT	TTC	1	1	All	0
N	258	P258Q	cCT	cAA	1	1	All	0
N	258	P258V	CCt	GTt	1	1	All	0
N	258	P258L	cCt	cTt	1	1	AU.2	0.002421
N	258	P258del	CCT	---	1	1	AY.100	0.000046
N	258	P258P	ccT	ccC	1	1	AY.100	0.000046
N	258	P258L	cCt	cTt	1	1	AY.100	0.000046
N	258	P258S	Cct	Tct	1	1	AY.102	0.000027
N	258	P258S	Cct	Tct	1	1	AY.103	0.000006
N	258	P258T	Cct	Act	1	1	AY.116	0.000287
N	258	P258P	ccT	ccC	1	1	AY.116	0.000287
N	258	P258S	Cct	Tct	1	1	AY.117	0.000085
N	258	P258L	cCt	cTt	1	1	AY.118	0.000063
N	258	P258L	cCt	cTt	1	1	AY.12	0.000316
N	258	P258P	ccT	ccC	1	1	AY.120	0.000037
N	258	P258H	cCt	cAt	1	1	AY.120	0.000037
N	258	P258T	Cct	Act	1	1	AY.120	0.000037
N	258	P258P	ccT	ccC	1	1	AY.120.2	0.001285
N	258	P258L	cCt	cTt	1	1	AY.13	0.000161
N	258	P258P	ccT	ccC	1	1	AY.13	0.000161
N	258	P258P	ccT	ccC	1	1	AY.16.1	0.00047
N	258	P258S	Cct	Tct	1	1	AY.20	0.000039
N	258	P258T	Cct	Act	1	1	AY.20	0.000039
N	258	P258P	ccT	ccC	1	1	AY.23	0.00007
N	258	P258T	Cct	Act	1	1	AY.25	0.000006
N	258	P258del2	cCT	c--	1	1	AY.25	0.000006
N	258	P258H	cCt	cAt	1	1	AY.26	0.000028
N	258	P258P	ccT	ccC	1	1	AY.27	0.000065
N	258	P258S	Cct	Tct	1	1	AY.27	0.000065
N	258	P258L	cCt	cTt	1	1	AY.29	0.000016
N	258	P258L	cCt	cTt	1	1	AY.3	0.00001
N	258	P258S	Cct	Tct	1	1	AY.3	0.00001
N	258	P258P	ccT	ccC	1	1	AY.34	0.000097
N	258	P258S	Cct	Tct	1	1	AY.34	0.000097
N	258	P258P	ccT	ccG	1	1	AY.36	0.000148
N	258	P258H	cCt	cAt	1	1	AY.39	0.000025
N	258	P258S	Cct	Tct	1	1	AY.39	0.000025
N	258	P258S	Cct	Tct	1	1	AY.39.1	0.00004
N	258	P258R	cCt	cGt	1	1	AY.4	0.000002
N	258	P258T	Cct	Act	1	1	AY.4	0.000002
N	258	P258P	ccT	ccA	1	1	AY.4.2	0.000022
N	258	P258S	Cct	Tct	1	1	AY.43	0.000004
N	258	P258del	CCT	---	1	1	AY.44	0.000006
N	258	P258del1	ccT	cc-	1	1	AY.44	0.000006
N	258	P258S	Cct	Tct	1	1	AY.45	0.000122
N	258	P258P	ccT	ccC	1	1	AY.46	0.000104
N	258	P258S	Cct	Tct	1	1	AY.47	0.000031
N	258	P258del1	Cct	-ct	1	1	AY.48	0.000465
N	258	P258T	Cct	Act	1	1	AY.5	0.000021
N	258	P258L	cCt	cTt	1	1	AY.53	0.000288
N	258	P258P	ccT	ccC	1	1	AY.57	0.000656
N	258	P258P	ccT	ccC	1	1	AY.6	0.000041
N	258	P258S	Cct	Tct	1	1	AY.6	0.000041
N	258	P258L	cCt	cTt	1	1	AY.61	0.000105
N	258	P258del	CCT	---	1	1	AY.67	0.000464
N	258	P258A	Cct	Gct	1	1	AY.68	0.000274
N	258	P258S	Cct	Tct	1	1	AY.7.1	0.000113
N	258	P258P	ccT	ccC	1	1	AY.71	0.000475
N	258	P258L	cCt	cTt	1	1	AY.74	0.000116
N	258	P258P	ccT	ccC	1	1	AY.74	0.000116
N	258	P258S	Cct	Tct	1	1	AY.75	0.000056
N	258	P258del	CCT	---	1	1	AY.75	0.000056
N	258	P258P	ccT	ccG	1	1	AY.85	0.000427
N	258	P258P	ccT	ccC	1	1	AY.9	0.000068
N	258	P258del1	ccT	cc-	1	1	AY.9.2	0.000037
N	258	P258P	ccT	ccG	1	1	AY.9.2	0.000037
N	258	P258del	CCT	---	1	1	AY.9.2	0.000037
N	258	P258H	cCt	cAt	1	1	AY.98	0.000079
N	258	P258L	cCt	cTt	1	1	AY.98.1	0.000048
N	258	P258del1	ccT	cc-	1	1	B	0.000128
N	258	P258F	CCT	TTC	1	1	B.1	0.000009
N	258	P258del1	CCt	-Tt	1	1	B.1	0.000009
N	258	P258A	Cct	Gct	1	1	B.1	0.000009
N	258	P258A	Cct	Gct	1	1	B.1.1	0.000018
N	258	P258del	CCT	---	1	1	B.1.1	0.000018
N	258	P258H	cCt	cAt	1	1	B.1.1	0.000018
N	258	P258T	Cct	Act	1	1	B.1.1	0.000018
N	258	P258L	cCt	cTt	1	1	B.1.1	0.000018
N	258	P258L	cCt	cTt	1	1	B.1.1.121	0.002427
N	258	P258S	Cct	Tct	1	1	B.1.1.134	0.011364
N	258	P258H	cCt	cAt	1	1	B.1.1.214	0.000055
N	258	P258S	Cct	Tct	1	1	B.1.1.214	0.000055
N	258	P258S	Cct	Tct	1	1	B.1.1.222	0.000204
N	258	P258V	CCt	GTt	1	1	B.1.1.27	0.00565
N	258	P258T	CcT	AcG	1	1	B.1.1.300	0.010753
N	258	P258L	cCt	cTt	1	1	B.1.1.307	0.002532
N	258	P258S	Cct	Tct	1	1	B.1.1.311	0.000358
N	258	P258P	ccT	ccC	1	1	B.1.1.337	0.003597
N	258	P258L	cCt	cTt	1	1	B.1.1.487	0.005587
N	258	P258L	cCt	cTt	1	1	B.1.1.519	0.00004
N	258	P258A	CcT	GcC	1	1	B.1.1.7	0.000001
N	258	P258Q	cCT	cAA	1	1	B.1.1.7	0.000001
N	258	P258del1	ccT	cc-	1	1	B.1.1.7	0.000001
N	258	P258T	CcT	AcA	1	1	B.1.1.7	0.000001
N	258	P258del1	Cct	-ct	1	1	B.1.110	0.004525
N	258	P258P	ccT	ccC	1	1	B.1.157	0.002985
N	258	P258H	cCt	cAt	1	1	B.1.177	0.000013
N	258	P258A	Cct	Gct	1	1	B.1.177	0.000013
N	258	P258P	ccT	ccC	1	1	B.1.177.55	0.002331
N	258	P258G	CCt	GGt	1	1	B.1.177.63	0.002703
N	258	P258L	cCt	cTt	1	1	B.1.177.73	0.000566
N	258	P258del	CCT	---	1	1	B.1.177.83	0.001481
N	258	P258T	Cct	Act	1	1	B.1.2	0.000009
N	258	P258del2	cCT	c--	1	1	B.1.2	0.000009
N	258	P258L	cCt	cTt	1	1	B.1.214.2	0.0006
N	258	P258L	cCt	cTt	1	1	B.1.258	0.000067
N	258	P258H	cCt	cAt	1	1	B.1.328	0.03125
N	258	P258P	ccT	ccC	1	1	B.1.336	0.002439
N	258	P258S	Cct	Tct	1	1	B.1.36	0.000146
N	258	P258P	ccT	ccC	1	1	B.1.36.10	0.004785
N	258	P258H	cCt	cAt	1	1	B.1.36.16	0.001425
N	258	P258P	ccT	ccC	1	1	B.1.36.39	0.002217
N	258	P258del	CCT	---	1	1	B.1.369	0.000285
N	258	P258P	ccT	ccC	1	1	B.1.39	0.003906
N	258	P258S	Cct	Tct	1	1	B.1.404	0.001302
N	258	P258L	cCt	cTt	1	1	B.1.427	0.00005
N	258	P258S	Cct	Tct	1	1	B.1.433	0.003195
N	258	P258del	CCT	---	1	1	B.1.439	0.005917
N	258	P258S	Cct	Tct	1	1	B.1.441	0.009615
N	258	P258P	ccT	ccC	1	1	B.1.441	0.009615
N	258	P258H	cCt	cAt	1	1	B.1.525	0.000113
N	258	P258H	cCt	cAt	1	1	B.1.526	0.000024
N	258	P258S	Cct	Tct	1	1	B.1.526	0.000024
N	258	P258P	ccT	ccC	1	1	B.1.538	0.008065
N	258	P258del1	ccT	cc-	1	1	B.1.595	0.000261
N	258	P258S	Cct	Tct	1	1	B.1.595	0.000261
N	258	P258T	Cct	Act	1	1	B.1.617.1	0.000129
N	258	P258del1	Cct	-ct	1	1	B.1.617.1	0.000129
N	258	P258A	Cct	Gct	1	1	B.1.617.2	0.000004
N	258	P258del	CCT	---	1	1	B.1.617.2	0.000004
N	258	P258T	Cct	Act	1	1	B.1.617.2	0.000004
N	258	P258P	ccT	ccA	1	1	B.1.618	0.004032
N	258	P258L	cCt	cTt	1	1	B.1.621	0.000089
N	258	P258P	ccT	ccC	1	1	B.1.623	0.000536
N	258	P258S	Cct	Tct	1	1	B.1.628	0.000352
N	258	P258H	cCt	cAt	1	1	B.1.637	0.000073
N	258	P258S	Cct	Tct	1	1	C.1.2	0.004255
N	258	P258H	cCt	cAt	1	1	C.28	0.04
N	258	P258P	ccT	ccC	1	1	C.37	0.000116
N	258	P258P	ccT	ccC	1	1	N.4	0.004255
N	258	P258del1	Cct	-ct	1	1	P.1	0.000016
N	258	P258P	ccT	ccG	1	1	P.1.1	0.000318
N	258	P258T	Cct	Act	1	1	P.1.10	0.000269
N	258	P258S	Cct	Tct	1	1	P.1.14	0.000048
N	258	P258L	cCt	cTt	1	1	P.1.14	0.000048
N	258	P258del	CCT	---	1	1	P.1.15	0.000232
N	258	P258P	ccT	ccC	1	1	P.1.7	0.000319
N	258	P258A	Cct	Gct	1	1	P.2	0.000187

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.