CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 214

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
M	214	S214I		nonsyn	aGt	aTt	1002	1002	1	27162-27164
M	214	S214del		del	AGT	---	169	169	1	27162-27164
M	214	S214S		syn	agT	agC	95	95	1	27162-27164
M	214	S214N		nonsyn	aGt	aAt	66	65	0.984848	27162-27164
M	214	S214N		nonsyn	aGT	aAC	66	1	0.0151515	27162-27164
M	214	S214G		nonsyn	Agt	Ggt	64	62	0.96875	27162-27164
M	214	S214G		nonsyn	AgT	GgA	64	2	0.03125	27162-27164
M	214	S214T		nonsyn	aGt	aCt	58	58	1	27162-27164
M	214	S214R		nonsyn	agT	agG	43	21	0.488372	27162-27164
M	214	S214R		nonsyn	Agt	Cgt	43	11	0.255814	27162-27164
M	214	S214R		nonsyn	agT	agA	43	10	0.232558	27162-27164
M	214	S214R		nonsyn	AgT	CgG	43	1	0.0232558	27162-27164
M	214	S214C		nonsyn	Agt	Tgt	30	30	1	27162-27164
M	214	S214K		nonsyn	aGT	aAA	6	3	0.5	27162-27164
M	214	S214K		nonsyn	aGT	aAG	6	3	0.5	27162-27164
M	214	S214D		nonsyn	AGt	GAt	3	2	0.666667	27162-27164
M	214	S214D		nonsyn	AGT	GAC	3	1	0.333333	27162-27164
M	214	S214del2		del	aGT	a--	1	1	1	27162-27164
M	214	S214E		nonsyn	AGT	GAA	1	1	1	27162-27164
M	214	S214H		nonsyn	AGt	CAt	1	1	1	27162-27164
M	214	S214Q		nonsyn	AGT	CAG	1	1	1	27162-27164
M	214	S214del1		del	Agt	-gt	1	1	1	27162-27164
M	214	S214X		nonsyn	AgT	TgA	1	1	1	27162-27164

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
M	214	S214I	aGt	aTt	1002	1002	All	0.000192
M	214	S214I	aGt	aTt	232	232	B.1.1.7	0.000208
M	214	S214del	AGT	---	169	169	All	0.000032
M	214	S214del	AGT	---	147	147	B.1.177.21	0.011241
M	214	S214I	aGt	aTt	101	101	AY.4	0.000157
M	214	S214S	agT	agC	95	95	All	0.000018
M	214	S214I	aGt	aTt	73	73	B.1.617.2	0.000275
M	214	S214N	aGt	aAt	65	66	All	0.000012
M	214	S214N	aGT	aAC	1	66	All	0
M	214	S214G	Agt	Ggt	62	64	All	0.000012
M	214	S214G	AgT	GgA	2	64	All	0
M	214	S214I	aGt	aTt	60	60	AY.43	0.000266
M	214	S214T	aGt	aCt	58	58	All	0.000011
M	214	S214I	aGt	aTt	57	57	AY.3.1	0.00486
M	214	S214I	aGt	aTt	56	56	AY.25	0.000337
M	214	S214R	agT	agG	21	43	All	0.000004
M	214	S214R	Agt	Cgt	11	43	All	0.000002
M	214	S214R	agT	agA	10	43	All	0.000002
M	214	S214R	AgT	CgG	1	43	All	0
M	214	S214I	aGt	aTt	31	31	AY.121	0.004195
M	214	S214C	Agt	Tgt	30	30	All	0.000006
M	214	S214I	aGt	aTt	30	30	B.1.2	0.000264
M	214	S214I	aGt	aTt	28	28	B.1	0.000256
M	214	S214T	aGt	aCt	21	21	B.1.1.7	0.000019
M	214	S214I	aGt	aTt	20	20	AY.103	0.000124
M	214	S214S	agT	agC	20	20	B.1.429	0.000471
M	214	S214N	aGt	aAt	17	17	AY.4	0.000026
M	214	S214del	AGT	---	16	16	B.1.1.7	0.000014
M	214	S214I	aGt	aTt	16	16	B.1.554	0.070485
M	214	S214I	aGt	aTt	12	12	AY.3	0.000119
M	214	S214R	agT	agG	11	11	B.1.184	0.647059
M	214	S214I	aGt	aTt	10	10	AY.106	0.003349
M	214	S214I	aGt	aTt	10	10	AY.44	0.000061
M	214	S214I	aGt	aTt	10	10	B.1.243	0.000696
M	214	S214S	agT	agC	9	9	AY.25	0.000054
M	214	S214I	aGt	aTt	9	9	AY.39	0.000222
M	214	S214I	aGt	aTt	9	9	B.1.160	0.000281
M	214	S214I	aGt	aTt	8	8	AY.33	0.000534
M	214	S214G	Agt	Ggt	8	8	AY.4	0.000012
M	214	S214C	Agt	Tgt	8	8	AY.43	0.000035
M	214	S214G	Agt	Ggt	8	8	B.1.1.7	0.000007
M	214	S214N	aGt	aAt	8	8	B.1.1.7	0.000007
M	214	S214I	aGt	aTt	8	8	B.1.177	0.000105
M	214	S214S	agT	agC	8	8	B.1.617.2	0.00003
M	214	S214G	Agt	Ggt	8	8	B.1.617.2	0.00003
M	214	S214I	aGt	aTt	8	8	P.1	0.000126
M	214	S214R	agT	agG	3	7		0.166667
M	214	S214R	agT	agA	2	7		0.111111
M	214	S214R	Agt	Cgt	1	7		0.055556
M	214	S214R	AgT	CgG	1	7		0.055556
M	214	S214I	aGt	aTt	7	7	AY.39.1	0.000277
M	214	S214I	aGt	aTt	7	7	AY.42	0.000282
M	214	S214I	aGt	aTt	7	7	AY.48	0.003256
M	214	S214I	aGt	aTt	7	7	B.1.1	0.000127
M	214	S214G	Agt	Ggt	7	7	B.1.525	0.000792
M	214	S214I	aGt	aTt	7	7	P.1.14	0.000335
M	214	S214N	aGt	aAt	5	6		0.277778
M	214	S214N	aGT	aAC	1	6		0.055556
M	214	S214K	aGT	aAA	3	6	All	0.000001
M	214	S214K	aGT	aAG	3	6	All	0.000001
M	214	S214I	aGt	aTt	6	6	AY.26	0.00017
M	214	S214I	aGt	aTt	6	6	AY.75	0.000336
M	214	S214I	aGt	aTt	6	6	AY.99	0.006296
M	214	S214I	aGt	aTt	6	6	B.1.565	0.004862
M	214	S214K	aGT	aAG	3	5		0.166667
M	214	S214K	aGT	aAA	2	5		0.111111
M	214	S214I	aGt	aTt	5	5	AY.100	0.00023
M	214	S214I	aGt	aTt	5	5	AY.20	0.000194
M	214	S214R	Agt	Cgt	5	5	AY.26	0.000142
M	214	S214I	aGt	aTt	5	5	AY.29	0.000079
M	214	S214C	Agt	Tgt	5	5	AY.3.1	0.000426
M	214	S214C	Agt	Tgt	5	5	AY.4	0.000008
M	214	S214T	aGt	aCt	5	5	AY.4.2	0.000108
M	214	S214T	aGt	aCt	5	5	AY.44	0.00003
M	214	S214S	agT	agC	5	5	AY.44	0.00003
M	214	S214I	aGt	aTt	5	5	AY.5	0.000103
M	214	S214I	aGt	aTt	5	5	AY.64	0.002976
M	214	S214S	agT	agC	5	5	B.1	0.000046
M	214	S214S	agT	agC	5	5	B.1.1.153	0.005476
M	214	S214S	agT	agC	5	5	B.1.1.7	0.000004
M	214	S214S	agT	agC	5	5	B.1.234	0.00066
M	214	S214I	aGt	aTt	4	4	AY.102	0.000106
M	214	S214I	aGt	aTt	4	4	AY.23	0.000279
M	214	S214T	aGt	aCt	4	4	AY.4	0.000006
M	214	S214I	aGt	aTt	4	4	AY.45	0.000487
M	214	S214R	agT	agA	4	4	B.1.1.274	0.020202
M	214	S214C	Agt	Tgt	4	4	B.1.1.7	0.000004
M	214	S214T	aGt	aCt	4	4	B.1.177.81	0.000757
M	214	S214I	aGt	aTt	4	4	B.1.199	0.016529
M	214	S214I	aGt	aTt	4	4	B.1.429	0.000094
M	214	S214I	aGt	aTt	4	4	B.1.526	0.000094
M	214	S214I	aGt	aTt	4	4	C.37	0.000464
M	214	S214D	AGt	GAt	2	3	All	0
M	214	S214D	AGT	GAC	1	3	All	0
M	214	S214G	Agt	Ggt	3	3	AY.13	0.000483
M	214	S214S	agT	agC	3	3	AY.4	0.000005
M	214	S214I	aGt	aTt	3	3	AY.4.2	0.000065
M	214	S214G	Agt	Ggt	2	3	AY.44	0.000012
M	214	S214G	AgT	GgA	1	3	AY.44	0.000006
M	214	S214I	aGt	aTt	3	3	AY.98.1	0.000145
M	214	S214del	AGT	---	3	3	B.1	0.000027
M	214	S214N	aGt	aAt	3	3	B.1.2	0.000026
M	214	S214I	aGt	aTt	3	3	B.1.320	0.003736
M	214	S214I	aGt	aTt	3	3	B.1.349	0.002144
M	214	S214G	Agt	Ggt	3	3	B.1.351	0.000089
M	214	S214I	aGt	aTt	3	3	B.1.351	0.000089
M	214	S214N	aGt	aAt	3	3	B.1.369	0.000856
M	214	S214I	aGt	aTt	3	3	B.1.617.1	0.000387
M	214	S214N	aGt	aAt	3	3	B.1.617.2	0.000011
M	214	S214R	Agt	Cgt	3	3	C.37	0.000348
M	214	S214G	AgT	GgA	1	2		0.055556
M	214	S214G	Agt	Ggt	1	2		0.055556
M	214	S214S	agT	agC	2	2	A.2.5.1	0.009615
M	214	S214G	Agt	Ggt	2	2	AY.1	0.000791
M	214	S214G	Agt	Ggt	2	2	AY.102	0.000053
M	214	S214I	aGt	aTt	2	2	AY.118	0.000125
M	214	S214N	aGt	aAt	2	2	AY.20	0.000078
M	214	S214T	aGt	aCt	2	2	AY.25	0.000012
M	214	S214S	agT	agC	2	2	AY.3	0.00002
M	214	S214I	aGt	aTt	2	2	AY.37	0.000632
M	214	S214N	aGt	aAt	2	2	AY.39	0.000049
M	214	S214G	Agt	Ggt	2	2	AY.43	0.000009
M	214	S214N	aGt	aAt	2	2	AY.43	0.000009
M	214	S214del	AGT	---	2	2	AY.44	0.000012
M	214	S214I	aGt	aTt	2	2	AY.6	0.000082
M	214	S214C	Agt	Tgt	2	2	AY.62	0.000871
M	214	S214I	aGt	aTt	2	2	AY.94	0.000885
M	214	S214I	aGt	aTt	2	2	B	0.000256
M	214	S214R	agT	agG	2	2	B.1	0.000018
M	214	S214R	agT	agA	2	2	B.1.1	0.000036
M	214	S214I	aGt	aTt	2	2	B.1.1.519	0.000079
M	214	S214N	aGt	aAt	2	2	B.1.177	0.000026
M	214	S214T	aGt	aCt	2	2	B.1.177	0.000026
M	214	S214S	agT	agC	2	2	B.1.177.10	0.001756
M	214	S214N	aGt	aAt	2	2	B.1.177.44	0.001038
M	214	S214I	aGt	aTt	2	2	B.1.177.86	0.000367
M	214	S214T	aGt	aCt	2	2	B.1.221	0.000142
M	214	S214G	Agt	Ggt	2	2	B.1.298	0.004228
M	214	S214I	aGt	aTt	2	2	B.1.36	0.000292
M	214	S214I	aGt	aTt	2	2	B.1.36.29	0.001035
M	214	S214R	agT	agG	2	2	B.1.36.8	0.002
M	214	S214I	aGt	aTt	2	2	B.1.396	0.001411
M	214	S214S	agT	agC	2	2	B.1.425	0.005988
M	214	S214I	aGt	aTt	2	2	B.1.517	0.000854
M	214	S214N	aGt	aAt	2	2	B.1.596	0.000174
M	214	S214S	agT	agC	2	2	B.1.596	0.000174
M	214	S214N	aGt	aAt	2	2	B.1.637	0.000146
M	214	S214I	aGt	aTt	2	2	B.1.637	0.000146
M	214	S214I	aGt	aTt	2	2	B.6	0.00182
M	214	S214T	aGt	aCt	2	2	D.2	0.00015
M	214	S214I	aGt	aTt	2	2	D.2	0.00015
M	214	S214S	agT	agC	2	2	P.1.12	0.000968
M	214	S214I	aGt	aTt	2	2	Q.1	0.000253
M	214	S214I	aGt	aTt	2	2	R.1	0.00018
M	214	S214E	AGT	GAA	1	1		0.055556
M	214	S214S	agT	agC	1	1		0.055556
M	214	S214Q	AGT	CAG	1	1		0.055556
M	214	S214H	AGt	CAt	1	1		0.055556
M	214	S214D	AGt	GAt	1	1		0.055556
M	214	S214I	aGt	aTt	1	1	A.2.4	0.003367
M	214	S214H	AGt	CAt	1	1	All	0
M	214	S214Q	AGT	CAG	1	1	All	0
M	214	S214del2	aGT	a--	1	1	All	0
M	214	S214del1	Agt	-gt	1	1	All	0
M	214	S214X	AgT	TgA	1	1	All	0
M	214	S214E	AGT	GAA	1	1	All	0
M	214	S214T	aGt	aCt	1	1	AY.100	0.000046
M	214	S214N	aGt	aAt	1	1	AY.100	0.000046
M	214	S214S	agT	agC	1	1	AY.102	0.000027
M	214	S214S	agT	agC	1	1	AY.103	0.000006
M	214	S214N	aGt	aAt	1	1	AY.103	0.000006
M	214	S214C	Agt	Tgt	1	1	AY.103	0.000006
M	214	S214T	aGt	aCt	1	1	AY.104	0.001984
M	214	S214I	aGt	aTt	1	1	AY.111	0.000183
M	214	S214T	aGt	aCt	1	1	AY.113	0.000142
M	214	S214G	Agt	Ggt	1	1	AY.116.1	0.000311
M	214	S214del1	Agt	-gt	1	1	AY.119	0.000035
M	214	S214I	aGt	aTt	1	1	AY.119	0.000035
M	214	S214S	agT	agC	1	1	AY.120	0.000037
M	214	S214G	Agt	Ggt	1	1	AY.120.1	0.000321
M	214	S214I	aGt	aTt	1	1	AY.16	0.00038
M	214	S214G	Agt	Ggt	1	1	AY.20	0.000039
M	214	S214C	Agt	Tgt	1	1	AY.23	0.00007
M	214	S214I	aGt	aTt	1	1	AY.23.1	0.000417
M	214	S214R	Agt	Cgt	1	1	AY.25	0.000006
M	214	S214N	aGt	aAt	1	1	AY.25	0.000006
M	214	S214G	Agt	Ggt	1	1	AY.25	0.000006
M	214	S214G	Agt	Ggt	1	1	AY.26	0.000028
M	214	S214I	aGt	aTt	1	1	AY.27	0.000065
M	214	S214N	aGt	aAt	1	1	AY.27	0.000065
M	214	S214G	Agt	Ggt	1	1	AY.29	0.000016
M	214	S214G	Agt	Ggt	1	1	AY.3	0.00001
M	214	S214I	aGt	aTt	1	1	AY.32	0.000532
M	214	S214I	aGt	aTt	1	1	AY.35	0.000233
M	214	S214T	aGt	aCt	1	1	AY.35	0.000233
M	214	S214S	agT	agC	1	1	AY.39	0.000025
M	214	S214C	Agt	Tgt	1	1	AY.39.1	0.00004
M	214	S214R	Agt	Cgt	1	1	AY.4	0.000002
M	214	S214S	agT	agC	1	1	AY.4.4	0.000409
M	214	S214I	aGt	aTt	1	1	AY.4.5	0.000107
M	214	S214T	aGt	aCt	1	1	AY.43	0.000004
M	214	S214S	agT	agC	1	1	AY.43	0.000004
M	214	S214S	agT	agC	1	1	AY.46.1	0.001027
M	214	S214I	aGt	aTt	1	1	AY.46.5	0.000198
M	214	S214I	aGt	aTt	1	1	AY.46.6	0.000072
M	214	S214T	aGt	aCt	1	1	AY.47	0.000031
M	214	S214G	Agt	Ggt	1	1	AY.47	0.000031
M	214	S214I	aGt	aTt	1	1	AY.5.3	0.000337
M	214	S214I	aGt	aTt	1	1	AY.53	0.000288
M	214	S214T	aGt	aCt	1	1	AY.61	0.000105
M	214	S214I	aGt	aTt	1	1	AY.61	0.000105
M	214	S214I	aGt	aTt	1	1	AY.62	0.000436
M	214	S214I	aGt	aTt	1	1	AY.66	0.00107
M	214	S214I	aGt	aTt	1	1	AY.68	0.000274
M	214	S214I	aGt	aTt	1	1	AY.7.1	0.000113
M	214	S214T	aGt	aCt	1	1	AY.7.1	0.000113
M	214	S214C	Agt	Tgt	1	1	AY.72	0.001361
M	214	S214I	aGt	aTt	1	1	AY.74	0.000116
M	214	S214S	agT	agC	1	1	AY.82	0.001357
M	214	S214I	aGt	aTt	1	1	AY.9	0.000068
M	214	S214G	Agt	Ggt	1	1	AY.9.1	0.000084
M	214	S214I	aGt	aTt	1	1	AY.9.2	0.000037
M	214	S214I	aGt	aTt	1	1	AY.93	0.000273
M	214	S214I	aGt	aTt	1	1	AY.98	0.000079
M	214	S214I	aGt	aTt	1	1	AZ.2	0.000821
M	214	S214S	agT	agC	1	1	AZ.2	0.000821
M	214	S214del2	aGT	a--	1	1	B	0.000128
M	214	S214N	aGt	aAt	1	1	B.1	0.000009
M	214	S214D	AGT	GAC	1	1	B.1	0.000009
M	214	S214S	agT	agC	1	1	B.1.1	0.000018
M	214	S214T	aGt	aCt	1	1	B.1.1	0.000018
M	214	S214I	aGt	aTt	1	1	B.1.1.214	0.000055
M	214	S214N	aGt	aAt	1	1	B.1.1.214	0.000055
M	214	S214N	aGt	aAt	1	1	B.1.1.222	0.000204
M	214	S214G	Agt	Ggt	1	1	B.1.1.28	0.000311
M	214	S214C	Agt	Tgt	1	1	B.1.1.311	0.000358
M	214	S214N	aGt	aAt	1	1	B.1.1.317	0.000412
M	214	S214I	aGt	aTt	1	1	B.1.1.318	0.000302
M	214	S214N	aGt	aAt	1	1	B.1.1.329	0.003846
M	214	S214I	aGt	aTt	1	1	B.1.1.388	0.045455
M	214	S214I	aGt	aTt	1	1	B.1.1.420	0.001006
M	214	S214I	aGt	aTt	1	1	B.1.1.526	0.003546
M	214	S214R	agT	agA	1	1	B.1.1.7	0.000001
M	214	S214I	aGt	aTt	1	1	B.1.139	0.000733
M	214	S214I	aGt	aTt	1	1	B.1.149	0.003425
M	214	S214C	Agt	Tgt	1	1	B.1.177	0.000013
M	214	S214T	aGt	aCt	1	1	B.1.177.17	0.000821
M	214	S214R	agT	agG	1	1	B.1.177.57	0.000281
M	214	S214I	aGt	aTt	1	1	B.1.177.57	0.000281
M	214	S214I	aGt	aTt	1	1	B.1.189	0.004292
M	214	S214S	agT	agC	1	1	B.1.2	0.000009
M	214	S214I	aGt	aTt	1	1	B.1.210	0.002132
M	214	S214S	agT	agC	1	1	B.1.221	0.000071
M	214	S214I	aGt	aTt	1	1	B.1.221	0.000071
M	214	S214R	agT	agA	1	1	B.1.221	0.000071
M	214	S214N	aGt	aAt	1	1	B.1.221	0.000071
M	214	S214K	aGT	aAA	1	1	B.1.221	0.000071
M	214	S214S	agT	agC	1	1	B.1.243	0.00007
M	214	S214T	aGt	aCt	1	1	B.1.243	0.00007
M	214	S214X	AgT	TgA	1	1	B.1.258.11	0.000396
M	214	S214D	AGt	GAt	1	1	B.1.258.11	0.000396
M	214	S214I	aGt	aTt	1	1	B.1.351.2	0.000303
M	214	S214I	aGt	aTt	1	1	B.1.351.3	0.000876
M	214	S214R	agT	agG	1	1	B.1.36.10	0.004785
M	214	S214I	aGt	aTt	1	1	B.1.36.10	0.004785
M	214	S214I	aGt	aTt	1	1	B.1.36.31	0.001751
M	214	S214I	aGt	aTt	1	1	B.1.367	0.000792
M	214	S214G	Agt	Ggt	1	1	B.1.369	0.000285
M	214	S214I	aGt	aTt	1	1	B.1.398	0.002976
M	214	S214I	aGt	aTt	1	1	B.1.400	0.000429
M	214	S214G	Agt	Ggt	1	1	B.1.426	0.001009
M	214	S214del	AGT	---	1	1	B.1.434	0.052632
M	214	S214I	aGt	aTt	1	1	B.1.466.2	0.000391
M	214	S214N	aGt	aAt	1	1	B.1.475	0.142857
M	214	S214I	aGt	aTt	1	1	B.1.499	0.00105
M	214	S214I	aGt	aTt	1	1	B.1.524	0.001406
M	214	S214S	agT	agC	1	1	B.1.575	0.000303
M	214	S214G	Agt	Ggt	1	1	B.1.595	0.000261
M	214	S214I	aGt	aTt	1	1	B.1.602	0.006536
M	214	S214N	aGt	aAt	1	1	B.1.617.1	0.000129
M	214	S214I	aGt	aTt	1	1	B.1.630	0.005236
M	214	S214G	Agt	Ggt	1	1	B.1.636	0.006711
M	214	S214R	agT	agG	1	1	B.1.637	0.000073
M	214	S214S	agT	agC	1	1	C.36	0.000911
M	214	S214I	aGt	aTt	1	1	C.36.3	0.000567
M	214	S214I	aGt	aTt	1	1	C.36.3.1	0.002717
M	214	S214S	agT	agC	1	1	D.2	0.000075
M	214	S214I	aGt	aTt	1	1	N.3	0.005814
M	214	S214S	agT	agC	1	1	P.1	0.000016
M	214	S214I	aGt	aTt	1	1	P.1.15	0.000232
M	214	S214I	aGt	aTt	1	1	P.4	0.003802

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.