CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 150

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	150	R150R		syn	cgT	cgC	25715	25704	0.999572	26970-26972
M	150	R150R		syn	cgT	cgG	25715	10	0.000388878	26970-26972
M	150	R150R		syn	cgT	cgA	25715	1	0.0000388878	26970-26972
M	150	R150del		del	CGT	---	125	125	1	26970-26972
M	150	R150C		nonsyn	Cgt	Tgt	11	8	0.727273	26970-26972
M	150	R150C		nonsyn	CgT	TgC	11	3	0.272727	26970-26972
M	150	R150L		nonsyn	cGt	cTt	10	10	1	26970-26972
M	150	R150S		nonsyn	Cgt	Agt	6	4	0.666667	26970-26972
M	150	R150S		nonsyn	CgT	AgC	6	2	0.333333	26970-26972
M	150	R150del1		del	Cgt	-gt	3	1	0.333333	26970-26972
M	150	R150del1		del	cGt	c-t	3	1	0.333333	26970-26972
M	150	R150del1		del	cgT	cg-	3	1	0.333333	26970-26972
M	150	R150P		nonsyn	cGt	cCt	2	2	1	26970-26972
M	150	R150H		nonsyn	cGt	cAt	2	2	1	26970-26972
M	150	R150del2		del	CGt	--t	2	1	0.5	26970-26972
M	150	R150del2		del	CGT	--G	2	1	0.5	26970-26972
M	150	R150Q		nonsyn	cGT	cAG	1	1	1	26970-26972

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	150	R150R	cgT	cgC	25704	25715	All	0.004916
M	150	R150R	cgT	cgG	10	25715	All	0.000002
M	150	R150R	cgT	cgA	1	25715	All	0
M	150	R150R	cgT	cgC	10324	10324	B.1.258	0.68703
M	150	R150R	cgT	cgC	9413	9413	B.1.258.17	0.978686
M	150	R150R	cgT	cgC	2483	2483	B.1.258.11	0.984146
M	150	R150R	cgT	cgC	523	523	B.1.258.7	1
M	150	R150R	cgT	cgC	372	372	B.1.258.22	0.992
M	150	R150R	cgT	cgC	290	290	B.1.258.4	1
M	150	R150R	cgT	cgC	255	255	B.1	0.002336
M	150	R150R	cgT	cgC	198	198	B.1.258.9	0.99
M	150	R150R	cgT	cgC	141	141	B.1.1.7	0.000126
M	150	R150R	cgT	cgC	141	141	B.1.258.19	1
M	150	R150del	CGT	---	125	125	All	0.000024
M	150	R150R	cgT	cgC	125	125	B.1.258.12	0.984252
M	150	R150R	cgT	cgC	125	125	B.1.258.21	0.968992
M	150	R150R	cgT	cgC	114	114	B.1.258.5	1
M	150	R150R	cgT	cgC	113	113	B.1.617.2	0.000425
M	150	R150del	CGT	---	102	102	B.1.177.21	0.0078
M	150	R150R	cgT	cgC	95	99	AY.4	0.000148
M	150	R150R	cgT	cgG	4	99	AY.4	0.000006
M	150	R150R	cgT	cgC	87	87	B.1.258.10	0.988636
M	150	R150R	cgT	cgC	63	63	B.1.258.20	1
M	150	R150R	cgT	cgC	57	61	AY.3	0.000567
M	150	R150R	cgT	cgG	4	61	AY.3	0.00004
M	150	R150R	cgT	cgC	53	53	AY.44	0.000323
M	150	R150R	cgT	cgC	51	51	B.1.258.6	1
M	150	R150R	cgT	cgC	44	44	B.1.621	0.003895
M	150	R150R	cgT	cgC	41	41	B.1.258.23	0.97619
M	150	R150R	cgT	cgC	37	37	B.1.2	0.000326
M	150	R150R	cgT	cgC	35	35	B.1.177	0.000461
M	150	R150R	cgT	cgC	35	35	B.1.221	0.002486
M	150	R150R	cgT	cgC	31	31	B.1.258.24	0.333333
M	150	R150R	cgT	cgC	30	30	B.1.1	0.000544
M	150	R150R	cgT	cgC	30	30	B.1.160	0.000936
M	150	R150R	cgT	cgC	29	29	AY.103	0.00018
M	150	R150R	cgT	cgC	28	28	B.1.609	0.013423
M	150	R150R	cgT	cgC	26	26	AY.36	0.003854
M	150	R150R	cgT	cgC	14	14	B.1.367	0.011094
M	150	R150R	cgT	cgC	13	13	B	0.001662
M	150	R150del	CGT	---	13	13	B.1.1.7	0.000012
M	150	R150R	cgT	cgC	13	13	B.1.258.14	0.012745
M	150	R150R	cgT	cgC	13	13	B.1.418	0.206349
M	150	R150R	cgT	cgC	12	12	AY.25	0.000072
M	150	R150R	cgT	cgC	12	12	AY.39	0.000297
M	150	R150R	cgT	cgC	12	12	AY.43	0.000053
M	150	R150C	Cgt	Tgt	8	11	All	0.000002
M	150	R150C	CgT	TgC	3	11	All	0.000001
M	150	R150L	cGt	cTt	10	10	All	0.000002
M	150	R150R	cgT	cgC	10	10	B.1.258.18	1
M	150	R150R	cgT	cgC	9	9	B.1.234	0.001187
M	150	R150R	cgT	cgC	8	8	A	0.003096
M	150	R150R	cgT	cgC	8	8	AY.7.1	0.000902
M	150	R150R	cgT	cgC	7	7	AY.4.2	0.000152
M	150	R150R	cgT	cgC	7	7	B.1.1.519	0.000278
M	150	R150R	cgT	cgC	7	7	B.1.222	0.011844
M	150	R150R	cgT	cgC	7	7	B.4.1	0.132075
M	150	R150S	Cgt	Agt	4	6	All	0.000001
M	150	R150S	CgT	AgC	2	6	All	0
M	150	R150R	cgT	cgC	6	6	AY.100	0.000276
M	150	R150R	cgT	cgC	6	6	AY.91	0.004383
M	150	R150R	cgT	cgC	6	6	B.1.375	0.004918
M	150	R150R	cgT	cgC	5	5	A.3	0.010482
M	150	R150R	cgT	cgC	5	5	AY.47	0.000156
M	150	R150R	cgT	cgC	5	5	B.1.411	0.018519
M	150	R150R	cgT	cgC	5	5	B.1.600	0.02924
M	150	R150R	cgT	cgC	5	5	P.1	0.000079
M	150	R150R	cgT	cgC	4	4	AY.46.6	0.000289
M	150	R150R	cgT	cgC	4	4	B.1.525	0.000453
M	150	R150R	cgT	cgC	4	4	R.1	0.00036
M	150	R150del1	Cgt	-gt	1	3	All	0
M	150	R150del1	cgT	cg-	1	3	All	0
M	150	R150del1	cGt	c-t	1	3	All	0
M	150	R150R	cgT	cgC	3	3	AY.77	0.003382
M	150	R150R	cgT	cgC	3	3	AY.98.1	0.000145
M	150	R150L	cGt	cTt	3	3	B.1	0.000027
M	150	R150R	cgT	cgC	3	3	B.1.160.8	0.003866
M	150	R150C	CgT	TgC	3	3	B.1.177.21	0.000229
M	150	R150R	cgT	cgC	2	3	B.1.177.73	0.001133
M	150	R150R	cgT	cgA	1	3	B.1.177.73	0.000566
M	150	R150R	cgT	cgC	3	3	B.1.258.15	0.056604
M	150	R150R	cgT	cgC	3	3	B.1.429	0.000071
M	150	R150R	cgT	cgC	3	3	Q.3	0.000435
M	150	R150H	cGt	cAt	2	2	All	0
M	150	R150P	cGt	cCt	2	2	All	0
M	150	R150del2	CGT	--G	1	2	All	0
M	150	R150del2	CGt	--t	1	2	All	0
M	150	R150R	cgT	cgC	2	2	AY.102	0.000053
M	150	R150R	cgT	cgC	2	2	AY.119	0.000071
M	150	R150R	cgT	cgC	2	2	AY.3.1	0.000171
M	150	R150R	cgT	cgC	2	2	AY.40	0.001929
M	150	R150R	cgT	cgC	2	2	AY.59	0.001059
M	150	R150R	cgT	cgC	2	2	AY.75.1	0.000361
M	150	R150C	Cgt	Tgt	2	2	B.1	0.000018
M	150	R150S	Cgt	Agt	1	2	B.1	0.000009
M	150	R150S	CgT	AgC	1	2	B.1	0.000009
M	150	R150R	cgT	cgC	2	2	B.1.1.153	0.002191
M	150	R150R	cgT	cgC	2	2	B.1.1.214	0.000111
M	150	R150L	cGt	cTt	2	2	B.1.1.7	0.000002
M	150	R150R	cgT	cgC	2	2	B.1.1.70	0.000682
M	150	R150R	cgT	cgC	2	2	B.1.160.7	0.004158
M	150	R150R	cgT	cgC	2	2	B.1.177.31	0.022989
M	150	R150R	cgT	cgC	2	2	B.1.177.6	0.001953
M	150	R150R	cgT	cgC	2	2	B.1.177.7	0.00033
M	150	R150R	cgT	cgC	2	2	B.1.237	0.00995
M	150	R150R	cgT	cgC	2	2	B.1.351	0.000059
M	150	R150R	cgT	cgC	2	2	B.1.36	0.000292
M	150	R150R	cgT	cgG	2	2	B.1.36.1	0.002281
M	150	R150R	cgT	cgC	2	2	B.1.466.2	0.000782
M	150	R150R	cgT	cgC	2	2	B.1.576	0.001813
M	150	R150R	cgT	cgC	2	2	B.1.590	0.009091
M	150	R150R	cgT	cgC	1	1		0.055556
M	150	R150R	cgT	cgC	1	1	A.2.4	0.003367
M	150	R150R	cgT	cgC	1	1	A.2.5	0.000499
M	150	R150Q	cGT	cAG	1	1	All	0
M	150	R150del2	CGT	--G	1	1	AY.103	0.000006
M	150	R150R	cgT	cgC	1	1	AY.11	0.001339
M	150	R150R	cgT	cgC	1	1	AY.16.1	0.00047
M	150	R150R	cgT	cgC	1	1	AY.20	0.000039
M	150	R150R	cgT	cgC	1	1	AY.23	0.00007
M	150	R150del2	CGt	--t	1	1	AY.25	0.000006
M	150	R150del	CGT	---	1	1	AY.26	0.000028
M	150	R150L	cGt	cTt	1	1	AY.27	0.000065
M	150	R150L	cGt	cTt	1	1	AY.4	0.000002
M	150	R150S	CgT	AgC	1	1	AY.42	0.00004
M	150	R150R	cgT	cgC	1	1	AY.42	0.00004
M	150	R150del	CGT	---	1	1	AY.43	0.000004
M	150	R150del	CGT	---	1	1	AY.44	0.000006
M	150	R150R	cgT	cgC	1	1	AY.45	0.000122
M	150	R150R	cgT	cgC	1	1	AY.46.4	0.000165
M	150	R150P	cGt	cCt	1	1	AY.47	0.000031
M	150	R150R	cgT	cgC	1	1	AY.52	0.000814
M	150	R150R	cgT	cgC	1	1	AY.61	0.000105
M	150	R150C	Cgt	Tgt	1	1	AY.61	0.000105
M	150	R150R	cgT	cgC	1	1	AY.62	0.000436
M	150	R150S	Cgt	Agt	1	1	AY.7.1	0.000113
M	150	R150Q	cGT	cAG	1	1	AY.85	0.000427
M	150	R150R	cgT	cgC	1	1	AY.9	0.000068
M	150	R150R	cgT	cgC	1	1	AY.98	0.000079
M	150	R150R	cgT	cgC	1	1	AY.99.2	0.000092
M	150	R150H	cGt	cAt	1	1	B.1	0.000009
M	150	R150del	CGT	---	1	1	B.1	0.000009
M	150	R150H	cGt	cAt	1	1	B.1.1	0.000018
M	150	R150C	Cgt	Tgt	1	1	B.1.1	0.000018
M	150	R150del	CGT	---	1	1	B.1.1.221	0.010101
M	150	R150R	cgT	cgC	1	1	B.1.1.225	0.007194
M	150	R150R	cgT	cgC	1	1	B.1.1.284	0.000107
M	150	R150R	cgT	cgC	1	1	B.1.1.317	0.000412
M	150	R150R	cgT	cgC	1	1	B.1.1.39	0.00051
M	150	R150R	cgT	cgC	1	1	B.1.1.409	0.002833
M	150	R150del	CGT	---	1	1	B.1.1.420	0.001006
M	150	R150R	cgT	cgC	1	1	B.1.1.466	0.008696
M	150	R150R	cgT	cgC	1	1	B.1.1.50	0.000679
M	150	R150R	cgT	cgC	1	1	B.1.146	0.004237
M	150	R150R	cgT	cgC	1	1	B.1.149	0.003425
M	150	R150R	cgT	cgC	1	1	B.1.157	0.002985
M	150	R150L	cGt	cTt	1	1	B.1.177	0.000013
M	150	R150R	cgT	cgC	1	1	B.1.177.12	0.000152
M	150	R150del1	Cgt	-gt	1	1	B.1.177.35	0.000691
M	150	R150C	Cgt	Tgt	1	1	B.1.177.52	0.001757
M	150	R150R	cgT	cgC	1	1	B.1.177.80	0.001912
M	150	R150C	Cgt	Tgt	1	1	B.1.177.86	0.000183
M	150	R150R	cgT	cgC	1	1	B.1.177.86	0.000183
M	150	R150S	Cgt	Agt	1	1	B.1.2	0.000009
M	150	R150R	cgT	cgC	1	1	B.1.223	0.002778
M	150	R150L	cGt	cTt	1	1	B.1.232	0.000537
M	150	R150C	Cgt	Tgt	1	1	B.1.234	0.000132
M	150	R150R	cgT	cgC	1	1	B.1.242	0.018868
M	150	R150del	CGT	---	1	1	B.1.258.11	0.000396
M	150	R150R	cgT	cgC	1	1	B.1.258.16	0.001637
M	150	R150R	cgT	cgC	1	1	B.1.258.3	0.001675
M	150	R150R	cgT	cgC	1	1	B.1.293	0.0125
M	150	R150R	cgT	cgC	1	1	B.1.329	0.000608
M	150	R150del	CGT	---	1	1	B.1.351	0.00003
M	150	R150R	cgT	cgC	1	1	B.1.36.17	0.000494
M	150	R150R	cgT	cgC	1	1	B.1.36.31	0.001751
M	150	R150R	cgT	cgC	1	1	B.1.36.9	0.003215
M	150	R150R	cgT	cgC	1	1	B.1.362	0.001541
M	150	R150R	cgT	cgC	1	1	B.1.366	0.004878
M	150	R150R	cgT	cgC	1	1	B.1.406	0.006061
M	150	R150del	CGT	---	1	1	B.1.427	0.00005
M	150	R150P	cGt	cCt	1	1	B.1.429	0.000024
M	150	R150R	cgT	cgC	1	1	B.1.432	0.011236
M	150	R150R	cgT	cgC	1	1	B.1.524	0.001406
M	150	R150R	cgT	cgC	1	1	B.1.526	0.000024
M	150	R150R	cgT	cgC	1	1	B.1.596	0.000087
M	150	R150del1	cgT	cg-	1	1	B.1.596	0.000087
M	150	R150R	cgT	cgC	1	1	B.1.599	0.00365
M	150	R150del	CGT	---	1	1	B.1.617.2	0.000004
M	150	R150del1	cGt	c-t	1	1	B.1.617.2	0.000004
M	150	R150L	cGt	cTt	1	1	B.1.617.2	0.000004
M	150	R150R	cgT	cgC	1	1	B.1.623	0.000536
M	150	R150R	cgT	cgC	1	1	B.1.627	0.00202
M	150	R150R	cgT	cgC	1	1	B.1.637	0.000073
M	150	R150R	cgT	cgC	1	1	B.1.94	0.027027
M	150	R150C	Cgt	Tgt	1	1	Q.1	0.000126
M	150	R150S	Cgt	Agt	1	1	Q.1	0.000126

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.