CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 44

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	44	R44K		nonsyn	aGg	aAg	850	847	0.996471	26652-26654
M	44	R44K		nonsyn	aGG	aAA	850	3	0.00352941	26652-26654
M	44	R44S		nonsyn	agG	agT	493	490	0.993915	26652-26654
M	44	R44S		nonsyn	agG	agC	493	3	0.00608519	26652-26654
M	44	R44R		syn	agG	agA	161	155	0.962733	26652-26654
M	44	R44R		syn	Agg	Cgg	161	6	0.0372671	26652-26654
M	44	R44M		nonsyn	aGg	aTg	76	76	1	26652-26654
M	44	R44del		del	AGG	---	36	36	1	26652-26654
M	44	R44G		nonsyn	Agg	Ggg	8	8	1	26652-26654
M	44	R44W		nonsyn	Agg	Tgg	3	3	1	26652-26654
M	44	R44C		nonsyn	AgG	TgT	1	1	1	26652-26654
M	44	R44X		nonsyn	AGG	TAA	1	1	1	26652-26654
M	44	R44del1		del	aGg	a-g	1	1	1	26652-26654
M	44	R44N		nonsyn	aGG	aAC	1	1	1	26652-26654

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	44	R44K	aGg	aAg	847	850	All	0.000162
M	44	R44K	aGG	aAA	3	850	All	0.000001
M	44	R44S	agG	agT	490	493	All	0.000094
M	44	R44S	agG	agC	3	493	All	0.000001
M	44	R44K	aGg	aAg	328	328	P.1.4	0.320312
M	44	R44S	agG	agT	188	188	B.1.517.1	0.989474
M	44	R44R	agG	agA	155	161	All	0.00003
M	44	R44R	Agg	Cgg	6	161	All	0.000001
M	44	R44K	aGg	aAg	146	146	AY.25	0.000878
M	44	R44S	agG	agT	126	126	B.1.517	0.0538
M	44	R44K	aGg	aAg	82	82	AY.103	0.000509
M	44	R44M	aGg	aTg	76	76	All	0.000015
M	44	R44R	agG	agA	63	63	AY.4	0.000098
M	44	R44K	aGg	aAg	60	61	B.1.2	0.000528
M	44	R44K	aGG	aAA	1	61	B.1.2	0.000009
M	44	R44K	aGg	aAg	58	58	B.1.258	0.00386
M	44	R44K	aGg	aAg	48	48	AY.44	0.000292
M	44	R44S	agG	agT	42	43	B.1.1.7	0.000038
M	44	R44S	agG	agC	1	43	B.1.1.7	0.000001
M	44	R44del	AGG	---	36	36	All	0.000007
M	44	R44K	aGg	aAg	36	36	B.1.617.2	0.000136
M	44	R44R	agG	agA	25	26	AY.39	0.000618
M	44	R44R	Agg	Cgg	1	26	AY.39	0.000025
M	44	R44S	agG	agT	26	26	AY.39.1	0.00103
M	44	R44del	AGG	---	16	16	B.1.177.21	0.001224
M	44	R44R	agG	agA	15	15	AY.43	0.000066
M	44	R44R	agG	agA	14	14	B.1.177.57	0.003934
M	44	R44S	agG	agT	12	12	B.1	0.00011
M	44	R44R	agG	agA	9	10	AY.44	0.000055
M	44	R44R	Agg	Cgg	1	10	AY.44	0.000006
M	44	R44M	aGg	aTg	9	9	B.1.1.7	0.000008
M	44	R44S	agG	agT	9	9	B.1.177	0.000119
M	44	R44G	Agg	Ggg	8	8	All	0.000002
M	44	R44del	AGG	---	8	8	B.1.1.7	0.000007
M	44	R44M	aGg	aTg	7	7	AY.4	0.000011
M	44	R44K	aGg	aAg	7	7	AY.46	0.000729
M	44	R44S	agG	agT	7	7	B.1.2	0.000062
M	44	R44M	aGg	aTg	7	7	B.1.617.2	0.000026
M	44	R44S	agG	agT	7	7	B.1.617.2	0.000026
M	44	R44M	aGg	aTg	6	6	B.1.177.21	0.000459
M	44	R44K	aGg	aAg	6	6	B.1.427	0.000303
M	44	R44K	aGg	aAg	5	5	AY.102	0.000133
M	44	R44K	aGg	aAg	5	5	AY.120	0.000186
M	44	R44S	agG	agT	5	5	AY.4	0.000008
M	44	R44K	aGg	aAg	5	5	AY.4	0.000008
M	44	R44K	aGg	aAg	5	5	AY.43	0.000022
M	44	R44K	aGg	aAg	5	5	B.1	0.000046
M	44	R44S	agG	agT	5	5	B.1.1	0.000091
M	44	R44R	agG	agA	4	5	B.1.2	0.000035
M	44	R44R	Agg	Cgg	1	5	B.1.2	0.000009
M	44	R44S	agG	agT	5	5	D.2	0.000375
M	44	R44K	aGg	aAg	4	4		0.222222
M	44	R44S	agG	agT	4	4	AY.103	0.000025
M	44	R44R	agG	agA	4	4	AY.27	0.000259
M	44	R44M	aGg	aTg	4	4	AY.42	0.000161
M	44	R44K	aGg	aAg	4	4	B.1.1	0.000073
M	44	R44R	agG	agA	4	4	B.1.1.222	0.000816
M	44	R44K	aGg	aAg	4	4	B.1.1.7	0.000004
M	44	R44S	agG	agT	4	4	B.1.160	0.000125
M	44	R44M	aGg	aTg	4	4	B.1.2	0.000035
M	44	R44W	Agg	Tgg	3	3	All	0.000001
M	44	R44M	aGg	aTg	3	3	AY.43	0.000013
M	44	R44S	agG	agT	3	3	B	0.000383
M	44	R44K	aGg	aAg	3	3	B.1.177.21	0.000229
M	44	R44S	agG	agT	3	3	B.1.177.21	0.000229
M	44	R44S	agG	agT	3	3	B.1.429	0.000071
M	44	R44K	aGg	aAg	3	3	B.1.526	0.000071
M	44	R44R	agG	agA	3	3	B.1.617.2	0.000011
M	44	R44G	Agg	Ggg	3	3	B.1.617.2	0.000011
M	44	R44M	aGg	aTg	3	3	P.1	0.000047
M	44	R44del	AGG	---	2	2		0.111111
M	44	R44S	agG	agC	2	2		0.111111
M	44	R44M	aGg	aTg	2	2	AY.103	0.000012
M	44	R44R	agG	agA	2	2	AY.25	0.000012
M	44	R44S	agG	agT	2	2	AY.25	0.000012
M	44	R44K	aGg	aAg	2	2	AY.29	0.000032
M	44	R44K	aGg	aAg	2	2	AY.3	0.00002
M	44	R44S	agG	agT	2	2	AY.3	0.00002
M	44	R44K	aGg	aAg	2	2	AY.33	0.000134
M	44	R44S	agG	agT	2	2	AY.39	0.000049
M	44	R44S	agG	agT	2	2	AY.43	0.000009
M	44	R44del	AGG	---	2	2	AY.43	0.000009
M	44	R44S	agG	agT	2	2	AY.44	0.000012
M	44	R44S	agG	agT	2	2	AY.47	0.000062
M	44	R44R	agG	agA	2	2	AY.5	0.000041
M	44	R44M	aGg	aTg	2	2	AY.5	0.000041
M	44	R44K	aGg	aAg	2	2	AY.99.2	0.000184
M	44	R44K	aGg	aAg	2	2	B	0.000256
M	44	R44M	aGg	aTg	2	2	B.1	0.000018
M	44	R44M	aGg	aTg	2	2	B.1.1.519	0.000079
M	44	R44K	aGg	aAg	2	2	B.1.160	0.000062
M	44	R44K	aGg	aAg	2	2	B.1.160.21	0.040816
M	44	R44R	agG	agA	2	2	B.1.240	0.000431
M	44	R44M	aGg	aTg	2	2	B.1.243	0.000139
M	44	R44M	aGg	aTg	2	2	B.1.367	0.001585
M	44	R44K	aGg	aAg	2	2	P.1	0.000032
M	44	R44S	agG	agT	2	2	P.1	0.000032
M	44	R44M	aGg	aTg	2	2	R.1	0.00018
M	44	R44K	aGg	aAg	1	1	A.2.5	0.000499
M	44	R44del1	aGg	a-g	1	1	All	0
M	44	R44N	aGG	aAC	1	1	All	0
M	44	R44C	AgG	TgT	1	1	All	0
M	44	R44X	AGG	TAA	1	1	All	0
M	44	R44M	aGg	aTg	1	1	AY.100	0.000046
M	44	R44S	agG	agT	1	1	AY.102	0.000027
M	44	R44M	aGg	aTg	1	1	AY.102	0.000027
M	44	R44R	agG	agA	1	1	AY.116	0.000287
M	44	R44K	aGG	aAA	1	1	AY.117	0.000085
M	44	R44M	aGg	aTg	1	1	AY.118	0.000063
M	44	R44del	AGG	---	1	1	AY.120	0.000037
M	44	R44R	agG	agA	1	1	AY.14	0.000088
M	44	R44R	agG	agA	1	1	AY.16	0.00038
M	44	R44K	aGg	aAg	1	1	AY.20	0.000039
M	44	R44M	aGg	aTg	1	1	AY.20	0.000039
M	44	R44S	agG	agT	1	1	AY.20	0.000039
M	44	R44R	agG	agA	1	1	AY.24	0.000431
M	44	R44S	agG	agT	1	1	AY.26	0.000028
M	44	R44M	aGg	aTg	1	1	AY.27	0.000065
M	44	R44S	agG	agT	1	1	AY.29.1	0.000221
M	44	R44R	agG	agA	1	1	AY.3	0.00001
M	44	R44M	aGg	aTg	1	1	AY.3	0.00001
M	44	R44R	agG	agA	1	1	AY.30	0.000396
M	44	R44M	aGg	aTg	1	1	AY.36	0.000148
M	44	R44K	aGg	aAg	1	1	AY.39	0.000025
M	44	R44M	aGg	aTg	1	1	AY.4.2	0.000022
M	44	R44S	agG	agT	1	1	AY.4.5	0.000107
M	44	R44K	aGg	aAg	1	1	AY.42	0.00004
M	44	R44W	Agg	Tgg	1	1	AY.43	0.000004
M	44	R44S	agG	agT	1	1	AY.46.2	0.000635
M	44	R44M	aGg	aTg	1	1	AY.46.6	0.000072
M	44	R44K	aGg	aAg	1	1	AY.6	0.000041
M	44	R44K	aGg	aAg	1	1	AY.61	0.000105
M	44	R44S	agG	agT	1	1	AY.68	0.000274
M	44	R44del	AGG	---	1	1	AY.68	0.000274
M	44	R44S	agG	agT	1	1	AY.75.1	0.00018
M	44	R44X	AGG	TAA	1	1	AY.84	0.000437
M	44	R44S	agG	agT	1	1	AY.9	0.000068
M	44	R44G	Agg	Ggg	1	1	AY.9	0.000068
M	44	R44S	agG	agT	1	1	AY.9.2	0.000037
M	44	R44K	aGg	aAg	1	1	AY.92	0.000287
M	44	R44R	Agg	Cgg	1	1	AY.98.1	0.000048
M	44	R44R	Agg	Cgg	1	1	B	0.000128
M	44	R44del	AGG	---	1	1	B.1	0.000009
M	44	R44C	AgG	TgT	1	1	B.1	0.000009
M	44	R44del1	aGg	a-g	1	1	B.1	0.000009
M	44	R44M	aGg	aTg	1	1	B.1.1	0.000018
M	44	R44N	aGG	aAC	1	1	B.1.1	0.000018
M	44	R44R	agG	agA	1	1	B.1.1.25	0.000569
M	44	R44S	agG	agT	1	1	B.1.1.277	0.000759
M	44	R44R	agG	agA	1	1	B.1.1.311	0.000358
M	44	R44M	aGg	aTg	1	1	B.1.1.348	0.000796
M	44	R44K	aGg	aAg	1	1	B.1.1.371	0.010417
M	44	R44M	aGg	aTg	1	1	B.1.1.39	0.00051
M	44	R44K	aGg	aAg	1	1	B.1.1.409	0.002833
M	44	R44S	agG	agT	1	1	B.1.1.409	0.002833
M	44	R44M	aGg	aTg	1	1	B.1.1.432	0.001266
M	44	R44R	Agg	Cgg	1	1	B.1.1.7	0.000001
M	44	R44G	Agg	Ggg	1	1	B.1.1.7	0.000001
M	44	R44S	agG	agT	1	1	B.1.104	0.00369
M	44	R44S	agG	agT	1	1	B.1.160.16	0.000929
M	44	R44K	aGG	aAA	1	1	B.1.161	0.017241
M	44	R44G	Agg	Ggg	1	1	B.1.177	0.000013
M	44	R44M	aGg	aTg	1	1	B.1.177	0.000013
M	44	R44K	aGg	aAg	1	1	B.1.177	0.000013
M	44	R44S	agG	agT	1	1	B.1.177.56	0.000668
M	44	R44S	agG	agT	1	1	B.1.177.60	0.000218
M	44	R44M	aGg	aTg	1	1	B.1.177.73	0.000566
M	44	R44W	Agg	Tgg	1	1	B.1.221	0.000071
M	44	R44S	agG	agT	1	1	B.1.234	0.000132
M	44	R44W	Agg	Tgg	1	1	B.1.258	0.000067
M	44	R44del	AGG	---	1	1	B.1.258.11	0.000396
M	44	R44K	aGg	aAg	1	1	B.1.258.14	0.00098
M	44	R44M	aGg	aTg	1	1	B.1.258.17	0.000104
M	44	R44K	aGg	aAg	1	1	B.1.324	0.001605
M	44	R44S	agG	agT	1	1	B.1.36.18	0.00042
M	44	R44S	agG	agT	1	1	B.1.36.39	0.002217
M	44	R44S	agG	agT	1	1	B.1.367	0.000792
M	44	R44S	agG	agT	1	1	B.1.396	0.000706
M	44	R44K	aGg	aAg	1	1	B.1.428	0.00102
M	44	R44K	aGg	aAg	1	1	B.1.466.2	0.000391
M	44	R44del	AGG	---	1	1	B.1.577	0.000687
M	44	R44K	aGg	aAg	1	1	B.1.577	0.000687
M	44	R44S	agG	agT	1	1	B.1.577	0.000687
M	44	R44K	aGg	aAg	1	1	B.1.596	0.000087
M	44	R44M	aGg	aTg	1	1	B.1.596	0.000087
M	44	R44M	aGg	aTg	1	1	B.1.610	0.003546
M	44	R44del	AGG	---	1	1	B.1.627	0.00202
M	44	R44S	agG	agT	1	1	B.1.76	0.011364
M	44	R44S	agG	agT	1	1	B.31	0.003731
M	44	R44S	agG	agT	1	1	C.37	0.000116
M	44	R44G	Agg	Ggg	1	1	D.2	0.000075
M	44	R44del	AGG	---	1	1	P.1	0.000016
M	44	R44G	Agg	Ggg	1	1	P.1.1	0.000318
M	44	R44del	AGG	---	1	1	P.1.15	0.000232
M	44	R44M	aGg	aTg	1	1	P.1.15	0.000232
M	44	R44S	agG	agT	1	1	P.1.15	0.000232
M	44	R44S	agG	agT	1	1	P.2	0.000187
M	44	R44K	aGg	aAg	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.