CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 81

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	81	A81S		nonsyn	Gct	Tct	21721	21721	1	26763-26765
M	81	A81A		syn	gcT	gcC	678	628	0.926254	26763-26765
M	81	A81A		syn	gcT	gcA	678	30	0.0442478	26763-26765
M	81	A81A		syn	gcT	gcG	678	20	0.0294985	26763-26765
M	81	A81del		del	GCT	---	87	87	1	26763-26765
M	81	A81V		nonsyn	gCt	gTt	10	10	1	26763-26765
M	81	A81G		nonsyn	gCt	gGt	6	6	1	26763-26765
M	81	A81P		nonsyn	Gct	Cct	5	5	1	26763-26765
M	81	A81D		nonsyn	gCt	gAt	3	3	1	26763-26765
M	81	A81T		nonsyn	Gct	Act	2	2	1	26763-26765
M	81	A81del1		del	gcT	gc-	2	1	0.5	26763-26765
M	81	A81del1		del	Gct	-ct	2	1	0.5	26763-26765

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	81	A81S	Gct	Tct	21721	21721	All	0.004154
M	81	A81S	Gct	Tct	15050	15050	AY.27	0.974047
M	81	A81S	Gct	Tct	3792	3792	AY.4	0.005902
M	81	A81S	Gct	Tct	1458	1458	B.1.1.7	0.001305
M	81	A81A	gcT	gcC	628	678	All	0.00012
M	81	A81A	gcT	gcA	30	678	All	0.000006
M	81	A81A	gcT	gcG	20	678	All	0.000004
M	81	A81S	Gct	Tct	249	249	B.1.617.2	0.000938
M	81	A81A	gcT	gcC	162	162	AY.29	0.002555
M	81	A81S	Gct	Tct	132	132	AY.4.2	0.002863
M	81	A81S	Gct	Tct	110	110	B.1.2	0.000969
M	81	A81A	gcT	gcC	105	105	AY.4	0.000163
M	81	A81S	Gct	Tct	98	98	AY.43	0.000434
M	81	A81del	GCT	---	87	87	All	0.000017
M	81	A81S	Gct	Tct	67	67	AY.37	0.021176
M	81	A81A	gcT	gcC	60	61	AY.3	0.000597
M	81	A81A	gcT	gcA	1	61	AY.3	0.00001
M	81	A81del	GCT	---	57	57	B.1.177.21	0.004359
M	81	A81S	Gct	Tct	51	51	AY.44	0.00031
M	81	A81A	gcT	gcC	50	50	B.1.617.2	0.000188
M	81	A81A	gcT	gcC	44	45	AY.103	0.000273
M	81	A81A	gcT	gcA	1	45	AY.103	0.000006
M	81	A81A	gcT	gcA	21	42	AY.43	0.000093
M	81	A81A	gcT	gcC	21	42	AY.43	0.000093
M	81	A81S	Gct	Tct	42	42	P.1	0.000662
M	81	A81S	Gct	Tct	37	37	AY.103	0.00023
M	81	A81S	Gct	Tct	37	37	B.1.575	0.011226
M	81	A81S	Gct	Tct	32	32	Q.8	0.005277
M	81	A81A	gcT	gcC	31	31	B.1.1.7	0.000028
M	81	A81S	Gct	Tct	27	27	AY.98.1	0.001308
M	81	A81S	Gct	Tct	23	23	AY.75	0.001289
M	81	A81S	Gct	Tct	23	23	B.1.177	0.000303
M	81	A81S	Gct	Tct	22	22	AY.42	0.000885
M	81	A81S	Gct	Tct	22	22	B.1.1.28	0.006847
M	81	A81S	Gct	Tct	21	21	B.1.1	0.000381
M	81	A81S	Gct	Tct	19	19	AY.69	0.003547
M	81	A81S	Gct	Tct	18	18	AY.39	0.000445
M	81	A81S	Gct	Tct	17	17	AY.16	0.006454
M	81	A81S	Gct	Tct	17	17	AY.25	0.000102
M	81	A81S	Gct	Tct	17	17	AY.75.1	0.003065
M	81	A81A	gcT	gcG	16	17	B.1.234	0.002111
M	81	A81A	gcT	gcC	1	17	B.1.234	0.000132
M	81	A81A	gcT	gcC	11	15	AY.25	0.000066
M	81	A81A	gcT	gcG	4	15	AY.25	0.000024
M	81	A81S	Gct	Tct	14	14	AY.102	0.000371
M	81	A81A	gcT	gcC	14	14	AY.44	0.000085
M	81	A81S	Gct	Tct	14	14	AY.74	0.001619
M	81	A81S	Gct	Tct	14	14	B.1	0.000128
M	81	A81S	Gct	Tct	13	13	B.1.110.3	0.009339
M	81	A81S	Gct	Tct	12	12	AY.100	0.000552
M	81	A81S	Gct	Tct	12	12	AY.111	0.002198
M	81	A81S	Gct	Tct	12	12	AY.47	0.000373
M	81	A81del	GCT	---	12	12	B.1.1.7	0.000011
M	81	A81A	gcT	gcC	11	11	AY.102	0.000292
M	81	A81A	gcT	gcC	11	11	AY.39.1	0.000436
M	81	A81V	gCt	gTt	10	10	All	0.000002
M	81	A81S	Gct	Tct	10	10	B.1.429	0.000235
M	81	A81S	Gct	Tct	10	10	B.1.526	0.000235
M	81	A81A	gcT	gcC	9	9	AY.9	0.000608
M	81	A81S	Gct	Tct	8	8	AY.121	0.001083
M	81	A81S	Gct	Tct	8	8	AY.26	0.000226
M	81	A81S	Gct	Tct	8	8	AY.5	0.000165
M	81	A81S	Gct	Tct	8	8	B.1.177.35	0.005529
M	81	A81A	gcT	gcC	8	8	B.1.2	0.00007
M	81	A81S	Gct	Tct	8	8	B.6.6	0.007111
M	81	A81A	gcT	gcC	7	7	AY.26	0.000198
M	81	A81S	Gct	Tct	7	7	AY.3	0.00007
M	81	A81S	Gct	Tct	7	7	AY.33	0.000467
M	81	A81G	gCt	gGt	6	6	All	0.000001
M	81	A81A	gcT	gcC	6	6	AY.20	0.000233
M	81	A81S	Gct	Tct	6	6	AY.61	0.000629
M	81	A81A	gcT	gcC	3	6	B.1	0.000027
M	81	A81A	gcT	gcA	3	6	B.1	0.000027
M	81	A81S	Gct	Tct	6	6	B.1.1.243	0.02449
M	81	A81P	Gct	Cct	5	5	All	0.000001
M	81	A81S	Gct	Tct	5	5	AY.119	0.000177
M	81	A81S	Gct	Tct	5	5	AY.120	0.000186
M	81	A81A	gcT	gcC	5	5	AY.3.1	0.000426
M	81	A81S	Gct	Tct	5	5	B.1.1.318	0.001509
M	81	A81S	Gct	Tct	5	5	B.1.221	0.000355
M	81	A81S	Gct	Tct	5	5	B.1.617.1	0.000645
M	81	A81S	Gct	Tct	5	5	C.37	0.00058
M	81	A81S	Gct	Tct	5	5	M.1	0.116279
M	81	A81del	GCT	---	4	4		0.222222
M	81	A81A	gcT	gcC	4	4	AY.100	0.000184
M	81	A81A	gcT	gcC	4	4	AY.113	0.00057
M	81	A81S	Gct	Tct	4	4	AY.117	0.000338
M	81	A81S	Gct	Tct	4	4	AY.46	0.000416
M	81	A81S	Gct	Tct	4	4	AY.9	0.00027
M	81	A81S	Gct	Tct	4	4	B.1.1.519	0.000159
M	81	A81S	Gct	Tct	4	4	B.1.258	0.000266
M	81	A81D	gCt	gAt	3	3	All	0.000001
M	81	A81S	Gct	Tct	3	3	AY.110	0.000338
M	81	A81A	gcT	gcC	3	3	AY.118	0.000188
M	81	A81S	Gct	Tct	3	3	AY.23	0.000209
M	81	A81S	Gct	Tct	3	3	AY.29	0.000047
M	81	A81A	gcT	gcC	3	3	AY.36	0.000445
M	81	A81G	gCt	gGt	3	3	AY.4	0.000005
M	81	A81S	Gct	Tct	3	3	AY.41	0.000882
M	81	A81V	gCt	gTt	3	3	B.1	0.000027
M	81	A81S	Gct	Tct	3	3	B.1.596	0.000261
M	81	A81S	Gct	Tct	3	3	B.1.637	0.000219
M	81	A81A	gcT	gcC	3	3	N.5	0.0053
M	81	A81S	Gct	Tct	3	3	P.1.14	0.000143
M	81	A81V	gCt	gTt	2	2		0.111111
M	81	A81G	gCt	gGt	2	2		0.111111
M	81	A81T	Gct	Act	2	2	All	0
M	81	A81del1	gcT	gc-	1	2	All	0
M	81	A81del1	Gct	-ct	1	2	All	0
M	81	A81S	Gct	Tct	2	2	AY.118	0.000125
M	81	A81A	gcT	gcC	2	2	AY.29.1	0.000441
M	81	A81A	gcT	gcC	2	2	AY.4.2	0.000043
M	81	A81S	Gct	Tct	2	2	AY.45	0.000243
M	81	A81A	gcT	gcC	2	2	AY.45	0.000243
M	81	A81S	Gct	Tct	2	2	AY.46.3	0.001867
M	81	A81A	gcT	gcC	2	2	AY.5	0.000041
M	81	A81A	gcT	gcC	2	2	AY.64	0.00119
M	81	A81S	Gct	Tct	2	2	AY.67	0.000929
M	81	A81del	GCT	---	2	2	AY.75.1	0.000361
M	81	A81S	Gct	Tct	2	2	AY.87	0.001665
M	81	A81A	gcT	gcC	2	2	AY.88	0.001768
M	81	A81S	Gct	Tct	2	2	AY.9.2	0.000073
M	81	A81S	Gct	Tct	2	2	AY.94	0.000885
M	81	A81A	gcT	gcC	2	2	AY.99.2	0.000184
M	81	A81P	Gct	Cct	2	2	B.1	0.000018
M	81	A81D	gCt	gAt	2	2	B.1	0.000018
M	81	A81S	Gct	Tct	2	2	B.1.1.214	0.000111
M	81	A81S	Gct	Tct	2	2	B.1.1.311	0.000716
M	81	A81S	Gct	Tct	2	2	B.1.1.369	0.000892
M	81	A81S	Gct	Tct	2	2	B.1.1.416	0.00181
M	81	A81A	gcT	gcC	2	2	B.1.1.519	0.000079
M	81	A81S	Gct	Tct	2	2	B.1.160	0.000062
M	81	A81A	gcT	gcC	2	2	B.1.177.86	0.000367
M	81	A81S	Gct	Tct	2	2	B.1.36.29	0.001035
M	81	A81S	Gct	Tct	2	2	B.1.427	0.000101
M	81	A81A	gcT	gcA	2	2	B.1.427	0.000101
M	81	A81S	Gct	Tct	2	2	B.1.604	0.034483
M	81	A81S	Gct	Tct	2	2	B.1.609	0.000959
M	81	A81del	GCT	---	2	2	B.1.617.2	0.000008
M	81	A81S	Gct	Tct	2	2	B.1.631	0.006734
M	81	A81A	gcT	gcC	2	2	B.1.632	0.013423
M	81	A81S	Gct	Tct	2	2	D.2	0.00015
M	81	A81A	gcT	gcC	2	2	P.1	0.000032
M	81	A81S	Gct	Tct	2	2	P.1.15	0.000465
M	81	A81S	Gct	Tct	1	1	AY.10	0.00053
M	81	A81S	Gct	Tct	1	1	AY.104	0.001984
M	81	A81A	gcT	gcC	1	1	AY.105	0.000643
M	81	A81S	Gct	Tct	1	1	AY.109	0.00074
M	81	A81S	Gct	Tct	1	1	AY.12	0.000316
M	81	A81del	GCT	---	1	1	AY.120	0.000037
M	81	A81A	gcT	gcC	1	1	AY.120	0.000037
M	81	A81A	gcT	gcC	1	1	AY.120.1	0.000321
M	81	A81S	Gct	Tct	1	1	AY.14	0.000088
M	81	A81S	Gct	Tct	1	1	AY.16.1	0.00047
M	81	A81S	Gct	Tct	1	1	AY.20	0.000039
M	81	A81A	gcT	gcC	1	1	AY.23	0.00007
M	81	A81S	Gct	Tct	1	1	AY.3.1	0.000085
M	81	A81A	gcT	gcC	1	1	AY.33	0.000067
M	81	A81A	gcT	gcC	1	1	AY.35	0.000233
M	81	A81A	gcT	gcC	1	1	AY.38	0.000499
M	81	A81S	Gct	Tct	1	1	AY.38	0.000499
M	81	A81T	Gct	Act	1	1	AY.4	0.000002
M	81	A81P	Gct	Cct	1	1	AY.4	0.000002
M	81	A81S	Gct	Tct	1	1	AY.4.4	0.000409
M	81	A81A	gcT	gcC	1	1	AY.4.5	0.000107
M	81	A81A	gcT	gcC	1	1	AY.46	0.000104
M	81	A81A	gcT	gcC	1	1	AY.46.6	0.000072
M	81	A81A	gcT	gcC	1	1	AY.47	0.000031
M	81	A81A	gcT	gcC	1	1	AY.5.4	0.000277
M	81	A81S	Gct	Tct	1	1	AY.52	0.000814
M	81	A81A	gcT	gcC	1	1	AY.55	0.000917
M	81	A81S	Gct	Tct	1	1	AY.60	0.000938
M	81	A81S	Gct	Tct	1	1	AY.7.1	0.000113
M	81	A81S	Gct	Tct	1	1	AY.71	0.000475
M	81	A81S	Gct	Tct	1	1	AY.72	0.001361
M	81	A81S	Gct	Tct	1	1	AY.77	0.001127
M	81	A81A	gcT	gcC	1	1	AY.9.1	0.000084
M	81	A81A	gcT	gcC	1	1	AY.9.2	0.000037
M	81	A81S	Gct	Tct	1	1	AY.93	0.000273
M	81	A81A	gcT	gcC	1	1	AY.98	0.000079
M	81	A81S	Gct	Tct	1	1	AY.98	0.000079
M	81	A81A	gcT	gcC	1	1	B	0.000128
M	81	A81del1	Gct	-ct	1	1	B.1	0.000009
M	81	A81del	GCT	---	1	1	B.1	0.000009
M	81	A81P	Gct	Cct	1	1	B.1.1	0.000018
M	81	A81G	gCt	gGt	1	1	B.1.1	0.000018
M	81	A81del1	gcT	gc-	1	1	B.1.1	0.000018
M	81	A81S	Gct	Tct	1	1	B.1.1.216	0.00089
M	81	A81S	Gct	Tct	1	1	B.1.1.222	0.000204
M	81	A81S	Gct	Tct	1	1	B.1.1.277	0.000759
M	81	A81D	gCt	gAt	1	1	B.1.1.326	0.001761
M	81	A81S	Gct	Tct	1	1	B.1.1.33	0.000421
M	81	A81A	gcT	gcA	1	1	B.1.1.348	0.000796
M	81	A81V	gCt	gTt	1	1	B.1.1.372	0.000689
M	81	A81del	GCT	---	1	1	B.1.1.372	0.000689
M	81	A81V	gCt	gTt	1	1	B.1.1.39	0.00051
M	81	A81S	Gct	Tct	1	1	B.1.1.397	0.002252
M	81	A81S	Gct	Tct	1	1	B.1.1.50	0.000679
M	81	A81S	Gct	Tct	1	1	B.1.1.58	0.005376
M	81	A81P	Gct	Cct	1	1	B.1.1.7	0.000001
M	81	A81T	Gct	Act	1	1	B.1.1.7	0.000001
M	81	A81A	gcT	gcA	1	1	B.1.1.70	0.000341
M	81	A81S	Gct	Tct	1	1	B.1.1.70	0.000341
M	81	A81A	gcT	gcC	1	1	B.1.1.77	0.041667
M	81	A81del	GCT	---	1	1	B.1.160	0.000031
M	81	A81A	gcT	gcC	1	1	B.1.160	0.000031
M	81	A81A	gcT	gcC	1	1	B.1.160.16	0.000929
M	81	A81del	GCT	---	1	1	B.1.161	0.017241
M	81	A81A	gcT	gcC	1	1	B.1.177	0.000013
M	81	A81A	gcT	gcC	1	1	B.1.177.21	0.000076
M	81	A81A	gcT	gcC	1	1	B.1.177.54	0.000606
M	81	A81S	Gct	Tct	1	1	B.1.177.57	0.000281
M	81	A81S	Gct	Tct	1	1	B.1.177.58	0.001332
M	81	A81S	Gct	Tct	1	1	B.1.177.81	0.000189
M	81	A81S	Gct	Tct	1	1	B.1.236	0.002053
M	81	A81del	GCT	---	1	1	B.1.258.11	0.000396
M	81	A81A	gcT	gcC	1	1	B.1.311	0.000275
M	81	A81S	Gct	Tct	1	1	B.1.351	0.00003
M	81	A81S	Gct	Tct	1	1	B.1.36	0.000146
M	81	A81A	gcT	gcC	1	1	B.1.36.38	0.001642
M	81	A81S	Gct	Tct	1	1	B.1.389	0.001002
M	81	A81S	Gct	Tct	1	1	B.1.409	0.000781
M	81	A81A	gcT	gcC	1	1	B.1.416.1	0.001563
M	81	A81S	Gct	Tct	1	1	B.1.426	0.001009
M	81	A81S	Gct	Tct	1	1	B.1.428	0.00102
M	81	A81S	Gct	Tct	1	1	B.1.436	0.001029
M	81	A81S	Gct	Tct	1	1	B.1.466.2	0.000391
M	81	A81S	Gct	Tct	1	1	B.1.525	0.000113
M	81	A81S	Gct	Tct	1	1	B.1.564	0.000426
M	81	A81A	gcT	gcC	1	1	B.1.575	0.000303
M	81	A81del	GCT	---	1	1	B.1.577	0.000687
M	81	A81S	Gct	Tct	1	1	B.1.589	0.007576
M	81	A81V	gCt	gTt	1	1	B.1.596	0.000087
M	81	A81A	gcT	gcC	1	1	B.1.596	0.000087
M	81	A81del	GCT	---	1	1	B.1.596	0.000087
M	81	A81V	gCt	gTt	1	1	B.1.606	0.006024
M	81	A81S	Gct	Tct	1	1	B.1.625	0.002353
M	81	A81del	GCT	---	1	1	B.1.627	0.00202
M	81	A81S	Gct	Tct	1	1	B.1.628	0.000352
M	81	A81S	Gct	Tct	1	1	B.61	0.005747
M	81	A81V	gCt	gTt	1	1	D.2	0.000075
M	81	A81A	gcT	gcC	1	1	D.2	0.000075
M	81	A81S	Gct	Tct	1	1	P.1.12	0.000484
M	81	A81A	gcT	gcC	1	1	P.1.14	0.000048
M	81	A81del	GCT	---	1	1	P.1.15	0.000232
M	81	A81S	Gct	Tct	1	1	P.1.17	0.000162
M	81	A81S	Gct	Tct	1	1	P.1.4	0.000977
M	81	A81S	Gct	Tct	1	1	P.2	0.000187
M	81	A81S	Gct	Tct	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.