CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : Mut = S4F

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	4	S4F		nonsyn	tCc	tTc	1911	1904	0.996337	26532-26534
M	4	S4F		nonsyn	tCC	tTT	1911	7	0.003663	26532-26534

Details of the mutation S4F 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	4	S4F	tCc	tTc	1904	1911	All	0.000364
M	4	S4F	tCC	tTT	7	1911	All	0.000001
M	4	S4F	tCc	tTc	213	213	B.1.1.7	0.000191
M	4	S4F	tCc	tTc	182	182	AY.4	0.000283
M	4	S4F	tCc	tTc	177	177	AY.34	0.017163
M	4	S4F	tCc	tTc	123	123	B.1.632	0.825503
M	4	S4F	tCc	tTc	78	78	B.1.617.2	0.000294
M	4	S4F	tCc	tTc	72	72	B.1.177	0.000948
M	4	S4F	tCc	tTc	50	50	AY.103	0.00031
M	4	S4F	tCc	tTc	45	46	B.1	0.000412
M	4	S4F	tCC	tTT	1	46	B.1	0.000009
M	4	S4F	tCc	tTc	45	45	AY.25	0.000271
M	4	S4F	tCc	tTc	43	43	B.1.160	0.001341
M	4	S4F	tCc	tTc	39	39	B.1.580	0.158537
M	4	S4F	tCc	tTc	32	32	AY.26	0.000906
M	4	S4F	tCc	tTc	29	29	B.1.1.519	0.001152
M	4	S4F	tCc	tTc	27	27	AY.39.1	0.00107
M	4	S4F	tCc	tTc	27	27	AY.4.2	0.000586
M	4	S4F	tCc	tTc	25	25	P.1	0.000394
M	4	S4F	tCc	tTc	24	24	AY.43	0.000106
M	4	S4F	tCc	tTc	24	24	B.1.1	0.000435
M	4	S4F	tCc	tTc	24	24	B.1.2	0.000211
M	4	S4F	tCc	tTc	23	23	AY.44	0.00014
M	4	S4F	tCc	tTc	23	23	B.1.258	0.001531
M	4	S4F	tCc	tTc	21	21	AY.119	0.000741
M	4	S4F	tCc	tTc	21	21	AY.23	0.001465
M	4	S4F	tCc	tTc	19	19	B.1.561	0.007543
M	4	S4F	tCc	tTc	18	18	B.1.573	0.109756
M	4	S4F	tCc	tTc	15	15	B.1.400	0.006435
M	4	S4F	tCc	tTc	14	14	B.1.1.214	0.000776
M	4	S4F	tCc	tTc	14	14	B.1.243	0.000974
M	4	S4F	tCc	tTc	9	13	AY.20	0.00035
M	4	S4F	tCC	tTT	4	13	AY.20	0.000155
M	4	S4F	tCc	tTc	13	13	AY.3	0.000129
M	4	S4F	tCc	tTc	13	13	B.1.351	0.000386
M	4	S4F	tCc	tTc	12	12	AY.102	0.000318
M	4	S4F	tCc	tTc	12	12	AY.29	0.000189
M	4	S4F	tCc	tTc	12	12	B	0.001534
M	4	S4F	tCc	tTc	10	10	AY.42	0.000402
M	4	S4F	tCc	tTc	9	9	AY.39	0.000222
M	4	S4F	tCc	tTc	9	9	AY.98.1	0.000436
M	4	S4F	tCc	tTc	9	9	B.1.429	0.000212
M	4	S4F	tCc	tTc	8	8	A.2.5	0.003992
M	4	S4F	tCc	tTc	8	8	B.1.526	0.000188
M	4	S4F	tCc	tTc	7	7	AY.107	0.003262
M	4	S4F	tCc	tTc	7	7	AY.3.1	0.000597
M	4	S4F	tCc	tTc	7	7	B.1.351.2	0.002118
M	4	S4F	tCc	tTc	7	7	B.1.525	0.000792
M	4	S4F	tCc	tTc	7	7	B.1.621	0.00062
M	4	S4F	tCc	tTc	6	6	P.1.7	0.001916
M	4	S4F	tCc	tTc	5	5	AY.6	0.000206
M	4	S4F	tCc	tTc	5	5	B.1.108	0.02907
M	4	S4F	tCc	tTc	5	5	B.1.234	0.00066
M	4	S4F	tCc	tTc	5	5	B.1.367	0.003962
M	4	S4F	tCc	tTc	5	5	B.1.565	0.004052
M	4	S4F	tCc	tTc	5	5	B.1.596	0.000436
M	4	S4F	tCc	tTc	5	5	P.1.1	0.001588
M	4	S4F	tCc	tTc	5	5	P.1.14	0.000239
M	4	S4F	tCc	tTc	4	4	AY.100	0.000184
M	4	S4F	tCc	tTc	4	4	AY.120	0.000149
M	4	S4F	tCc	tTc	4	4	AY.27	0.000259
M	4	S4F	tCc	tTc	4	4	AY.33	0.000267
M	4	S4F	tCc	tTc	4	4	AY.57	0.002625
M	4	S4F	tCc	tTc	4	4	AY.98	0.000316
M	4	S4F	tCc	tTc	4	4	B.1.1.284	0.00043
M	4	S4F	tCc	tTc	4	4	B.1.177.4	0.000844
M	4	S4F	tCc	tTc	4	4	B.1.221	0.000284
M	4	S4F	tCc	tTc	4	4	B.1.258.17	0.000416
M	4	S4F	tCc	tTc	4	4	D.2	0.0003
M	4	S4F	tCc	tTc	4	4	N.3	0.023256
M	4	S4F	tCc	tTc	4	4	W.4	0.005405
M	4	S4F	tCc	tTc	2	3		0.111111
M	4	S4F	tCC	tTT	1	3		0.055556
M	4	S4F	tCc	tTc	3	3	AA.6	0.048387
M	4	S4F	tCc	tTc	3	3	AY.117	0.000254
M	4	S4F	tCc	tTc	3	3	AY.118	0.000188
M	4	S4F	tCc	tTc	3	3	AY.121	0.000406
M	4	S4F	tCc	tTc	3	3	AY.13	0.000483
M	4	S4F	tCc	tTc	3	3	AY.2	0.001068
M	4	S4F	tCc	tTc	3	3	AY.46	0.000312
M	4	S4F	tCc	tTc	3	3	AY.46.5	0.000595
M	4	S4F	tCc	tTc	3	3	AY.5	0.000062
M	4	S4F	tCc	tTc	3	3	AY.9	0.000203
M	4	S4F	tCc	tTc	3	3	AY.93	0.000819
M	4	S4F	tCc	tTc	3	3	B.1.1.121	0.007282
M	4	S4F	tCc	tTc	3	3	B.1.1.311	0.001074
M	4	S4F	tCc	tTc	3	3	B.1.1.411	0.044118
M	4	S4F	tCc	tTc	2	3	B.1.1.63	0.000772
M	4	S4F	tCC	tTT	1	3	B.1.1.63	0.000386
M	4	S4F	tCc	tTc	3	3	B.1.177.60	0.000655
M	4	S4F	tCc	tTc	3	3	B.1.177.81	0.000568
M	4	S4F	tCc	tTc	3	3	B.1.36.18	0.001261
M	4	S4F	tCc	tTc	3	3	B.1.517	0.001281
M	4	S4F	tCc	tTc	3	3	B.1.609	0.001438
M	4	S4F	tCc	tTc	3	3	B.4.8	0.214286
M	4	S4F	tCc	tTc	2	2	AM.4	0.007143
M	4	S4F	tCc	tTc	2	2	AY.34.1	0.00102
M	4	S4F	tCc	tTc	2	2	AY.35	0.000466
M	4	S4F	tCc	tTc	2	2	AY.47	0.000062
M	4	S4F	tCc	tTc	2	2	AY.48	0.00093
M	4	S4F	tCc	tTc	2	2	AY.55	0.001835
M	4	S4F	tCc	tTc	2	2	AY.75	0.000112
M	4	S4F	tCc	tTc	2	2	B.1.1.1	0.000653
M	4	S4F	tCc	tTc	2	2	B.1.1.33	0.000842
M	4	S4F	tCc	tTc	2	2	B.1.128	0.001271
M	4	S4F	tCc	tTc	2	2	B.1.160.16	0.001859
M	4	S4F	tCc	tTc	2	2	B.1.160.26	0.004843
M	4	S4F	tCc	tTc	2	2	B.1.240	0.000431
M	4	S4F	tCc	tTc	2	2	B.1.241	0.001623
M	4	S4F	tCc	tTc	2	2	B.1.396	0.001411
M	4	S4F	tCc	tTc	2	2	B.1.438.1	0.000215
M	4	S4F	tCc	tTc	2	2	B.1.474	0.003802
M	4	S4F	tCc	tTc	2	2	B.1.623	0.001073
M	4	S4F	tCc	tTc	2	2	B.40	0.000729
M	4	S4F	tCc	tTc	2	2	C.14	0.008658
M	4	S4F	tCc	tTc	2	2	Q.1	0.000253
M	4	S4F	tCc	tTc	1	1	A	0.000387
M	4	S4F	tCc	tTc	1	1	A.2.2	0.001689
M	4	S4F	tCc	tTc	1	1	A.23.1	0.000704
M	4	S4F	tCc	tTc	1	1	A.29	0.005319
M	4	S4F	tCc	tTc	1	1	AU.1	0.001266
M	4	S4F	tCc	tTc	1	1	AU.3	0.00211
M	4	S4F	tCc	tTc	1	1	AY.101	0.00049
M	4	S4F	tCc	tTc	1	1	AY.105	0.000643
M	4	S4F	tCc	tTc	1	1	AY.110	0.000113
M	4	S4F	tCc	tTc	1	1	AY.116	0.000287
M	4	S4F	tCc	tTc	1	1	AY.12	0.000316
M	4	S4F	tCc	tTc	1	1	AY.120.2.1	0.000498
M	4	S4F	tCc	tTc	1	1	AY.14	0.000088
M	4	S4F	tCc	tTc	1	1	AY.22	0.002092
M	4	S4F	tCc	tTc	1	1	AY.23.1	0.000417
M	4	S4F	tCc	tTc	1	1	AY.29.1	0.000221
M	4	S4F	tCc	tTc	1	1	AY.32	0.000532
M	4	S4F	tCc	tTc	1	1	AY.4.3	0.000842
M	4	S4F	tCc	tTc	1	1	AY.4.5	0.000107
M	4	S4F	tCc	tTc	1	1	AY.46.6	0.000072
M	4	S4F	tCc	tTc	1	1	AY.53	0.000288
M	4	S4F	tCc	tTc	1	1	AY.59	0.00053
M	4	S4F	tCc	tTc	1	1	AY.61	0.000105
M	4	S4F	tCc	tTc	1	1	AY.70	0.000209
M	4	S4F	tCc	tTc	1	1	AY.72	0.001361
M	4	S4F	tCc	tTc	1	1	AY.74	0.000116
M	4	S4F	tCc	tTc	1	1	AY.77	0.001127
M	4	S4F	tCc	tTc	1	1	AY.78	0.001541
M	4	S4F	tCc	tTc	1	1	AY.99	0.001049
M	4	S4F	tCc	tTc	1	1	B.1.1.170	0.001247
M	4	S4F	tCc	tTc	1	1	B.1.1.176	0.000439
M	4	S4F	tCc	tTc	1	1	B.1.1.25	0.000569
M	4	S4F	tCc	tTc	1	1	B.1.1.253	0.002506
M	4	S4F	tCc	tTc	1	1	B.1.1.28	0.000311
M	4	S4F	tCc	tTc	1	1	B.1.1.280	0.003086
M	4	S4F	tCc	tTc	1	1	B.1.1.294	0.001266
M	4	S4F	tCc	tTc	1	1	B.1.1.309	0.005848
M	4	S4F	tCc	tTc	1	1	B.1.1.316	0.000925
M	4	S4F	tCc	tTc	1	1	B.1.1.318	0.000302
M	4	S4F	tCc	tTc	1	1	B.1.1.322	0.008772
M	4	S4F	tCc	tTc	1	1	B.1.1.369	0.000446
M	4	S4F	tCc	tTc	1	1	B.1.1.37	0.000193
M	4	S4F	tCc	tTc	1	1	B.1.1.391	0.008547
M	4	S4F	tCc	tTc	1	1	B.1.1.402	0.011111
M	4	S4F	tCc	tTc	1	1	B.1.1.416	0.000905
M	4	S4F	tCc	tTc	1	1	B.1.1.420	0.001006
M	4	S4F	tCc	tTc	1	1	B.1.1.526	0.003546
M	4	S4F	tCc	tTc	1	1	B.1.1.61	0.008772
M	4	S4F	tCc	tTc	1	1	B.1.1.70	0.000341
M	4	S4F	tCc	tTc	1	1	B.1.147	0.000756
M	4	S4F	tCc	tTc	1	1	B.1.157	0.002985
M	4	S4F	tCc	tTc	1	1	B.1.160.15	0.00495
M	4	S4F	tCc	tTc	1	1	B.1.170	0.00431
M	4	S4F	tCc	tTc	1	1	B.1.177.10	0.000878
M	4	S4F	tCc	tTc	1	1	B.1.177.21	0.000076
M	4	S4F	tCc	tTc	1	1	B.1.177.56	0.000668
M	4	S4F	tCc	tTc	1	1	B.1.177.7	0.000165
M	4	S4F	tCc	tTc	1	1	B.1.177.73	0.000566
M	4	S4F	tCc	tTc	1	1	B.1.177.8	0.000752
M	4	S4F	tCc	tTc	1	1	B.1.177.87	0.000728
M	4	S4F	tCc	tTc	1	1	B.1.179	0.003759
M	4	S4F	tCc	tTc	1	1	B.1.210	0.002132
M	4	S4F	tCc	tTc	1	1	B.1.236	0.002053
M	4	S4F	tCc	tTc	1	1	B.1.258.14	0.00098
M	4	S4F	tCc	tTc	1	1	B.1.298	0.002114
M	4	S4F	tCc	tTc	1	1	B.1.311	0.000275
M	4	S4F	tCc	tTc	1	1	B.1.325	0.006897
M	4	S4F	tCc	tTc	1	1	B.1.351.3	0.000876
M	4	S4F	tCc	tTc	1	1	B.1.36	0.000146
M	4	S4F	tCc	tTc	1	1	B.1.36.29	0.000517
M	4	S4F	tCc	tTc	1	1	B.1.36.36	0.000602
M	4	S4F	tCc	tTc	1	1	B.1.409	0.000781
M	4	S4F	tCc	tTc	1	1	B.1.411	0.003704
M	4	S4F	tCc	tTc	1	1	B.1.420	0.010417
M	4	S4F	tCc	tTc	1	1	B.1.427	0.00005
M	4	S4F	tCc	tTc	1	1	B.1.428	0.00102
M	4	S4F	tCc	tTc	1	1	B.1.432	0.011236
M	4	S4F	tCc	tTc	1	1	B.1.478	0.011765
M	4	S4F	tCc	tTc	1	1	B.1.480	0.002488
M	4	S4F	tCc	tTc	1	1	B.1.536	0.02381
M	4	S4F	tCc	tTc	1	1	B.1.575	0.000303
M	4	S4F	tCc	tTc	1	1	B.1.595	0.000261
M	4	S4F	tCc	tTc	1	1	B.1.630	0.005236
M	4	S4F	tCc	tTc	1	1	B.1.637	0.000073
M	4	S4F	tCc	tTc	1	1	B.1.9	0.006173
M	4	S4F	tCc	tTc	1	1	B.11	0.005128
M	4	S4F	tCc	tTc	1	1	B.28	0.003279
M	4	S4F	tCc	tTc	1	1	B.3	0.000831
M	4	S4F	tCc	tTc	1	1	B.4	0.002208
M	4	S4F	tCc	tTc	1	1	C.16	0.00106
M	4	S4F	tCc	tTc	1	1	C.31	0.017857
M	4	S4F	tCc	tTc	1	1	C.36	0.000911
M	4	S4F	tCc	tTc	1	1	P.1.6	0.001946
M	4	S4F	tCc	tTc	1	1	R.1	0.00009

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.