CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : Mut = F100F

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	100	F100F		syn	ttC	ttT	8300	8300	1	26820-26822

Details of the mutation F100F 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	100	F100F	ttC	ttT	8300	8300	All	0.001587
M	100	F100F	ttC	ttT	2511	2511	AY.4	0.003908
M	100	F100F	ttC	ttT	1125	1125	B.1.1.7	0.001007
M	100	F100F	ttC	ttT	782	782	AY.75	0.04381
M	100	F100F	ttC	ttT	694	694	B.1.617.2	0.002613
M	100	F100F	ttC	ttT	547	547	B.1.2	0.004817
M	100	F100F	ttC	ttT	280	280	AY.5	0.005782
M	100	F100F	ttC	ttT	124	124	P.1	0.001953
M	100	F100F	ttC	ttT	123	123	B.1.243	0.008559
M	100	F100F	ttC	ttT	118	118	AY.44	0.000718
M	100	F100F	ttC	ttT	88	88	B.1.177	0.001159
M	100	F100F	ttC	ttT	78	78	AY.46	0.008118
M	100	F100F	ttC	ttT	71	71	AY.43	0.000315
M	100	F100F	ttC	ttT	67	67	B.1	0.000614
M	100	F100F	ttC	ttT	66	66	B.1.429	0.001553
M	100	F100F	ttC	ttT	65	65	AY.103	0.000404
M	100	F100F	ttC	ttT	62	62	AY.3	0.000617
M	100	F100F	ttC	ttT	59	59	AY.113	0.008401
M	100	F100F	ttC	ttT	58	58	AY.100	0.002668
M	100	F100F	ttC	ttT	49	49	AY.20	0.001904
M	100	F100F	ttC	ttT	49	49	B.1.177.80	0.09369
M	100	F100F	ttC	ttT	48	48	B.1.427	0.002424
M	100	F100F	ttC	ttT	47	47	AY.25	0.000283
M	100	F100F	ttC	ttT	43	43	AY.39	0.001063
M	100	F100F	ttC	ttT	43	43	B.1.1	0.00078
M	100	F100F	ttC	ttT	38	38	AY.33	0.002538
M	100	F100F	ttC	ttT	31	31	AY.108	0.034179
M	100	F100F	ttC	ttT	26	26	B.1.594	0.8125
M	100	F100F	ttC	ttT	26	26	C.37	0.003018
M	100	F100F	ttC	ttT	24	24	AY.70	0.005004
M	100	F100F	ttC	ttT	24	24	B.1.210	0.051173
M	100	F100F	ttC	ttT	22	22	C.16	0.02333
M	100	F100F	ttC	ttT	20	20	AY.102	0.00053
M	100	F100F	ttC	ttT	19	19	AY.4.2	0.000412
M	100	F100F	ttC	ttT	19	19	B.1.637	0.001388
M	100	F100F	ttC	ttT	18	18	AY.26	0.00051
M	100	F100F	ttC	ttT	17	17	B.1.497	0.005351
M	100	F100F	ttC	ttT	16	16	B.1.1.288	0.030651
M	100	F100F	ttC	ttT	16	16	B.1.351	0.000476
M	100	F100F	ttC	ttT	15	15	B.1.1.434	0.005228
M	100	F100F	ttC	ttT	15	15	B.1.36	0.002189
M	100	F100F	ttC	ttT	15	15	B.1.526	0.000353
M	100	F100F	ttC	ttT	14	14	B.1.160.17	0.02381
M	100	F100F	ttC	ttT	14	14	B.1.239	0.017094
M	100	F100F	ttC	ttT	14	14	B.1.438.1	0.001502
M	100	F100F	ttC	ttT	14	14	Q.1	0.001769
M	100	F100F	ttC	ttT	13	13	AY.119	0.000459
M	100	F100F	ttC	ttT	13	13	B.1.1.28	0.004046
M	100	F100F	ttC	ttT	13	13	B.1.621	0.001151
M	100	F100F	ttC	ttT	12	12	AU.1	0.01519
M	100	F100F	ttC	ttT	12	12	AY.45	0.00146
M	100	F100F	ttC	ttT	12	12	B.1.160	0.000374
M	100	F100F	ttC	ttT	12	12	B.1.36.1	0.013683
M	100	F100F	ttC	ttT	11	11	B.1.177.65	0.007319
M	100	F100F	ttC	ttT	11	11	B.1.311	0.00302
M	100	F100F	ttC	ttT	11	11	P.1.2	0.012717
M	100	F100F	ttC	ttT	10	10	AY.39.1	0.000396
M	100	F100F	ttC	ttT	10	10	AY.67	0.004643
M	100	F100F	ttC	ttT	10	10	B.1.1.519	0.000397
M	100	F100F	ttC	ttT	10	10	B.1.596	0.000871
M	100	F100F	ttC	ttT	10	10	P.1.17	0.001618
M	100	F100F	ttC	ttT	10	10	R.1	0.0009
M	100	F100F	ttC	ttT	9	9	AY.29	0.000142
M	100	F100F	ttC	ttT	9	9	AY.6	0.00037
M	100	F100F	ttC	ttT	9	9	B.1.1.258	0.029316
M	100	F100F	ttC	ttT	8	8	B.1.111	0.009401
M	100	F100F	ttC	ttT	8	8	B.1.602	0.052288
M	100	F100F	ttC	ttT	8	8	B.4	0.01766
M	100	F100F	ttC	ttT	7	7	AY.117	0.000592
M	100	F100F	ttC	ttT	7	7	AY.88	0.006189
M	100	F100F	ttC	ttT	7	7	B.1.1.214	0.000388
M	100	F100F	ttC	ttT	7	7	B.1.1.416	0.006335
M	100	F100F	ttC	ttT	7	7	B.1.220	0.076087
M	100	F100F	ttC	ttT	7	7	B.1.221	0.000497
M	100	F100F	ttC	ttT	7	7	B.1.258.17	0.000728
M	100	F100F	ttC	ttT	7	7	B.1.623	0.003755
M	100	F100F	ttC	ttT	7	7	B.1.627	0.014141
M	100	F100F	ttC	ttT	7	7	P.1.1	0.002224
M	100	F100F	ttC	ttT	7	7	P.2	0.001306
M	100	F100F	ttC	ttT	6	6	AA.8	0.133333
M	100	F100F	ttC	ttT	6	6	AY.23	0.000418
M	100	F100F	ttC	ttT	6	6	AY.97	0.010204
M	100	F100F	ttC	ttT	6	6	B.1.1.273	0.040541
M	100	F100F	ttC	ttT	6	6	B.1.1.464	0.008837
M	100	F100F	ttC	ttT	6	6	B.1.258	0.000399
M	100	F100F	ttC	ttT	6	6	B.1.628	0.002114
M	100	F100F	ttC	ttT	5	5	AY.120	0.000186
M	100	F100F	ttC	ttT	5	5	AY.37	0.00158
M	100	F100F	ttC	ttT	5	5	AY.53	0.001438
M	100	F100F	ttC	ttT	5	5	AY.61	0.000524
M	100	F100F	ttC	ttT	5	5	B	0.000639
M	100	F100F	ttC	ttT	5	5	B.1.1.277	0.003794
M	100	F100F	ttC	ttT	5	5	B.1.177.21	0.000382
M	100	F100F	ttC	ttT	5	5	B.1.177.86	0.000917
M	100	F100F	ttC	ttT	5	5	B.1.306	0.028571
M	100	F100F	ttC	ttT	5	5	B.1.36.29	0.002587
M	100	F100F	ttC	ttT	5	5	B.1.369	0.001426
M	100	F100F	ttC	ttT	5	5	N.5	0.008834
M	100	F100F	ttC	ttT	5	5	Q.8	0.000825
M	100	F100F	ttC	ttT	4	4	A.2.5	0.001996
M	100	F100F	ttC	ttT	4	4	AY.110	0.000451
M	100	F100F	ttC	ttT	4	4	AY.121	0.000541
M	100	F100F	ttC	ttT	4	4	AY.47	0.000124
M	100	F100F	ttC	ttT	4	4	AY.7	0.000784
M	100	F100F	ttC	ttT	4	4	AY.77	0.00451
M	100	F100F	ttC	ttT	4	4	AY.9	0.00027
M	100	F100F	ttC	ttT	4	4	AY.98.1	0.000194
M	100	F100F	ttC	ttT	4	4	B.1.1.153	0.004381
M	100	F100F	ttC	ttT	4	4	B.1.1.176	0.001757
M	100	F100F	ttC	ttT	4	4	B.1.1.222	0.000816
M	100	F100F	ttC	ttT	4	4	B.1.177.7	0.000659
M	100	F100F	ttC	ttT	4	4	B.1.240	0.000862
M	100	F100F	ttC	ttT	4	4	B.1.425	0.011976
M	100	F100F	ttC	ttT	4	4	B.1.595	0.001044
M	100	F100F	ttC	ttT	4	4	P.1.10	0.001078
M	100	F100F	ttC	ttT	3	3	AD.2	0.000657
M	100	F100F	ttC	ttT	3	3	AE.8	0.001467
M	100	F100F	ttC	ttT	3	3	AY.118	0.000188
M	100	F100F	ttC	ttT	3	3	AY.30	0.001187
M	100	F100F	ttC	ttT	3	3	AY.4.5	0.000322
M	100	F100F	ttC	ttT	3	3	AY.46.4	0.000494
M	100	F100F	ttC	ttT	3	3	AY.9.1	0.000251
M	100	F100F	ttC	ttT	3	3	AY.9.2	0.00011
M	100	F100F	ttC	ttT	3	3	B.1.110.3	0.002155
M	100	F100F	ttC	ttT	3	3	B.1.160.16	0.002788
M	100	F100F	ttC	ttT	3	3	B.1.446	0.06
M	100	F100F	ttC	ttT	3	3	B.1.618	0.012097
M	100	F100F	ttC	ttT	3	3	P.1.14	0.000143
M	100	F100F	ttC	ttT	3	3	P.1.15	0.000697
M	100	F100F	ttC	ttT	3	3	P.1.7	0.000958
M	100	F100F	ttC	ttT	2	2		0.111111
M	100	F100F	ttC	ttT	2	2	AY.101	0.000981
M	100	F100F	ttC	ttT	2	2	AY.105	0.001286
M	100	F100F	ttC	ttT	2	2	AY.111	0.000366
M	100	F100F	ttC	ttT	2	2	AY.16	0.000759
M	100	F100F	ttC	ttT	2	2	AY.2	0.000712
M	100	F100F	ttC	ttT	2	2	AY.27	0.000129
M	100	F100F	ttC	ttT	2	2	AY.34	0.000194
M	100	F100F	ttC	ttT	2	2	AY.4.2.1	0.000298
M	100	F100F	ttC	ttT	2	2	AY.46.1	0.002053
M	100	F100F	ttC	ttT	2	2	AY.54	0.000191
M	100	F100F	ttC	ttT	2	2	AY.62	0.000871
M	100	F100F	ttC	ttT	2	2	AY.65	0.001066
M	100	F100F	ttC	ttT	2	2	AY.69	0.000373
M	100	F100F	ttC	ttT	2	2	AY.75.1	0.000361
M	100	F100F	ttC	ttT	2	2	AY.98	0.000158
M	100	F100F	ttC	ttT	2	2	AY.99.2	0.000184
M	100	F100F	ttC	ttT	2	2	AZ.1	0.001735
M	100	F100F	ttC	ttT	2	2	B.1.1.192	0.004619
M	100	F100F	ttC	ttT	2	2	B.1.128	0.001271
M	100	F100F	ttC	ttT	2	2	B.1.177.42	0.001789
M	100	F100F	ttC	ttT	2	2	B.1.177.54	0.001213
M	100	F100F	ttC	ttT	2	2	B.1.184	0.117647
M	100	F100F	ttC	ttT	2	2	B.1.36.18	0.00084
M	100	F100F	ttC	ttT	2	2	B.1.36.7	0.008
M	100	F100F	ttC	ttT	2	2	B.1.36.8	0.002
M	100	F100F	ttC	ttT	2	2	B.1.396	0.001411
M	100	F100F	ttC	ttT	2	2	B.1.404	0.002604
M	100	F100F	ttC	ttT	2	2	B.1.525	0.000226
M	100	F100F	ttC	ttT	2	2	B.1.577	0.001375
M	100	F100F	ttC	ttT	2	2	B.1.617.1	0.000258
M	100	F100F	ttC	ttT	2	2	B.1.621.1	0.001012
M	100	F100F	ttC	ttT	2	2	C.1	0.004785
M	100	F100F	ttC	ttT	2	2	C.36.3	0.001134
M	100	F100F	ttC	ttT	2	2	D.2	0.00015
M	100	F100F	ttC	ttT	1	1	A	0.000387
M	100	F100F	ttC	ttT	1	1	A.3	0.002096
M	100	F100F	ttC	ttT	1	1	AY.10	0.00053
M	100	F100F	ttC	ttT	1	1	AY.106	0.000335
M	100	F100F	ttC	ttT	1	1	AY.12	0.000316
M	100	F100F	ttC	ttT	1	1	AY.13	0.000161
M	100	F100F	ttC	ttT	1	1	AY.23.1	0.000417
M	100	F100F	ttC	ttT	1	1	AY.24	0.000431
M	100	F100F	ttC	ttT	1	1	AY.35	0.000233
M	100	F100F	ttC	ttT	1	1	AY.36	0.000148
M	100	F100F	ttC	ttT	1	1	AY.38	0.000499
M	100	F100F	ttC	ttT	1	1	AY.4.3	0.000842
M	100	F100F	ttC	ttT	1	1	AY.42	0.00004
M	100	F100F	ttC	ttT	1	1	AY.48	0.000465
M	100	F100F	ttC	ttT	1	1	AY.49	0.003195
M	100	F100F	ttC	ttT	1	1	AY.5.3	0.000337
M	100	F100F	ttC	ttT	1	1	AY.5.4	0.000277
M	100	F100F	ttC	ttT	1	1	AY.56	0.001605
M	100	F100F	ttC	ttT	1	1	AY.58	0.000907
M	100	F100F	ttC	ttT	1	1	AY.64	0.000595
M	100	F100F	ttC	ttT	1	1	AY.7.1	0.000113
M	100	F100F	ttC	ttT	1	1	AY.87	0.000833
M	100	F100F	ttC	ttT	1	1	AY.95	0.000761
M	100	F100F	ttC	ttT	1	1	B.1.1.10	0.001115
M	100	F100F	ttC	ttT	1	1	B.1.1.117	0.009709
M	100	F100F	ttC	ttT	1	1	B.1.1.123	0.017857
M	100	F100F	ttC	ttT	1	1	B.1.1.165	0.015385
M	100	F100F	ttC	ttT	1	1	B.1.1.189	0.001513
M	100	F100F	ttC	ttT	1	1	B.1.1.194	0.00495
M	100	F100F	ttC	ttT	1	1	B.1.1.216	0.00089
M	100	F100F	ttC	ttT	1	1	B.1.1.261	0.008621
M	100	F100F	ttC	ttT	1	1	B.1.1.279	0.001121
M	100	F100F	ttC	ttT	1	1	B.1.1.306	0.000438
M	100	F100F	ttC	ttT	1	1	B.1.1.307	0.002532
M	100	F100F	ttC	ttT	1	1	B.1.1.317	0.000412
M	100	F100F	ttC	ttT	1	1	B.1.1.318	0.000302
M	100	F100F	ttC	ttT	1	1	B.1.1.33	0.000421
M	100	F100F	ttC	ttT	1	1	B.1.1.368	0.003086
M	100	F100F	ttC	ttT	1	1	B.1.1.371	0.010417
M	100	F100F	ttC	ttT	1	1	B.1.1.389	0.006061
M	100	F100F	ttC	ttT	1	1	B.1.1.393	0.111111
M	100	F100F	ttC	ttT	1	1	B.1.1.461	0.012048
M	100	F100F	ttC	ttT	1	1	B.1.1.523	0.001563
M	100	F100F	ttC	ttT	1	1	B.1.1.67	0.004566
M	100	F100F	ttC	ttT	1	1	B.1.153	0.018868
M	100	F100F	ttC	ttT	1	1	B.1.160.11	0.005714
M	100	F100F	ttC	ttT	1	1	B.1.160.9	0.007194
M	100	F100F	ttC	ttT	1	1	B.1.177.10	0.000878
M	100	F100F	ttC	ttT	1	1	B.1.177.16	0.000664
M	100	F100F	ttC	ttT	1	1	B.1.177.17	0.000821
M	100	F100F	ttC	ttT	1	1	B.1.177.23	0.003236
M	100	F100F	ttC	ttT	1	1	B.1.177.28	0.007407
M	100	F100F	ttC	ttT	1	1	B.1.177.45	0.000381
M	100	F100F	ttC	ttT	1	1	B.1.177.60	0.000218
M	100	F100F	ttC	ttT	1	1	B.1.177.73	0.000566
M	100	F100F	ttC	ttT	1	1	B.1.177.81	0.000189
M	100	F100F	ttC	ttT	1	1	B.1.177.83	0.001481
M	100	F100F	ttC	ttT	1	1	B.1.177.87	0.000728
M	100	F100F	ttC	ttT	1	1	B.1.201	0.005682
M	100	F100F	ttC	ttT	1	1	B.1.247	0.014925
M	100	F100F	ttC	ttT	1	1	B.1.252	0.006623
M	100	F100F	ttC	ttT	1	1	B.1.279	0.000514
M	100	F100F	ttC	ttT	1	1	B.1.351.2	0.000303
M	100	F100F	ttC	ttT	1	1	B.1.351.3	0.000876
M	100	F100F	ttC	ttT	1	1	B.1.36.10	0.004785
M	100	F100F	ttC	ttT	1	1	B.1.36.22	0.001208
M	100	F100F	ttC	ttT	1	1	B.1.380	0.006623
M	100	F100F	ttC	ttT	1	1	B.1.399	0.001934
M	100	F100F	ttC	ttT	1	1	B.1.416	0.001269
M	100	F100F	ttC	ttT	1	1	B.1.417	0.028571
M	100	F100F	ttC	ttT	1	1	B.1.422	0.000812
M	100	F100F	ttC	ttT	1	1	B.1.443	0.004673
M	100	F100F	ttC	ttT	1	1	B.1.456	0.003268
M	100	F100F	ttC	ttT	1	1	B.1.466.2	0.000391
M	100	F100F	ttC	ttT	1	1	B.1.468	0.005714
M	100	F100F	ttC	ttT	1	1	B.1.523	0.002451
M	100	F100F	ttC	ttT	1	1	B.1.560	0.00463
M	100	F100F	ttC	ttT	1	1	B.1.561	0.000397
M	100	F100F	ttC	ttT	1	1	B.1.564	0.000426
M	100	F100F	ttC	ttT	1	1	B.1.576	0.000907
M	100	F100F	ttC	ttT	1	1	B.1.600	0.005848
M	100	F100F	ttC	ttT	1	1	B.1.619	0.000871
M	100	F100F	ttC	ttT	1	1	B.1.620	0.000946
M	100	F100F	ttC	ttT	1	1	B.1.634	0.003425
M	100	F100F	ttC	ttT	1	1	B.1.78	0.008547
M	100	F100F	ttC	ttT	1	1	B.40	0.000364
M	100	F100F	ttC	ttT	1	1	C.26	0.007353
M	100	F100F	ttC	ttT	1	1	C.30	0.001727
M	100	F100F	ttC	ttT	1	1	C.36	0.000911
M	100	F100F	ttC	ttT	1	1	K.3	0.006173
M	100	F100F	ttC	ttT	1	1	P.1.12	0.000484
M	100	F100F	ttC	ttT	1	1	P.1.16	0.000374

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.