CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = A67S

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
S	67	A67S		nonsyn	Gct	Tct	5358	5349	0.99832	21761-21763
S	67	A67S		nonsyn	GcT	TcA	5358	5	0.000933184	21761-21763
S	67	A67S		nonsyn	GCt	AGt	5358	2	0.000373274	21761-21763
S	67	A67S		nonsyn	GcT	TcG	5358	1	0.000186637	21761-21763
S	67	A67S		nonsyn	GcT	TcC	5358	1	0.000186637	21761-21763

Details of the mutation A67S 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
S	67	A67S	Gct	Tct	5349	5358	All	0.001023
S	67	A67S	GcT	TcA	5	5358	All	0.000001
S	67	A67S	GCt	AGt	2	5358	All	0
S	67	A67S	GcT	TcC	1	5358	All	0
S	67	A67S	GcT	TcG	1	5358	All	0
S	67	A67S	Gct	Tct	1878	1878	AY.43	0.00832
S	67	A67S	Gct	Tct	1053	1053	B.1.1.7	0.000943
S	67	A67S	Gct	Tct	591	591	AY.4	0.00092
S	67	A67S	Gct	Tct	236	236	B.1.617.2	0.000889
S	67	A67S	Gct	Tct	124	126	P.1	0.001953
S	67	A67S	GcT	TcA	2	126	P.1	0.000032
S	67	A67S	Gct	Tct	123	123	B.1.541	0.544248
S	67	A67S	Gct	Tct	74	74	B.1.1.50	0.050238
S	67	A67S	Gct	Tct	71	71	B.1.177.7	0.011705
S	67	A67S	Gct	Tct	69	69	AY.25	0.000415
S	67	A67S	Gct	Tct	68	68	AY.103	0.000422
S	67	A67S	Gct	Tct	58	58	B.1.177	0.000764
S	67	A67S	Gct	Tct	49	49	B.1.1	0.000889
S	67	A67S	Gct	Tct	47	47	AY.9.2	0.001726
S	67	A67S	Gct	Tct	41	41	AY.113	0.005838
S	67	A67S	Gct	Tct	40	41	B.1.2	0.000352
S	67	A67S	GCt	AGt	1	41	B.1.2	0.000009
S	67	A67S	Gct	Tct	36	36	AY.9.1	0.003014
S	67	A67S	Gct	Tct	31	31	B.1	0.000284
S	67	A67S	Gct	Tct	30	30	B.1.1.214	0.001664
S	67	A67S	Gct	Tct	29	29	AY.102	0.000769
S	67	A67S	Gct	Tct	29	29	B.1.596	0.002527
S	67	A67S	Gct	Tct	26	26	AY.5	0.000537
S	67	A67S	Gct	Tct	25	25	AY.26	0.000708
S	67	A67S	Gct	Tct	22	22	B.1.1.277	0.016692
S	67	A67S	Gct	Tct	21	21	AY.20	0.000816
S	67	A67S	Gct	Tct	21	21	AY.3.1	0.00179
S	67	A67S	Gct	Tct	20	20	AY.3	0.000199
S	67	A67S	Gct	Tct	19	19	AY.119	0.000671
S	67	A67S	Gct	Tct	19	19	B.1.427	0.000959
S	67	A67S	Gct	Tct	19	19	P.1.10	0.00512
S	67	A67S	Gct	Tct	17	17	AY.46.4	0.002797
S	67	A67S	Gct	Tct	16	16	B.1.258.17	0.001664
S	67	A67S	Gct	Tct	16	16	B.1.351	0.000476
S	67	A67S	Gct	Tct	14	14	AY.39	0.000346
S	67	A67S	Gct	Tct	11	11	AY.29	0.000174
S	67	A67S	Gct	Tct	11	11	AY.44	0.000067
S	67	A67S	Gct	Tct	11	11	AY.46	0.001145
S	67	A67S	Gct	Tct	11	11	B.1.1.186	0.037801
S	67	A67S	Gct	Tct	11	11	P.1.15	0.002556
S	67	A67S	Gct	Tct	10	10	AY.9	0.000676
S	67	A67S	Gct	Tct	10	10	B.1.1.25	0.005685
S	67	A67S	Gct	Tct	9	9	AY.4.2	0.000195
S	67	A67S	Gct	Tct	9	9	B.1.1.519	0.000357
S	67	A67S	Gct	Tct	9	9	B.1.258	0.000599
S	67	A67S	Gct	Tct	8	8	AY.6	0.000329
S	67	A67S	Gct	Tct	8	8	B.1.526	0.000188
S	67	A67S	Gct	Tct	8	8	C.36.3	0.004538
S	67	A67S	Gct	Tct	7	7	AY.96	0.014523
S	67	A67S	Gct	Tct	7	7	AY.99.2	0.000645
S	67	A67S	Gct	Tct	7	7	B.1.91	0.014523
S	67	A67S	Gct	Tct	7	7	Q.8	0.001154
S	67	A67S	Gct	Tct	6	6	AY.23	0.000418
S	67	A67S	Gct	Tct	5	6	B.1.1.28	0.001556
S	67	A67S	GcT	TcA	1	6	B.1.1.28	0.000311
S	67	A67S	Gct	Tct	6	6	B.1.160	0.000187
S	67	A67S	Gct	Tct	5	5	AY.100	0.00023
S	67	A67S	Gct	Tct	5	5	AY.117	0.000423
S	67	A67S	Gct	Tct	5	5	AY.47	0.000156
S	67	A67S	Gct	Tct	5	5	B.1.1.174	0.016892
S	67	A67S	Gct	Tct	5	5	B.1.177.86	0.000917
S	67	A67S	Gct	Tct	5	5	B.1.621	0.000443
S	67	A67S	Gct	Tct	5	5	P.1.7	0.001596
S	67	A67S	Gct	Tct	4	5	P.2	0.000747
S	67	A67S	GcT	TcA	1	5	P.2	0.000187
S	67	A67S	Gct	Tct	4	4	AY.120	0.000149
S	67	A67S	Gct	Tct	4	4	AY.33	0.000267
S	67	A67S	Gct	Tct	4	4	AY.98.1	0.000194
S	67	A67S	Gct	Tct	4	4	B.1.1.163	0.030534
S	67	A67S	Gct	Tct	4	4	B.1.1.176	0.001757
S	67	A67S	Gct	Tct	4	4	B.1.1.294	0.005063
S	67	A67S	Gct	Tct	4	4	B.1.177.48	0.0125
S	67	A67S	Gct	Tct	4	4	B.1.311	0.001098
S	67	A67S	Gct	Tct	4	4	B.1.566	0.076923
S	67	A67S	Gct	Tct	4	4	P.1.12	0.001936
S	67	A67S	Gct	Tct	4	4	P.1.14	0.000191
S	67	A67S	Gct	Tct	4	4	P.1.17	0.000647
S	67	A67S	Gct	Tct	2	3		0.111111
S	67	A67S	GcT	TcC	1	3		0.055556
S	67	A67S	Gct	Tct	3	3	AY.14	0.000264
S	67	A67S	Gct	Tct	2	3	AY.30	0.000791
S	67	A67S	GcT	TcA	1	3	AY.30	0.000396
S	67	A67S	Gct	Tct	3	3	AY.42	0.000121
S	67	A67S	Gct	Tct	3	3	AY.5.4	0.00083
S	67	A67S	Gct	Tct	3	3	AY.61	0.000314
S	67	A67S	Gct	Tct	3	3	B.1.1.196	0.017143
S	67	A67S	Gct	Tct	1	3	B.1.1.33	0.000421
S	67	A67S	GcT	TcG	1	3	B.1.1.33	0.000421
S	67	A67S	GCt	AGt	1	3	B.1.1.33	0.000421
S	67	A67S	Gct	Tct	3	3	B.1.1.523	0.004687
S	67	A67S	Gct	Tct	3	3	B.1.160.7	0.006237
S	67	A67S	Gct	Tct	3	3	B.1.177.73	0.001699
S	67	A67S	Gct	Tct	3	3	B.1.177.81	0.000568
S	67	A67S	Gct	Tct	3	3	B.1.240	0.000647
S	67	A67S	Gct	Tct	3	3	B.1.637	0.000219
S	67	A67S	Gct	Tct	3	3	B.6	0.00273
S	67	A67S	Gct	Tct	3	3	P.1.2	0.003468
S	67	A67S	Gct	Tct	2	2	AY.118	0.000125
S	67	A67S	Gct	Tct	2	2	AY.27	0.000129
S	67	A67S	Gct	Tct	2	2	AY.34	0.000194
S	67	A67S	Gct	Tct	2	2	AY.34.1	0.00102
S	67	A67S	Gct	Tct	2	2	AY.4.5	0.000215
S	67	A67S	Gct	Tct	2	2	AY.46.5	0.000397
S	67	A67S	Gct	Tct	2	2	AY.5.3	0.000675
S	67	A67S	Gct	Tct	2	2	AY.54	0.000191
S	67	A67S	Gct	Tct	2	2	AY.67	0.000929
S	67	A67S	Gct	Tct	2	2	AY.98	0.000158
S	67	A67S	Gct	Tct	2	2	B.1.177.60	0.000437
S	67	A67S	Gct	Tct	2	2	B.1.243	0.000139
S	67	A67S	Gct	Tct	2	2	B.1.279	0.001027
S	67	A67S	Gct	Tct	2	2	B.1.351.2	0.000605
S	67	A67S	Gct	Tct	2	2	B.1.36	0.000292
S	67	A67S	Gct	Tct	2	2	B.1.429	0.000047
S	67	A67S	Gct	Tct	2	2	B.1.621.1	0.001012
S	67	A67S	Gct	Tct	2	2	B.1.627	0.00404
S	67	A67S	Gct	Tct	2	2	B.40	0.000729
S	67	A67S	Gct	Tct	2	2	C.37	0.000232
S	67	A67S	Gct	Tct	2	2	D.2	0.00015
S	67	A67S	Gct	Tct	2	2	P.1.13	0.001797
S	67	A67S	Gct	Tct	2	2	P.1.17.1	0.00175
S	67	A67S	Gct	Tct	2	2	P.3	0.00319
S	67	A67S	Gct	Tct	2	2	Q.1	0.000253
S	67	A67S	Gct	Tct	2	2	Q.7	0.002222
S	67	A67S	Gct	Tct	1	1	A	0.000387
S	67	A67S	Gct	Tct	1	1	AA.2	0.007692
S	67	A67S	Gct	Tct	1	1	AY.104	0.001984
S	67	A67S	Gct	Tct	1	1	AY.106	0.000335
S	67	A67S	Gct	Tct	1	1	AY.107	0.000466
S	67	A67S	Gct	Tct	1	1	AY.114	0.000231
S	67	A67S	Gct	Tct	1	1	AY.121	0.000135
S	67	A67S	Gct	Tct	1	1	AY.19	0.00114
S	67	A67S	Gct	Tct	1	1	AY.36	0.000148
S	67	A67S	Gct	Tct	1	1	AY.37	0.000316
S	67	A67S	Gct	Tct	1	1	AY.39.1	0.00004
S	67	A67S	Gct	Tct	1	1	AY.39.2	0.001541
S	67	A67S	Gct	Tct	1	1	AY.4.1	0.000737
S	67	A67S	Gct	Tct	1	1	AY.4.4	0.000409
S	67	A67S	Gct	Tct	1	1	AY.45	0.000122
S	67	A67S	Gct	Tct	1	1	AY.46.6	0.000072
S	67	A67S	Gct	Tct	1	1	AY.55	0.000917
S	67	A67S	Gct	Tct	1	1	AY.58	0.000907
S	67	A67S	Gct	Tct	1	1	AY.85	0.000427
S	67	A67S	Gct	Tct	1	1	AY.91	0.00073
S	67	A67S	Gct	Tct	1	1	AY.92	0.000287
S	67	A67S	Gct	Tct	1	1	AY.93	0.000273
S	67	A67S	Gct	Tct	1	1	AY.94	0.000443
S	67	A67S	Gct	Tct	1	1	B	0.000128
S	67	A67S	Gct	Tct	1	1	B.1.1.1	0.000327
S	67	A67S	Gct	Tct	1	1	B.1.1.161	0.003534
S	67	A67S	Gct	Tct	1	1	B.1.1.207	0.001182
S	67	A67S	Gct	Tct	1	1	B.1.1.222	0.000204
S	67	A67S	Gct	Tct	1	1	B.1.1.305	0.003861
S	67	A67S	Gct	Tct	1	1	B.1.1.317	0.000412
S	67	A67S	Gct	Tct	1	1	B.1.1.347	0.018182
S	67	A67S	Gct	Tct	1	1	B.1.1.369	0.000446
S	67	A67S	Gct	Tct	1	1	B.1.1.37	0.000193
S	67	A67S	Gct	Tct	1	1	B.1.1.420	0.001006
S	67	A67S	Gct	Tct	1	1	B.1.1.528	0.004808
S	67	A67S	Gct	Tct	1	1	B.1.1.63	0.000386
S	67	A67S	Gct	Tct	1	1	B.1.177.44	0.000519
S	67	A67S	Gct	Tct	1	1	B.1.195	0.005025
S	67	A67S	Gct	Tct	1	1	B.1.214.2	0.0006
S	67	A67S	Gct	Tct	1	1	B.1.221	0.000071
S	67	A67S	Gct	Tct	1	1	B.1.234	0.000132
S	67	A67S	Gct	Tct	1	1	B.1.276	0.016949
S	67	A67S	Gct	Tct	1	1	B.1.308	0.034483
S	67	A67S	Gct	Tct	1	1	B.1.321	0.034483
S	67	A67S	Gct	Tct	1	1	B.1.351.5	0.0006
S	67	A67S	Gct	Tct	1	1	B.1.36.19	0.009259
S	67	A67S	Gct	Tct	1	1	B.1.36.29	0.000517
S	67	A67S	Gct	Tct	1	1	B.1.362	0.001541
S	67	A67S	Gct	Tct	1	1	B.1.375	0.00082
S	67	A67S	Gct	Tct	1	1	B.1.400	0.000429
S	67	A67S	Gct	Tct	1	1	B.1.409	0.000781
S	67	A67S	Gct	Tct	1	1	B.1.426	0.001009
S	67	A67S	Gct	Tct	1	1	B.1.438.1	0.000107
S	67	A67S	Gct	Tct	1	1	B.1.565	0.00081
S	67	A67S	Gct	Tct	1	1	B.1.595	0.000261
S	67	A67S	Gct	Tct	1	1	B.1.609	0.000479
S	67	A67S	Gct	Tct	1	1	B.1.617.1	0.000129
S	67	A67S	Gct	Tct	1	1	B.1.618	0.004032
S	67	A67S	Gct	Tct	1	1	B.1.619.1	0.000641
S	67	A67S	Gct	Tct	1	1	B.1.9.5	0.005682
S	67	A67S	Gct	Tct	1	1	C.31	0.017857
S	67	A67S	Gct	Tct	1	1	P.1.16	0.000374
S	67	A67S	Gct	Tct	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.