CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = P162P

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
N	162	P162P		syn	ccT	ccC	5592	4955	0.886087	28757-28759
N	162	P162P		syn	ccT	ccA	5592	458	0.0819027	28757-28759
N	162	P162P		syn	ccT	ccG	5592	179	0.03201	28757-28759

Details of the mutation P162P 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
N	162	P162P	ccT	ccC	4955	5592	All	0.000948
N	162	P162P	ccT	ccA	458	5592	All	0.000088
N	162	P162P	ccT	ccG	179	5592	All	0.000034
N	162	P162P	ccT	ccC	2807	2807	B.1.1.70	0.957367
N	162	P162P	ccT	ccC	665	665	AP.1	0.998498
N	162	P162P	ccT	ccC	240	323	AY.44	0.001461
N	162	P162P	ccT	ccG	82	323	AY.44	0.000499
N	162	P162P	ccT	ccA	1	323	AY.44	0.000006
N	162	P162P	ccT	ccA	251	313	B.1.1.7	0.000225
N	162	P162P	ccT	ccC	46	313	B.1.1.7	0.000041
N	162	P162P	ccT	ccG	16	313	B.1.1.7	0.000014
N	162	P162P	ccT	ccC	205	232	AY.4	0.000319
N	162	P162P	ccT	ccA	24	232	AY.4	0.000037
N	162	P162P	ccT	ccG	3	232	AY.4	0.000005
N	162	P162P	ccT	ccC	154	210	B.1	0.001411
N	162	P162P	ccT	ccA	43	210	B.1	0.000394
N	162	P162P	ccT	ccG	13	210	B.1	0.000119
N	162	P162P	ccT	ccC	124	126	AY.103	0.00077
N	162	P162P	ccT	ccA	1	126	AY.103	0.000006
N	162	P162P	ccT	ccG	1	126	AY.103	0.000006
N	162	P162P	ccT	ccC	110	110	AY.94	0.048694
N	162	P162P	ccT	ccC	73	89	B.1.617.2	0.000275
N	162	P162P	ccT	ccA	15	89	B.1.617.2	0.000056
N	162	P162P	ccT	ccG	1	89	B.1.617.2	0.000004
N	162	P162P	ccT	ccC	65	80	B.1.177	0.000856
N	162	P162P	ccT	ccA	13	80	B.1.177	0.000171
N	162	P162P	ccT	ccG	2	80	B.1.177	0.000026
N	162	P162P	ccT	ccC	54	70	B.1.1	0.00098
N	162	P162P	ccT	ccA	10	70	B.1.1	0.000181
N	162	P162P	ccT	ccG	6	70	B.1.1	0.000109
N	162	P162P	ccT	ccC	51	51	AY.99.2	0.0047
N	162	P162P	ccT	ccC	22	33	B.1.2	0.000194
N	162	P162P	ccT	ccG	6	33	B.1.2	0.000053
N	162	P162P	ccT	ccA	5	33	B.1.2	0.000044
N	162	P162P	ccT	ccA	28	30	AY.4.2	0.000607
N	162	P162P	ccT	ccG	2	30	AY.4.2	0.000043
N	162	P162P	ccT	ccC	25	25	AY.9.2	0.000918
N	162	P162P	ccT	ccC	22	24	B.1.221	0.001563
N	162	P162P	ccT	ccA	2	24	B.1.221	0.000142
N	162	P162P	ccT	ccC	17	22	AY.100	0.000782
N	162	P162P	ccT	ccA	5	22	AY.100	0.00023
N	162	P162P	ccT	ccC	12	21	B.1.160	0.000374
N	162	P162P	ccT	ccG	5	21	B.1.160	0.000156
N	162	P162P	ccT	ccA	4	21	B.1.160	0.000125
N	162	P162P	ccT	ccC	18	20	AY.43	0.00008
N	162	P162P	ccT	ccG	1	20	AY.43	0.000004
N	162	P162P	ccT	ccA	1	20	AY.43	0.000004
N	162	P162P	ccT	ccC	16	16	B.1.620	0.015137
N	162	P162P	ccT	ccA	8	15	AY.25	0.000048
N	162	P162P	ccT	ccC	4	15	AY.25	0.000024
N	162	P162P	ccT	ccG	3	15	AY.25	0.000018
N	162	P162P	ccT	ccG	11	15	AY.3	0.000109
N	162	P162P	ccT	ccC	3	15	AY.3	0.00003
N	162	P162P	ccT	ccA	1	15	AY.3	0.00001
N	162	P162P	ccT	ccA	7	13	B.1.258	0.000466
N	162	P162P	ccT	ccC	6	13	B.1.258	0.000399
N	162	P162P	ccT	ccG	11	11	B.1.160.12	0.070513
N	162	P162P	ccT	ccC	11	11	B.1.177.86	0.002018
N	162	P162P	ccT	ccC	11	11	B.1.351	0.000327
N	162	P162P	ccT	ccC	7	9	B.1.177.44	0.003633
N	162	P162P	ccT	ccA	2	9	B.1.177.44	0.001038
N	162	P162P	ccT	ccC	8	8	B.1.160.32	0.034335
N	162	P162P	ccT	ccC	7	7	AY.39	0.000173
N	162	P162P	ccT	ccC	4	7	B.1.1.39	0.002039
N	162	P162P	ccT	ccA	2	7	B.1.1.39	0.001019
N	162	P162P	ccT	ccG	1	7	B.1.1.39	0.00051
N	162	P162P	ccT	ccC	7	7	P.1	0.00011
N	162	P162P	ccT	ccC	6	6	AY.113	0.000854
N	162	P162P	ccT	ccC	3	6	B.1.596	0.000261
N	162	P162P	ccT	ccA	3	6	B.1.596	0.000261
N	162	P162P	ccT	ccC	3	5	AY.102	0.00008
N	162	P162P	ccT	ccG	1	5	AY.102	0.000027
N	162	P162P	ccT	ccA	1	5	AY.102	0.000027
N	162	P162P	ccT	ccC	5	5	B	0.000639
N	162	P162P	ccT	ccC	3	5	B.1.1.385	0.013393
N	162	P162P	ccT	ccA	2	5	B.1.1.385	0.008929
N	162	P162P	ccT	ccC	5	5	B.1.221.2	0.02008
N	162	P162P	ccT	ccC	4	4	AD.2	0.000876
N	162	P162P	ccT	ccG	4	4	AY.30	0.001583
N	162	P162P	ccT	ccC	3	4	B.1.1.189	0.004539
N	162	P162P	ccT	ccA	1	4	B.1.1.189	0.001513
N	162	P162P	ccT	ccA	2	4	B.1.1.372	0.001377
N	162	P162P	ccT	ccC	2	4	B.1.1.372	0.001377
N	162	P162P	ccT	ccC	4	4	B.1.1.519	0.000159
N	162	P162P	ccT	ccC	4	4	B.1.236	0.008214
N	162	P162P	ccT	ccC	4	4	B.1.36	0.000584
N	162	P162P	ccT	ccC	3	4	B.1.427	0.000151
N	162	P162P	ccT	ccG	1	4	B.1.427	0.00005
N	162	P162P	ccT	ccC	2	3		0.111111
N	162	P162P	ccT	ccA	1	3		0.055556
N	162	P162P	ccT	ccC	3	3	AY.38	0.001498
N	162	P162P	ccT	ccA	3	3	AY.47	0.000093
N	162	P162P	ccT	ccC	3	3	AY.6	0.000123
N	162	P162P	ccT	ccA	2	3	B.1.1.170	0.002494
N	162	P162P	ccT	ccC	1	3	B.1.1.170	0.001247
N	162	P162P	ccT	ccC	3	3	B.1.139	0.002199
N	162	P162P	ccT	ccC	3	3	B.1.177.73	0.001699
N	162	P162P	ccT	ccC	2	3	B.1.177.75	0.002081
N	162	P162P	ccT	ccG	1	3	B.1.177.75	0.001041
N	162	P162P	ccT	ccC	2	3	B.1.258.11	0.000793
N	162	P162P	ccT	ccA	1	3	B.1.258.11	0.000396
N	162	P162P	ccT	ccC	3	3	B.1.354	0.130435
N	162	P162P	ccT	ccC	3	3	C.14	0.012987
N	162	P162P	ccT	ccC	3	3	P.1.14	0.000143
N	162	P162P	ccT	ccC	2	2	AY.117	0.000169
N	162	P162P	ccT	ccA	1	2	AY.119	0.000035
N	162	P162P	ccT	ccC	1	2	AY.119	0.000035
N	162	P162P	ccT	ccG	1	2	AY.120	0.000037
N	162	P162P	ccT	ccA	1	2	AY.120	0.000037
N	162	P162P	ccT	ccC	2	2	AY.16	0.000759
N	162	P162P	ccT	ccC	2	2	AY.26	0.000057
N	162	P162P	ccT	ccC	2	2	AY.29	0.000032
N	162	P162P	ccT	ccA	1	2	AY.3.1	0.000085
N	162	P162P	ccT	ccC	1	2	AY.3.1	0.000085
N	162	P162P	ccT	ccC	2	2	AY.46.6	0.000144
N	162	P162P	ccT	ccC	2	2	AY.59	0.001059
N	162	P162P	ccT	ccA	1	2	B.1.1.301	0.001179
N	162	P162P	ccT	ccC	1	2	B.1.1.301	0.001179
N	162	P162P	ccT	ccC	2	2	B.1.1.409	0.005666
N	162	P162P	ccT	ccA	1	2	B.1.1.515	0.02
N	162	P162P	ccT	ccC	1	2	B.1.1.515	0.02
N	162	P162P	ccT	ccC	2	2	B.1.160.17	0.003401
N	162	P162P	ccT	ccC	2	2	B.1.177.16	0.001329
N	162	P162P	ccT	ccC	2	2	B.1.177.77	0.001452
N	162	P162P	ccT	ccC	1	2	B.1.293	0.0125
N	162	P162P	ccT	ccA	1	2	B.1.293	0.0125
N	162	P162P	ccT	ccC	2	2	B.1.375	0.001639
N	162	P162P	ccT	ccC	1	2	B.1.389	0.001002
N	162	P162P	ccT	ccA	1	2	B.1.389	0.001002
N	162	P162P	ccT	ccC	1	2	B.1.429	0.000024
N	162	P162P	ccT	ccG	1	2	B.1.429	0.000024
N	162	P162P	ccT	ccG	1	2	B.1.575	0.000303
N	162	P162P	ccT	ccC	1	2	B.1.575	0.000303
N	162	P162P	ccT	ccG	1	2	B.1.609	0.000479
N	162	P162P	ccT	ccA	1	2	B.1.609	0.000479
N	162	P162P	ccT	ccC	1	2	B.1.78	0.008547
N	162	P162P	ccT	ccA	1	2	B.1.78	0.008547
N	162	P162P	ccT	ccC	2	2	C.35	0.001548
N	162	P162P	ccT	ccC	1	2	P.2	0.000187
N	162	P162P	ccT	ccA	1	2	P.2	0.000187
N	162	P162P	ccT	ccC	1	1	A	0.000387
N	162	P162P	ccT	ccC	1	1	A.2	0.000662
N	162	P162P	ccT	ccC	1	1	AY.1	0.000396
N	162	P162P	ccT	ccC	1	1	AY.110	0.000113
N	162	P162P	ccT	ccC	1	1	AY.111	0.000183
N	162	P162P	ccT	ccC	1	1	AY.120.1	0.000321
N	162	P162P	ccT	ccC	1	1	AY.14	0.000088
N	162	P162P	ccT	ccA	1	1	AY.19	0.00114
N	162	P162P	ccT	ccC	1	1	AY.23	0.00007
N	162	P162P	ccT	ccC	1	1	AY.33	0.000067
N	162	P162P	ccT	ccC	1	1	AY.4.4	0.000409
N	162	P162P	ccT	ccC	1	1	AY.46	0.000104
N	162	P162P	ccT	ccG	1	1	AY.5	0.000021
N	162	P162P	ccT	ccC	1	1	AY.52	0.000814
N	162	P162P	ccT	ccA	1	1	AY.71	0.000475
N	162	P162P	ccT	ccC	1	1	AY.75.1	0.00018
N	162	P162P	ccT	ccC	1	1	AY.8	0.000606
N	162	P162P	ccT	ccC	1	1	AY.98	0.000079
N	162	P162P	ccT	ccC	1	1	AY.99	0.001049
N	162	P162P	ccT	ccG	1	1	B.1.1.148	0.008772
N	162	P162P	ccT	ccG	1	1	B.1.1.157	0.000913
N	162	P162P	ccT	ccC	1	1	B.1.1.171	0.003676
N	162	P162P	ccT	ccA	1	1	B.1.1.193	0.111111
N	162	P162P	ccT	ccC	1	1	B.1.1.198	0.001468
N	162	P162P	ccT	ccC	1	1	B.1.1.253	0.002506
N	162	P162P	ccT	ccA	1	1	B.1.1.277	0.000759
N	162	P162P	ccT	ccC	1	1	B.1.1.348	0.000796
N	162	P162P	ccT	ccC	1	1	B.1.1.507	0.008696
N	162	P162P	ccT	ccC	1	1	B.1.1.56	0.017857
N	162	P162P	ccT	ccC	1	1	B.1.103	0.019231
N	162	P162P	ccT	ccC	1	1	B.1.177.12	0.000152
N	162	P162P	ccT	ccC	1	1	B.1.177.20	0.001517
N	162	P162P	ccT	ccA	1	1	B.1.177.33	0.001645
N	162	P162P	ccT	ccC	1	1	B.1.177.50	0.004695
N	162	P162P	ccT	ccC	1	1	B.1.177.57	0.000281
N	162	P162P	ccT	ccC	1	1	B.1.177.60	0.000218
N	162	P162P	ccT	ccC	1	1	B.1.210	0.002132
N	162	P162P	ccT	ccC	1	1	B.1.234	0.000132
N	162	P162P	ccT	ccA	1	1	B.1.284	0.013158
N	162	P162P	ccT	ccC	1	1	B.1.301	0.005917
N	162	P162P	ccT	ccC	1	1	B.1.329	0.000608
N	162	P162P	ccT	ccC	1	1	B.1.36.27	0.000763
N	162	P162P	ccT	ccC	1	1	B.1.369	0.000285
N	162	P162P	ccT	ccC	1	1	B.1.466.2	0.000391
N	162	P162P	ccT	ccC	1	1	B.1.525	0.000113
N	162	P162P	ccT	ccC	1	1	B.1.541	0.004425
N	162	P162P	ccT	ccA	1	1	B.1.576	0.000907
N	162	P162P	ccT	ccC	1	1	B.1.577	0.000687
N	162	P162P	ccT	ccA	1	1	B.1.618	0.004032
N	162	P162P	ccT	ccC	1	1	B.1.621	0.000089
N	162	P162P	ccT	ccC	1	1	B.1.623	0.000536
N	162	P162P	ccT	ccC	1	1	B.1.627	0.00202
N	162	P162P	ccT	ccA	1	1	B.1.83	0.015385
N	162	P162P	ccT	ccC	1	1	B.29	0.003509
N	162	P162P	ccT	ccC	1	1	C.30	0.001727
N	162	P162P	ccT	ccC	1	1	C.37	0.000116
N	162	P162P	ccT	ccC	1	1	K.1	0.02381
N	162	P162P	ccT	ccC	1	1	P.1.1	0.000318
N	162	P162P	ccT	ccC	1	1	P.1.12	0.000484
N	162	P162P	ccT	ccC	1	1	P.1.15	0.000232
N	162	P162P	ccT	ccG	1	1	P.1.16	0.000374
N	162	P162P	ccT	ccC	1	1	Q.8	0.000165
N	162	P162P	ccT	ccC	1	1	W.4	0.001351

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.