CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp10 : CodonNum = 85

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
ORF1ab/nsp10	85	N85N	N4338N	syn	aaT	aaC	3554	3554	1	13277-13279
ORF1ab/nsp10	85	N85D	N4338D	nonsyn	Aat	Gat	593	593	1	13277-13279
ORF1ab/nsp10	85	N85S	N4338S	nonsyn	aAt	aGt	442	442	1	13277-13279
ORF1ab/nsp10	85	N85del	N4338del	del	AAT	---	74	74	1	13277-13279
ORF1ab/nsp10	85	N85K	N4338K	nonsyn	aaT	aaG	24	23	0.958333	13277-13279
ORF1ab/nsp10	85	N85K	N4338K	nonsyn	aaT	aaA	24	1	0.0416667	13277-13279
ORF1ab/nsp10	85	N85T	N4338T	nonsyn	aAt	aCt	19	19	1	13277-13279
ORF1ab/nsp10	85	N85I	N4338I	nonsyn	aAt	aTt	9	8	0.888889	13277-13279
ORF1ab/nsp10	85	N85I	N4338I	nonsyn	aAT	aTC	9	1	0.111111	13277-13279
ORF1ab/nsp10	85	N85Y	N4338Y	nonsyn	Aat	Tat	7	7	1	13277-13279
ORF1ab/nsp10	85	N85H	N4338H	nonsyn	Aat	Cat	7	7	1	13277-13279
ORF1ab/nsp10	85	N85del1	N4338del1	del	Aat	-at	1	1	1	13277-13279
ORF1ab/nsp10	85	N85R	N4338R	nonsyn	AAt	CGt	1	1	1	13277-13279

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
ORF1ab/nsp10	85	N85N	aaT	aaC	3554	3554	All	0.00068
ORF1ab/nsp10	85	N85N	aaT	aaC	3229	3229	B.1.1.7	0.002891
ORF1ab/nsp10	85	N85D	Aat	Gat	593	593	All	0.000113
ORF1ab/nsp10	85	N85D	Aat	Gat	583	583	B.1.160.17	0.991497
ORF1ab/nsp10	85	N85S	aAt	aGt	442	442	All	0.000085
ORF1ab/nsp10	85	N85S	aAt	aGt	131	131	B.1.221	0.009305
ORF1ab/nsp10	85	N85S	aAt	aGt	96	96	AY.42	0.003862
ORF1ab/nsp10	85	N85del	AAT	---	74	74	All	0.000014
ORF1ab/nsp10	85	N85N	aaT	aaC	65	65	AY.20	0.002526
ORF1ab/nsp10	85	N85S	aAt	aGt	61	61	AY.6	0.002509
ORF1ab/nsp10	85	N85S	aAt	aGt	54	54	AY.44	0.000329
ORF1ab/nsp10	85	N85del	AAT	---	31	31	B.1.1.7	0.000028
ORF1ab/nsp10	85	N85N	aaT	aaC	27	27	AY.7.1	0.003043
ORF1ab/nsp10	85	N85K	aaT	aaG	23	24	All	0.000004
ORF1ab/nsp10	85	N85K	aaT	aaA	1	24	All	0
ORF1ab/nsp10	85	N85N	aaT	aaC	24	24	B.1.617.2	0.00009
ORF1ab/nsp10	85	N85K	aaT	aaG	21	21	B.1.2	0.000185
ORF1ab/nsp10	85	N85S	aAt	aGt	20	20	B.1.1.7	0.000018
ORF1ab/nsp10	85	N85T	aAt	aCt	19	19	All	0.000004
ORF1ab/nsp10	85	N85N	aaT	aaC	18	18	AY.4	0.000028
ORF1ab/nsp10	85	N85N	aaT	aaC	18	18	B.1.351.2	0.005446
ORF1ab/nsp10	85	N85N	aaT	aaC	18	18	B.1.429	0.000424
ORF1ab/nsp10	85	N85T	aAt	aCt	15	15	B.1.1.7	0.000013
ORF1ab/nsp10	85	N85N	aaT	aaC	15	15	C.37	0.001741
ORF1ab/nsp10	85	N85N	aaT	aaC	12	12	B.1	0.00011
ORF1ab/nsp10	85	N85N	aaT	aaC	11	11	AY.43	0.000049
ORF1ab/nsp10	85	N85N	aaT	aaC	11	11	B.1.177	0.000145
ORF1ab/nsp10	85	N85N	aaT	aaC	11	11	B.1.2	0.000097
ORF1ab/nsp10	85	N85I	aAt	aTt	8	9	All	0.000002
ORF1ab/nsp10	85	N85I	aAT	aTC	1	9	All	0
ORF1ab/nsp10	85	N85Y	Aat	Tat	7	7	All	0.000001
ORF1ab/nsp10	85	N85H	Aat	Cat	7	7	All	0.000001
ORF1ab/nsp10	85	N85S	aAt	aGt	7	7	B.1.1.398	0.022581
ORF1ab/nsp10	85	N85S	aAt	aGt	7	7	B.1.617.2	0.000026
ORF1ab/nsp10	85	N85I	aAt	aTt	6	6		0.333333
ORF1ab/nsp10	85	N85N	aaT	aaC	6	6	AY.117	0.000507
ORF1ab/nsp10	85	N85N	aaT	aaC	6	6	AY.3	0.00006
ORF1ab/nsp10	85	N85N	aaT	aaC	6	6	AY.44	0.000037
ORF1ab/nsp10	85	N85S	aAt	aGt	6	6	B.1.429	0.000141
ORF1ab/nsp10	85	N85S	aAt	aGt	5	5	AY.4	0.000008
ORF1ab/nsp10	85	N85N	aaT	aaC	5	5	B.1.1	0.000091
ORF1ab/nsp10	85	N85S	aAt	aGt	5	5	B.1.1	0.000091
ORF1ab/nsp10	85	N85S	aAt	aGt	5	5	B.1.1.519	0.000199
ORF1ab/nsp10	85	N85del	AAT	---	5	5	B.1.177	0.000066
ORF1ab/nsp10	85	N85N	aaT	aaC	4	4	AY.103	0.000025
ORF1ab/nsp10	85	N85N	aaT	aaC	4	4	AY.50	0.003197
ORF1ab/nsp10	85	N85N	aaT	aaC	4	4	AY.64	0.002381
ORF1ab/nsp10	85	N85S	aAt	aGt	4	4	AY.99.2	0.000369
ORF1ab/nsp10	85	N85D	Aat	Gat	4	4	B.1.160	0.000125
ORF1ab/nsp10	85	N85N	aaT	aaC	3	3	AY.29	0.000047
ORF1ab/nsp10	85	N85del	AAT	---	3	3	AY.4.5	0.000322
ORF1ab/nsp10	85	N85del	AAT	---	3	3	AY.43	0.000013
ORF1ab/nsp10	85	N85N	aaT	aaC	3	3	AY.48	0.001395
ORF1ab/nsp10	85	N85N	aaT	aaC	3	3	AY.6	0.000123
ORF1ab/nsp10	85	N85N	aaT	aaC	3	3	AY.62	0.001307
ORF1ab/nsp10	85	N85H	Aat	Cat	3	3	B.1.1.1	0.00098
ORF1ab/nsp10	85	N85S	aAt	aGt	3	3	B.1.1.189	0.004539
ORF1ab/nsp10	85	N85S	aAt	aGt	3	3	B.1.1.284	0.000322
ORF1ab/nsp10	85	N85S	aAt	aGt	3	3	B.1.1.317	0.001235
ORF1ab/nsp10	85	N85S	aAt	aGt	3	3	B.1.2	0.000026
ORF1ab/nsp10	85	N85N	aaT	aaC	3	3	B.1.351	0.000089
ORF1ab/nsp10	85	N85Y	Aat	Tat	2	2		0.111111
ORF1ab/nsp10	85	N85N	aaT	aaC	2	2	AU.2	0.004843
ORF1ab/nsp10	85	N85N	aaT	aaC	2	2	AY.25	0.000012
ORF1ab/nsp10	85	N85del	AAT	---	2	2	AY.25	0.000012
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	AY.26	0.000057
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	AY.29	0.000032
ORF1ab/nsp10	85	N85N	aaT	aaC	2	2	AY.36	0.000296
ORF1ab/nsp10	85	N85del	AAT	---	2	2	AY.4	0.000003
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	B.1.1.153	0.002191
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	B.1.1.28	0.000622
ORF1ab/nsp10	85	N85Y	Aat	Tat	2	2	B.1.1.7	0.000002
ORF1ab/nsp10	85	N85K	aaT	aaG	2	2	B.1.1.7	0.000002
ORF1ab/nsp10	85	N85Y	Aat	Tat	2	2	B.1.2	0.000018
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	B.1.258.17	0.000208
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	B.1.351	0.000059
ORF1ab/nsp10	85	N85N	aaT	aaC	2	2	B.1.596	0.000174
ORF1ab/nsp10	85	N85N	aaT	aaC	2	2	B.1.637	0.000146
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	P.1	0.000032
ORF1ab/nsp10	85	N85S	aAt	aGt	2	2	P.1.4	0.001953
ORF1ab/nsp10	85	N85N	aaT	aaC	2	2	Q.1	0.000253
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	A	0.000387
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	A.2	0.000662
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AH.3	0.003802
ORF1ab/nsp10	85	N85del1	Aat	-at	1	1	All	0
ORF1ab/nsp10	85	N85R	AAt	CGt	1	1	All	0
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.1	0.000396
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.100	0.000046
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.102	0.000027
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.103	0.000006
ORF1ab/nsp10	85	N85D	Aat	Gat	1	1	AY.103	0.000006
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.106	0.000335
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.111	0.000183
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.114	0.000231
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.119	0.000035
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.121	0.000135
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.16.1	0.00047
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.19	0.00114
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.20	0.000039
ORF1ab/nsp10	85	N85D	Aat	Gat	1	1	AY.25	0.000006
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.26	0.000028
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.3	0.00001
ORF1ab/nsp10	85	N85T	aAt	aCt	1	1	AY.3	0.00001
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.3	0.00001
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.35	0.000233
ORF1ab/nsp10	85	N85I	aAt	aTt	1	1	AY.39	0.000025
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.39	0.000025
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.39	0.000025
ORF1ab/nsp10	85	N85H	Aat	Cat	1	1	AY.4	0.000002
ORF1ab/nsp10	85	N85Y	Aat	Tat	1	1	AY.4	0.000002
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.4.5	0.000107
ORF1ab/nsp10	85	N85D	Aat	Gat	1	1	AY.41	0.000294
ORF1ab/nsp10	85	N85H	Aat	Cat	1	1	AY.43	0.000004
ORF1ab/nsp10	85	N85H	Aat	Cat	1	1	AY.44	0.000006
ORF1ab/nsp10	85	N85I	aAT	aTC	1	1	AY.44	0.000006
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.46.2	0.000635
ORF1ab/nsp10	85	N85D	Aat	Gat	1	1	AY.47	0.000031
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.5	0.000021
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.59	0.00053
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.60	0.000938
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.62	0.000436
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.67	0.000464
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.68	0.000274
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.7	0.000196
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.74	0.000116
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.9	0.000068
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.9.2	0.000037
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	AY.93	0.000273
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	AY.98.1	0.000048
ORF1ab/nsp10	85	N85del	AAT	---	1	1	AY.99	0.001049
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1	0.000009
ORF1ab/nsp10	85	N85T	aAt	aCt	1	1	B.1	0.000009
ORF1ab/nsp10	85	N85K	aaT	aaA	1	1	B.1.1	0.000018
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.1.1	0.000327
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.1.277	0.000759
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.1.279	0.001121
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.1.318	0.000302
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	B.1.1.37	0.000193
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.1.39	0.00051
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.1.519	0.00004
ORF1ab/nsp10	85	N85D	Aat	Gat	1	1	B.1.1.7	0.000001
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.1.70	0.000341
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.160	0.000031
ORF1ab/nsp10	85	N85D	Aat	Gat	1	1	B.1.177	0.000013
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.177.17	0.000821
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.177.18	0.00116
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.177.6	0.000977
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.177.69	0.001484
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.177.83	0.001481
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.206	0.000816
ORF1ab/nsp10	85	N85del1	Aat	-at	1	1	B.1.206	0.000816
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.23	0.006061
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.234	0.000132
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.243	0.00007
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.258.11	0.000396
ORF1ab/nsp10	85	N85I	aAt	aTt	1	1	B.1.36	0.000146
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.36	0.000146
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.36.36	0.000602
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.36.38	0.001642
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	B.1.406	0.006061
ORF1ab/nsp10	85	N85T	aAt	aCt	1	1	B.1.466.2	0.000391
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	B.1.499	0.00105
ORF1ab/nsp10	85	N85S	aAt	aGt	1	1	B.1.526	0.000024
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.526	0.000024
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.575.1	0.002439
ORF1ab/nsp10	85	N85H	Aat	Cat	1	1	B.1.617.2	0.000004
ORF1ab/nsp10	85	N85R	AAt	CGt	1	1	B.1.617.2	0.000004
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.617.3	0.002985
ORF1ab/nsp10	85	N85del	AAT	---	1	1	B.1.630	0.005236
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	B.1.631	0.003367
ORF1ab/nsp10	85	N85T	aAt	aCt	1	1	D.2	0.000075
ORF1ab/nsp10	85	N85N	aaT	aaC	1	1	P.1	0.000016
ORF1ab/nsp10	85	N85del	AAT	---	1	1	P.1	0.000016

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.