CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF6 : Mut = X62del1

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
ORF6	62	X62del1		del	tAa	t-a	835	754	0.902994	27385-27387
ORF6	62	X62del1		del	taA	ta-	835	70	0.0838323	27385-27387
ORF6	62	X62del1		del	Taa	-aa	835	11	0.0131737	27385-27387

Details of the mutation X62del1 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
ORF6	62	X62del1	tAa	t-a	754	835	All	0.000144
ORF6	62	X62del1	taA	ta-	70	835	All	0.000013
ORF6	62	X62del1	Taa	-aa	11	835	All	0.000002
ORF6	62	X62del1	tAa	t-a	480	480	A.27	0.794702
ORF6	62	X62del1	tAa	t-a	80	85	AY.4	0.000125
ORF6	62	X62del1	taA	ta-	5	85	AY.4	0.000008
ORF6	62	X62del1	tAa	t-a	18	27	AY.44	0.00011
ORF6	62	X62del1	taA	ta-	9	27	AY.44	0.000055
ORF6	62	X62del1	tAa	t-a	20	25	B.1.1.7	0.000018
ORF6	62	X62del1	taA	ta-	3	25	B.1.1.7	0.000003
ORF6	62	X62del1	Taa	-aa	2	25	B.1.1.7	0.000002
ORF6	62	X62del1	tAa	t-a	13	15	B.1.1	0.000236
ORF6	62	X62del1	Taa	-aa	1	15	B.1.1	0.000018
ORF6	62	X62del1	taA	ta-	1	15	B.1.1	0.000018
ORF6	62	X62del1	taA	ta-	11	14	P.1	0.000173
ORF6	62	X62del1	tAa	t-a	2	14	P.1	0.000032
ORF6	62	X62del1	Taa	-aa	1	14	P.1	0.000016
ORF6	62	X62del1	tAa	t-a	12	12	B.1.240	0.002587
ORF6	62	X62del1	tAa	t-a	9	11	B.1	0.000082
ORF6	62	X62del1	Taa	-aa	1	11	B.1	0.000009
ORF6	62	X62del1	taA	ta-	1	11	B.1	0.000009
ORF6	62	X62del1	tAa	t-a	11	11	B.1.575	0.003337
ORF6	62	X62del1	tAa	t-a	10	11	B.1.617.2	0.000038
ORF6	62	X62del1	taA	ta-	1	11	B.1.617.2	0.000004
ORF6	62	X62del1	taA	ta-	8	10	AY.3	0.00008
ORF6	62	X62del1	tAa	t-a	2	10	AY.3	0.00002
ORF6	62	X62del1	tAa	t-a	10	10	AY.38	0.004993
ORF6	62	X62del1	tAa	t-a	6	9	AY.25	0.000036
ORF6	62	X62del1	taA	ta-	3	9	AY.25	0.000018
ORF6	62	X62del1	taA	ta-	9	9	B.1.525	0.001018
ORF6	62	X62del1	tAa	t-a	7	7	A	0.002709
ORF6	62	X62del1	tAa	t-a	4	7	AY.103	0.000025
ORF6	62	X62del1	Taa	-aa	2	7	AY.103	0.000012
ORF6	62	X62del1	taA	ta-	1	7	AY.103	0.000006
ORF6	62	X62del1	tAa	t-a	5	6	AY.39	0.000124
ORF6	62	X62del1	taA	ta-	1	6	AY.39	0.000025
ORF6	62	X62del1	tAa	t-a	6	6	B.1.1.519	0.000238
ORF6	62	X62del1	tAa	t-a	5	5	B	0.000639
ORF6	62	X62del1	tAa	t-a	4	4	AY.102	0.000106
ORF6	62	X62del1	tAa	t-a	3	3	A.29	0.015957
ORF6	62	X62del1	tAa	t-a	2	3	AY.100	0.000092
ORF6	62	X62del1	taA	ta-	1	3	AY.100	0.000046
ORF6	62	X62del1	tAa	t-a	2	3	AY.34	0.000194
ORF6	62	X62del1	taA	ta-	1	3	AY.34	0.000097
ORF6	62	X62del1	taA	ta-	3	3	AY.4.5	0.000322
ORF6	62	X62del1	taA	ta-	3	3	B.1.139	0.002199
ORF6	62	X62del1	tAa	t-a	2	2	AY.26	0.000057
ORF6	62	X62del1	tAa	t-a	1	2	AY.4.2	0.000022
ORF6	62	X62del1	taA	ta-	1	2	AY.4.2	0.000022
ORF6	62	X62del1	taA	ta-	1	2	B.1.1.28	0.000311
ORF6	62	X62del1	tAa	t-a	1	2	B.1.1.28	0.000311
ORF6	62	X62del1	tAa	t-a	1	2	B.1.1.33	0.000421
ORF6	62	X62del1	Taa	-aa	1	2	B.1.1.33	0.000421
ORF6	62	X62del1	tAa	t-a	2	2	B.1.1.434	0.000697
ORF6	62	X62del1	tAa	t-a	1	2	B.1.160	0.000031
ORF6	62	X62del1	Taa	-aa	1	2	B.1.160	0.000031
ORF6	62	X62del1	tAa	t-a	1	2	B.1.177	0.000013
ORF6	62	X62del1	taA	ta-	1	2	B.1.177	0.000013
ORF6	62	X62del1	tAa	t-a	2	2	B.1.177.6	0.001953
ORF6	62	X62del1	tAa	t-a	2	2	B.1.2	0.000018
ORF6	62	X62del1	taA	ta-	1	2	B.1.243	0.00007
ORF6	62	X62del1	tAa	t-a	1	2	B.1.243	0.00007
ORF6	62	X62del1	tAa	t-a	2	2	P.1.1	0.000635
ORF6	62	X62del1	tAa	t-a	1	1	A.1	0.000282
ORF6	62	X62del1	tAa	t-a	1	1	A.2	0.000662
ORF6	62	X62del1	tAa	t-a	1	1	AY.113	0.000142
ORF6	62	X62del1	tAa	t-a	1	1	AY.116.1	0.000311
ORF6	62	X62del1	tAa	t-a	1	1	AY.119	0.000035
ORF6	62	X62del1	tAa	t-a	1	1	AY.14	0.000088
ORF6	62	X62del1	tAa	t-a	1	1	AY.32	0.000532
ORF6	62	X62del1	tAa	t-a	1	1	AY.43	0.000004
ORF6	62	X62del1	tAa	t-a	1	1	AY.45	0.000122
ORF6	62	X62del1	tAa	t-a	1	1	AY.47	0.000031
ORF6	62	X62del1	taA	ta-	1	1	AY.78	0.001541
ORF6	62	X62del1	tAa	t-a	1	1	B.1.1.161	0.003534
ORF6	62	X62del1	tAa	t-a	1	1	B.1.1.261	0.008621
ORF6	62	X62del1	tAa	t-a	1	1	B.1.1.298	0.000862
ORF6	62	X62del1	tAa	t-a	1	1	B.1.1.369	0.000446
ORF6	62	X62del1	tAa	t-a	1	1	B.1.111	0.001175
ORF6	62	X62del1	tAa	t-a	1	1	B.1.160.33	0.004425
ORF6	62	X62del1	tAa	t-a	1	1	B.1.177.12	0.000152
ORF6	62	X62del1	tAa	t-a	1	1	B.1.177.7	0.000165
ORF6	62	X62del1	Taa	-aa	1	1	B.1.234	0.000132
ORF6	62	X62del1	tAa	t-a	1	1	B.1.320	0.001245
ORF6	62	X62del1	tAa	t-a	1	1	B.1.351.2	0.000303
ORF6	62	X62del1	taA	ta-	1	1	B.1.369	0.000285
ORF6	62	X62del1	tAa	t-a	1	1	B.1.416	0.001269
ORF6	62	X62del1	taA	ta-	1	1	B.1.526	0.000024
ORF6	62	X62del1	tAa	t-a	1	1	B.1.564	0.000426
ORF6	62	X62del1	tAa	t-a	1	1	B.1.595	0.000261
ORF6	62	X62del1	tAa	t-a	1	1	B.1.596	0.000087
ORF6	62	X62del1	taA	ta-	1	1	B.1.629	0.013333
ORF6	62	X62del1	Taa	-aa	1	1	B.1.637	0.000073
ORF6	62	X62del1	tAa	t-a	1	1	B.40	0.000364
ORF6	62	X62del1	taA	ta-	1	1	C.37	0.000116
ORF6	62	X62del1	tAa	t-a	1	1	P.1.17	0.000162
ORF6	62	X62del1	tAa	t-a	1	1	P.2	0.000187

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.