CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : Mut = A79del1

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
ORF7a	79	A79del1		del	Gcc	-cc	1716	1679	0.978438	27628-27630
ORF7a	79	A79del1		del	gcC	gc-	1716	17	0.00990676	27628-27630
ORF7a	79	A79del1		del	gCc	g-c	1716	6	0.0034965	27628-27630
ORF7a	79	A79del1		del	GCc	-Nc	1716	4	0.002331	27628-27630
ORF7a	79	A79del1		del	GCc	-Ac	1716	3	0.00174825	27628-27630
ORF7a	79	A79del1		del	gCC	g-N	1716	2	0.0011655	27628-27630
ORF7a	79	A79del1		del	GCC	-NN	1716	2	0.0011655	27628-27630
ORF7a	79	A79del1		del	GCc	-Tc	1716	2	0.0011655	27628-27630
ORF7a	79	A79del1		del	GcC	-cN	1716	1	0.000582751	27628-27630

Details of the mutation A79del1 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
ORF7a	79	A79del1	Gcc	-cc	1679	1716	All	0.000321
ORF7a	79	A79del1	gcC	gc-	17	1716	All	0.000003
ORF7a	79	A79del1	gCc	g-c	6	1716	All	0.000001
ORF7a	79	A79del1	GCc	-Nc	4	1716	All	0.000001
ORF7a	79	A79del1	GCc	-Ac	3	1716	All	0.000001
ORF7a	79	A79del1	gCC	g-N	2	1716	All	0
ORF7a	79	A79del1	GCC	-NN	2	1716	All	0
ORF7a	79	A79del1	GCc	-Tc	2	1716	All	0
ORF7a	79	A79del1	GcC	-cN	1	1716	All	0
ORF7a	79	A79del1	Gcc	-cc	982	984	B.1.617.2	0.003698
ORF7a	79	A79del1	GCc	-Nc	2	984	B.1.617.2	0.000008
ORF7a	79	A79del1	Gcc	-cc	166	169	AY.102	0.004401
ORF7a	79	A79del1	GCc	-Nc	2	169	AY.102	0.000053
ORF7a	79	A79del1	GCC	-NN	1	169	AY.102	0.000027
ORF7a	79	A79del1	Gcc	-cc	95	96	AY.43	0.000421
ORF7a	79	A79del1	gcC	gc-	1	96	AY.43	0.000004
ORF7a	79	A79del1	Gcc	-cc	64	72	AY.39	0.001582
ORF7a	79	A79del1	gcC	gc-	7	72	AY.39	0.000173
ORF7a	79	A79del1	GCC	-NN	1	72	AY.39	0.000025
ORF7a	79	A79del1	Gcc	-cc	70	70	AY.120	0.002603
ORF7a	79	A79del1	Gcc	-cc	49	49	AY.46.4	0.008061
ORF7a	79	A79del1	Gcc	-cc	33	37	AY.4	0.000051
ORF7a	79	A79del1	gcC	gc-	3	37	AY.4	0.000005
ORF7a	79	A79del1	GcC	-cN	1	37	AY.4	0.000002
ORF7a	79	A79del1	Gcc	-cc	30	33	AY.103	0.000186
ORF7a	79	A79del1	gCC	g-N	1	33	AY.103	0.000006
ORF7a	79	A79del1	gcC	gc-	1	33	AY.103	0.000006
ORF7a	79	A79del1	gCc	g-c	1	33	AY.103	0.000006
ORF7a	79	A79del1	Gcc	-cc	20	20	AY.54	0.001907
ORF7a	79	A79del1	Gcc	-cc	13	14	AY.44	0.000079
ORF7a	79	A79del1	gCc	g-c	1	14	AY.44	0.000006
ORF7a	79	A79del1	Gcc	-cc	12	12	AY.68	0.003285
ORF7a	79	A79del1	Gcc	-cc	7	11	B.1.1.7	0.000006
ORF7a	79	A79del1	gCc	g-c	1	11	B.1.1.7	0.000001
ORF7a	79	A79del1	gcC	gc-	1	11	B.1.1.7	0.000001
ORF7a	79	A79del1	GCc	-Tc	1	11	B.1.1.7	0.000001
ORF7a	79	A79del1	gCC	g-N	1	11	B.1.1.7	0.000001
ORF7a	79	A79del1	Gcc	-cc	10	10	AY.106	0.003349
ORF7a	79	A79del1	Gcc	-cc	10	10	AY.37	0.003161
ORF7a	79	A79del1	Gcc	-cc	7	8	AY.42	0.000282
ORF7a	79	A79del1	gcC	gc-	1	8	AY.42	0.00004
ORF7a	79	A79del1	Gcc	-cc	8	8	AY.46.2	0.005083
ORF7a	79	A79del1	Gcc	-cc	7	7	AY.119	0.000247
ORF7a	79	A79del1	Gcc	-cc	6	6	AY.110	0.000676
ORF7a	79	A79del1	Gcc	-cc	5	5	AY.46.1	0.005133
ORF7a	79	A79del1	Gcc	-cc	5	5	AY.98	0.000395
ORF7a	79	A79del1	Gcc	-cc	4	4	AY.111	0.000733
ORF7a	79	A79del1	Gcc	-cc	4	4	AY.45	0.000487
ORF7a	79	A79del1	Gcc	-cc	4	4	AY.47	0.000124
ORF7a	79	A79del1	Gcc	-cc	4	4	AY.74	0.000463
ORF7a	79	A79del1	Gcc	-cc	3	3	AY.118	0.000188
ORF7a	79	A79del1	Gcc	-cc	3	3	AY.23	0.000209
ORF7a	79	A79del1	Gcc	-cc	2	3	AY.25	0.000012
ORF7a	79	A79del1	gcC	gc-	1	3	AY.25	0.000006
ORF7a	79	A79del1	Gcc	-cc	3	3	AY.3	0.00003
ORF7a	79	A79del1	Gcc	-cc	3	3	AY.40	0.002893
ORF7a	79	A79del1	Gcc	-cc	3	3	AY.84	0.001312
ORF7a	79	A79del1	Gcc	-cc	3	3	AY.98.1	0.000145
ORF7a	79	A79del1	Gcc	-cc	2	3	AY.99.2	0.000184
ORF7a	79	A79del1	gcC	gc-	1	3	AY.99.2	0.000092
ORF7a	79	A79del1	gCc	g-c	2	3	B.1	0.000018
ORF7a	79	A79del1	GCc	-Tc	1	3	B.1	0.000009
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.1	0.000791
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.113	0.000285
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.117	0.000169
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.121	0.000271
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.19	0.002281
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.33	0.000134
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.34.1	0.00102
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.4.1	0.001475
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.46	0.000208
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.5	0.000041
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.66	0.002139
ORF7a	79	A79del1	GCc	-Ac	2	2	AY.7.2	0.001119
ORF7a	79	A79del1	Gcc	-cc	2	2	AY.88	0.001768
ORF7a	79	A79del1	Gcc	-cc	1	2	C.37	0.000116
ORF7a	79	A79del1	gcC	gc-	1	2	C.37	0.000116
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.100	0.000046
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.114	0.000231
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.116	0.000287
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.22	0.002092
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.36	0.000148
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.53	0.000288
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.65	0.000533
ORF7a	79	A79del1	GCc	-Ac	1	1	AY.7	0.000196
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.73	0.000665
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.81	0.001992
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.85	0.000427
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.90	0.000684
ORF7a	79	A79del1	Gcc	-cc	1	1	AY.95	0.000761
ORF7a	79	A79del1	Gcc	-cc	1	1	B.1.1.519	0.00004
ORF7a	79	A79del1	Gcc	-cc	1	1	B.1.243	0.00007
ORF7a	79	A79del1	gCc	g-c	1	1	B.1.399	0.001934
ORF7a	79	A79del1	Gcc	-cc	1	1	P.1	0.000016
ORF7a	79	A79del1	Gcc	-cc	1	1	P.2	0.000187
ORF7a	79	A79del1	Gcc	-cc	1	1	Q.8	0.000165

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.