CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp15A1-B : Mut = A137A

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/nsp15A1-B	137	A137A	A6589A	syn	gcC	gcT	5233	5094	0.973438	20029-20031
ORF1ab/nsp15A1-B	137	A137A	A6589A	syn	gcC	gcA	5233	138	0.0263711	20029-20031
ORF1ab/nsp15A1-B	137	A137A	A6589A	syn	gcC	gcG	5233	1	0.000191095	20029-20031

Details of the mutation A137A 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/nsp15A1-B	137	A137A	gcC	gcT	5094	5233	All	0.000974
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	138	5233	All	0.000026
ORF1ab/nsp15A1-B	137	A137A	gcC	gcG	1	5233	All	0
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	3192	3192	AY.53	0.917769
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	731	731	AY.103	0.004539
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	343	343	B.1.177	0.004516
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	156	156	B.1.429	0.003671
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	94	100	B.1.1.7	0.000084
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	6	100	B.1.1.7	0.000005
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	86	86	B.1.1.257	0.834951
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	80	80	P.1.10	0.021558
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	58	58	AY.111	0.010623
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	57	57	AY.4	0.000089
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	42	50	B.1.1	0.000762
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	8	50	B.1.1	0.000145
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	45	45	B.1.177.35	0.031099
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	19	26	B.1	0.000174
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	6	26	B.1	0.000055
ORF1ab/nsp15A1-B	137	A137A	gcC	gcG	1	26	B.1	0.000009
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	26	26	B.1.234	0.003431
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	24	24	AY.9.1	0.002009
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	18	18	B.1.177.21	0.001376
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	16	16	A.1	0.00451
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	15	16	AY.25	0.00009
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	16	AY.25	0.000006
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	16	16	B.1.160	0.000499
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	14	14	B.1.582	0.006869
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	11	13	AY.43	0.000049
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	2	13	AY.43	0.000009
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	9	9	AY.44	0.000055
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	9	9	B.1.617.2	0.000034
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	6	8	B.1.2	0.000053
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	2	8	B.1.2	0.000018
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	5	6	AY.42	0.000201
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	6	AY.42	0.00004
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	6	6	B.1.551	0.007742
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	6	6	P.1	0.000095
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	5	5	AY.20	0.000194
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	5	5	AY.4.2	0.000108
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	4	AY.4.5	0.000215
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	2	4	AY.4.5	0.000215
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	4	4	B.1.1.214	0.000222
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	4	4	B.1.1.33	0.001684
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	4	4	B.1.427	0.000202
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	4	4	B.1.526	0.000094
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	4	4	B.1.589	0.030303
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	4	4	B.1.609	0.001918
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	4	4	B.1.9.5	0.022727
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	3	3	AY.9.2	0.00011
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	3	3	B	0.000383
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	3	3	B.1.1.271	0.166667
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	3	3	B.1.1.277	0.002276
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	3	3	B.1.1.486	0.004732
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	3	3	B.1.221	0.000213
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2		0.111111
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	2	2	AY.117	0.000169
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	AY.26	0.000057
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	2	2	AY.29	0.000032
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	AY.47	0.000062
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	AY.61	0.00021
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	AY.75	0.000112
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	B.1.1.391	0.017094
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	B.1.177.46	0.001837
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	B.1.177.56	0.001335
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	B.1.243	0.000139
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	B.1.351	0.000059
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	B.1.36.29	0.001035
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	2	2	C.37	0.000232
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	A.2.4	0.003367
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	1	AY.24	0.000431
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	1	AY.3	0.00001
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	AY.33	0.000067
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	AY.35	0.000233
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	AY.39.1	0.00004
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	1	AY.5	0.000021
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	1	AY.69	0.000187
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	AY.74	0.000116
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	AY.96	0.002075
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	AY.98	0.000079
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.1.348	0.000796
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.1.413	0.006897
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.1.519	0.00004
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.177.12	0.000152
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.177.15	0.000631
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.177.31	0.011494
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.177.4	0.000211
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.177.7	0.000165
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.240	0.000216
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.241	0.000812
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.260	0.003344
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	1	B.1.36.36	0.000602
ORF1ab/nsp15A1-B	137	A137A	gcC	gcA	1	1	B.1.378	0.006849
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.404	0.001302
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.533	0.009615
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.595	0.000261
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.596	0.000087
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.621	0.000089
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.1.8	0.001972
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.4	0.002208
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	B.6.6	0.000889
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	P.1.9	0.004808
ORF1ab/nsp15A1-B	137	A137A	gcC	gcT	1	1	Q.3	0.000145

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.