CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 899

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/nsp3	899	Y899Y	Y1717Y	syn	taC	taT	604	604	1	5414-5416
ORF1ab/nsp3	899	Y899H	Y1717H	nonsyn	Tac	Cac	52	50	0.961538	5414-5416
ORF1ab/nsp3	899	Y899H	Y1717H	nonsyn	TaC	CaT	52	2	0.0384615	5414-5416
ORF1ab/nsp3	899	Y899del	Y1717del	del	TAC	---	51	51	1	5414-5416
ORF1ab/nsp3	899	Y899F	Y1717F	nonsyn	tAc	tTc	5	5	1	5414-5416
ORF1ab/nsp3	899	Y899X	Y1717X	nonsyn	taC	taA	5	3	0.6	5414-5416
ORF1ab/nsp3	899	Y899X	Y1717X	nonsyn	taC	taG	5	2	0.4	5414-5416
ORF1ab/nsp3	899	Y899C	Y1717C	nonsyn	tAc	tGc	4	4	1	5414-5416
ORF1ab/nsp3	899	Y899D	Y1717D	nonsyn	Tac	Gac	2	2	1	5414-5416
ORF1ab/nsp3	899	Y899Q	Y1717Q	nonsyn	TaC	CaA	1	1	1	5414-5416
ORF1ab/nsp3	899	Y899del2	Y1717del2	del	TAc	--c	1	1	1	5414-5416
ORF1ab/nsp3	899	Y899N	Y1717N	nonsyn	Tac	Aac	1	1	1	5414-5416
ORF1ab/nsp3	899	Y899del1	Y1717del1	del	Tac	-ac	1	1	1	5414-5416

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/nsp3	899	Y899Y	taC	taT	604	604	All	0.000116
ORF1ab/nsp3	899	Y899Y	taC	taT	78	78	B.1.445	0.917647
ORF1ab/nsp3	899	Y899Y	taC	taT	77	77	AY.43	0.000341
ORF1ab/nsp3	899	Y899Y	taC	taT	62	62	AY.5	0.00128
ORF1ab/nsp3	899	Y899Y	taC	taT	56	56	AY.4	0.000087
ORF1ab/nsp3	899	Y899H	Tac	Cac	50	52	All	0.00001
ORF1ab/nsp3	899	Y899H	TaC	CaT	2	52	All	0
ORF1ab/nsp3	899	Y899del	TAC	---	51	51	All	0.00001
ORF1ab/nsp3	899	Y899Y	taC	taT	40	40	AY.46	0.004163
ORF1ab/nsp3	899	Y899Y	taC	taT	36	36	B.1.1.7	0.000032
ORF1ab/nsp3	899	Y899H	Tac	Cac	27	27	AY.4	0.000042
ORF1ab/nsp3	899	Y899Y	taC	taT	25	25	AY.44	0.000152
ORF1ab/nsp3	899	Y899Y	taC	taT	22	22	B.1.160	0.000686
ORF1ab/nsp3	899	Y899Y	taC	taT	21	21	B.1.621	0.001859
ORF1ab/nsp3	899	Y899del	TAC	---	17	17	B.1.1.7	0.000015
ORF1ab/nsp3	899	Y899Y	taC	taT	16	16	AY.33	0.001068
ORF1ab/nsp3	899	Y899Y	taC	taT	15	15	B.1.1	0.000272
ORF1ab/nsp3	899	Y899Y	taC	taT	15	15	B.1.2	0.000132
ORF1ab/nsp3	899	Y899Y	taC	taT	14	14	B.1.617.2	0.000053
ORF1ab/nsp3	899	Y899Y	taC	taT	11	11	B.1.1.519	0.000437
ORF1ab/nsp3	899	Y899Y	taC	taT	10	10	AY.29	0.000158
ORF1ab/nsp3	899	Y899Y	taC	taT	9	9	B.1	0.000082
ORF1ab/nsp3	899	Y899Y	taC	taT	8	8	AY.25	0.000048
ORF1ab/nsp3	899	Y899Y	taC	taT	6	6	B.1.427	0.000303
ORF1ab/nsp3	899	Y899F	tAc	tTc	5	5	All	0.000001
ORF1ab/nsp3	899	Y899X	taC	taA	3	5	All	0.000001
ORF1ab/nsp3	899	Y899X	taC	taG	2	5	All	0
ORF1ab/nsp3	899	Y899Y	taC	taT	5	5	AY.102	0.000133
ORF1ab/nsp3	899	Y899Y	taC	taT	5	5	AY.118	0.000313
ORF1ab/nsp3	899	Y899C	tAc	tGc	4	4	All	0.000001
ORF1ab/nsp3	899	Y899Y	taC	taT	4	4	AY.103	0.000025
ORF1ab/nsp3	899	Y899Y	taC	taT	4	4	AY.20	0.000155
ORF1ab/nsp3	899	Y899H	Tac	Cac	4	4	AY.3	0.00004
ORF1ab/nsp3	899	Y899Y	taC	taT	4	4	AY.47	0.000124
ORF1ab/nsp3	899	Y899Y	taC	taT	4	4	B.1.637	0.000292
ORF1ab/nsp3	899	Y899Y	taC	taT	4	4	P.1	0.000063
ORF1ab/nsp3	899	Y899del	TAC	---	3	3	AY.25	0.000018
ORF1ab/nsp3	899	Y899Y	taC	taT	3	3	AY.46.6	0.000217
ORF1ab/nsp3	899	Y899Y	taC	taT	3	3	B.1.1.434	0.001046
ORF1ab/nsp3	899	Y899del	TAC	---	3	3	B.1.2	0.000026
ORF1ab/nsp3	899	Y899H	Tac	Cac	3	3	B.1.617.2	0.000011
ORF1ab/nsp3	899	Y899H	Tac	Cac	3	3	P.1	0.000047
ORF1ab/nsp3	899	Y899H	Tac	Cac	3	3	P.1.14	0.000143
ORF1ab/nsp3	899	Y899D	Tac	Gac	2	2	All	0
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	AY.121	0.000271
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	AY.26	0.000057
ORF1ab/nsp3	899	Y899del	TAC	---	2	2	AY.4	0.000003
ORF1ab/nsp3	899	Y899del	TAC	---	2	2	AY.43	0.000009
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	AY.6	0.000082
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	B	0.000256
ORF1ab/nsp3	899	Y899H	Tac	Cac	2	2	B.1	0.000018
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	B.1.1.222	0.000408
ORF1ab/nsp3	899	Y899del	TAC	---	2	2	B.1.160	0.000062
ORF1ab/nsp3	899	Y899H	Tac	Cac	2	2	B.1.160	0.000062
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	B.1.177	0.000026
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	B.1.177.7	0.00033
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	B.1.243	0.000139
ORF1ab/nsp3	899	Y899del	TAC	---	2	2	B.1.36	0.000292
ORF1ab/nsp3	899	Y899H	TaC	CaT	2	2	B.1.411	0.007407
ORF1ab/nsp3	899	Y899Y	taC	taT	2	2	B.1.617.1	0.000258
ORF1ab/nsp3	899	Y899C	tAc	tGc	2	2	P.1	0.000032
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	899	Y899H	Tac	Cac	1	1	A.2.4	0.003367
ORF1ab/nsp3	899	Y899del2	TAc	--c	1	1	All	0
ORF1ab/nsp3	899	Y899Q	TaC	CaA	1	1	All	0
ORF1ab/nsp3	899	Y899del1	Tac	-ac	1	1	All	0
ORF1ab/nsp3	899	Y899N	Tac	Aac	1	1	All	0
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	AY.108	0.001103
ORF1ab/nsp3	899	Y899H	Tac	Cac	1	1	AY.116.1	0.000311
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.23	0.00007
ORF1ab/nsp3	899	Y899H	Tac	Cac	1	1	AY.25	0.000006
ORF1ab/nsp3	899	Y899C	tAc	tGc	1	1	AY.25	0.000006
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	AY.26	0.000028
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.27	0.000065
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.3	0.00001
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.3.1	0.000085
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.39	0.000025
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.4.2	0.000022
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	AY.44	0.000006
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.45	0.000122
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.61	0.000105
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	AY.66	0.00107
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.86	0.00083
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.9.1	0.000084
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.9.2	0.000037
ORF1ab/nsp3	899	Y899del1	Tac	-ac	1	1	AY.93	0.000273
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	AY.99	0.001049
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	AY.99.2	0.000092
ORF1ab/nsp3	899	Y899X	taC	taA	1	1	B.1	0.000009
ORF1ab/nsp3	899	Y899D	Tac	Gac	1	1	B.1	0.000009
ORF1ab/nsp3	899	Y899X	taC	taG	1	1	B.1.1	0.000018
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.1	0.000018
ORF1ab/nsp3	899	Y899D	Tac	Gac	1	1	B.1.1	0.000018
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.1.129	0.009174
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.1.163	0.007634
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	899	Y899F	tAc	tTc	1	1	B.1.1.300	0.010753
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.1.316	0.000925
ORF1ab/nsp3	899	Y899X	taC	taA	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	899	Y899H	Tac	Cac	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	899	Y899H	Tac	Cac	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.157	0.002985
ORF1ab/nsp3	899	Y899X	taC	taA	1	1	B.1.177	0.000013
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp3	899	Y899F	tAc	tTc	1	1	B.1.184	0.058824
ORF1ab/nsp3	899	Y899del2	TAc	--c	1	1	B.1.23	0.006061
ORF1ab/nsp3	899	Y899Q	TaC	CaA	1	1	B.1.258	0.000067
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.258.3	0.001675
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	899	Y899X	taC	taG	1	1	B.1.338	0.008621
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.36.8	0.001
ORF1ab/nsp3	899	Y899F	tAc	tTc	1	1	B.1.36.8	0.001
ORF1ab/nsp3	899	Y899N	Tac	Aac	1	1	B.1.362	0.001541
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.400	0.000429
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.429	0.000024
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.438.1	0.000107
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.452	0.013699
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.499	0.00105
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.564	0.000426
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.577	0.000687
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.587	0.001898
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.595	0.000261
ORF1ab/nsp3	899	Y899F	tAc	tTc	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.1.620	0.000946
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	B.15	0.017544
ORF1ab/nsp3	899	Y899Y	taC	taT	1	1	B.40	0.000364
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	C.36	0.000911
ORF1ab/nsp3	899	Y899F	tAc	tTc	1	1	D.2	0.000075
ORF1ab/nsp3	899	Y899C	tAc	tGc	1	1	D.2	0.000075
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	P.1	0.000016
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	P.1.1	0.000318
ORF1ab/nsp3	899	Y899del	TAC	---	1	1	Q.2	0.000613
ORF1ab/nsp3	899	Y899H	Tac	Cac	1	1	R.1	0.00009

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.