CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 90

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
M	90	L90L		syn	Ttg	Ctg	343	210	0.612245	26790-26792
M	90	L90L		syn	ttG	ttA	343	133	0.387755	26790-26792
M	90	L90F		nonsyn	ttG	ttT	328	319	0.972561	26790-26792
M	90	L90F		nonsyn	ttG	ttC	328	9	0.027439	26790-26792
M	90	L90del		del	TTG	---	232	232	1	26790-26792
M	90	L90S		nonsyn	tTg	tCg	71	70	0.985915	26790-26792
M	90	L90S		nonsyn	tTG	tCC	71	1	0.0140845	26790-26792
M	90	L90V		nonsyn	Ttg	Gtg	11	11	1	26790-26792
M	90	L90M		nonsyn	Ttg	Atg	9	9	1	26790-26792
M	90	L90W		nonsyn	tTg	tGg	4	4	1	26790-26792
M	90	L90X		nonsyn	tTg	tAg	2	2	1	26790-26792
M	90	L90C		nonsyn	tTG	tGT	2	2	1	26790-26792
M	90	L90P		nonsyn	TTg	CCg	1	1	1	26790-26792
M	90	L90del1		del	ttG	tt-	1	1	1	26790-26792
M	90	L90T		nonsyn	TTg	ACg	1	1	1	26790-26792
M	90	L90del2		del	TTg	--g	1	1	1	26790-26792
M	90	L90I		nonsyn	TtG	AtT	1	1	1	26790-26792

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
M	90	L90L	Ttg	Ctg	210	343	All	0.00004
M	90	L90L	ttG	ttA	133	343	All	0.000025
M	90	L90F	ttG	ttT	319	328	All	0.000061
M	90	L90F	ttG	ttC	9	328	All	0.000002
M	90	L90del	TTG	---	232	232	All	0.000044
M	90	L90F	ttG	ttT	97	99	B.1.1.7	0.000087
M	90	L90F	ttG	ttC	2	99	B.1.1.7	0.000002
M	90	L90L	Ttg	Ctg	89	89	B.1.160	0.002776
M	90	L90S	tTg	tCg	70	71	All	0.000013
M	90	L90S	tTG	tCC	1	71	All	0
M	90	L90del	TTG	---	61	61	B.1.1.7	0.000055
M	90	L90del	TTG	---	59	59	B.1.177.21	0.004512
M	90	L90S	tTg	tCg	47	47	B.1.1.7	0.000042
M	90	L90F	ttG	ttT	43	43	AY.103	0.000267
M	90	L90L	ttG	ttA	38	43	B.1.1.7	0.000034
M	90	L90L	Ttg	Ctg	5	43	B.1.1.7	0.000004
M	90	L90del	TTG	---	25	25	B.1	0.000229
M	90	L90L	ttG	ttA	18	22	AY.44	0.00011
M	90	L90L	Ttg	Ctg	4	22	AY.44	0.000024
M	90	L90L	ttG	ttA	15	19	B.1.258	0.000998
M	90	L90L	Ttg	Ctg	4	19	B.1.258	0.000266
M	90	L90L	Ttg	Ctg	14	18	B.1.617.2	0.000053
M	90	L90L	ttG	ttA	4	18	B.1.617.2	0.000015
M	90	L90L	Ttg	Ctg	12	15	AY.3	0.000119
M	90	L90L	ttG	ttA	3	15	AY.3	0.00003
M	90	L90L	ttG	ttA	10	15	AY.4	0.000016
M	90	L90L	Ttg	Ctg	5	15	AY.4	0.000008
M	90	L90F	ttG	ttT	14	14	AY.43	0.000062
M	90	L90F	ttG	ttT	13	13	B.1	0.000119
M	90	L90F	ttG	ttT	13	13	B.1.516	0.02544
M	90	L90F	ttG	ttT	12	12	B.1.1.88	0.857143
M	90	L90L	Ttg	Ctg	12	12	B.1.160.20	0.107143
M	90	L90F	ttG	ttT	11	12	B.1.617.2	0.000041
M	90	L90F	ttG	ttC	1	12	B.1.617.2	0.000004
M	90	L90V	Ttg	Gtg	11	11	All	0.000002
M	90	L90L	Ttg	Ctg	6	10	AY.43	0.000027
M	90	L90L	ttG	ttA	4	10	AY.43	0.000018
M	90	L90L	Ttg	Ctg	10	10	B.1.2	0.000088
M	90	L90M	Ttg	Atg	9	9	All	0.000002
M	90	L90L	Ttg	Ctg	6	8	B.1	0.000055
M	90	L90L	ttG	ttA	2	8	B.1	0.000018
M	90	L90L	ttG	ttA	8	8	B.1.526	0.000188
M	90	L90F	ttG	ttT	7	7	AY.102	0.000186
M	90	L90L	Ttg	Ctg	7	7	AY.121	0.000947
M	90	L90F	ttG	ttT	7	7	AY.4	0.000011
M	90	L90F	ttG	ttT	7	7	B.1.1.402	0.077778
M	90	L90L	Ttg	Ctg	6	7	B.1.621	0.000531
M	90	L90L	ttG	ttA	1	7	B.1.621	0.000089
M	90	L90F	ttG	ttT	7	7	P.1.14	0.000335
M	90	L90F	ttG	ttT	6	6	AY.3	0.00006
M	90	L90F	ttG	ttT	5	6	B.1.1	0.000091
M	90	L90F	ttG	ttC	1	6	B.1.1	0.000018
M	90	L90F	ttG	ttT	4	6	B.1.2	0.000035
M	90	L90F	ttG	ttC	2	6	B.1.2	0.000018
M	90	L90F	ttG	ttT	5	5	AY.25	0.00003
M	90	L90del	TTG	---	5	5	AY.43	0.000022
M	90	L90F	ttG	ttT	5	5	B.1.1.153	0.005476
M	90	L90W	tTg	tGg	4	4	All	0.000001
M	90	L90L	ttG	ttA	3	4	AY.102	0.00008
M	90	L90L	Ttg	Ctg	1	4	AY.102	0.000027
M	90	L90F	ttG	ttT	4	4	AY.20	0.000155
M	90	L90del	TTG	---	4	4	AY.25	0.000024
M	90	L90L	Ttg	Ctg	4	4	AY.25	0.000024
M	90	L90S	tTg	tCg	4	4	AY.4	0.000006
M	90	L90F	ttG	ttT	4	4	AY.4.2	0.000087
M	90	L90del	TTG	---	4	4	AY.99.2	0.000369
M	90	L90del	TTG	---	4	4	B.1.2	0.000035
M	90	L90F	ttG	ttT	4	4	B.1.427	0.000202
M	90	L90L	ttG	ttA	2	3	AY.103	0.000012
M	90	L90L	Ttg	Ctg	1	3	AY.103	0.000006
M	90	L90F	ttG	ttT	3	3	AY.16.1	0.00141
M	90	L90S	tTg	tCg	3	3	AY.26	0.000085
M	90	L90F	ttG	ttT	3	3	AY.39	0.000074
M	90	L90del	TTG	---	3	3	AY.46.3	0.002801
M	90	L90L	ttG	ttA	3	3	AY.46.6	0.000217
M	90	L90S	tTg	tCg	3	3	AY.61	0.000314
M	90	L90L	Ttg	Ctg	3	3	AY.85	0.001282
M	90	L90L	Ttg	Ctg	2	3	B.1.1	0.000036
M	90	L90L	ttG	ttA	1	3	B.1.1	0.000018
M	90	L90del	TTG	---	3	3	B.1.1.343	0.0625
M	90	L90del	TTG	---	3	3	B.1.160	0.000094
M	90	L90del	TTG	---	3	3	B.1.177	0.00004
M	90	L90F	ttG	ttT	3	3	B.1.351	0.000089
M	90	L90W	tTg	tGg	3	3	B.1.480	0.007463
M	90	L90F	ttG	ttT	3	3	B.1.526	0.000071
M	90	L90del	TTG	---	3	3	B.1.596	0.000261
M	90	L90S	tTg	tCg	3	3	B.1.617.2	0.000011
M	90	L90del	TTG	---	3	3	B.1.617.2	0.000011
M	90	L90F	ttG	ttT	3	3	C.37	0.000348
M	90	L90del	TTG	---	3	3	D.2	0.000225
M	90	L90L	ttG	ttA	3	3	P.1	0.000047
M	90	L90F	ttG	ttC	2	2		0.111111
M	90	L90del	TTG	---	2	2		0.111111
M	90	L90C	tTG	tGT	2	2		0.111111
M	90	L90X	tTg	tAg	2	2	All	0
M	90	L90C	tTG	tGT	2	2	All	0
M	90	L90L	ttG	ttA	2	2	AY.1	0.000791
M	90	L90L	Ttg	Ctg	2	2	AY.120	0.000074
M	90	L90del	TTG	---	2	2	AY.13	0.000322
M	90	L90S	tTg	tCg	2	2	AY.27	0.000129
M	90	L90F	ttG	ttC	1	2	AY.32	0.000532
M	90	L90F	ttG	ttT	1	2	AY.32	0.000532
M	90	L90F	ttG	ttT	2	2	AY.36	0.000296
M	90	L90F	ttG	ttT	2	2	AY.4.5	0.000215
M	90	L90del	TTG	---	2	2	AY.45	0.000243
M	90	L90del	TTG	---	2	2	AY.47	0.000062
M	90	L90F	ttG	ttT	2	2	AY.67	0.000929
M	90	L90L	Ttg	Ctg	2	2	AY.75.1	0.000361
M	90	L90del	TTG	---	2	2	AY.75.1	0.000361
M	90	L90M	Ttg	Atg	2	2	AY.75.1	0.000361
M	90	L90V	Ttg	Gtg	2	2	AY.98	0.000158
M	90	L90F	ttG	ttT	2	2	B	0.000256
M	90	L90M	Ttg	Atg	2	2	B.1	0.000018
M	90	L90M	Ttg	Atg	2	2	B.1.1.7	0.000002
M	90	L90L	Ttg	Ctg	2	2	B.1.221	0.000142
M	90	L90del	TTG	---	2	2	B.1.265	0.002541
M	90	L90del	TTG	---	2	2	B.1.400	0.000858
M	90	L90V	Ttg	Gtg	2	2	B.1.526	0.000047
M	90	L90F	ttG	ttT	2	2	P.1	0.000032
M	90	L90F	ttG	ttT	1	1	AD.2	0.000219
M	90	L90P	TTg	CCg	1	1	All	0
M	90	L90I	TtG	AtT	1	1	All	0
M	90	L90T	TTg	ACg	1	1	All	0
M	90	L90del1	ttG	tt-	1	1	All	0
M	90	L90del2	TTg	--g	1	1	All	0
M	90	L90del	TTG	---	1	1	AY.103	0.000006
M	90	L90L	Ttg	Ctg	1	1	AY.106	0.000335
M	90	L90V	Ttg	Gtg	1	1	AY.107	0.000466
M	90	L90F	ttG	ttT	1	1	AY.117	0.000085
M	90	L90F	ttG	ttT	1	1	AY.118	0.000063
M	90	L90del	TTG	---	1	1	AY.118	0.000063
M	90	L90L	ttG	ttA	1	1	AY.119	0.000035
M	90	L90del	TTG	---	1	1	AY.120	0.000037
M	90	L90L	Ttg	Ctg	1	1	AY.120.1	0.000321
M	90	L90F	ttG	ttT	1	1	AY.23	0.00007
M	90	L90S	tTg	tCg	1	1	AY.25	0.000006
M	90	L90del	TTG	---	1	1	AY.26	0.000028
M	90	L90L	ttG	ttA	1	1	AY.26	0.000028
M	90	L90L	Ttg	Ctg	1	1	AY.27	0.000065
M	90	L90S	tTg	tCg	1	1	AY.29	0.000016
M	90	L90F	ttG	ttT	1	1	AY.29	0.000016
M	90	L90M	Ttg	Atg	1	1	AY.29	0.000016
M	90	L90L	ttG	ttA	1	1	AY.3.1	0.000085
M	90	L90del	TTG	---	1	1	AY.34.1	0.00051
M	90	L90del	TTG	---	1	1	AY.39	0.000025
M	90	L90L	Ttg	Ctg	1	1	AY.39	0.000025
M	90	L90F	ttG	ttT	1	1	AY.39.1	0.00004
M	90	L90M	Ttg	Atg	1	1	AY.39.1	0.00004
M	90	L90del	TTG	---	1	1	AY.4	0.000002
M	90	L90S	tTg	tCg	1	1	AY.43	0.000004
M	90	L90del	TTG	---	1	1	AY.44	0.000006
M	90	L90F	ttG	ttT	1	1	AY.44	0.000006
M	90	L90del	TTG	---	1	1	AY.46	0.000104
M	90	L90S	tTg	tCg	1	1	AY.47	0.000031
M	90	L90L	ttG	ttA	1	1	AY.5	0.000021
M	90	L90F	ttG	ttT	1	1	AY.5	0.000021
M	90	L90L	Ttg	Ctg	1	1	AY.5.3	0.000337
M	90	L90L	ttG	ttA	1	1	AY.54	0.000095
M	90	L90L	ttG	ttA	1	1	AY.55	0.000917
M	90	L90F	ttG	ttT	1	1	AY.59	0.00053
M	90	L90del	TTG	---	1	1	AY.60	0.000938
M	90	L90F	ttG	ttT	1	1	AY.61	0.000105
M	90	L90del2	TTg	--g	1	1	AY.67	0.000464
M	90	L90L	ttG	ttA	1	1	AY.68	0.000274
M	90	L90del	TTG	---	1	1	AY.70	0.000209
M	90	L90F	ttG	ttT	1	1	AY.75	0.000056
M	90	L90L	Ttg	Ctg	1	1	AY.75	0.000056
M	90	L90L	ttG	ttA	1	1	AY.9.2	0.000037
M	90	L90del	TTG	---	1	1	AY.98	0.000079
M	90	L90L	ttG	ttA	1	1	AY.99	0.001049
M	90	L90S	tTg	tCg	1	1	B	0.000128
M	90	L90X	tTg	tAg	1	1	B	0.000128
M	90	L90L	Ttg	Ctg	1	1	B	0.000128
M	90	L90S	tTg	tCg	1	1	B.1	0.000009
M	90	L90del	TTG	---	1	1	B.1.1	0.000018
M	90	L90I	TtG	AtT	1	1	B.1.1	0.000018
M	90	L90V	Ttg	Gtg	1	1	B.1.1	0.000018
M	90	L90L	Ttg	Ctg	1	1	B.1.1.207	0.001182
M	90	L90del	TTG	---	1	1	B.1.1.207	0.001182
M	90	L90del	TTG	---	1	1	B.1.1.221	0.010101
M	90	L90L	ttG	ttA	1	1	B.1.1.28	0.000311
M	90	L90del	TTG	---	1	1	B.1.1.288	0.001916
M	90	L90F	ttG	ttT	1	1	B.1.1.311	0.000358
M	90	L90del	TTG	---	1	1	B.1.1.372	0.000689
M	90	L90F	ttG	ttT	1	1	B.1.1.432	0.001266
M	90	L90P	TTg	CCg	1	1	B.1.1.7	0.000001
M	90	L90V	Ttg	Gtg	1	1	B.1.1.7	0.000001
M	90	L90del	TTG	---	1	1	B.1.1.70	0.000341
M	90	L90F	ttG	ttT	1	1	B.1.1.71	0.006061
M	90	L90X	tTg	tAg	1	1	B.1.160	0.000031
M	90	L90del	TTG	---	1	1	B.1.160.16	0.000929
M	90	L90L	Ttg	Ctg	1	1	B.1.160.7	0.002079
M	90	L90del	TTG	---	1	1	B.1.161	0.017241
M	90	L90L	Ttg	Ctg	1	1	B.1.177	0.000013
M	90	L90V	Ttg	Gtg	1	1	B.1.177	0.000013
M	90	L90T	TTg	ACg	1	1	B.1.177.21	0.000076
M	90	L90L	ttG	ttA	1	1	B.1.177.21	0.000076
M	90	L90del1	ttG	tt-	1	1	B.1.177.54	0.000606
M	90	L90del	TTG	---	1	1	B.1.177.73	0.000566
M	90	L90F	ttG	ttT	1	1	B.1.214.2	0.0006
M	90	L90F	ttG	ttT	1	1	B.1.221	0.000071
M	90	L90F	ttG	ttT	1	1	B.1.258	0.000067
M	90	L90del	TTG	---	1	1	B.1.258	0.000067
M	90	L90W	tTg	tGg	1	1	B.1.258	0.000067
M	90	L90V	Ttg	Gtg	1	1	B.1.258.10	0.011364
M	90	L90del	TTG	---	1	1	B.1.258.11	0.000396
M	90	L90L	Ttg	Ctg	1	1	B.1.326	0.007576
M	90	L90del	TTG	---	1	1	B.1.329	0.000608
M	90	L90L	ttG	ttA	1	1	B.1.334	0.018182
M	90	L90del	TTG	---	1	1	B.1.351	0.00003
M	90	L90L	ttG	ttA	1	1	B.1.351.5	0.0006
M	90	L90L	ttG	ttA	1	1	B.1.36	0.000146
M	90	L90S	tTg	tCg	1	1	B.1.36.31	0.001751
M	90	L90L	ttG	ttA	1	1	B.1.36.35	0.002604
M	90	L90F	ttG	ttT	1	1	B.1.391	0.001127
M	90	L90F	ttG	ttT	1	1	B.1.429	0.000024
M	90	L90del	TTG	---	1	1	B.1.429	0.000024
M	90	L90L	ttG	ttA	1	1	B.1.429	0.000024
M	90	L90del	TTG	---	1	1	B.1.459	0.004082
M	90	L90F	ttG	ttT	1	1	B.1.524	0.001406
M	90	L90S	tTG	tCC	1	1	B.1.538	0.008065
M	90	L90del	TTG	---	1	1	B.1.561	0.000397
M	90	L90F	ttG	ttT	1	1	B.1.577	0.000687
M	90	L90del	TTG	---	1	1	B.1.577	0.000687
M	90	L90del	TTG	---	1	1	B.1.595	0.000261
M	90	L90del	TTG	---	1	1	B.1.617.1	0.000129
M	90	L90M	Ttg	Atg	1	1	B.1.617.2	0.000004
M	90	L90F	ttG	ttT	1	1	B.1.621	0.000089
M	90	L90del	TTG	---	1	1	B.1.627	0.00202
M	90	L90del	TTG	---	1	1	B.1.91	0.002075
M	90	L90L	Ttg	Ctg	1	1	B.4	0.002208
M	90	L90L	Ttg	Ctg	1	1	B.40	0.000364
M	90	L90V	Ttg	Gtg	1	1	D.2	0.000075
M	90	L90del	TTG	---	1	1	P.1	0.000016
M	90	L90del	TTG	---	1	1	P.1.15	0.000232
M	90	L90S	tTg	tCg	1	1	P.1.15	0.000232
M	90	L90F	ttG	ttT	1	1	P.1.17	0.000162
M	90	L90F	ttG	ttT	1	1	P.7	0.004367
M	90	L90F	ttG	ttT	1	1	Q.6	0.006623
M	90	L90V	Ttg	Gtg	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.