CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 77

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
S	77	K77T		nonsyn	aAg	aCg	14184	14181	0.999789	21791-21793
S	77	K77T		nonsyn	aAG	aCA	14184	2	0.000141004	21791-21793
S	77	K77T		nonsyn	aAG	aCC	14184	1	0.000070502	21791-21793
S	77	K77K		syn	aaG	aaA	1363	1363	1	21791-21793
S	77	K77N		nonsyn	aaG	aaT	829	681	0.821472	21791-21793
S	77	K77N		nonsyn	aaG	aaC	829	148	0.178528	21791-21793
S	77	K77del		del	AAG	---	504	504	1	21791-21793
S	77	K77R		nonsyn	aAg	aGg	114	110	0.964912	21791-21793
S	77	K77R		nonsyn	aAG	aGA	114	3	0.0263158	21791-21793
S	77	K77R		nonsyn	AAg	CGg	114	1	0.00877193	21791-21793
S	77	K77M		nonsyn	aAg	aTg	75	75	1	21791-21793
S	77	K77E		nonsyn	Aag	Gag	46	42	0.913043	21791-21793
S	77	K77E		nonsyn	AaG	GaA	46	4	0.0869565	21791-21793
S	77	K77X		nonsyn	Aag	Tag	16	11	0.6875	21791-21793
S	77	K77X		nonsyn	AaG	TaA	16	3	0.1875	21791-21793
S	77	K77X		nonsyn	AAG	TGA	16	2	0.125	21791-21793
S	77	K77Q		nonsyn	Aag	Cag	12	12	1	21791-21793
S	77	K77I		nonsyn	aAG	aTT	10	5	0.5	21791-21793
S	77	K77I		nonsyn	aAG	aTA	10	5	0.5	21791-21793
S	77	K77del2		del	aAG	a--	4	2	0.5	21791-21793
S	77	K77del2		del	AAG	G--	4	2	0.5	21791-21793
S	77	K77del1		del	aaG	aa-	4	1	0.25	21791-21793
S	77	K77del1		del	Aag	-ag	4	1	0.25	21791-21793
S	77	K77del1		del	AAG	-NN	4	1	0.25	21791-21793
S	77	K77del1		del	AaG	Ca-	4	1	0.25	21791-21793
S	77	K77C		nonsyn	AAG	TGT	2	1	0.5	21791-21793
S	77	K77C		nonsyn	AAG	TGC	2	1	0.5	21791-21793
S	77	K77Y		nonsyn	AaG	TaC	1	1	1	21791-21793
S	77	K77G		nonsyn	AAg	GGg	1	1	1	21791-21793
S	77	K77P		nonsyn	AAg	CCg	1	1	1	21791-21793

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
S	77	K77T	aAg	aCg	14181	14184	All	0.002712
S	77	K77T	aAG	aCA	2	14184	All	0
S	77	K77T	aAG	aCC	1	14184	All	0
S	77	K77T	aAg	aCg	8172	8174	B.1.617.2	0.030771
S	77	K77T	aAG	aCA	2	8174	B.1.617.2	0.000008
S	77	K77T	aAg	aCg	3118	3119	AY.35	0.726637
S	77	K77T	aAG	aCC	1	3119	AY.35	0.000233
S	77	K77T	aAg	aCg	1468	1468	AY.48	0.682791
S	77	K77K	aaG	aaA	1363	1363	All	0.000261
S	77	K77K	aaG	aaA	1025	1025	AY.116.1	0.319215
S	77	K77N	aaG	aaT	681	829	All	0.00013
S	77	K77N	aaG	aaC	148	829	All	0.000028
S	77	K77del	AAG	---	504	504	All	0.000096
S	77	K77N	aaG	aaT	371	374	B.1.526	0.00872
S	77	K77N	aaG	aaC	3	374	B.1.526	0.000071
S	77	K77T	aAg	aCg	245	245	AY.16.1	0.115132
S	77	K77T	aAg	aCg	243	243	AY.44	0.001479
S	77	K77T	aAg	aCg	128	128	AY.108	0.141125
S	77	K77R	aAg	aGg	110	114	All	0.000021
S	77	K77R	aAG	aGA	3	114	All	0.000001
S	77	K77R	AAg	CGg	1	114	All	0
S	77	K77T	aAg	aCg	114	114	AY.13	0.018352
S	77	K77N	aaG	aaC	54	103	B.1.1.7	0.000048
S	77	K77N	aaG	aaT	49	103	B.1.1.7	0.000044
S	77	K77T	aAg	aCg	91	91	AY.102	0.002413
S	77	K77del	AAG	---	90	90	B.1.617.2	0.000339
S	77	K77del	AAG	---	87	87	AY.43	0.000385
S	77	K77M	aAg	aTg	75	75	All	0.000014
S	77	K77T	aAg	aCg	59	59	AY.92	0.016949
S	77	K77T	aAg	aCg	54	54	AY.23	0.003766
S	77	K77K	aaG	aaA	54	54	B.1.497	0.016997
S	77	K77T	aAg	aCg	52	52	AY.85	0.022213
S	77	K77E	Aag	Gag	42	46	All	0.000008
S	77	K77E	AaG	GaA	4	46	All	0.000001
S	77	K77del	AAG	---	46	46	B.1.1.7	0.000041
S	77	K77M	aAg	aTg	36	36	B.6	0.032757
S	77	K77T	aAg	aCg	35	35	AY.59	0.018538
S	77	K77N	aaG	aaT	27	30	AY.4	0.000042
S	77	K77N	aaG	aaC	3	30	AY.4	0.000005
S	77	K77T	aAg	aCg	29	29	AY.54	0.002765
S	77	K77T	aAg	aCg	29	29	AY.66	0.031016
S	77	K77del	AAG	---	28	28	AY.44	0.00017
S	77	K77N	aaG	aaC	26	27	AY.3	0.000259
S	77	K77N	aaG	aaT	1	27	AY.3	0.00001
S	77	K77T	aAg	aCg	27	27	AY.37	0.008534
S	77	K77del	AAG	---	27	27	AY.9	0.001825
S	77	K77K	aaG	aaA	27	27	B.1.2	0.000238
S	77	K77N	aaG	aaT	25	27	B.1.617.2	0.000094
S	77	K77N	aaG	aaC	2	27	B.1.617.2	0.000008
S	77	K77T	aAg	aCg	26	26	AY.98	0.002054
S	77	K77T	aAg	aCg	22	22	AY.19	0.025086
S	77	K77del	AAG	---	22	22	AY.25	0.000132
S	77	K77K	aaG	aaA	21	21	B.1.617.2	0.000079
S	77	K77del	AAG	---	20	20	AY.4	0.000031
S	77	K77T	aAg	aCg	20	20	AY.5.4	0.005534
S	77	K77K	aaG	aaA	20	20	B.1.577	0.013746
S	77	K77R	aAg	aGg	19	19	B.1.1.7	0.000017
S	77	K77N	aaG	aaT	16	17	AY.43	0.000071
S	77	K77N	aaG	aaC	1	17	AY.43	0.000004
S	77	K77K	aaG	aaA	17	17	B.1.177.4	0.003588
S	77	K77X	Aag	Tag	11	16	All	0.000002
S	77	K77X	AaG	TaA	3	16	All	0.000001
S	77	K77X	AAG	TGA	2	16	All	0
S	77	K77del	AAG	---	16	16	AY.102	0.000424
S	77	K77T	aAg	aCg	16	16	AY.43	0.000071
S	77	K77T	aAg	aCg	16	16	AY.84	0.006999
S	77	K77N	aaG	aaT	15	15	AY.99.2	0.001382
S	77	K77N	aaG	aaT	13	15	B.1.160	0.000405
S	77	K77N	aaG	aaC	2	15	B.1.160	0.000062
S	77	K77del	AAG	---	13	13	AY.34.1	0.006629
S	77	K77R	aAg	aGg	13	13	AY.4	0.00002
S	77	K77K	aaG	aaA	13	13	AY.61	0.001362
S	77	K77K	aaG	aaA	13	13	B.1.429	0.000306
S	77	K77Q	Aag	Cag	12	12	All	0.000002
S	77	K77T	aAg	aCg	12	12	AY.47	0.000373
S	77	K77N	aaG	aaT	7	12	C.37	0.000812
S	77	K77N	aaG	aaC	5	12	C.37	0.00058
S	77	K77N	aaG	aaT	8	11	AY.44	0.000049
S	77	K77N	aaG	aaC	3	11	AY.44	0.000018
S	77	K77T	aAg	aCg	11	11	AY.62	0.004793
S	77	K77N	aaG	aaT	8	11	B.1	0.000073
S	77	K77N	aaG	aaC	3	11	B.1	0.000027
S	77	K77K	aaG	aaA	11	11	B.1.1.7	0.00001
S	77	K77I	aAG	aTA	5	10	All	0.000001
S	77	K77I	aAG	aTT	5	10	All	0.000001
S	77	K77N	aaG	aaT	10	10	AY.117	0.000845
S	77	K77R	aAg	aGg	10	10	AY.23	0.000697
S	77	K77T	aAg	aCg	10	10	AY.25	0.00006
S	77	K77M	aAg	aTg	10	10	B.1.1.7	0.000009
S	77	K77N	aaG	aaT	9	10	P.1	0.000142
S	77	K77N	aaG	aaC	1	10	P.1	0.000016
S	77	K77R	aAg	aGg	9	9	AY.103	0.000056
S	77	K77T	aAg	aCg	9	9	AY.116	0.002581
S	77	K77T	aAg	aCg	9	9	AY.75	0.000504
S	77	K77T	aAg	aCg	8	8	AY.103	0.00005
S	77	K77N	aaG	aaT	6	8	AY.103	0.000037
S	77	K77N	aaG	aaC	2	8	AY.103	0.000012
S	77	K77T	aAg	aCg	8	8	AY.24	0.003448
S	77	K77K	aaG	aaA	8	8	AY.4	0.000012
S	77	K77K	aaG	aaA	8	8	AY.46	0.000833
S	77	K77N	aaG	aaC	5	8	AY.5	0.000103
S	77	K77N	aaG	aaT	3	8	AY.5	0.000062
S	77	K77T	aAg	aCg	8	8	AY.55	0.007339
S	77	K77N	aaG	aaT	8	8	B.1.258	0.000532
S	77	K77K	aaG	aaA	8	8	P.1	0.000126
S	77	K77T	aAg	aCg	7	7	AY.119	0.000247
S	77	K77del	AAG	---	7	7	AY.3	0.00007
S	77	K77T	aAg	aCg	7	7	AY.61	0.000733
S	77	K77T	aAg	aCg	7	7	AY.87	0.005828
S	77	K77T	aAg	aCg	7	7	AY.98.1	0.000339
S	77	K77K	aaG	aaA	7	7	B.1	0.000064
S	77	K77del	AAG	---	7	7	B.1.1	0.000127
S	77	K77del	AAG	---	6	6	AY.103	0.000037
S	77	K77K	aaG	aaA	6	6	AY.116	0.001721
S	77	K77T	aAg	aCg	6	6	AY.121	0.000812
S	77	K77T	aAg	aCg	6	6	AY.3	0.00006
S	77	K77del	AAG	---	6	6	AY.33	0.000401
S	77	K77K	aaG	aaA	6	6	AY.54	0.000572
S	77	K77R	aAg	aGg	6	6	B.1.1.214	0.000333
S	77	K77E	Aag	Gag	6	6	B.1.1.7	0.000005
S	77	K77del	AAG	---	6	6	B.1.177	0.000079
S	77	K77K	aaG	aaA	6	6	B.1.221	0.000426
S	77	K77E	Aag	Gag	6	6	B.1.427	0.000303
S	77	K77K	aaG	aaA	5	5	AY.103	0.000031
S	77	K77T	aAg	aCg	5	5	AY.118	0.000313
S	77	K77N	aaG	aaC	5	5	AY.20	0.000194
S	77	K77K	aaG	aaA	5	5	AY.25	0.00003
S	77	K77N	aaG	aaT	5	5	AY.39	0.000124
S	77	K77M	aAg	aTg	5	5	AY.4	0.000008
S	77	K77del	AAG	---	5	5	AY.4.5	0.000537
S	77	K77del	AAG	---	5	5	AY.46	0.00052
S	77	K77del	AAG	---	5	5	AY.9.2	0.000184
S	77	K77X	Aag	Tag	5	5	B	0.000639
S	77	K77N	aaG	aaT	5	5	B.1.1.298	0.00431
S	77	K77N	aaG	aaT	5	5	B.1.1.519	0.000199
S	77	K77K	aaG	aaA	5	5	B.1.160	0.000156
S	77	K77N	aaG	aaT	5	5	B.1.2	0.000044
S	77	K77I	aAG	aTA	5	5	B.1.429	0.000118
S	77	K77K	aaG	aaA	5	5	B.1.436	0.005144
S	77	K77E	Aag	Gag	5	5	B.1.438.1	0.000536
S	77	K77T	aAg	aCg	5	5	C.35	0.00387
S	77	K77X	AAG	TGA	2	4		0.111111
S	77	K77X	AaG	TaA	2	4		0.111111
S	77	K77del2	AAG	G--	2	4	All	0
S	77	K77del2	aAG	a--	2	4	All	0
S	77	K77del1	aaG	aa-	1	4	All	0
S	77	K77del1	Aag	-ag	1	4	All	0
S	77	K77del1	AaG	Ca-	1	4	All	0
S	77	K77del1	AAG	-NN	1	4	All	0
S	77	K77T	aAg	aCg	4	4	AY.100	0.000184
S	77	K77K	aaG	aaA	4	4	AY.102	0.000106
S	77	K77T	aAg	aCg	4	4	AY.117	0.000338
S	77	K77del	AAG	---	4	4	AY.121	0.000541
S	77	K77del	AAG	---	4	4	AY.26	0.000113
S	77	K77del	AAG	---	4	4	AY.39	0.000099
S	77	K77T	aAg	aCg	4	4	AY.4	0.000006
S	77	K77N	aaG	aaT	4	4	AY.4.5	0.00043
S	77	K77K	aaG	aaA	4	4	AY.43	0.000018
S	77	K77del	AAG	---	4	4	AY.5	0.000083
S	77	K77del	AAG	---	4	4	AY.61	0.000419
S	77	K77T	aAg	aCg	4	4	AY.68	0.001095
S	77	K77T	aAg	aCg	4	4	AY.77	0.00451
S	77	K77del	AAG	---	4	4	AY.85	0.001709
S	77	K77T	aAg	aCg	4	4	AY.88	0.003537
S	77	K77del	AAG	---	4	4	B.1	0.000037
S	77	K77M	aAg	aTg	4	4	B.1.1	0.000073
S	77	K77N	aaG	aaC	3	4	B.1.36	0.000438
S	77	K77N	aaG	aaT	1	4	B.1.36	0.000146
S	77	K77N	aaG	aaC	3	4	B.1.427	0.000151
S	77	K77N	aaG	aaT	1	4	B.1.427	0.00005
S	77	K77R	aAg	aGg	4	4	B.1.617.2	0.000015
S	77	K77R	aAg	aGg	4	4	P.1	0.000063
S	77	K77N	aaG	aaT	4	4	P.1.17	0.000647
S	77	K77del	AAG	---	3	3	AY.101	0.001471
S	77	K77N	aaG	aaT	2	3	AY.102	0.000053
S	77	K77N	aaG	aaC	1	3	AY.102	0.000027
S	77	K77del	AAG	---	3	3	AY.20	0.000117
S	77	K77K	aaG	aaA	3	3	AY.24	0.001293
S	77	K77E	Aag	Gag	3	3	AY.25	0.000018
S	77	K77X	Aag	Tag	3	3	AY.4	0.000005
S	77	K77E	Aag	Gag	3	3	AY.4	0.000005
S	77	K77M	aAg	aTg	3	3	AY.4.5	0.000322
S	77	K77R	aAg	aGg	2	3	AY.43	0.000009
S	77	K77R	AAg	CGg	1	3	AY.43	0.000004
S	77	K77R	aAg	aGg	3	3	AY.44	0.000018
S	77	K77K	aaG	aaA	3	3	AY.44	0.000018
S	77	K77T	aAg	aCg	3	3	AY.45	0.000365
S	77	K77del	AAG	---	3	3	AY.47	0.000093
S	77	K77T	aAg	aCg	3	3	AY.52	0.002443
S	77	K77T	aAg	aCg	3	3	AY.53	0.000863
S	77	K77del	AAG	---	3	3	AY.54	0.000286
S	77	K77T	aAg	aCg	3	3	AY.56	0.004815
S	77	K77R	aAg	aGg	3	3	AY.61	0.000314
S	77	K77T	aAg	aCg	3	3	AY.71	0.001425
S	77	K77del	AAG	---	3	3	AY.75	0.000168
S	77	K77K	aaG	aaA	3	3	AY.75.1	0.000541
S	77	K77T	aAg	aCg	3	3	AY.75.1	0.000541
S	77	K77T	aAg	aCg	3	3	AY.9.2	0.00011
S	77	K77E	Aag	Gag	3	3	B.1	0.000027
S	77	K77N	aaG	aaT	3	3	B.1.1	0.000054
S	77	K77N	aaG	aaT	3	3	B.1.1.358	0.103448
S	77	K77R	aAg	aGg	3	3	B.1.1.432	0.003797
S	77	K77K	aaG	aaA	3	3	B.1.1.432	0.003797
S	77	K77R	aAg	aGg	3	3	B.1.160	0.000094
S	77	K77K	aaG	aaA	3	3	B.1.177	0.00004
S	77	K77N	aaG	aaT	3	3	B.1.177	0.00004
S	77	K77N	aaG	aaT	3	3	B.1.234	0.000396
S	77	K77del	AAG	---	3	3	B.1.429	0.000071
S	77	K77K	aaG	aaA	3	3	B.1.526	0.000071
S	77	K77T	aAg	aCg	3	3	B.1.617.1	0.000387
S	77	K77M	aAg	aTg	3	3	B.1.617.2	0.000011
S	77	K77R	aAg	aGg	3	3	C.16	0.003181
S	77	K77K	aaG	aaA	3	3	C.33	0.176471
S	77	K77N	aaG	aaT	3	3	P.1.14	0.000143
S	77	K77N	aaG	aaC	2	3	P.2	0.000373
S	77	K77N	aaG	aaT	1	3	P.2	0.000187
S	77	K77K	aaG	aaA	3	3	Q.2	0.00184
S	77	K77K	aaG	aaA	2	2		0.111111
S	77	K77R	aAG	aGA	2	2		0.111111
S	77	K77E	AaG	GaA	2	2		0.111111
S	77	K77del	AAG	---	2	2		0.111111
S	77	K77R	aAg	aGg	2	2	A	0.000774
S	77	K77C	AAG	TGC	1	2	All	0
S	77	K77C	AAG	TGT	1	2	All	0
S	77	K77T	aAg	aCg	2	2	AY.10	0.00106
S	77	K77T	aAg	aCg	2	2	AY.101	0.000981
S	77	K77K	aaG	aaA	2	2	AY.107	0.000932
S	77	K77del	AAG	---	2	2	AY.108	0.002205
S	77	K77T	aAg	aCg	2	2	AY.110	0.000225
S	77	K77K	aaG	aaA	2	2	AY.118	0.000125
S	77	K77del	AAG	---	2	2	AY.118	0.000125
S	77	K77E	Aag	Gag	2	2	AY.13	0.000322
S	77	K77T	aAg	aCg	2	2	AY.20	0.000078
S	77	K77K	aaG	aaA	2	2	AY.20	0.000078
S	77	K77T	aAg	aCg	2	2	AY.22	0.004184
S	77	K77N	aaG	aaC	1	2	AY.25	0.000006
S	77	K77N	aaG	aaT	1	2	AY.25	0.000006
S	77	K77K	aaG	aaA	2	2	AY.26	0.000057
S	77	K77K	aaG	aaA	2	2	AY.29	0.000032
S	77	K77K	aaG	aaA	2	2	AY.3	0.00002
S	77	K77N	aaG	aaT	2	2	AY.33	0.000134
S	77	K77K	aaG	aaA	2	2	AY.34	0.000194
S	77	K77Q	Aag	Cag	2	2	AY.34	0.000194
S	77	K77I	aAG	aTT	2	2	AY.4	0.000003
S	77	K77del	AAG	---	2	2	AY.42	0.00008
S	77	K77T	aAg	aCg	2	2	AY.46	0.000208
S	77	K77T	aAg	aCg	2	2	AY.5.3	0.000675
S	77	K77T	aAg	aCg	2	2	AY.64	0.00119
S	77	K77del	AAG	---	2	2	AY.68	0.000547
S	77	K77N	aaG	aaC	1	2	AY.69	0.000187
S	77	K77N	aaG	aaT	1	2	AY.69	0.000187
S	77	K77del	AAG	---	2	2	AY.7.2	0.001119
S	77	K77del	AAG	---	2	2	AY.75.1	0.000361
S	77	K77E	Aag	Gag	1	2	AY.79	0.001211
S	77	K77E	AaG	GaA	1	2	AY.79	0.001211
S	77	K77T	aAg	aCg	2	2	AY.82	0.002714
S	77	K77T	aAg	aCg	2	2	AY.95	0.001522
S	77	K77del	AAG	---	2	2	AY.98.1	0.000097
S	77	K77M	aAg	aTg	2	2	B.1	0.000018
S	77	K77Q	Aag	Cag	2	2	B.1.1.170	0.002494
S	77	K77K	aaG	aaA	2	2	B.1.1.434	0.000697
S	77	K77R	aAg	aGg	2	2	B.1.1.63	0.000772
S	77	K77T	aAg	aCg	2	2	B.1.1.7	0.000002
S	77	K77K	aaG	aaA	2	2	B.1.110.3	0.001437
S	77	K77K	aaG	aaA	2	2	B.1.177.8	0.001505
S	77	K77del	AAG	---	2	2	B.1.2	0.000018
S	77	K77N	aaG	aaC	2	2	B.1.258.11	0.000793
S	77	K77N	aaG	aaT	1	2	B.1.351	0.00003
S	77	K77N	aaG	aaC	1	2	B.1.351	0.00003
S	77	K77R	aAg	aGg	2	2	B.1.351.2	0.000605
S	77	K77K	aaG	aaA	2	2	B.1.36.17	0.000988
S	77	K77N	aaG	aaT	2	2	B.1.396	0.001411
S	77	K77N	aaG	aaT	2	2	B.1.416.1	0.003125
S	77	K77E	Aag	Gag	2	2	B.1.429	0.000047
S	77	K77N	aaG	aaT	2	2	B.1.429	0.000047
S	77	K77N	aaG	aaT	2	2	B.1.492	0.014085
S	77	K77del	AAG	---	2	2	B.1.525	0.000226
S	77	K77N	aaG	aaT	2	2	B.1.588	0.00182
S	77	K77T	aAg	aCg	2	2	B.1.596	0.000174
S	77	K77X	Aag	Tag	1	2	B.1.617.1	0.000129
S	77	K77X	AaG	TaA	1	2	B.1.617.1	0.000129
S	77	K77N	aaG	aaT	2	2	B.1.621	0.000177
S	77	K77R	aAg	aGg	2	2	B.1.621	0.000177
S	77	K77K	aaG	aaA	2	2	N.5	0.003534
S	77	K77M	aAg	aTg	2	2	P.1	0.000032
S	77	K77M	aAg	aTg	2	2	P.1.7	0.000639
S	77	K77N	aaG	aaC	2	2	Q.8	0.00033
S	77	K77del	AAG	---	2	2	R.1	0.00018
S	77	K77N	aaG	aaT	1	1	AD.2	0.000219
S	77	K77G	AAg	GGg	1	1	All	0
S	77	K77Y	AaG	TaC	1	1	All	0
S	77	K77P	AAg	CCg	1	1	All	0
S	77	K77N	aaG	aaC	1	1	AM.4	0.003571
S	77	K77K	aaG	aaA	1	1	AY.10	0.00053
S	77	K77del	AAG	---	1	1	AY.100	0.000046
S	77	K77M	aAg	aTg	1	1	AY.100	0.000046
S	77	K77K	aaG	aaA	1	1	AY.100	0.000046
S	77	K77R	aAg	aGg	1	1	AY.102	0.000027
S	77	K77E	Aag	Gag	1	1	AY.102	0.000027
S	77	K77Q	Aag	Cag	1	1	AY.103	0.000006
S	77	K77del	AAG	---	1	1	AY.105	0.000643
S	77	K77T	aAg	aCg	1	1	AY.106	0.000335
S	77	K77Q	Aag	Cag	1	1	AY.106	0.000335
S	77	K77Q	Aag	Cag	1	1	AY.110	0.000113
S	77	K77P	AAg	CCg	1	1	AY.110	0.000113
S	77	K77del	AAG	---	1	1	AY.111	0.000183
S	77	K77del1	AAG	-NN	1	1	AY.113	0.000142
S	77	K77Q	Aag	Cag	1	1	AY.118	0.000063
S	77	K77N	aaG	aaC	1	1	AY.119	0.000035
S	77	K77K	aaG	aaA	1	1	AY.119	0.000035
S	77	K77T	aAg	aCg	1	1	AY.12	0.000316
S	77	K77del	AAG	---	1	1	AY.12	0.000316
S	77	K77del	AAG	---	1	1	AY.120	0.000037
S	77	K77R	aAG	aGA	1	1	AY.120.1	0.000321
S	77	K77K	aaG	aaA	1	1	AY.13	0.000161
S	77	K77K	aaG	aaA	1	1	AY.23	0.00007
S	77	K77del	AAG	---	1	1	AY.23	0.00007
S	77	K77K	aaG	aaA	1	1	AY.23.1	0.000417
S	77	K77R	aAg	aGg	1	1	AY.25	0.000006
S	77	K77C	AAG	TGT	1	1	AY.25	0.000006
S	77	K77N	aaG	aaT	1	1	AY.26	0.000028
S	77	K77R	aAg	aGg	1	1	AY.26	0.000028
S	77	K77T	aAg	aCg	1	1	AY.26	0.000028
S	77	K77T	aAg	aCg	1	1	AY.28	0.00189
S	77	K77N	aaG	aaC	1	1	AY.29	0.000016
S	77	K77del1	AaG	Ca-	1	1	AY.3	0.00001
S	77	K77del	AAG	---	1	1	AY.3.1	0.000085
S	77	K77del	AAG	---	1	1	AY.30	0.000396
S	77	K77T	aAg	aCg	1	1	AY.32	0.000532
S	77	K77N	aaG	aaC	1	1	AY.34	0.000097
S	77	K77N	aaG	aaT	1	1	AY.36	0.000148
S	77	K77K	aaG	aaA	1	1	AY.37	0.000316
S	77	K77T	aAg	aCg	1	1	AY.38	0.000499
S	77	K77T	aAg	aCg	1	1	AY.39.1.1	0.000725
S	77	K77N	aaG	aaT	1	1	AY.4.2	0.000022
S	77	K77del	AAG	---	1	1	AY.4.4	0.000409
S	77	K77R	aAg	aGg	1	1	AY.4.5	0.000107
S	77	K77K	aaG	aaA	1	1	AY.4.5	0.000107
S	77	K77T	aAg	aCg	1	1	AY.41	0.000294
S	77	K77Q	Aag	Cag	1	1	AY.42	0.00004
S	77	K77N	aaG	aaT	1	1	AY.42	0.00004
S	77	K77Q	Aag	Cag	1	1	AY.43	0.000004
S	77	K77E	Aag	Gag	1	1	AY.43	0.000004
S	77	K77M	aAg	aTg	1	1	AY.43	0.000004
S	77	K77E	AaG	GaA	1	1	AY.44	0.000006
S	77	K77del	AAG	---	1	1	AY.45	0.000122
S	77	K77N	aaG	aaC	1	1	AY.46.2	0.000635
S	77	K77Q	Aag	Cag	1	1	AY.46.5	0.000198
S	77	K77K	aaG	aaA	1	1	AY.46.5	0.000198
S	77	K77del	AAG	---	1	1	AY.46.6	0.000072
S	77	K77X	Aag	Tag	1	1	AY.46.6	0.000072
S	77	K77N	aaG	aaT	1	1	AY.46.6	0.000072
S	77	K77N	aaG	aaT	1	1	AY.47	0.000031
S	77	K77del2	AAG	G--	1	1	AY.47	0.000031
S	77	K77T	aAg	aCg	1	1	AY.5	0.000021
S	77	K77K	aaG	aaA	1	1	AY.5.3	0.000337
S	77	K77del	AAG	---	1	1	AY.52	0.000814
S	77	K77M	aAg	aTg	1	1	AY.53	0.000288
S	77	K77N	aaG	aaT	1	1	AY.58	0.000907
S	77	K77M	aAg	aTg	1	1	AY.58	0.000907
S	77	K77I	aAG	aTT	1	1	AY.58	0.000907
S	77	K77R	aAg	aGg	1	1	AY.59	0.00053
S	77	K77del2	AAG	G--	1	1	AY.59	0.00053
S	77	K77K	aaG	aaA	1	1	AY.6	0.000041
S	77	K77del	AAG	---	1	1	AY.60	0.000938
S	77	K77N	aaG	aaC	1	1	AY.61	0.000105
S	77	K77N	aaG	aaT	1	1	AY.63	0.000387
S	77	K77del	AAG	---	1	1	AY.64	0.000595
S	77	K77del	AAG	---	1	1	AY.67	0.000464
S	77	K77M	aAg	aTg	1	1	AY.7.1	0.000113
S	77	K77N	aaG	aaT	1	1	AY.7.1	0.000113
S	77	K77I	aAG	aTT	1	1	AY.7.1	0.000113
S	77	K77del	AAG	---	1	1	AY.70	0.000209
S	77	K77R	aAg	aGg	1	1	AY.70	0.000209
S	77	K77T	aAg	aCg	1	1	AY.70	0.000209
S	77	K77N	aaG	aaT	1	1	AY.71	0.000475
S	77	K77del	AAG	---	1	1	AY.72	0.001361
S	77	K77K	aaG	aaA	1	1	AY.75	0.000056
S	77	K77del1	aaG	aa-	1	1	AY.75.1	0.00018
S	77	K77K	aaG	aaA	1	1	AY.79	0.001211
S	77	K77Q	Aag	Cag	1	1	AY.84	0.000437
S	77	K77T	aAg	aCg	1	1	AY.9	0.000068
S	77	K77N	aaG	aaT	1	1	AY.9	0.000068
S	77	K77K	aaG	aaA	1	1	AY.9	0.000068
S	77	K77K	aaG	aaA	1	1	AY.9.2	0.000037
S	77	K77N	aaG	aaT	1	1	AY.92	0.000287
S	77	K77T	aAg	aCg	1	1	AY.93	0.000273
S	77	K77del	AAG	---	1	1	AY.94	0.000443
S	77	K77N	aaG	aaT	1	1	AY.95	0.000761
S	77	K77N	aaG	aaT	1	1	AY.98	0.000079
S	77	K77R	aAg	aGg	1	1	AY.98.1	0.000048
S	77	K77del	AAG	---	1	1	AY.99	0.001049
S	77	K77del	AAG	---	1	1	AZ.2	0.000821
S	77	K77T	aAg	aCg	1	1	B.1	0.000009
S	77	K77R	aAg	aGg	1	1	B.1	0.000009
S	77	K77del2	aAG	a--	1	1	B.1	0.000009
S	77	K77G	AAg	GGg	1	1	B.1	0.000009
S	77	K77I	aAG	aTT	1	1	B.1	0.000009
S	77	K77E	Aag	Gag	1	1	B.1.1	0.000018
S	77	K77T	aAg	aCg	1	1	B.1.1	0.000018
S	77	K77X	Aag	Tag	1	1	B.1.1	0.000018
S	77	K77R	aAg	aGg	1	1	B.1.1	0.000018
S	77	K77K	aaG	aaA	1	1	B.1.1	0.000018
S	77	K77N	aaG	aaC	1	1	B.1.1.196	0.005714
S	77	K77R	aAg	aGg	1	1	B.1.1.216	0.00089
S	77	K77K	aaG	aaA	1	1	B.1.1.222	0.000204
S	77	K77N	aaG	aaT	1	1	B.1.1.263	0.001558
S	77	K77N	aaG	aaT	1	1	B.1.1.304	0.002809
S	77	K77del	AAG	---	1	1	B.1.1.306	0.000438
S	77	K77del	AAG	---	1	1	B.1.1.311	0.000358
S	77	K77N	aaG	aaT	1	1	B.1.1.312	0.001912
S	77	K77R	aAg	aGg	1	1	B.1.1.312	0.001912
S	77	K77del	AAG	---	1	1	B.1.1.315	0.008475
S	77	K77del	AAG	---	1	1	B.1.1.318	0.000302
S	77	K77K	aaG	aaA	1	1	B.1.1.326	0.001761
S	77	K77N	aaG	aaC	1	1	B.1.1.351	0.002793
S	77	K77R	aAg	aGg	1	1	B.1.1.368	0.003086
S	77	K77N	aaG	aaC	1	1	B.1.1.37	0.000193
S	77	K77K	aaG	aaA	1	1	B.1.1.37	0.000193
S	77	K77T	aAg	aCg	1	1	B.1.1.37	0.000193
S	77	K77N	aaG	aaT	1	1	B.1.1.374	0.002375
S	77	K77K	aaG	aaA	1	1	B.1.1.413	0.006897
S	77	K77R	aAg	aGg	1	1	B.1.1.414	0.142857
S	77	K77del	AAG	---	1	1	B.1.1.434	0.000349
S	77	K77N	aaG	aaC	1	1	B.1.1.462	0.008621
S	77	K77N	aaG	aaT	1	1	B.1.1.481	0.071429
S	77	K77del	AAG	---	1	1	B.1.1.523	0.001563
S	77	K77del2	aAG	a--	1	1	B.1.1.7	0.000001
S	77	K77del1	Aag	-ag	1	1	B.1.1.7	0.000001
S	77	K77K	aaG	aaA	1	1	B.1.1.70	0.000341
S	77	K77N	aaG	aaC	1	1	B.1.116	0.011628
S	77	K77del	AAG	---	1	1	B.1.160	0.000031
S	77	K77N	aaG	aaT	1	1	B.1.160.18	0.007299
S	77	K77N	aaG	aaT	1	1	B.1.177.12	0.000152
S	77	K77del	AAG	---	1	1	B.1.177.17	0.000821
S	77	K77del	AAG	---	1	1	B.1.177.18	0.00116
S	77	K77del	AAG	---	1	1	B.1.177.21	0.000076
S	77	K77E	Aag	Gag	1	1	B.1.177.21	0.000076
S	77	K77N	aaG	aaC	1	1	B.1.177.44	0.000519
S	77	K77del	AAG	---	1	1	B.1.177.51	0.004566
S	77	K77del	AAG	---	1	1	B.1.177.56	0.000668
S	77	K77K	aaG	aaA	1	1	B.1.177.58	0.001332
S	77	K77K	aaG	aaA	1	1	B.1.177.60	0.000218
S	77	K77N	aaG	aaT	1	1	B.1.177.65	0.000665
S	77	K77N	aaG	aaT	1	1	B.1.177.7	0.000165
S	77	K77N	aaG	aaT	1	1	B.1.177.75	0.001041
S	77	K77T	aAg	aCg	1	1	B.1.177.81	0.000189
S	77	K77N	aaG	aaT	1	1	B.1.177.81	0.000189
S	77	K77K	aaG	aaA	1	1	B.1.177.81	0.000189
S	77	K77del	AAG	---	1	1	B.1.179	0.003759
S	77	K77N	aaG	aaT	1	1	B.1.181	0.019608
S	77	K77R	aAg	aGg	1	1	B.1.2	0.000009
S	77	K77T	aAg	aCg	1	1	B.1.2	0.000009
S	77	K77E	Aag	Gag	1	1	B.1.2	0.000009
S	77	K77K	aaG	aaA	1	1	B.1.206	0.000816
S	77	K77N	aaG	aaT	1	1	B.1.206	0.000816
S	77	K77R	aAg	aGg	1	1	B.1.218	0.005155
S	77	K77K	aaG	aaA	1	1	B.1.225	0.015385
S	77	K77M	aAg	aTg	1	1	B.1.234	0.000132
S	77	K77R	aAg	aGg	1	1	B.1.240	0.000216
S	77	K77R	aAg	aGg	1	1	B.1.243	0.00007
S	77	K77N	aaG	aaT	1	1	B.1.243	0.00007
S	77	K77N	aaG	aaT	1	1	B.1.258.16	0.001637
S	77	K77N	aaG	aaT	1	1	B.1.258.17	0.000104
S	77	K77K	aaG	aaA	1	1	B.1.258.17	0.000104
S	77	K77E	Aag	Gag	1	1	B.1.258.17	0.000104
S	77	K77K	aaG	aaA	1	1	B.1.311	0.000275
S	77	K77K	aaG	aaA	1	1	B.1.36	0.000146
S	77	K77K	aaG	aaA	1	1	B.1.36.22	0.001208
S	77	K77N	aaG	aaT	1	1	B.1.36.29	0.000517
S	77	K77K	aaG	aaA	1	1	B.1.36.38	0.001642
S	77	K77T	aAg	aCg	1	1	B.1.366	0.004878
S	77	K77N	aaG	aaT	1	1	B.1.391	0.001127
S	77	K77M	aAg	aTg	1	1	B.1.427	0.00005
S	77	K77R	aAg	aGg	1	1	B.1.427	0.00005
S	77	K77R	aAg	aGg	1	1	B.1.429	0.000024
S	77	K77M	aAg	aTg	1	1	B.1.429	0.000024
S	77	K77N	aaG	aaC	1	1	B.1.438.1	0.000107
S	77	K77N	aaG	aaT	1	1	B.1.525	0.000113
S	77	K77C	AAG	TGC	1	1	B.1.525	0.000113
S	77	K77T	aAg	aCg	1	1	B.1.526	0.000024
S	77	K77E	Aag	Gag	1	1	B.1.596	0.000087
S	77	K77N	aaG	aaC	1	1	B.1.596	0.000087
S	77	K77K	aaG	aaA	1	1	B.1.596	0.000087
S	77	K77K	aaG	aaA	1	1	B.1.617.1	0.000129
S	77	K77N	aaG	aaC	1	1	B.1.617.1	0.000129
S	77	K77Y	AaG	TaC	1	1	B.1.617.1	0.000129
S	77	K77E	Aag	Gag	1	1	B.1.617.2	0.000004
S	77	K77E	Aag	Gag	1	1	B.1.619.1	0.000641
S	77	K77del	AAG	---	1	1	B.1.620	0.000946
S	77	K77del	AAG	---	1	1	B.1.621	0.000089
S	77	K77N	aaG	aaT	1	1	B.1.628	0.000352
S	77	K77E	Aag	Gag	1	1	B.1.637	0.000073
S	77	K77K	aaG	aaA	1	1	B.4.1	0.018868
S	77	K77del	AAG	---	1	1	B.61	0.005747
S	77	K77K	aaG	aaA	1	1	C.11	0.010638
S	77	K77del	AAG	---	1	1	C.35	0.000774
S	77	K77del	AAG	---	1	1	C.36.3	0.000567
S	77	K77N	aaG	aaT	1	1	D.2	0.000075
S	77	K77T	aAg	aCg	1	1	D.2	0.000075
S	77	K77E	Aag	Gag	1	1	P.1	0.000016
S	77	K77del	AAG	---	1	1	P.1.1	0.000318
S	77	K77N	aaG	aaC	1	1	P.1.12	0.000484
S	77	K77N	aaG	aaT	1	1	P.1.7	0.000319
S	77	K77N	aaG	aaT	1	1	P.7	0.004367
S	77	K77del	AAG	---	1	1	Q.1	0.000126
S	77	K77N	aaG	aaC	1	1	Q.3	0.000145
S	77	K77N	aaG	aaT	1	1	Q.4	0.000455
S	77	K77R	aAg	aGg	1	1	Q.8	0.000165
S	77	K77N	aaG	aaT	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.