CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp1 : CodonNum = 100

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/nsp1	100	S100N	S100N	nonsyn	aGt	aAt	4392	4392	1	563-565
ORF1ab/nsp1	100	S100C	S100C	nonsyn	Agt	Tgt	1317	1316	0.999241	563-565
ORF1ab/nsp1	100	S100C	S100C	nonsyn	AgT	TgC	1317	1	0.000759301	563-565
ORF1ab/nsp1	100	S100G	S100G	nonsyn	Agt	Ggt	603	602	0.998342	563-565
ORF1ab/nsp1	100	S100G	S100G	nonsyn	AgT	GgC	603	1	0.00165837	563-565
ORF1ab/nsp1	100	S100S	S100S	syn	agT	agC	477	477	1	563-565
ORF1ab/nsp1	100	S100R	S100R	nonsyn	agT	agG	75	30	0.4	563-565
ORF1ab/nsp1	100	S100R	S100R	nonsyn	Agt	Cgt	75	22	0.293333	563-565
ORF1ab/nsp1	100	S100R	S100R	nonsyn	agT	agA	75	18	0.24	563-565
ORF1ab/nsp1	100	S100R	S100R	nonsyn	AgT	CgG	75	5	0.0666667	563-565
ORF1ab/nsp1	100	S100del	S100del	del	AGT	---	68	68	1	563-565
ORF1ab/nsp1	100	S100I	S100I	nonsyn	aGt	aTt	57	57	1	563-565
ORF1ab/nsp1	100	S100W	S100W	nonsyn	AgT	TgG	19	19	1	563-565
ORF1ab/nsp1	100	S100T	S100T	nonsyn	aGt	aCt	7	7	1	563-565
ORF1ab/nsp1	100	S100del1	S100del1	del	Agt	-gt	4	2	0.5	563-565
ORF1ab/nsp1	100	S100del1	S100del1	del	aGt	a-t	4	1	0.25	563-565
ORF1ab/nsp1	100	S100del1	S100del1	del	agT	ag-	4	1	0.25	563-565
ORF1ab/nsp1	100	S100del2	S100del2	del	AGt	--t	2	2	1	563-565
ORF1ab/nsp1	100	S100Y	S100Y	nonsyn	AGt	TAt	2	1	0.5	563-565
ORF1ab/nsp1	100	S100Y	S100Y	nonsyn	AGT	TAC	2	1	0.5	563-565
ORF1ab/nsp1	100	S100X	S100X	nonsyn	AGT	TAG	1	1	1	563-565
ORF1ab/nsp1	100	S100K	S100K	nonsyn	aGT	aAG	1	1	1	563-565
ORF1ab/nsp1	100	S100H	S100H	nonsyn	AGt	CAt	1	1	1	563-565

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/nsp1	100	S100N	aGt	aAt	4392	4392	All	0.00084
ORF1ab/nsp1	100	S100N	aGt	aAt	3771	3771	AY.4	0.005869
ORF1ab/nsp1	100	S100C	Agt	Tgt	1316	1317	All	0.000252
ORF1ab/nsp1	100	S100C	AgT	TgC	1	1317	All	0
ORF1ab/nsp1	100	S100C	Agt	Tgt	884	884	AY.4.3	0.744108
ORF1ab/nsp1	100	S100G	Agt	Ggt	602	603	All	0.000115
ORF1ab/nsp1	100	S100G	AgT	GgC	1	603	All	0
ORF1ab/nsp1	100	S100S	agT	agC	477	477	All	0.000091
ORF1ab/nsp1	100	S100N	aGt	aAt	325	325	AY.3	0.003233
ORF1ab/nsp1	100	S100C	Agt	Tgt	247	247	AY.4	0.000384
ORF1ab/nsp1	100	S100G	Agt	Ggt	134	134	AY.120	0.004982
ORF1ab/nsp1	100	S100S	agT	agC	108	108	AY.25	0.00065
ORF1ab/nsp1	100	S100G	Agt	Ggt	105	105	AY.102	0.002784
ORF1ab/nsp1	100	S100G	Agt	Ggt	103	104	B.1.617.2	0.000388
ORF1ab/nsp1	100	S100G	AgT	GgC	1	104	B.1.617.2	0.000004
ORF1ab/nsp1	100	S100S	agT	agC	100	100	AY.46.6	0.007221
ORF1ab/nsp1	100	S100N	aGt	aAt	100	100	B.1.617.2	0.000377
ORF1ab/nsp1	100	S100R	agT	agG	30	75	All	0.000006
ORF1ab/nsp1	100	S100R	Agt	Cgt	22	75	All	0.000004
ORF1ab/nsp1	100	S100R	agT	agA	18	75	All	0.000003
ORF1ab/nsp1	100	S100R	AgT	CgG	5	75	All	0.000001
ORF1ab/nsp1	100	S100del	AGT	---	68	68	All	0.000013
ORF1ab/nsp1	100	S100I	aGt	aTt	57	57	All	0.000011
ORF1ab/nsp1	100	S100G	Agt	Ggt	43	43	AY.26	0.001217
ORF1ab/nsp1	100	S100S	agT	agC	40	40	AY.39	0.000988
ORF1ab/nsp1	100	S100S	agT	agC	39	39	B.1.1.519	0.001549
ORF1ab/nsp1	100	S100N	aGt	aAt	37	37	B.1.1.7	0.000033
ORF1ab/nsp1	100	S100S	agT	agC	35	35	B.1.1.7	0.000031
ORF1ab/nsp1	100	S100G	Agt	Ggt	31	31	AY.39	0.000766
ORF1ab/nsp1	100	S100R	agT	agG	13	24	AY.4	0.00002
ORF1ab/nsp1	100	S100R	Agt	Cgt	5	24	AY.4	0.000008
ORF1ab/nsp1	100	S100R	agT	agA	3	24	AY.4	0.000005
ORF1ab/nsp1	100	S100R	AgT	CgG	3	24	AY.4	0.000005
ORF1ab/nsp1	100	S100G	Agt	Ggt	24	24	B.1.234	0.003167
ORF1ab/nsp1	100	S100S	agT	agC	22	22	B.1.429	0.000518
ORF1ab/nsp1	100	S100S	agT	agC	21	21	AY.4	0.000033
ORF1ab/nsp1	100	S100G	Agt	Ggt	20	20	AY.20	0.000777
ORF1ab/nsp1	100	S100S	agT	agC	20	20	B.1.177	0.000263
ORF1ab/nsp1	100	S100W	AgT	TgG	19	19	All	0.000004
ORF1ab/nsp1	100	S100N	aGt	aAt	17	17	AY.43	0.000075
ORF1ab/nsp1	100	S100N	aGt	aAt	17	17	B.1.351.5	0.010192
ORF1ab/nsp1	100	S100R	agT	agG	10	16	AY.4.5	0.001075
ORF1ab/nsp1	100	S100R	Agt	Cgt	4	16	AY.4.5	0.00043
ORF1ab/nsp1	100	S100R	AgT	CgG	2	16	AY.4.5	0.000215
ORF1ab/nsp1	100	S100G	Agt	Ggt	15	15	AY.44	0.000091
ORF1ab/nsp1	100	S100G	Agt	Ggt	14	14	AY.43	0.000062
ORF1ab/nsp1	100	S100C	Agt	Tgt	14	14	AY.44	0.000085
ORF1ab/nsp1	100	S100C	Agt	Tgt	14	14	B.1	0.000128
ORF1ab/nsp1	100	S100G	Agt	Ggt	13	13	AY.116	0.003728
ORF1ab/nsp1	100	S100C	Agt	Tgt	13	13	AY.4.5	0.001397
ORF1ab/nsp1	100	S100C	Agt	Tgt	13	13	B.1.617.2	0.000049
ORF1ab/nsp1	100	S100C	Agt	Tgt	12	12	B.1.1.7	0.000011
ORF1ab/nsp1	100	S100N	aGt	aAt	11	11	B.1.177	0.000145
ORF1ab/nsp1	100	S100S	agT	agC	11	11	B.1.617.2	0.000041
ORF1ab/nsp1	100	S100C	Agt	Tgt	10	10	AY.42	0.000402
ORF1ab/nsp1	100	S100N	aGt	aAt	10	10	AY.44	0.000061
ORF1ab/nsp1	100	S100S	agT	agC	10	10	AY.96	0.020747
ORF1ab/nsp1	100	S100S	agT	agC	9	9	AY.110	0.001014
ORF1ab/nsp1	100	S100G	Agt	Ggt	9	9	AY.25	0.000054
ORF1ab/nsp1	100	S100C	Agt	Tgt	9	9	AY.37	0.002845
ORF1ab/nsp1	100	S100G	Agt	Ggt	9	9	AY.4	0.000014
ORF1ab/nsp1	100	S100I	aGt	aTt	9	9	AY.4	0.000014
ORF1ab/nsp1	100	S100S	agT	agC	9	9	AY.43	0.00004
ORF1ab/nsp1	100	S100G	Agt	Ggt	9	9	B.1.1.7	0.000008
ORF1ab/nsp1	100	S100W	AgT	TgG	8	8	AY.4	0.000012
ORF1ab/nsp1	100	S100N	aGt	aAt	8	8	AY.42	0.000322
ORF1ab/nsp1	100	S100del	AGT	---	8	8	B.1.1.7	0.000007
ORF1ab/nsp1	100	S100T	aGt	aCt	7	7	All	0.000001
ORF1ab/nsp1	100	S100C	Agt	Tgt	7	7	AY.45	0.000852
ORF1ab/nsp1	100	S100C	Agt	Tgt	7	7	B.1.2	0.000062
ORF1ab/nsp1	100	S100N	aGt	aAt	6	6	AY.4.5	0.000645
ORF1ab/nsp1	100	S100G	Agt	Ggt	6	6	AY.5	0.000124
ORF1ab/nsp1	100	S100I	aGt	aTt	6	6	B.1	0.000055
ORF1ab/nsp1	100	S100N	aGt	aAt	6	6	B.1.2	0.000053
ORF1ab/nsp1	100	S100S	agT	agC	6	6	B.1.2	0.000053
ORF1ab/nsp1	100	S100I	aGt	aTt	6	6	B.1.617.2	0.000023
ORF1ab/nsp1	100	S100N	aGt	aAt	5	5	AY.117	0.000423
ORF1ab/nsp1	100	S100N	aGt	aAt	5	5	AY.25	0.00003
ORF1ab/nsp1	100	S100W	AgT	TgG	5	5	AY.4.5	0.000537
ORF1ab/nsp1	100	S100C	Agt	Tgt	5	5	AY.43	0.000022
ORF1ab/nsp1	100	S100I	aGt	aTt	5	5	AY.6	0.000206
ORF1ab/nsp1	100	S100G	Agt	Ggt	5	5	B.1	0.000046
ORF1ab/nsp1	100	S100C	Agt	Tgt	5	5	B.1.177.87	0.003639
ORF1ab/nsp1	100	S100N	aGt	aAt	5	5	B.1.36.8	0.005
ORF1ab/nsp1	100	S100C	Agt	Tgt	5	5	C.37	0.00058
ORF1ab/nsp1	100	S100del1	Agt	-gt	2	4	All	0
ORF1ab/nsp1	100	S100del1	agT	ag-	1	4	All	0
ORF1ab/nsp1	100	S100del1	aGt	a-t	1	4	All	0
ORF1ab/nsp1	100	S100S	agT	agC	4	4	AY.102	0.000106
ORF1ab/nsp1	100	S100G	Agt	Ggt	4	4	AY.3	0.00004
ORF1ab/nsp1	100	S100N	aGt	aAt	4	4	AY.32	0.00213
ORF1ab/nsp1	100	S100C	Agt	Tgt	4	4	AY.39	0.000099
ORF1ab/nsp1	100	S100del	AGT	---	4	4	AY.4.5	0.00043
ORF1ab/nsp1	100	S100del	AGT	---	4	4	AY.43	0.000018
ORF1ab/nsp1	100	S100G	Agt	Ggt	4	4	AY.58	0.00363
ORF1ab/nsp1	100	S100N	aGt	aAt	4	4	B.1	0.000037
ORF1ab/nsp1	100	S100del	AGT	---	4	4	B.1.1.33	0.001684
ORF1ab/nsp1	100	S100del	AGT	---	4	4	B.1.1.348	0.003185
ORF1ab/nsp1	100	S100G	Agt	Ggt	4	4	B.1.177.17	0.003284
ORF1ab/nsp1	100	S100G	Agt	Ggt	4	4	B.1.429	0.000094
ORF1ab/nsp1	100	S100N	aGt	aAt	3	3	AY.100	0.000138
ORF1ab/nsp1	100	S100C	Agt	Tgt	3	3	AY.100	0.000138
ORF1ab/nsp1	100	S100G	Agt	Ggt	3	3	AY.103	0.000019
ORF1ab/nsp1	100	S100S	agT	agC	3	3	AY.20	0.000117
ORF1ab/nsp1	100	S100I	aGt	aTt	3	3	AY.26	0.000085
ORF1ab/nsp1	100	S100C	Agt	Tgt	3	3	AY.3	0.00003
ORF1ab/nsp1	100	S100N	aGt	aAt	3	3	AY.35	0.000699
ORF1ab/nsp1	100	S100R	agT	agA	3	3	AY.39	0.000074
ORF1ab/nsp1	100	S100del	AGT	---	3	3	AY.4	0.000005
ORF1ab/nsp1	100	S100C	Agt	Tgt	3	3	AY.46.6	0.000217
ORF1ab/nsp1	100	S100N	aGt	aAt	3	3	AY.6	0.000123
ORF1ab/nsp1	100	S100C	Agt	Tgt	3	3	AY.8	0.001818
ORF1ab/nsp1	100	S100C	Agt	Tgt	3	3	AY.9	0.000203
ORF1ab/nsp1	100	S100R	Agt	Cgt	2	3	AY.9	0.000135
ORF1ab/nsp1	100	S100R	agT	agG	1	3	AY.9	0.000068
ORF1ab/nsp1	100	S100R	agT	agA	3	3	B.1.1.7	0.000003
ORF1ab/nsp1	100	S100del	AGT	---	3	3	B.1.177.4	0.000633
ORF1ab/nsp1	100	S100S	agT	agC	3	3	B.1.177.9	0.003995
ORF1ab/nsp1	100	S100del	AGT	---	3	3	B.1.2	0.000026
ORF1ab/nsp1	100	S100C	Agt	Tgt	3	3	B.1.351	0.000089
ORF1ab/nsp1	100	S100N	aGt	aAt	3	3	B.1.36	0.000438
ORF1ab/nsp1	100	S100G	Agt	Ggt	3	3	B.1.36.17	0.001482
ORF1ab/nsp1	100	S100N	aGt	aAt	3	3	B.1.429	0.000071
ORF1ab/nsp1	100	S100S	agT	agC	3	3	B.1.526	0.000071
ORF1ab/nsp1	100	S100C	Agt	Tgt	3	3	P.1	0.000047
ORF1ab/nsp1	100	S100del2	AGt	--t	2	2	All	0
ORF1ab/nsp1	100	S100Y	AGT	TAC	1	2	All	0
ORF1ab/nsp1	100	S100Y	AGt	TAt	1	2	All	0
ORF1ab/nsp1	100	S100G	Agt	Ggt	2	2	AY.100	0.000092
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	AY.102	0.000053
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.102	0.000053
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.103	0.000012
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	AY.103	0.000012
ORF1ab/nsp1	100	S100I	aGt	aTt	2	2	AY.103	0.000012
ORF1ab/nsp1	100	S100G	Agt	Ggt	2	2	AY.110	0.000225
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.12	0.000632
ORF1ab/nsp1	100	S100I	aGt	aTt	2	2	AY.12	0.000632
ORF1ab/nsp1	100	S100W	AgT	TgG	2	2	AY.120	0.000074
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	AY.120	0.000074
ORF1ab/nsp1	100	S100R	agT	agG	2	2	AY.120	0.000074
ORF1ab/nsp1	100	S100G	Agt	Ggt	2	2	AY.23	0.000139
ORF1ab/nsp1	100	S100del	AGT	---	2	2	AY.25	0.000012
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	AY.26	0.000057
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	AY.29	0.000032
ORF1ab/nsp1	100	S100G	Agt	Ggt	2	2	AY.33	0.000134
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.36	0.000296
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.39	0.000049
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	AY.39.1	0.000079
ORF1ab/nsp1	100	S100G	Agt	Ggt	2	2	AY.4.2	0.000043
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.4.2	0.000043
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	AY.4.2	0.000043
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.4.4	0.000818
ORF1ab/nsp1	100	S100S	agT	agC	2	2	AY.44	0.000012
ORF1ab/nsp1	100	S100S	agT	agC	2	2	AY.46	0.000208
ORF1ab/nsp1	100	S100S	agT	agC	2	2	AY.5	0.000041
ORF1ab/nsp1	100	S100S	agT	agC	2	2	AY.75	0.000112
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	2	AY.8	0.000606
ORF1ab/nsp1	100	S100R	agT	agG	1	2	AY.8	0.000606
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	AY.84	0.000875
ORF1ab/nsp1	100	S100S	agT	agC	2	2	B	0.000256
ORF1ab/nsp1	100	S100S	agT	agC	2	2	B.1.1	0.000036
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	B.1.1	0.000036
ORF1ab/nsp1	100	S100T	aGt	aCt	2	2	B.1.1.7	0.000002
ORF1ab/nsp1	100	S100I	aGt	aTt	2	2	B.1.1.7	0.000002
ORF1ab/nsp1	100	S100S	agT	agC	2	2	B.1.189	0.008584
ORF1ab/nsp1	100	S100G	Agt	Ggt	2	2	B.1.2	0.000018
ORF1ab/nsp1	100	S100I	aGt	aTt	2	2	B.1.2	0.000018
ORF1ab/nsp1	100	S100R	agT	agA	1	2	B.1.2	0.000009
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	2	B.1.2	0.000009
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	B.1.240	0.000431
ORF1ab/nsp1	100	S100G	Agt	Ggt	2	2	B.1.243	0.000139
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	B.1.260	0.006689
ORF1ab/nsp1	100	S100N	aGt	aAt	2	2	B.1.36.24	0.012346
ORF1ab/nsp1	100	S100C	Agt	Tgt	2	2	B.1.429	0.000047
ORF1ab/nsp1	100	S100del	AGT	---	2	2	B.1.617.2	0.000008
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	2	B.1.617.2	0.000004
ORF1ab/nsp1	100	S100R	agT	agA	1	2	B.1.617.2	0.000004
ORF1ab/nsp1	100	S100T	aGt	aCt	2	2	B.1.637	0.000146
ORF1ab/nsp1	100	S100del	AGT	---	2	2	N.4	0.008511
ORF1ab/nsp1	100	S100del	AGT	---	2	2	N.6	0.014184
ORF1ab/nsp1	100	S100del	AGT	---	2	2	P.2	0.000373
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1		0.055556
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1		0.055556
ORF1ab/nsp1	100	S100K	aGT	aAG	1	1		0.055556
ORF1ab/nsp1	100	S100R	agT	agG	1	1		0.055556
ORF1ab/nsp1	100	S100X	AGT	TAG	1	1		0.055556
ORF1ab/nsp1	100	S100Y	AGt	TAt	1	1		0.055556
ORF1ab/nsp1	100	S100W	AgT	TgG	1	1		0.055556
ORF1ab/nsp1	100	S100del	AGT	---	1	1	A	0.000387
ORF1ab/nsp1	100	S100S	agT	agC	1	1	A.2.5.2	0.001572
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AD.2	0.000219
ORF1ab/nsp1	100	S100X	AGT	TAG	1	1	All	0
ORF1ab/nsp1	100	S100K	aGT	aAG	1	1	All	0
ORF1ab/nsp1	100	S100H	AGt	CAt	1	1	All	0
ORF1ab/nsp1	100	S100R	agT	agA	1	1	AY.102	0.000027
ORF1ab/nsp1	100	S100R	agT	agA	1	1	AY.103	0.000006
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.116	0.000287
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.117	0.000085
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.117	0.000085
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.117	0.000085
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.118	0.000063
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.118	0.000063
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	AY.119	0.000035
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.119	0.000035
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.119	0.000035
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.12	0.000316
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.120.1	0.000321
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.120.2	0.001285
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.121	0.000135
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.13	0.000161
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.14	0.000088
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.14	0.000088
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.16	0.00038
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.16.1	0.00047
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.19	0.00114
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.19	0.00114
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.20	0.000039
ORF1ab/nsp1	100	S100C	AgT	TgC	1	1	AY.23	0.00007
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.23	0.00007
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.25	0.000006
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.25	0.000006
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.26	0.000028
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.27	0.000065
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.29	0.000016
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.3	0.00001
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.3.1	0.000085
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.34	0.000097
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.34	0.000097
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.38	0.000499
ORF1ab/nsp1	100	S100T	aGt	aCt	1	1	AY.39	0.000025
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.39.1	0.00004
ORF1ab/nsp1	100	S100T	aGt	aCt	1	1	AY.4	0.000002
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.4.2.1	0.000149
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.41	0.000294
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.42	0.00004
ORF1ab/nsp1	100	S100Y	AGT	TAC	1	1	AY.43	0.000004
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.43	0.000004
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.44	0.000006
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.44	0.000006
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.46	0.000104
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.46	0.000104
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.47	0.000031
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.5	0.000021
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.5	0.000021
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.5	0.000021
ORF1ab/nsp1	100	S100R	agT	agA	1	1	AY.51	0.000909
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.52	0.000814
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.53	0.000288
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.54	0.000095
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	AY.58	0.000907
ORF1ab/nsp1	100	S100R	agT	agG	1	1	AY.6	0.000041
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.60	0.000938
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.61	0.000105
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.62	0.000436
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.65	0.000533
ORF1ab/nsp1	100	S100S	agT	agC	1	1	AY.69	0.000187
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.7.2	0.000559
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.74	0.000116
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.75.1	0.00018
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.75.1	0.00018
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.77	0.001127
ORF1ab/nsp1	100	S100W	AgT	TgG	1	1	AY.8	0.000606
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.82	0.001357
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.85	0.000427
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.87	0.000833
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.9	0.000068
ORF1ab/nsp1	100	S100W	AgT	TgG	1	1	AY.9	0.000068
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.9.1	0.000084
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.9.1	0.000084
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.9.2	0.000037
ORF1ab/nsp1	100	S100R	agT	agA	1	1	AY.91	0.00073
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.92	0.000287
ORF1ab/nsp1	100	S100del	AGT	---	1	1	AY.95	0.000761
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.95	0.000761
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.98	0.000079
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	AY.98.1	0.000048
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	AY.98.1	0.000048
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.99.1	0.001553
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	AY.99.2	0.000092
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	AY.99.2	0.000092
ORF1ab/nsp1	100	S100del1	aGt	a-t	1	1	B.1	0.000009
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1	0.000009
ORF1ab/nsp1	100	S100R	agT	agA	1	1	B.1	0.000009
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1	0.000009
ORF1ab/nsp1	100	S100R	agT	agA	1	1	B.1.1	0.000018
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.1	0.000018
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.1	0.000018
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.1.1	0.000327
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.1.207	0.001182
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.1.214	0.000055
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.1.222	0.000204
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.1.273	0.006757
ORF1ab/nsp1	100	S100del1	agT	ag-	1	1	B.1.1.306	0.000438
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.1.318	0.000302
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	B.1.1.348	0.000796
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	B.1.1.519	0.00004
ORF1ab/nsp1	100	S100del1	Agt	-gt	1	1	B.1.1.7	0.000001
ORF1ab/nsp1	100	S100del2	AGt	--t	1	1	B.1.1.7	0.000001
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.118	0.006711
ORF1ab/nsp1	100	S100R	agT	agA	1	1	B.1.160	0.000031
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.177	0.000013
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.177	0.000013
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.177.15	0.000631
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.177.17	0.000821
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.177.4	0.000211
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	B.1.177.4	0.000211
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.177.4	0.000211
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.177.43	0.001477
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	B.1.177.44	0.000519
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp1	100	S100T	aGt	aCt	1	1	B.1.177.56	0.000668
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.177.77	0.000726
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.179	0.003759
ORF1ab/nsp1	100	S100del2	AGt	--t	1	1	B.1.2	0.000009
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.211	0.025
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.221	0.000071
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.221	0.000071
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.243	0.00007
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	B.1.258	0.000067
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	B.1.258.17	0.000104
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.258.17	0.000104
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.258.17	0.000104
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	B.1.265	0.001271
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.349	0.000715
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.351	0.00003
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.351	0.00003
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	B.1.351	0.00003
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.36	0.000146
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.36.18	0.00042
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.36.29	0.000517
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.36.36	0.000602
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.367	0.000792
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.367	0.000792
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.399	0.001934
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.427	0.00005
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.429	0.000024
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.433	0.003195
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.436	0.001029
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	B.1.466.2	0.000391
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.526	0.000024
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	B.1.538	0.008065
ORF1ab/nsp1	100	S100S	agT	agC	1	1	B.1.551	0.00129
ORF1ab/nsp1	100	S100H	AGt	CAt	1	1	B.1.560	0.00463
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.564	0.000426
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	B.1.577	0.000687
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.1.595	0.000261
ORF1ab/nsp1	100	S100W	AgT	TgG	1	1	B.1.599	0.00365
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	B.1.599	0.00365
ORF1ab/nsp1	100	S100R	agT	agG	1	1	B.1.599	0.00365
ORF1ab/nsp1	100	S100del1	Agt	-gt	1	1	B.1.606	0.006024
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	B.1.617.1	0.000129
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	B.1.84	0.020833
ORF1ab/nsp1	100	S100del	AGT	---	1	1	B.30	0.014706
ORF1ab/nsp1	100	S100del	AGT	---	1	1	C.17	0.055556
ORF1ab/nsp1	100	S100del	AGT	---	1	1	C.35	0.000774
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	C.35	0.000774
ORF1ab/nsp1	100	S100R	Agt	Cgt	1	1	D.2	0.000075
ORF1ab/nsp1	100	S100C	Agt	Tgt	1	1	G.1	0.041667
ORF1ab/nsp1	100	S100I	aGt	aTt	1	1	N.5	0.001767
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	P.1	0.000016
ORF1ab/nsp1	100	S100N	aGt	aAt	1	1	P.1	0.000016
ORF1ab/nsp1	100	S100G	Agt	Ggt	1	1	P.1.10	0.000269
ORF1ab/nsp1	100	S100N	aGt	aAt	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.