CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 40

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
N	40	R40C		nonsyn	Cgt	Tgt	1936	1936	1	28391-28393
N	40	R40L		nonsyn	cGt	cTt	1161	1161	1	28391-28393
N	40	R40H		nonsyn	cGt	cAt	934	934	1	28391-28393
N	40	R40R		syn	cgT	cgC	514	452	0.879377	28391-28393
N	40	R40R		syn	cgT	cgG	514	55	0.107004	28391-28393
N	40	R40R		syn	cgT	cgA	514	7	0.0136187	28391-28393
N	40	R40S		nonsyn	Cgt	Agt	80	80	1	28391-28393
N	40	R40del		del	CGT	---	32	32	1	28391-28393
N	40	R40P		nonsyn	cGt	cCt	27	24	0.888889	28391-28393
N	40	R40P		nonsyn	cGT	cCG	27	2	0.0740741	28391-28393
N	40	R40P		nonsyn	cGT	cCA	27	1	0.037037	28391-28393
N	40	R40G		nonsyn	Cgt	Ggt	6	6	1	28391-28393
N	40	R40Q		nonsyn	cGT	cAA	3	2	0.666667	28391-28393
N	40	R40Q		nonsyn	cGT	cAG	3	1	0.333333	28391-28393
N	40	R40N		nonsyn	CGt	AAt	1	1	1	28391-28393
N	40	R40del2		del	cGT	c--	1	1	1	28391-28393
N	40	R40del1		del	cGt	c-t	1	1	1	28391-28393
N	40	R40E		nonsyn	CGT	GAG	1	1	1	28391-28393

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
N	40	R40C	Cgt	Tgt	1936	1936	All	0.00037
N	40	R40L	cGt	cTt	1161	1161	All	0.000222
N	40	R40H	cGt	cAt	934	934	All	0.000179
N	40	R40C	Cgt	Tgt	531	531	B.1.1.7	0.000475
N	40	R40R	cgT	cgC	452	514	All	0.000086
N	40	R40R	cgT	cgG	55	514	All	0.000011
N	40	R40R	cgT	cgA	7	514	All	0.000001
N	40	R40L	cGt	cTt	381	381	AY.4	0.000593
N	40	R40C	Cgt	Tgt	201	201	S.1	0.99505
N	40	R40H	cGt	cAt	187	187	B.1.617.2	0.000704
N	40	R40L	cGt	cTt	184	184	AY.75	0.010308
N	40	R40C	Cgt	Tgt	176	176	B.1.1.217	0.64
N	40	R40L	cGt	cTt	156	156	B.1.1.284	0.016754
N	40	R40C	Cgt	Tgt	136	136	AY.3	0.001353
N	40	R40H	cGt	cAt	132	132	B.1.221	0.009376
N	40	R40C	Cgt	Tgt	118	118	AY.4	0.000184
N	40	R40H	cGt	cAt	116	116	AY.44	0.000706
N	40	R40R	cgT	cgC	104	108	B.1.1.7	0.000093
N	40	R40R	cgT	cgA	2	108	B.1.1.7	0.000002
N	40	R40R	cgT	cgG	2	108	B.1.1.7	0.000002
N	40	R40L	cGt	cTt	94	94	B.1.617.2	0.000354
N	40	R40S	Cgt	Agt	80	80	All	0.000015
N	40	R40L	cGt	cTt	59	59	B.1.1.7	0.000053
N	40	R40C	Cgt	Tgt	52	52	B.1.617.2	0.000196
N	40	R40H	cGt	cAt	51	51	AY.71	0.024228
N	40	R40H	cGt	cAt	50	50	AY.4	0.000078
N	40	R40L	cGt	cTt	47	47	AY.103	0.000292
N	40	R40H	cGt	cAt	45	45	AY.33	0.003005
N	40	R40R	cgT	cgC	31	43	B.1.351	0.000922
N	40	R40R	cgT	cgG	12	43	B.1.351	0.000357
N	40	R40R	cgT	cgC	41	41	AY.72	0.055782
N	40	R40C	Cgt	Tgt	36	36	B.1	0.00033
N	40	R40del	CGT	---	32	32	All	0.000006
N	40	R40R	cgT	cgC	31	31	B.1.525	0.003508
N	40	R40L	cGt	cTt	30	30	AY.43	0.000133
N	40	R40R	cgT	cgC	21	30	B.1.2	0.000185
N	40	R40R	cgT	cgG	7	30	B.1.2	0.000062
N	40	R40R	cgT	cgA	2	30	B.1.2	0.000018
N	40	R40C	Cgt	Tgt	30	30	C.36.3	0.017016
N	40	R40C	Cgt	Tgt	28	28	R.1	0.00252
N	40	R40P	cGt	cCt	24	27	All	0.000005
N	40	R40P	cGT	cCG	2	27	All	0
N	40	R40P	cGT	cCA	1	27	All	0
N	40	R40H	cGt	cAt	25	25	AY.3	0.000249
N	40	R40L	cGt	cTt	25	25	B.1	0.000229
N	40	R40H	cGt	cAt	24	24	AY.25	0.000144
N	40	R40H	cGt	cAt	24	24	B.1.1.7	0.000021
N	40	R40R	cgT	cgC	22	24	B.1.617.2	0.000083
N	40	R40R	cgT	cgG	2	24	B.1.617.2	0.000008
N	40	R40C	Cgt	Tgt	23	23	AY.103	0.000143
N	40	R40C	Cgt	Tgt	23	23	AY.44	0.00014
N	40	R40C	Cgt	Tgt	23	23	B.1.526	0.000541
N	40	R40C	Cgt	Tgt	22	22	AY.43	0.000097
N	40	R40C	Cgt	Tgt	22	22	B.1.1	0.000399
N	40	R40S	Cgt	Agt	22	22	B.1.595	0.005741
N	40	R40C	Cgt	Tgt	22	22	C.37	0.002553
N	40	R40R	cgT	cgC	21	21	AY.121	0.002842
N	40	R40H	cGt	cAt	21	21	P.1	0.000331
N	40	R40C	Cgt	Tgt	19	19	AY.26	0.000538
N	40	R40R	cgT	cgC	17	18	P.1	0.000268
N	40	R40R	cgT	cgG	1	18	P.1	0.000016
N	40	R40H	cGt	cAt	17	17	AY.23	0.001186
N	40	R40L	cGt	cTt	17	17	P.1	0.000268
N	40	R40C	Cgt	Tgt	16	16	AY.25	0.000096
N	40	R40C	Cgt	Tgt	16	16	AY.46.6	0.001155
N	40	R40H	cGt	cAt	15	15	AY.43	0.000066
N	40	R40H	cGt	cAt	14	14	AY.103	0.000087
N	40	R40R	cgT	cgC	12	14	AY.4	0.000019
N	40	R40R	cgT	cgG	2	14	AY.4	0.000003
N	40	R40R	cgT	cgC	13	13	B.1.147	0.009826
N	40	R40C	Cgt	Tgt	13	13	B.1.160	0.000405
N	40	R40R	cgT	cgC	12	13	B.1.177	0.000158
N	40	R40R	cgT	cgG	1	13	B.1.177	0.000013
N	40	R40C	Cgt	Tgt	13	13	B.1.2	0.000114
N	40	R40C	Cgt	Tgt	13	13	P.1	0.000205
N	40	R40R	cgT	cgC	12	12	AY.20	0.000466
N	40	R40C	Cgt	Tgt	12	12	AY.34	0.001164
N	40	R40R	cgT	cgC	7	12	AY.43	0.000031
N	40	R40R	cgT	cgG	5	12	AY.43	0.000022
N	40	R40R	cgT	cgC	12	12	B.1.1.28	0.003735
N	40	R40C	Cgt	Tgt	11	11	AY.119	0.000388
N	40	R40H	cGt	cAt	11	11	AY.32	0.005857
N	40	R40L	cGt	cTt	11	11	AY.44	0.000067
N	40	R40C	Cgt	Tgt	11	11	AY.64	0.006548
N	40	R40H	cGt	cAt	11	11	B.1.1	0.0002
N	40	R40C	Cgt	Tgt	11	11	B.1.1.311	0.00394
N	40	R40S	Cgt	Agt	11	11	B.1.1.7	0.00001
N	40	R40S	Cgt	Agt	10	10	AY.25	0.00006
N	40	R40H	cGt	cAt	10	10	AY.9.1	0.000837
N	40	R40R	cgT	cgC	9	10	B.1.1	0.000163
N	40	R40R	cgT	cgG	1	10	B.1.1	0.000018
N	40	R40H	cGt	cAt	10	10	B.1.2	0.000088
N	40	R40H	cGt	cAt	10	10	B.1.214.3	0.071429
N	40	R40R	cgT	cgC	10	10	B.1.524	0.014065
N	40	R40C	Cgt	Tgt	10	10	P.1.14	0.000478
N	40	R40C	Cgt	Tgt	9	9	AY.1	0.003562
N	40	R40C	Cgt	Tgt	9	9	AY.113	0.001282
N	40	R40H	cGt	cAt	9	9	AY.14	0.000792
N	40	R40L	cGt	cTt	9	9	AY.26	0.000255
N	40	R40H	cGt	cAt	9	9	AY.39	0.000222
N	40	R40C	Cgt	Tgt	9	9	AY.61	0.000943
N	40	R40L	cGt	cTt	9	9	B.1.243	0.000626
N	40	R40R	cgT	cgC	8	8	AY.3	0.00008
N	40	R40S	Cgt	Agt	8	8	AY.43	0.000035
N	40	R40C	Cgt	Tgt	8	8	B.1.1.50	0.005431
N	40	R40C	Cgt	Tgt	8	8	B.1.177.46	0.007346
N	40	R40H	cGt	cAt	8	8	B.1.258	0.000532
N	40	R40C	Cgt	Tgt	8	8	B.1.427	0.000404
N	40	R40C	Cgt	Tgt	7	7	AY.47	0.000218
N	40	R40C	Cgt	Tgt	7	7	AY.5	0.000145
N	40	R40C	Cgt	Tgt	7	7	B	0.000895
N	40	R40L	cGt	cTt	7	7	B.1.1	0.000127
N	40	R40C	Cgt	Tgt	7	7	B.1.1.519	0.000278
N	40	R40C	Cgt	Tgt	7	7	B.1.177	0.000092
N	40	R40G	Cgt	Ggt	6	6	All	0.000001
N	40	R40H	cGt	cAt	6	6	AY.119	0.000212
N	40	R40L	cGt	cTt	6	6	AY.25	0.000036
N	40	R40H	cGt	cAt	6	6	AY.26	0.00017
N	40	R40L	cGt	cTt	6	6	AY.3	0.00006
N	40	R40C	Cgt	Tgt	6	6	AY.46	0.000624
N	40	R40R	cgT	cgC	6	6	AY.5	0.000124
N	40	R40L	cGt	cTt	6	6	AY.9.2	0.00022
N	40	R40H	cGt	cAt	6	6	B.1	0.000055
N	40	R40C	Cgt	Tgt	6	6	B.1.1.10	0.006689
N	40	R40H	cGt	cAt	6	6	B.1.1.297	0.013423
N	40	R40L	cGt	cTt	6	6	B.1.1.519	0.000238
N	40	R40L	cGt	cTt	5	5	AY.1	0.001979
N	40	R40L	cGt	cTt	5	5	AY.102	0.000133
N	40	R40L	cGt	cTt	5	5	AY.120	0.000186
N	40	R40C	Cgt	Tgt	5	5	AY.3.1	0.000426
N	40	R40C	Cgt	Tgt	5	5	AY.7.1	0.000564
N	40	R40C	Cgt	Tgt	5	5	AY.74	0.000578
N	40	R40C	Cgt	Tgt	5	5	B.1.1.329	0.019231
N	40	R40C	Cgt	Tgt	5	5	B.1.1.70	0.001705
N	40	R40C	Cgt	Tgt	5	5	B.1.147	0.003779
N	40	R40C	Cgt	Tgt	5	5	B.1.177.7	0.000824
N	40	R40C	Cgt	Tgt	5	5	B.1.234	0.00066
N	40	R40C	Cgt	Tgt	5	5	B.1.258	0.000333
N	40	R40L	cGt	cTt	5	5	B.1.466.2	0.001956
N	40	R40C	Cgt	Tgt	5	5	B.1.621	0.000443
N	40	R40C	Cgt	Tgt	5	5	N.5	0.008834
N	40	R40R	cgT	cgG	3	4		0.166667
N	40	R40R	cgT	cgA	1	4		0.055556
N	40	R40H	cGt	cAt	4	4	AY.100	0.000184
N	40	R40R	cgT	cgC	3	4	AY.103	0.000019
N	40	R40R	cgT	cgG	1	4	AY.103	0.000006
N	40	R40C	Cgt	Tgt	4	4	AY.120	0.000149
N	40	R40P	cGt	cCt	4	4	AY.25	0.000024
N	40	R40C	Cgt	Tgt	4	4	AY.39	0.000099
N	40	R40S	Cgt	Agt	4	4	AY.4	0.000006
N	40	R40H	cGt	cAt	4	4	AY.47	0.000124
N	40	R40del	CGT	---	4	4	AY.5	0.000083
N	40	R40C	Cgt	Tgt	4	4	AY.54	0.000381
N	40	R40C	Cgt	Tgt	4	4	AY.6	0.000165
N	40	R40C	Cgt	Tgt	4	4	AY.75	0.000224
N	40	R40H	cGt	cAt	4	4	AY.75.1	0.000721
N	40	R40H	cGt	cAt	4	4	AY.90	0.002738
N	40	R40S	Cgt	Agt	4	4	B.1	0.000037
N	40	R40C	Cgt	Tgt	4	4	B.1.1.1	0.001307
N	40	R40C	Cgt	Tgt	4	4	B.1.1.157	0.003653
N	40	R40R	cgT	cgC	4	4	B.1.1.526	0.014184
N	40	R40del	CGT	---	4	4	B.1.1.7	0.000004
N	40	R40C	Cgt	Tgt	4	4	B.1.22	0.00527
N	40	R40L	cGt	cTt	4	4	B.1.305	0.008602
N	40	R40R	cgT	cgG	4	4	P.1.15	0.000929
N	40	R40P	cGt	cCt	1	3		0.055556
N	40	R40P	cGT	cCA	1	3		0.055556
N	40	R40P	cGT	cCG	1	3		0.055556
N	40	R40Q	cGT	cAA	2	3	All	0
N	40	R40Q	cGT	cAG	1	3	All	0
N	40	R40R	cgT	cgC	3	3	AY.100	0.000138
N	40	R40H	cGt	cAt	3	3	AY.102	0.00008
N	40	R40C	Cgt	Tgt	3	3	AY.102	0.00008
N	40	R40L	cGt	cTt	3	3	AY.117	0.000254
N	40	R40L	cGt	cTt	3	3	AY.118	0.000188
N	40	R40L	cGt	cTt	3	3	AY.2	0.001068
N	40	R40R	cgT	cgC	2	3	AY.25	0.000012
N	40	R40R	cgT	cgG	1	3	AY.25	0.000006
N	40	R40R	cgT	cgC	3	3	AY.26	0.000085
N	40	R40C	Cgt	Tgt	3	3	AY.33	0.0002
N	40	R40L	cGt	cTt	3	3	AY.39	0.000074
N	40	R40R	cgT	cgC	2	3	AY.39	0.000049
N	40	R40R	cgT	cgG	1	3	AY.39	0.000025
N	40	R40del	CGT	---	3	3	AY.43	0.000013
N	40	R40L	cGt	cTt	3	3	AY.46	0.000312
N	40	R40C	Cgt	Tgt	3	3	AY.46.4	0.000494
N	40	R40H	cGt	cAt	3	3	AY.5	0.000062
N	40	R40R	cgT	cgC	2	3	AY.59	0.001059
N	40	R40R	cgT	cgG	1	3	AY.59	0.00053
N	40	R40H	cGt	cAt	3	3	AY.6	0.000123
N	40	R40C	Cgt	Tgt	3	3	AY.98.1	0.000145
N	40	R40C	Cgt	Tgt	3	3	B.1.1.141	0.006036
N	40	R40C	Cgt	Tgt	3	3	B.1.1.433	0.004274
N	40	R40R	cgT	cgG	2	3	B.1.160	0.000062
N	40	R40R	cgT	cgC	1	3	B.1.160	0.000031
N	40	R40S	Cgt	Agt	3	3	B.1.160.12	0.019231
N	40	R40S	Cgt	Agt	3	3	B.1.2	0.000026
N	40	R40H	cGt	cAt	3	3	B.1.351	0.000089
N	40	R40C	Cgt	Tgt	3	3	B.1.36.35	0.007812
N	40	R40C	Cgt	Tgt	3	3	B.1.429	0.000071
N	40	R40L	cGt	cTt	3	3	B.1.576	0.00272
N	40	R40C	Cgt	Tgt	3	3	B.1.582	0.001472
N	40	R40C	Cgt	Tgt	3	3	B.1.617.1	0.000387
N	40	R40del	CGT	---	3	3	B.1.617.2	0.000011
N	40	R40S	Cgt	Agt	3	3	B.1.617.2	0.000011
N	40	R40H	cGt	cAt	3	3	B.1.637	0.000219
N	40	R40C	Cgt	Tgt	3	3	B.6	0.00273
N	40	R40Q	cGT	cAG	1	2		0.055556
N	40	R40Q	cGT	cAA	1	2		0.055556
N	40	R40C	Cgt	Tgt	2	2	A.1	0.000564
N	40	R40H	cGt	cAt	2	2	AY.10	0.00106
N	40	R40R	cgT	cgC	2	2	AY.102	0.000053
N	40	R40L	cGt	cTt	2	2	AY.106	0.00067
N	40	R40C	Cgt	Tgt	2	2	AY.107	0.000932
N	40	R40C	Cgt	Tgt	2	2	AY.118	0.000125
N	40	R40P	cGt	cCt	2	2	AY.121	0.000271
N	40	R40R	cgT	cgC	2	2	AY.14	0.000176
N	40	R40L	cGt	cTt	2	2	AY.14	0.000176
N	40	R40C	Cgt	Tgt	2	2	AY.16	0.000759
N	40	R40H	cGt	cAt	2	2	AY.20	0.000078
N	40	R40del	CGT	---	2	2	AY.23	0.000139
N	40	R40L	cGt	cTt	2	2	AY.23	0.000139
N	40	R40H	cGt	cAt	2	2	AY.23.1	0.000835
N	40	R40C	Cgt	Tgt	2	2	AY.29	0.000032
N	40	R40G	Cgt	Ggt	2	2	AY.3	0.00002
N	40	R40H	cGt	cAt	2	2	AY.3.1	0.000171
N	40	R40C	Cgt	Tgt	2	2	AY.30	0.000791
N	40	R40H	cGt	cAt	2	2	AY.34	0.000194
N	40	R40R	cgT	cgC	2	2	AY.36	0.000296
N	40	R40del	CGT	---	2	2	AY.4	0.000003
N	40	R40P	cGt	cCt	2	2	AY.4.2	0.000043
N	40	R40L	cGt	cTt	2	2	AY.4.2	0.000043
N	40	R40C	Cgt	Tgt	2	2	AY.4.2	0.000043
N	40	R40H	cGt	cAt	2	2	AY.4.5	0.000215
N	40	R40C	Cgt	Tgt	2	2	AY.4.5	0.000215
N	40	R40L	cGt	cTt	2	2	AY.40	0.001929
N	40	R40H	cGt	cAt	2	2	AY.45	0.000243
N	40	R40del	CGT	---	2	2	AY.46	0.000208
N	40	R40H	cGt	cAt	2	2	AY.46.4	0.000329
N	40	R40L	cGt	cTt	2	2	AY.5	0.000041
N	40	R40C	Cgt	Tgt	2	2	AY.57	0.001312
N	40	R40C	Cgt	Tgt	2	2	AY.59	0.001059
N	40	R40R	cgT	cgC	2	2	AY.9	0.000135
N	40	R40C	Cgt	Tgt	2	2	AY.91	0.001461
N	40	R40C	Cgt	Tgt	2	2	AY.92	0.000575
N	40	R40H	cGt	cAt	2	2	AY.92	0.000575
N	40	R40L	cGt	cTt	2	2	AY.98	0.000158
N	40	R40H	cGt	cAt	2	2	AY.98.1	0.000097
N	40	R40R	cgT	cgC	2	2	B.1	0.000018
N	40	R40L	cGt	cTt	2	2	B.1.1.214	0.000111
N	40	R40C	Cgt	Tgt	2	2	B.1.1.261	0.017241
N	40	R40C	Cgt	Tgt	2	2	B.1.1.28	0.000622
N	40	R40L	cGt	cTt	2	2	B.1.1.322	0.017544
N	40	R40H	cGt	cAt	2	2	B.1.1.33	0.000842
N	40	R40C	Cgt	Tgt	2	2	B.1.1.337	0.007194
N	40	R40C	Cgt	Tgt	2	2	B.1.1.39	0.001019
N	40	R40C	Cgt	Tgt	2	2	B.1.1.449	0.045455
N	40	R40P	cGt	cCt	2	2	B.1.1.7	0.000002
N	40	R40H	cGt	cAt	2	2	B.1.177	0.000026
N	40	R40R	cgT	cgC	2	2	B.1.177.75	0.002081
N	40	R40L	cGt	cTt	2	2	B.1.2	0.000018
N	40	R40C	Cgt	Tgt	2	2	B.1.221	0.000142
N	40	R40L	cGt	cTt	2	2	B.1.221	0.000142
N	40	R40R	cgT	cgG	2	2	B.1.221	0.000142
N	40	R40P	cGt	cCt	1	2	B.1.221	0.000071
N	40	R40P	cGT	cCG	1	2	B.1.221	0.000071
N	40	R40C	Cgt	Tgt	2	2	B.1.243	0.000139
N	40	R40C	Cgt	Tgt	2	2	B.1.306	0.011429
N	40	R40C	Cgt	Tgt	2	2	B.1.344	0.016393
N	40	R40L	cGt	cTt	2	2	B.1.351	0.000059
N	40	R40C	Cgt	Tgt	2	2	B.1.36	0.000292
N	40	R40H	cGt	cAt	2	2	B.1.36.36	0.001204
N	40	R40H	cGt	cAt	2	2	B.1.36.8	0.002
N	40	R40C	Cgt	Tgt	2	2	B.1.369	0.00057
N	40	R40L	cGt	cTt	2	2	B.1.416.1	0.003125
N	40	R40R	cgT	cgG	2	2	B.1.427	0.000101
N	40	R40H	cGt	cAt	2	2	B.1.427	0.000101
N	40	R40H	cGt	cAt	2	2	B.1.438.1	0.000215
N	40	R40H	cGt	cAt	2	2	B.1.526	0.000047
N	40	R40C	Cgt	Tgt	2	2	B.1.595	0.000522
N	40	R40H	cGt	cAt	2	2	B.1.596	0.000174
N	40	R40C	Cgt	Tgt	2	2	B.1.596	0.000174
N	40	R40P	cGt	cCt	2	2	B.1.617.2	0.000008
N	40	R40L	cGt	cTt	2	2	B.1.621	0.000177
N	40	R40R	cgT	cgC	2	2	B.1.628	0.000705
N	40	R40H	cGt	cAt	2	2	C.37	0.000232
N	40	R40C	Cgt	Tgt	2	2	P.1.15	0.000465
N	40	R40R	cgT	cgC	2	2	P.4	0.007605
N	40	R40C	Cgt	Tgt	2	2	Q.1	0.000253
N	40	R40H	cGt	cAt	1	1		0.055556
N	40	R40L	cGt	cTt	1	1	A.1	0.000282
N	40	R40H	cGt	cAt	1	1	A.2	0.000662
N	40	R40R	cgT	cgC	1	1	A.23.1	0.000704
N	40	R40C	Cgt	Tgt	1	1	A.5	0.001923
N	40	R40C	Cgt	Tgt	1	1	AD.2	0.000219
N	40	R40C	Cgt	Tgt	1	1	AE.8	0.000489
N	40	R40del1	cGt	c-t	1	1	All	0
N	40	R40del2	cGT	c--	1	1	All	0
N	40	R40E	CGT	GAG	1	1	All	0
N	40	R40N	CGt	AAt	1	1	All	0
N	40	R40C	Cgt	Tgt	1	1	AM.4	0.003571
N	40	R40C	Cgt	Tgt	1	1	AU.3	0.00211
N	40	R40H	cGt	cAt	1	1	AY.1	0.000396
N	40	R40C	Cgt	Tgt	1	1	AY.100	0.000046
N	40	R40P	cGt	cCt	1	1	AY.102	0.000027
N	40	R40S	Cgt	Agt	1	1	AY.102	0.000027
N	40	R40P	cGt	cCt	1	1	AY.103	0.000006
N	40	R40S	Cgt	Agt	1	1	AY.103	0.000006
N	40	R40C	Cgt	Tgt	1	1	AY.105	0.000643
N	40	R40H	cGt	cAt	1	1	AY.105	0.000643
N	40	R40C	Cgt	Tgt	1	1	AY.109	0.00074
N	40	R40H	cGt	cAt	1	1	AY.110	0.000113
N	40	R40C	Cgt	Tgt	1	1	AY.114	0.000231
N	40	R40C	Cgt	Tgt	1	1	AY.116	0.000287
N	40	R40H	cGt	cAt	1	1	AY.116	0.000287
N	40	R40C	Cgt	Tgt	1	1	AY.116.1	0.000311
N	40	R40R	cgT	cgG	1	1	AY.117	0.000085
N	40	R40P	cGt	cCt	1	1	AY.118	0.000063
N	40	R40H	cGt	cAt	1	1	AY.118	0.000063
N	40	R40C	Cgt	Tgt	1	1	AY.12	0.000316
N	40	R40H	cGt	cAt	1	1	AY.12	0.000316
N	40	R40H	cGt	cAt	1	1	AY.120	0.000037
N	40	R40H	cGt	cAt	1	1	AY.13	0.000161
N	40	R40L	cGt	cTt	1	1	AY.13	0.000161
N	40	R40C	Cgt	Tgt	1	1	AY.16.1	0.00047
N	40	R40R	cgT	cgC	1	1	AY.18	0.010101
N	40	R40L	cGt	cTt	1	1	AY.19	0.00114
N	40	R40C	Cgt	Tgt	1	1	AY.2	0.000356
N	40	R40L	cGt	cTt	1	1	AY.20	0.000039
N	40	R40C	Cgt	Tgt	1	1	AY.23	0.00007
N	40	R40S	Cgt	Agt	1	1	AY.23	0.00007
N	40	R40C	Cgt	Tgt	1	1	AY.24	0.000431
N	40	R40C	Cgt	Tgt	1	1	AY.27	0.000065
N	40	R40R	cgT	cgC	1	1	AY.29	0.000016
N	40	R40L	cGt	cTt	1	1	AY.29	0.000016
N	40	R40S	Cgt	Agt	1	1	AY.3	0.00001
N	40	R40P	cGt	cCt	1	1	AY.3	0.00001
N	40	R40R	cgT	cgC	1	1	AY.3.1	0.000085
N	40	R40H	cGt	cAt	1	1	AY.30	0.000396
N	40	R40C	Cgt	Tgt	1	1	AY.32	0.000532
N	40	R40C	Cgt	Tgt	1	1	AY.36	0.000148
N	40	R40R	cgT	cgC	1	1	AY.37	0.000316
N	40	R40H	cGt	cAt	1	1	AY.37	0.000316
N	40	R40C	Cgt	Tgt	1	1	AY.39.1	0.00004
N	40	R40G	Cgt	Ggt	1	1	AY.4	0.000002
N	40	R40R	cgT	cgC	1	1	AY.4.2	0.000022
N	40	R40R	cgT	cgC	1	1	AY.4.3	0.000842
N	40	R40C	Cgt	Tgt	1	1	AY.4.4	0.000409
N	40	R40del	CGT	---	1	1	AY.4.4	0.000409
N	40	R40L	cGt	cTt	1	1	AY.42	0.00004
N	40	R40C	Cgt	Tgt	1	1	AY.42	0.00004
N	40	R40H	cGt	cAt	1	1	AY.42	0.00004
N	40	R40P	cGt	cCt	1	1	AY.43	0.000004
N	40	R40R	cgT	cgC	1	1	AY.44	0.000006
N	40	R40R	cgT	cgC	1	1	AY.45	0.000122
N	40	R40L	cGt	cTt	1	1	AY.45	0.000122
N	40	R40C	Cgt	Tgt	1	1	AY.45	0.000122
N	40	R40S	Cgt	Agt	1	1	AY.45	0.000122
N	40	R40S	Cgt	Agt	1	1	AY.46	0.000104
N	40	R40C	Cgt	Tgt	1	1	AY.46.1	0.001027
N	40	R40del	CGT	---	1	1	AY.46.6	0.000072
N	40	R40R	cgT	cgG	1	1	AY.46.6	0.000072
N	40	R40S	Cgt	Agt	1	1	AY.47	0.000031
N	40	R40del	CGT	---	1	1	AY.5.3	0.000337
N	40	R40L	cGt	cTt	1	1	AY.5.4	0.000277
N	40	R40C	Cgt	Tgt	1	1	AY.5.4	0.000277
N	40	R40L	cGt	cTt	1	1	AY.54	0.000095
N	40	R40R	cgT	cgC	1	1	AY.55	0.000917
N	40	R40L	cGt	cTt	1	1	AY.55	0.000917
N	40	R40H	cGt	cAt	1	1	AY.59	0.00053
N	40	R40L	cGt	cTt	1	1	AY.6	0.000041
N	40	R40del	CGT	---	1	1	AY.60	0.000938
N	40	R40L	cGt	cTt	1	1	AY.61	0.000105
N	40	R40L	cGt	cTt	1	1	AY.64	0.000595
N	40	R40L	cGt	cTt	1	1	AY.69	0.000187
N	40	R40L	cGt	cTt	1	1	AY.70	0.000209
N	40	R40H	cGt	cAt	1	1	AY.75	0.000056
N	40	R40L	cGt	cTt	1	1	AY.75.1	0.00018
N	40	R40H	cGt	cAt	1	1	AY.77	0.001127
N	40	R40C	Cgt	Tgt	1	1	AY.77	0.001127
N	40	R40C	Cgt	Tgt	1	1	AY.79	0.001211
N	40	R40R	cgT	cgC	1	1	AY.79	0.001211
N	40	R40C	Cgt	Tgt	1	1	AY.82	0.001357
N	40	R40C	Cgt	Tgt	1	1	AY.84	0.000437
N	40	R40H	cGt	cAt	1	1	AY.87	0.000833
N	40	R40del	CGT	---	1	1	AY.9.1	0.000084
N	40	R40H	cGt	cAt	1	1	AY.9.2	0.000037
N	40	R40G	Cgt	Ggt	1	1	AY.98	0.000079
N	40	R40del	CGT	---	1	1	AY.99	0.001049
N	40	R40H	cGt	cAt	1	1	AY.99.1	0.001553
N	40	R40C	Cgt	Tgt	1	1	AY.99.2	0.000092
N	40	R40L	cGt	cTt	1	1	AZ.2	0.000821
N	40	R40H	cGt	cAt	1	1	B	0.000128
N	40	R40L	cGt	cTt	1	1	B	0.000128
N	40	R40R	cgT	cgC	1	1	B	0.000128
N	40	R40P	cGt	cCt	1	1	B.1	0.000009
N	40	R40del	CGT	---	1	1	B.1.1	0.000018
N	40	R40C	Cgt	Tgt	1	1	B.1.1.121	0.002427
N	40	R40del	CGT	---	1	1	B.1.1.139	0.022727
N	40	R40H	cGt	cAt	1	1	B.1.1.176	0.000439
N	40	R40C	Cgt	Tgt	1	1	B.1.1.176	0.000439
N	40	R40R	cgT	cgC	1	1	B.1.1.176	0.000439
N	40	R40C	Cgt	Tgt	1	1	B.1.1.214	0.000055
N	40	R40H	cGt	cAt	1	1	B.1.1.214	0.000055
N	40	R40S	Cgt	Agt	1	1	B.1.1.214	0.000055
N	40	R40del	CGT	---	1	1	B.1.1.216	0.00089
N	40	R40H	cGt	cAt	1	1	B.1.1.222	0.000204
N	40	R40C	Cgt	Tgt	1	1	B.1.1.231	0.003096
N	40	R40C	Cgt	Tgt	1	1	B.1.1.240	0.004695
N	40	R40R	cgT	cgG	1	1	B.1.1.244	0.015385
N	40	R40L	cGt	cTt	1	1	B.1.1.26	0.005236
N	40	R40C	Cgt	Tgt	1	1	B.1.1.263	0.001558
N	40	R40C	Cgt	Tgt	1	1	B.1.1.275	0.011236
N	40	R40L	cGt	cTt	1	1	B.1.1.28	0.000311
N	40	R40C	Cgt	Tgt	1	1	B.1.1.307	0.002532
N	40	R40C	Cgt	Tgt	1	1	B.1.1.315	0.008475
N	40	R40C	Cgt	Tgt	1	1	B.1.1.317	0.000412
N	40	R40P	cGt	cCt	1	1	B.1.1.318	0.000302
N	40	R40C	Cgt	Tgt	1	1	B.1.1.318	0.000302
N	40	R40R	cgT	cgC	1	1	B.1.1.33	0.000421
N	40	R40C	Cgt	Tgt	1	1	B.1.1.33	0.000421
N	40	R40L	cGt	cTt	1	1	B.1.1.368	0.003086
N	40	R40C	Cgt	Tgt	1	1	B.1.1.37	0.000193
N	40	R40C	Cgt	Tgt	1	1	B.1.1.409	0.002833
N	40	R40C	Cgt	Tgt	1	1	B.1.1.434	0.000349
N	40	R40L	cGt	cTt	1	1	B.1.1.50	0.000679
N	40	R40C	Cgt	Tgt	1	1	B.1.1.518	0.006329
N	40	R40H	cGt	cAt	1	1	B.1.1.519	0.00004
N	40	R40R	cgT	cgC	1	1	B.1.1.519	0.00004
N	40	R40L	cGt	cTt	1	1	B.1.1.61	0.008772
N	40	R40Q	cGT	cAA	1	1	B.1.1.7	0.000001
N	40	R40C	Cgt	Tgt	1	1	B.1.1.71	0.006061
N	40	R40L	cGt	cTt	1	1	B.1.1.72	0.030303
N	40	R40R	cgT	cgC	1	1	B.1.103	0.019231
N	40	R40H	cGt	cAt	1	1	B.1.160	0.000031
N	40	R40H	cGt	cAt	1	1	B.1.160.10	0.008065
N	40	R40C	Cgt	Tgt	1	1	B.1.160.23	0.004831
N	40	R40C	Cgt	Tgt	1	1	B.1.160.24	0.004425
N	40	R40L	cGt	cTt	1	1	B.1.177	0.000013
N	40	R40L	cGt	cTt	1	1	B.1.177.24	0.001295
N	40	R40C	Cgt	Tgt	1	1	B.1.177.32	0.00135
N	40	R40R	cgT	cgC	1	1	B.1.177.56	0.000668
N	40	R40H	cGt	cAt	1	1	B.1.177.58	0.001332
N	40	R40E	CGT	GAG	1	1	B.1.177.63	0.002703
N	40	R40del	CGT	---	1	1	B.1.177.75	0.001041
N	40	R40R	cgT	cgC	1	1	B.1.177.8	0.000752
N	40	R40L	cGt	cTt	1	1	B.1.177.81	0.000189
N	40	R40C	Cgt	Tgt	1	1	B.1.177.82	0.000477
N	40	R40del1	cGt	c-t	1	1	B.1.2	0.000009
N	40	R40P	cGt	cCt	1	1	B.1.2	0.000009
N	40	R40L	cGt	cTt	1	1	B.1.206	0.000816
N	40	R40del	CGT	---	1	1	B.1.221	0.000071
N	40	R40R	cgT	cgC	1	1	B.1.236	0.002053
N	40	R40C	Cgt	Tgt	1	1	B.1.240	0.000216
N	40	R40L	cGt	cTt	1	1	B.1.258	0.000067
N	40	R40R	cgT	cgG	1	1	B.1.258	0.000067
N	40	R40H	cGt	cAt	1	1	B.1.258.17	0.000104
N	40	R40C	Cgt	Tgt	1	1	B.1.268	0.010417
N	40	R40S	Cgt	Agt	1	1	B.1.279	0.000514
N	40	R40G	Cgt	Ggt	1	1	B.1.332	0.003497
N	40	R40C	Cgt	Tgt	1	1	B.1.346	0.001311
N	40	R40S	Cgt	Agt	1	1	B.1.349	0.000715
N	40	R40C	Cgt	Tgt	1	1	B.1.351	0.00003
N	40	R40L	cGt	cTt	1	1	B.1.36	0.000146
N	40	R40H	cGt	cAt	1	1	B.1.36.17	0.000494
N	40	R40R	cgT	cgC	1	1	B.1.36.29	0.000517
N	40	R40H	cGt	cAt	1	1	B.1.36.29	0.000517
N	40	R40C	Cgt	Tgt	1	1	B.1.36.36	0.000602
N	40	R40C	Cgt	Tgt	1	1	B.1.36.38	0.001642
N	40	R40H	cGt	cAt	1	1	B.1.361	0.001289
N	40	R40C	Cgt	Tgt	1	1	B.1.361	0.001289
N	40	R40R	cgT	cgA	1	1	B.1.369	0.000285
N	40	R40C	Cgt	Tgt	1	1	B.1.396	0.000706
N	40	R40H	cGt	cAt	1	1	B.1.400	0.000429
N	40	R40R	cgT	cgA	1	1	B.1.400	0.000429
N	40	R40C	Cgt	Tgt	1	1	B.1.411	0.003704
N	40	R40P	cGt	cCt	1	1	B.1.416	0.001269
N	40	R40L	cGt	cTt	1	1	B.1.429	0.000024
N	40	R40del2	cGT	c--	1	1	B.1.429	0.000024
N	40	R40R	cgT	cgC	1	1	B.1.429	0.000024
N	40	R40C	Cgt	Tgt	1	1	B.1.438	0.006536
N	40	R40del	CGT	---	1	1	B.1.439	0.005917
N	40	R40C	Cgt	Tgt	1	1	B.1.452	0.013699
N	40	R40C	Cgt	Tgt	1	1	B.1.468	0.005714
N	40	R40C	Cgt	Tgt	1	1	B.1.497	0.000315
N	40	R40L	cGt	cTt	1	1	B.1.516	0.001957
N	40	R40C	Cgt	Tgt	1	1	B.1.525	0.000113
N	40	R40C	Cgt	Tgt	1	1	B.1.546	0.003704
N	40	R40C	Cgt	Tgt	1	1	B.1.575.1	0.002439
N	40	R40H	cGt	cAt	1	1	B.1.575.1	0.002439
N	40	R40H	cGt	cAt	1	1	B.1.595	0.000261
N	40	R40L	cGt	cTt	1	1	B.1.595	0.000261
N	40	R40R	cgT	cgC	1	1	B.1.596	0.000087
N	40	R40R	cgT	cgC	1	1	B.1.597	0.00463
N	40	R40G	Cgt	Ggt	1	1	B.1.617.2	0.000004
N	40	R40R	cgT	cgC	1	1	B.1.620	0.000946
N	40	R40R	cgT	cgC	1	1	B.1.621	0.000089
N	40	R40H	cGt	cAt	1	1	B.1.621	0.000089
N	40	R40H	cGt	cAt	1	1	B.1.621.1	0.000506
N	40	R40R	cgT	cgG	1	1	B.1.623	0.000536
N	40	R40C	Cgt	Tgt	1	1	B.1.628	0.000352
N	40	R40C	Cgt	Tgt	1	1	B.1.637	0.000073
N	40	R40C	Cgt	Tgt	1	1	B.43	0.014286
N	40	R40L	cGt	cTt	1	1	B.60	0.015873
N	40	R40H	cGt	cAt	1	1	C.31	0.017857
N	40	R40L	cGt	cTt	1	1	C.35	0.000774
N	40	R40C	Cgt	Tgt	1	1	C.36	0.000911
N	40	R40C	Cgt	Tgt	1	1	C.36.1	0.004149
N	40	R40L	cGt	cTt	1	1	C.37	0.000116
N	40	R40L	cGt	cTt	1	1	C.37.1	0.002618
N	40	R40S	Cgt	Agt	1	1	D.2	0.000075
N	40	R40C	Cgt	Tgt	1	1	D.2	0.000075
N	40	R40H	cGt	cAt	1	1	N.5	0.001767
N	40	R40S	Cgt	Agt	1	1	P.1	0.000016
N	40	R40N	CGt	AAt	1	1	P.1	0.000016
N	40	R40P	cGt	cCt	1	1	P.1	0.000016
N	40	R40R	cgT	cgC	1	1	P.1.13	0.000898
N	40	R40H	cGt	cAt	1	1	P.1.14	0.000048
N	40	R40H	cGt	cAt	1	1	P.1.15	0.000232
N	40	R40C	Cgt	Tgt	1	1	P.1.17	0.000162
N	40	R40H	cGt	cAt	1	1	P.1.7	0.000319
N	40	R40R	cgT	cgC	1	1	P.1.7	0.000319
N	40	R40H	cGt	cAt	1	1	P.5	0.013699
N	40	R40C	Cgt	Tgt	1	1	Q.4	0.000455
N	40	R40C	Cgt	Tgt	1	1	Q.8	0.000165
N	40	R40L	cGt	cTt	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.