CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 46

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	46	P46S		nonsyn	Ccc	Tcc	3515	3513	0.999431	28409-28411
N	46	P46S		nonsyn	CCc	AGc	3515	1	0.000284495	28409-28411
N	46	P46S		nonsyn	CcC	TcT	3515	1	0.000284495	28409-28411
N	46	P46P		syn	ccC	ccT	813	796	0.97909	28409-28411
N	46	P46P		syn	ccC	ccA	813	13	0.0159902	28409-28411
N	46	P46P		syn	ccC	ccG	813	4	0.00492005	28409-28411
N	46	P46L		nonsyn	cCc	cTc	274	273	0.99635	28409-28411
N	46	P46L		nonsyn	cCC	cTT	274	1	0.00364964	28409-28411
N	46	P46del		del	CCC	---	73	73	1	28409-28411
N	46	P46A		nonsyn	Ccc	Gcc	15	12	0.8	28409-28411
N	46	P46A		nonsyn	CcC	GcG	15	2	0.133333	28409-28411
N	46	P46A		nonsyn	CcC	GcA	15	1	0.0666667	28409-28411
N	46	P46T		nonsyn	Ccc	Acc	13	12	0.923077	28409-28411
N	46	P46T		nonsyn	CcC	AcG	13	1	0.0769231	28409-28411
N	46	P46R		nonsyn	cCc	cGc	11	6	0.545455	28409-28411
N	46	P46R		nonsyn	cCC	cGG	11	3	0.272727	28409-28411
N	46	P46R		nonsyn	cCC	cGA	11	1	0.0909091	28409-28411
N	46	P46R		nonsyn	CCC	AGG	11	1	0.0909091	28409-28411
N	46	P46H		nonsyn	cCc	cAc	9	9	1	28409-28411
N	46	P46G		nonsyn	CCC	GGG	5	2	0.4	28409-28411
N	46	P46G		nonsyn	CCc	GGc	5	2	0.4	28409-28411
N	46	P46G		nonsyn	CCC	GGA	5	1	0.2	28409-28411
N	46	P46del1		del	CcC	-cN	2	1	0.5	28409-28411
N	46	P46del1		del	Ccc	-cc	2	1	0.5	28409-28411
N	46	P46Q		nonsyn	cCC	cAG	1	1	1	28409-28411
N	46	P46K		nonsyn	CCC	AAG	1	1	1	28409-28411
N	46	P46N		nonsyn	CCc	AAc	1	1	1	28409-28411
N	46	P46del2		del	cCC	c--	1	1	1	28409-28411

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	46	P46S	Ccc	Tcc	3513	3515	All	0.000672
N	46	P46S	CcC	TcT	1	3515	All	0
N	46	P46S	CCc	AGc	1	3515	All	0
N	46	P46S	Ccc	Tcc	832	832	AY.73	0.55356
N	46	P46P	ccC	ccT	796	813	All	0.000152
N	46	P46P	ccC	ccA	13	813	All	0.000002
N	46	P46P	ccC	ccG	4	813	All	0.000001
N	46	P46S	Ccc	Tcc	500	500	B.1.1.7	0.000448
N	46	P46S	Ccc	Tcc	297	297	AY.4	0.000462
N	46	P46L	cCc	cTc	273	274	All	0.000052
N	46	P46L	cCC	cTT	1	274	All	0
N	46	P46S	Ccc	Tcc	166	166	B.1.617.2	0.000625
N	46	P46S	Ccc	Tcc	163	163	AY.3	0.001621
N	46	P46S	Ccc	Tcc	158	158	AY.103	0.000981
N	46	P46P	ccC	ccT	116	118	B.1.1.7	0.000104
N	46	P46P	ccC	ccA	1	118	B.1.1.7	0.000001
N	46	P46P	ccC	ccG	1	118	B.1.1.7	0.000001
N	46	P46S	Ccc	Tcc	112	112	AY.120	0.004164
N	46	P46S	Ccc	Tcc	106	106	AY.44	0.000645
N	46	P46S	Ccc	Tcc	103	103	AY.43	0.000456
N	46	P46S	Ccc	Tcc	83	83	AY.25	0.000499
N	46	P46S	Ccc	Tcc	81	81	AY.4.2	0.001757
N	46	P46del	CCC	---	73	73	All	0.000014
N	46	P46P	ccC	ccT	69	69	B.1.2	0.000608
N	46	P46S	Ccc	Tcc	56	56	B.1.2	0.000493
N	46	P46S	Ccc	Tcc	56	56	B.1.234	0.007389
N	46	P46P	ccC	ccT	51	51	AY.4	0.000079
N	46	P46S	Ccc	Tcc	49	49	B.1	0.000449
N	46	P46L	cCc	cTc	44	44	B.1.1.7	0.000039
N	46	P46P	ccC	ccT	37	37	AY.29	0.000584
N	46	P46P	ccC	ccT	34	34	B.1.1.214	0.001886
N	46	P46S	Ccc	Tcc	33	33	AY.39.2	0.050847
N	46	P46L	cCc	cTc	32	33	B.1.177	0.000421
N	46	P46L	cCC	cTT	1	33	B.1.177	0.000013
N	46	P46S	Ccc	Tcc	31	31	B.1.177	0.000408
N	46	P46L	cCc	cTc	29	29	AY.4	0.000045
N	46	P46S	Ccc	Tcc	28	28	B.1.429	0.000659
N	46	P46S	Ccc	Tcc	27	27	AY.47	0.00084
N	46	P46P	ccC	ccT	25	27	B.1	0.000229
N	46	P46P	ccC	ccA	2	27	B.1	0.000018
N	46	P46P	ccC	ccT	22	23	B.1.1	0.000399
N	46	P46P	ccC	ccA	1	23	B.1.1	0.000018
N	46	P46S	Ccc	Tcc	23	23	B.1.623	0.012339
N	46	P46P	ccC	ccT	20	20	B.1.177	0.000263
N	46	P46P	ccC	ccT	17	18	AY.44	0.000103
N	46	P46P	ccC	ccA	1	18	AY.44	0.000006
N	46	P46L	cCc	cTc	18	18	B.1.637	0.001315
N	46	P46P	ccC	ccT	17	17	B.1.617.2	0.000064
N	46	P46P	ccC	ccT	16	16	AY.43	0.000071
N	46	P46S	Ccc	Tcc	16	16	B.1.177.75	0.016649
N	46	P46P	ccC	ccT	16	16	B.1.427	0.000808
N	46	P46A	Ccc	Gcc	12	15	All	0.000002
N	46	P46A	CcC	GcG	2	15	All	0
N	46	P46A	CcC	GcA	1	15	All	0
N	46	P46S	Ccc	Tcc	15	15	AY.23	0.001046
N	46	P46P	ccC	ccT	15	15	AY.25	0.00009
N	46	P46S	Ccc	Tcc	15	15	AY.29	0.000237
N	46	P46P	ccC	ccT	15	15	B.1.177.21	0.001147
N	46	P46P	ccC	ccT	15	15	B.1.526	0.000353
N	46	P46P	ccC	ccT	14	14	AY.103	0.000087
N	46	P46T	Ccc	Acc	12	13	All	0.000002
N	46	P46T	CcC	AcG	1	13	All	0
N	46	P46S	Ccc	Tcc	13	13	AY.102	0.000345
N	46	P46S	Ccc	Tcc	13	13	AY.39	0.000321
N	46	P46P	ccC	ccT	13	13	AY.7.1	0.001465
N	46	P46S	Ccc	Tcc	13	13	B.1.1.222	0.002652
N	46	P46S	Ccc	Tcc	13	13	B.1.427	0.000656
N	46	P46S	Ccc	Tcc	13	13	B.1.617.1	0.001677
N	46	P46S	Ccc	Tcc	13	13	B.1.637	0.00095
N	46	P46S	Ccc	Tcc	13	13	C.37	0.001509
N	46	P46S	Ccc	Tcc	13	13	P.1	0.000205
N	46	P46S	Ccc	Tcc	12	12	AY.46.6	0.000866
N	46	P46L	cCc	cTc	12	12	B.1	0.00011
N	46	P46R	cCc	cGc	6	11	All	0.000001
N	46	P46R	cCC	cGG	3	11	All	0.000001
N	46	P46R	CCC	AGG	1	11	All	0
N	46	P46R	cCC	cGA	1	11	All	0
N	46	P46S	Ccc	Tcc	11	11	AY.20	0.000428
N	46	P46P	ccC	ccT	11	11	AY.3	0.000109
N	46	P46S	Ccc	Tcc	11	11	AY.34	0.001067
N	46	P46S	Ccc	Tcc	11	11	B.1.146	0.04661
N	46	P46S	Ccc	Tcc	11	11	B.1.177.82	0.005251
N	46	P46L	cCc	cTc	11	11	B.1.2	0.000097
N	46	P46S	Ccc	Tcc	10	10	AY.119	0.000353
N	46	P46S	Ccc	Tcc	10	10	AY.3.1	0.000853
N	46	P46P	ccC	ccT	10	10	AY.47	0.000311
N	46	P46S	Ccc	Tcc	10	10	B.1.1.434	0.003486
N	46	P46S	Ccc	Tcc	10	10	B.1.177.81	0.001893
N	46	P46S	Ccc	Tcc	10	10	B.1.346	0.013106
N	46	P46L	cCc	cTc	10	10	B.1.526	0.000235
N	46	P46P	ccC	ccT	10	10	K.3	0.061728
N	46	P46H	cCc	cAc	9	9	All	0.000002
N	46	P46S	Ccc	Tcc	9	9	AY.100	0.000414
N	46	P46S	Ccc	Tcc	9	9	AY.5	0.000186
N	46	P46S	Ccc	Tcc	9	9	B.1.1.316	0.008326
N	46	P46del	CCC	---	9	9	B.1.1.7	0.000008
N	46	P46P	ccC	ccT	9	9	B.1.160	0.000281
N	46	P46S	Ccc	Tcc	8	8	AY.117	0.000676
N	46	P46S	Ccc	Tcc	8	8	AY.26	0.000226
N	46	P46del	CCC	---	8	8	AY.4	0.000012
N	46	P46P	ccC	ccT	8	8	AY.4.2	0.000174
N	46	P46L	cCc	cTc	8	8	AY.43	0.000035
N	46	P46S	Ccc	Tcc	8	8	AY.78	0.012327
N	46	P46P	ccC	ccT	8	8	B.1.1.277	0.00607
N	46	P46P	ccC	ccT	8	8	B.1.1.519	0.000318
N	46	P46A	Ccc	Gcc	8	8	B.1.1.7	0.000007
N	46	P46P	ccC	ccT	8	8	B.1.258	0.000532
N	46	P46L	cCc	cTc	8	8	B.1.516	0.015656
N	46	P46S	Ccc	Tcc	7	7	B.1.1	0.000127
N	46	P46S	Ccc	Tcc	7	7	B.1.1.519	0.000278
N	46	P46S	Ccc	Tcc	7	7	B.1.160	0.000218
N	46	P46S	Ccc	Tcc	7	7	B.1.177.17	0.005747
N	46	P46P	ccC	ccT	5	7	B.1.221	0.000355
N	46	P46P	ccC	ccG	2	7	B.1.221	0.000142
N	46	P46S	Ccc	Tcc	7	7	B.1.526	0.000165
N	46	P46S	Ccc	Tcc	7	7	Q.7	0.007778
N	46	P46P	ccC	ccT	6	6	AY.120	0.000223
N	46	P46L	cCc	cTc	6	6	AY.25	0.000036
N	46	P46L	cCc	cTc	6	6	AY.44	0.000037
N	46	P46P	ccC	ccT	6	6	AY.6	0.000247
N	46	P46P	ccC	ccT	6	6	B.1.243	0.000418
N	46	P46S	Ccc	Tcc	6	6	B.1.351	0.000178
N	46	P46del	CCC	---	6	6	B.1.617.2	0.000023
N	46	P46S	Ccc	Tcc	6	6	D.2	0.00045
N	46	P46P	ccC	ccT	6	6	P.1	0.000095
N	46	P46L	cCc	cTc	5	5	A.23.1	0.003521
N	46	P46G	CCC	GGG	2	5	All	0
N	46	P46G	CCc	GGc	2	5	All	0
N	46	P46G	CCC	GGA	1	5	All	0
N	46	P46S	Ccc	Tcc	5	5	AY.120.1	0.001605
N	46	P46del	CCC	---	5	5	AY.43	0.000022
N	46	P46S	Ccc	Tcc	5	5	AY.6	0.000206
N	46	P46S	Ccc	Tcc	5	5	AY.74	0.000578
N	46	P46S	Ccc	Tcc	5	5	AY.98.1	0.000242
N	46	P46S	Ccc	Tcc	5	5	B.1.1.46	0.021834
N	46	P46del	CCC	---	5	5	B.1.2	0.000044
N	46	P46S	Ccc	Tcc	4	5	B.1.221	0.000284
N	46	P46R	cCC	cGG	2	5	B.1.221	0.000142
N	46	P46R	cCc	cGc	2	5	B.1.221	0.000142
N	46	P46R	CCC	AGG	1	5	B.1.221	0.000071
N	46	P46S	CCc	AGc	1	5	B.1.221	0.000071
N	46	P46S	Ccc	Tcc	5	5	B.1.243	0.000348
N	46	P46L	cCc	cTc	5	5	B.1.351	0.000149
N	46	P46L	cCc	cTc	5	5	B.1.617.2	0.000019
N	46	P46L	cCc	cTc	5	5	P.1	0.000079
N	46	P46S	Ccc	Tcc	5	5	P.1.14	0.000239
N	46	P46S	Ccc	Tcc	5	5	P.1.15	0.001162
N	46	P46P	ccC	ccT	4	4	AY.102	0.000106
N	46	P46P	ccC	ccT	4	4	AY.119	0.000141
N	46	P46S	Ccc	Tcc	4	4	AY.16.1	0.00188
N	46	P46P	ccC	ccT	4	4	AY.23	0.000279
N	46	P46H	cCc	cAc	4	4	AY.4	0.000006
N	46	P46L	cCc	cTc	4	4	AY.4.2	0.000087
N	46	P46S	Ccc	Tcc	4	4	AY.45	0.000487
N	46	P46P	ccC	ccT	4	4	AY.46.6	0.000289
N	46	P46P	ccC	ccT	4	4	AY.5	0.000083
N	46	P46P	ccC	ccT	4	4	AY.9.1	0.000335
N	46	P46S	Ccc	Tcc	4	4	AY.99.2	0.000369
N	46	P46S	Ccc	Tcc	4	4	B	0.000511
N	46	P46T	Ccc	Acc	4	4	B.1	0.000037
N	46	P46P	ccC	ccT	4	4	B.1.177.4	0.000844
N	46	P46P	ccC	ccT	4	4	B.1.177.73	0.002265
N	46	P46S	Ccc	Tcc	4	4	B.1.236	0.008214
N	46	P46S	Ccc	Tcc	4	4	B.1.258	0.000266
N	46	P46S	Ccc	Tcc	4	4	B.1.311	0.001098
N	46	P46P	ccC	ccT	4	4	B.1.351	0.000119
N	46	P46P	ccC	ccT	4	4	B.1.36.31	0.007005
N	46	P46S	Ccc	Tcc	4	4	B.1.561	0.001588
N	46	P46S	Ccc	Tcc	4	4	Q.3	0.00058
N	46	P46R	cCc	cGc	1	3		0.055556
N	46	P46R	cCC	cGA	1	3		0.055556
N	46	P46A	Ccc	Gcc	1	3		0.055556
N	46	P46A	CcC	GcA	1	3		0.055556
N	46	P46R	cCC	cGG	1	3		0.055556
N	46	P46A	CcC	GcG	1	3		0.055556
N	46	P46G	CCc	GGc	1	3		0.055556
N	46	P46G	CCC	GGA	1	3		0.055556
N	46	P46G	CCC	GGG	1	3		0.055556
N	46	P46L	cCc	cTc	3	3	AY.103	0.000019
N	46	P46S	Ccc	Tcc	3	3	AY.116.1	0.000934
N	46	P46P	ccC	ccT	2	3	AY.20	0.000078
N	46	P46P	ccC	ccA	1	3	AY.20	0.000039
N	46	P46del	CCC	---	3	3	AY.25	0.000018
N	46	P46del	CCC	---	3	3	AY.29	0.000047
N	46	P46S	Ccc	Tcc	3	3	AY.33	0.0002
N	46	P46P	ccC	ccT	3	3	AY.39	0.000074
N	46	P46S	Ccc	Tcc	3	3	AY.40	0.002893
N	46	P46S	Ccc	Tcc	3	3	AY.42	0.000121
N	46	P46L	cCc	cTc	3	3	AY.47	0.000093
N	46	P46P	ccC	ccA	3	3	AY.54	0.000286
N	46	P46S	Ccc	Tcc	3	3	AY.70	0.000626
N	46	P46S	Ccc	Tcc	3	3	AY.71	0.001425
N	46	P46S	Ccc	Tcc	3	3	AY.75	0.000168
N	46	P46S	Ccc	Tcc	3	3	AY.75.1	0.000541
N	46	P46P	ccC	ccT	3	3	AY.98.1	0.000145
N	46	P46L	cCc	cTc	3	3	AY.98.1	0.000145
N	46	P46L	cCc	cTc	3	3	B.1.1	0.000054
N	46	P46T	Ccc	Acc	3	3	B.1.1	0.000054
N	46	P46P	ccC	ccT	3	3	B.1.1.284	0.000322
N	46	P46S	Ccc	Tcc	3	3	B.1.1.306	0.001315
N	46	P46P	ccC	ccT	3	3	B.1.1.311	0.001074
N	46	P46L	cCc	cTc	3	3	B.1.1.519	0.000119
N	46	P46S	Ccc	Tcc	3	3	B.1.177.46	0.002755
N	46	P46S	Ccc	Tcc	3	3	B.1.369	0.000856
N	46	P46L	cCc	cTc	3	3	B.1.398	0.008929
N	46	P46L	cCc	cTc	3	3	B.1.429	0.000071
N	46	P46P	ccC	ccT	3	3	B.1.429	0.000071
N	46	P46S	Ccc	Tcc	3	3	B.1.438.1	0.000322
N	46	P46P	ccC	ccT	3	3	B.1.517	0.001281
N	46	P46S	Ccc	Tcc	3	3	B.1.551	0.003871
N	46	P46P	ccC	ccT	3	3	D.2	0.000225
N	46	P46P	ccC	ccT	3	3	N.5	0.0053
N	46	P46S	Ccc	Tcc	3	3	P.1.17	0.000485
N	46	P46P	ccC	ccG	1	2		0.055556
N	46	P46P	ccC	ccA	1	2		0.055556
N	46	P46P	ccC	ccT	2	2	A.23.1	0.001408
N	46	P46del1	Ccc	-cc	1	2	All	0
N	46	P46del1	CcC	-cN	1	2	All	0
N	46	P46L	cCc	cTc	2	2	AY.102	0.000053
N	46	P46S	Ccc	Tcc	2	2	AY.121	0.000271
N	46	P46S	Ccc	Tcc	2	2	AY.19	0.002281
N	46	P46del	CCC	---	2	2	AY.23	0.000139
N	46	P46del	CCC	---	2	2	AY.3	0.00002
N	46	P46L	cCc	cTc	2	2	AY.3	0.00002
N	46	P46P	ccC	ccT	2	2	AY.33	0.000134
N	46	P46S	Ccc	Tcc	2	2	AY.4.2.1	0.000298
N	46	P46S	Ccc	Tcc	2	2	AY.4.4	0.000818
N	46	P46S	Ccc	Tcc	2	2	AY.4.5	0.000215
N	46	P46del	CCC	---	2	2	AY.42	0.00008
N	46	P46del	CCC	---	2	2	AY.44	0.000012
N	46	P46S	Ccc	Tcc	2	2	AY.62	0.000871
N	46	P46S	Ccc	Tcc	2	2	AY.65	0.001066
N	46	P46P	ccC	ccT	2	2	AY.75	0.000112
N	46	P46S	Ccc	Tcc	2	2	AY.98	0.000158
N	46	P46P	ccC	ccT	2	2	AY.98	0.000158
N	46	P46P	ccC	ccT	2	2	AY.99.2	0.000184
N	46	P46S	Ccc	Tcc	2	2	AZ.2	0.001642
N	46	P46P	ccC	ccA	1	2	B	0.000128
N	46	P46P	ccC	ccT	1	2	B	0.000128
N	46	P46del	CCC	---	2	2	B.1	0.000018
N	46	P46S	Ccc	Tcc	2	2	B.1.1.1	0.000653
N	46	P46P	ccC	ccT	2	2	B.1.1.194	0.009901
N	46	P46S	Ccc	Tcc	2	2	B.1.1.284	0.000215
N	46	P46S	Ccc	Tcc	2	2	B.1.1.311	0.000716
N	46	P46P	ccC	ccT	2	2	B.1.1.317	0.000823
N	46	P46P	ccC	ccT	2	2	B.1.1.362	0.011236
N	46	P46L	cCc	cTc	2	2	B.1.160	0.000062
N	46	P46P	ccC	ccT	2	2	B.1.160.18	0.014599
N	46	P46S	Ccc	Tcc	2	2	B.1.177.15	0.001262
N	46	P46S	Ccc	Tcc	2	2	B.1.177.20	0.003035
N	46	P46S	Ccc	Tcc	2	2	B.1.177.35	0.001382
N	46	P46P	ccC	ccT	2	2	B.1.177.44	0.001038
N	46	P46S	Ccc	Tcc	2	2	B.1.177.57	0.000562
N	46	P46S	Ccc	Tcc	2	2	B.1.177.60	0.000437
N	46	P46P	ccC	ccT	2	2	B.1.177.75	0.002081
N	46	P46L	cCc	cTc	2	2	B.1.221	0.000142
N	46	P46T	Ccc	Acc	1	2	B.1.221	0.000071
N	46	P46T	CcC	AcG	1	2	B.1.221	0.000071
N	46	P46A	CcC	GcG	1	2	B.1.221	0.000071
N	46	P46A	Ccc	Gcc	1	2	B.1.221	0.000071
N	46	P46G	CCC	GGG	1	2	B.1.221	0.000071
N	46	P46G	CCc	GGc	1	2	B.1.221	0.000071
N	46	P46P	ccC	ccT	2	2	B.1.258.17	0.000208
N	46	P46S	Ccc	Tcc	2	2	B.1.287	0.060606
N	46	P46P	ccC	ccT	2	2	B.1.336	0.004878
N	46	P46P	ccC	ccT	2	2	B.1.338	0.017241
N	46	P46S	Ccc	Tcc	1	2	B.1.36	0.000146
N	46	P46S	CcC	TcT	1	2	B.1.36	0.000146
N	46	P46S	Ccc	Tcc	2	2	B.1.406	0.012121
N	46	P46S	Ccc	Tcc	2	2	B.1.428.3	0.025641
N	46	P46S	Ccc	Tcc	2	2	B.1.438	0.013072
N	46	P46P	ccC	ccT	2	2	B.1.441	0.019231
N	46	P46S	Ccc	Tcc	2	2	B.1.470	0.002809
N	46	P46L	cCc	cTc	2	2	B.1.525	0.000226
N	46	P46P	ccC	ccT	2	2	B.1.561	0.000794
N	46	P46P	ccC	ccT	2	2	B.1.564	0.000852
N	46	P46L	cCc	cTc	2	2	B.1.565	0.001621
N	46	P46P	ccC	ccT	2	2	B.1.577	0.001375
N	46	P46S	Ccc	Tcc	2	2	B.1.588	0.00182
N	46	P46P	ccC	ccT	2	2	B.1.596	0.000174
N	46	P46S	Ccc	Tcc	2	2	B.1.599	0.007299
N	46	P46S	Ccc	Tcc	2	2	B.1.621	0.000177
N	46	P46P	ccC	ccT	2	2	N.6	0.014184
N	46	P46T	Ccc	Acc	1	1		0.055556
N	46	P46S	Ccc	Tcc	1	1	A	0.000387
N	46	P46P	ccC	ccT	1	1	A.1	0.000282
N	46	P46N	CCc	AAc	1	1	All	0
N	46	P46del2	cCC	c--	1	1	All	0
N	46	P46Q	cCC	cAG	1	1	All	0
N	46	P46K	CCC	AAG	1	1	All	0
N	46	P46S	Ccc	Tcc	1	1	AP.1	0.001502
N	46	P46S	Ccc	Tcc	1	1	AY.1	0.000396
N	46	P46P	ccC	ccT	1	1	AY.100	0.000046
N	46	P46del	CCC	---	1	1	AY.103	0.000006
N	46	P46S	Ccc	Tcc	1	1	AY.110	0.000113
N	46	P46P	ccC	ccT	1	1	AY.110	0.000113
N	46	P46S	Ccc	Tcc	1	1	AY.114	0.000231
N	46	P46del1	CcC	-cN	1	1	AY.117	0.000085
N	46	P46P	ccC	ccT	1	1	AY.117	0.000085
N	46	P46S	Ccc	Tcc	1	1	AY.118	0.000063
N	46	P46P	ccC	ccT	1	1	AY.118	0.000063
N	46	P46L	cCc	cTc	1	1	AY.118	0.000063
N	46	P46P	ccC	ccT	1	1	AY.12	0.000316
N	46	P46L	cCc	cTc	1	1	AY.120	0.000037
N	46	P46L	cCc	cTc	1	1	AY.121	0.000135
N	46	P46S	Ccc	Tcc	1	1	AY.14	0.000088
N	46	P46L	cCc	cTc	1	1	AY.20	0.000039
N	46	P46del	CCC	---	1	1	AY.20	0.000039
N	46	P46S	Ccc	Tcc	1	1	AY.23.1	0.000417
N	46	P46L	cCc	cTc	1	1	AY.26	0.000028
N	46	P46P	ccC	ccT	1	1	AY.26	0.000028
N	46	P46S	Ccc	Tcc	1	1	AY.27	0.000065
N	46	P46P	ccC	ccT	1	1	AY.27	0.000065
N	46	P46S	Ccc	Tcc	1	1	AY.28	0.00189
N	46	P46P	ccC	ccT	1	1	AY.29.1	0.000221
N	46	P46P	ccC	ccT	1	1	AY.3.1	0.000085
N	46	P46L	cCc	cTc	1	1	AY.33	0.000067
N	46	P46P	ccC	ccT	1	1	AY.34	0.000097
N	46	P46del	CCC	---	1	1	AY.34	0.000097
N	46	P46S	Ccc	Tcc	1	1	AY.36	0.000148
N	46	P46L	cCc	cTc	1	1	AY.39	0.000025
N	46	P46P	ccC	ccT	1	1	AY.39.1	0.00004
N	46	P46S	Ccc	Tcc	1	1	AY.39.1	0.00004
N	46	P46L	cCc	cTc	1	1	AY.39.1	0.00004
N	46	P46R	cCc	cGc	1	1	AY.4	0.000002
N	46	P46del	CCC	---	1	1	AY.4.2.1	0.000149
N	46	P46S	Ccc	Tcc	1	1	AY.4.3	0.000842
N	46	P46S	Ccc	Tcc	1	1	AY.41	0.000294
N	46	P46P	ccC	ccT	1	1	AY.41	0.000294
N	46	P46T	Ccc	Acc	1	1	AY.44	0.000006
N	46	P46L	cCc	cTc	1	1	AY.46	0.000104
N	46	P46S	Ccc	Tcc	1	1	AY.46	0.000104
N	46	P46P	ccC	ccT	1	1	AY.46.4	0.000165
N	46	P46S	Ccc	Tcc	1	1	AY.46.4	0.000165
N	46	P46P	ccC	ccT	1	1	AY.46.5	0.000198
N	46	P46del	CCC	---	1	1	AY.46.6	0.000072
N	46	P46P	ccC	ccT	1	1	AY.53	0.000288
N	46	P46L	cCc	cTc	1	1	AY.53	0.000288
N	46	P46T	Ccc	Acc	1	1	AY.59	0.00053
N	46	P46del	CCC	---	1	1	AY.59	0.00053
N	46	P46del	CCC	---	1	1	AY.6	0.000041
N	46	P46del	CCC	---	1	1	AY.60	0.000938
N	46	P46S	Ccc	Tcc	1	1	AY.61	0.000105
N	46	P46P	ccC	ccT	1	1	AY.65	0.000533
N	46	P46S	Ccc	Tcc	1	1	AY.68	0.000274
N	46	P46H	cCc	cAc	1	1	AY.68	0.000274
N	46	P46S	Ccc	Tcc	1	1	AY.69	0.000187
N	46	P46P	ccC	ccT	1	1	AY.69	0.000187
N	46	P46L	cCc	cTc	1	1	AY.7.1	0.000113
N	46	P46S	Ccc	Tcc	1	1	AY.7.2	0.000559
N	46	P46R	cCc	cGc	1	1	AY.75.1	0.00018
N	46	P46S	Ccc	Tcc	1	1	AY.79	0.001211
N	46	P46L	cCc	cTc	1	1	AY.8	0.000606
N	46	P46P	ccC	ccT	1	1	AY.80	0.001129
N	46	P46P	ccC	ccT	1	1	AY.82	0.001357
N	46	P46S	Ccc	Tcc	1	1	AY.84	0.000437
N	46	P46P	ccC	ccA	1	1	AY.85	0.000427
N	46	P46S	Ccc	Tcc	1	1	AY.85	0.000427
N	46	P46S	Ccc	Tcc	1	1	AY.9	0.000068
N	46	P46P	ccC	ccT	1	1	AY.9	0.000068
N	46	P46del	CCC	---	1	1	AY.9	0.000068
N	46	P46S	Ccc	Tcc	1	1	AY.9.1	0.000084
N	46	P46P	ccC	ccT	1	1	AY.9.2	0.000037
N	46	P46del2	cCC	c--	1	1	AY.9.2	0.000037
N	46	P46S	Ccc	Tcc	1	1	AY.9.2	0.000037
N	46	P46P	ccC	ccT	1	1	AY.92	0.000287
N	46	P46S	Ccc	Tcc	1	1	AY.92	0.000287
N	46	P46L	cCc	cTc	1	1	AY.93	0.000273
N	46	P46S	Ccc	Tcc	1	1	AY.93	0.000273
N	46	P46del	CCC	---	1	1	AY.98.1	0.000048
N	46	P46del	CCC	---	1	1	B	0.000128
N	46	P46H	cCc	cAc	1	1	B.1	0.000009
N	46	P46R	cCc	cGc	1	1	B.1	0.000009
N	46	P46del	CCC	---	1	1	B.1.1	0.000018
N	46	P46P	ccC	ccT	1	1	B.1.1.121	0.002427
N	46	P46P	ccC	ccT	1	1	B.1.1.135	0.004695
N	46	P46del	CCC	---	1	1	B.1.1.139	0.022727
N	46	P46del	CCC	---	1	1	B.1.1.161	0.003534
N	46	P46P	ccC	ccT	1	1	B.1.1.176	0.000439
N	46	P46S	Ccc	Tcc	1	1	B.1.1.196	0.005714
N	46	P46S	Ccc	Tcc	1	1	B.1.1.198	0.001468
N	46	P46del	CCC	---	1	1	B.1.1.216	0.00089
N	46	P46S	Ccc	Tcc	1	1	B.1.1.216	0.00089
N	46	P46S	Ccc	Tcc	1	1	B.1.1.231	0.003096
N	46	P46P	ccC	ccT	1	1	B.1.1.232	0.001815
N	46	P46S	Ccc	Tcc	1	1	B.1.1.27	0.00565
N	46	P46P	ccC	ccT	1	1	B.1.1.28	0.000311
N	46	P46S	Ccc	Tcc	1	1	B.1.1.28	0.000311
N	46	P46S	Ccc	Tcc	1	1	B.1.1.291	0.000742
N	46	P46P	ccC	ccT	1	1	B.1.1.312	0.001912
N	46	P46S	Ccc	Tcc	1	1	B.1.1.318	0.000302
N	46	P46S	Ccc	Tcc	1	1	B.1.1.37	0.000193
N	46	P46S	Ccc	Tcc	1	1	B.1.1.378	0.007299
N	46	P46S	Ccc	Tcc	1	1	B.1.1.39	0.00051
N	46	P46P	ccC	ccT	1	1	B.1.1.409	0.002833
N	46	P46P	ccC	ccT	1	1	B.1.1.434	0.000349
N	46	P46P	ccC	ccT	1	1	B.1.1.50	0.000679
N	46	P46P	ccC	ccT	1	1	B.1.1.52	0.012195
N	46	P46S	Ccc	Tcc	1	1	B.1.1.523	0.001563
N	46	P46del	CCC	---	1	1	B.1.1.63	0.000386
N	46	P46S	Ccc	Tcc	1	1	B.1.104	0.00369
N	46	P46P	ccC	ccT	1	1	B.1.139	0.000733
N	46	P46P	ccC	ccT	1	1	B.1.149	0.003425
N	46	P46L	cCc	cTc	1	1	B.1.160.33	0.004425
N	46	P46del	CCC	---	1	1	B.1.177	0.000013
N	46	P46L	cCc	cTc	1	1	B.1.177.12	0.000152
N	46	P46S	Ccc	Tcc	1	1	B.1.177.12	0.000152
N	46	P46P	ccC	ccT	1	1	B.1.177.16	0.000664
N	46	P46P	ccC	ccT	1	1	B.1.177.20	0.001517
N	46	P46S	Ccc	Tcc	1	1	B.1.177.21	0.000076
N	46	P46P	ccC	ccT	1	1	B.1.177.23	0.003236
N	46	P46S	Ccc	Tcc	1	1	B.1.177.33	0.001645
N	46	P46S	Ccc	Tcc	1	1	B.1.177.44	0.000519
N	46	P46P	ccC	ccT	1	1	B.1.177.51	0.004566
N	46	P46S	Ccc	Tcc	1	1	B.1.177.54	0.000606
N	46	P46S	Ccc	Tcc	1	1	B.1.177.56	0.000668
N	46	P46L	cCc	cTc	1	1	B.1.177.58	0.001332
N	46	P46P	ccC	ccT	1	1	B.1.177.60	0.000218
N	46	P46del	CCC	---	1	1	B.1.177.63	0.002703
N	46	P46P	ccC	ccT	1	1	B.1.177.65	0.000665
N	46	P46L	cCc	cTc	1	1	B.1.177.69	0.001484
N	46	P46P	ccC	ccT	1	1	B.1.177.7	0.000165
N	46	P46S	Ccc	Tcc	1	1	B.1.177.7	0.000165
N	46	P46L	cCc	cTc	1	1	B.1.177.7	0.000165
N	46	P46del	CCC	---	1	1	B.1.177.75	0.001041
N	46	P46S	Ccc	Tcc	1	1	B.1.177.77	0.000726
N	46	P46L	cCc	cTc	1	1	B.1.177.80	0.001912
N	46	P46P	ccC	ccT	1	1	B.1.177.82	0.000477
N	46	P46P	ccC	ccT	1	1	B.1.177.84	0.006667
N	46	P46del1	Ccc	-cc	1	1	B.1.2	0.000009
N	46	P46S	Ccc	Tcc	1	1	B.1.214.2	0.0006
N	46	P46N	CCc	AAc	1	1	B.1.221	0.000071
N	46	P46Q	cCC	cAG	1	1	B.1.221	0.000071
N	46	P46del	CCC	---	1	1	B.1.221	0.000071
N	46	P46K	CCC	AAG	1	1	B.1.221	0.000071
N	46	P46H	cCc	cAc	1	1	B.1.221	0.000071
N	46	P46P	ccC	ccT	1	1	B.1.23	0.006061
N	46	P46P	ccC	ccT	1	1	B.1.232	0.000537
N	46	P46P	ccC	ccT	1	1	B.1.234	0.000132
N	46	P46P	ccC	ccT	1	1	B.1.236	0.002053
N	46	P46P	ccC	ccT	1	1	B.1.240	0.000216
N	46	P46S	Ccc	Tcc	1	1	B.1.258.17	0.000104
N	46	P46P	ccC	ccT	1	1	B.1.311	0.000275
N	46	P46L	cCc	cTc	1	1	B.1.320	0.001245
N	46	P46S	Ccc	Tcc	1	1	B.1.349	0.000715
N	46	P46S	Ccc	Tcc	1	1	B.1.351.2	0.000303
N	46	P46P	ccC	ccT	1	1	B.1.36	0.000146
N	46	P46P	ccC	ccT	1	1	B.1.36.10	0.004785
N	46	P46L	cCc	cTc	1	1	B.1.36.17	0.000494
N	46	P46L	cCc	cTc	1	1	B.1.36.18	0.00042
N	46	P46P	ccC	ccT	1	1	B.1.36.18	0.00042
N	46	P46S	Ccc	Tcc	1	1	B.1.36.22	0.001208
N	46	P46P	ccC	ccT	1	1	B.1.369	0.000285
N	46	P46L	cCc	cTc	1	1	B.1.372	0.010989
N	46	P46P	ccC	ccT	1	1	B.1.389	0.001002
N	46	P46S	Ccc	Tcc	1	1	B.1.396	0.000706
N	46	P46S	Ccc	Tcc	1	1	B.1.403	0.003268
N	46	P46S	Ccc	Tcc	1	1	B.1.405	0.012346
N	46	P46L	cCc	cTc	1	1	B.1.411	0.003704
N	46	P46S	Ccc	Tcc	1	1	B.1.416.1	0.001563
N	46	P46del	CCC	---	1	1	B.1.439	0.005917
N	46	P46P	ccC	ccT	1	1	B.1.525	0.000113
N	46	P46P	ccC	ccT	1	1	B.1.530	0.007143
N	46	P46P	ccC	ccT	1	1	B.1.540	0.009709
N	46	P46S	Ccc	Tcc	1	1	B.1.558	0.004566
N	46	P46L	cCc	cTc	1	1	B.1.561	0.000397
N	46	P46S	Ccc	Tcc	1	1	B.1.564	0.000426
N	46	P46P	ccC	ccT	1	1	B.1.567	0.003333
N	46	P46S	Ccc	Tcc	1	1	B.1.568	0.001111
N	46	P46P	ccC	ccT	1	1	B.1.573	0.006098
N	46	P46P	ccC	ccT	1	1	B.1.575.1	0.002439
N	46	P46S	Ccc	Tcc	1	1	B.1.587	0.001898
N	46	P46H	cCc	cAc	1	1	B.1.595	0.000261
N	46	P46S	Ccc	Tcc	1	1	B.1.595	0.000261
N	46	P46del	CCC	---	1	1	B.1.596	0.000087
N	46	P46L	cCc	cTc	1	1	B.1.596	0.000087
N	46	P46S	Ccc	Tcc	1	1	B.1.603	0.010638
N	46	P46S	Ccc	Tcc	1	1	B.1.609	0.000479
N	46	P46P	ccC	ccT	1	1	B.1.617.1	0.000129
N	46	P46H	cCc	cAc	1	1	B.1.617.1	0.000129
N	46	P46A	Ccc	Gcc	1	1	B.1.617.2	0.000004
N	46	P46S	Ccc	Tcc	1	1	B.1.617.3	0.002985
N	46	P46L	cCc	cTc	1	1	B.1.618	0.004032
N	46	P46S	Ccc	Tcc	1	1	B.1.619.1	0.000641
N	46	P46P	ccC	ccT	1	1	B.1.621	0.000089
N	46	P46S	Ccc	Tcc	1	1	B.1.621.1	0.000506
N	46	P46P	ccC	ccT	1	1	B.1.623	0.000536
N	46	P46P	ccC	ccT	1	1	B.1.627	0.00202
N	46	P46P	ccC	ccT	1	1	B.1.628	0.000352
N	46	P46P	ccC	ccT	1	1	B.1.637	0.000073
N	46	P46P	ccC	ccT	1	1	B.1.93	0.000934
N	46	P46S	Ccc	Tcc	1	1	B.40	0.000364
N	46	P46P	ccC	ccT	1	1	C.1.2	0.004255
N	46	P46S	Ccc	Tcc	1	1	C.13	0.025641
N	46	P46P	ccC	ccT	1	1	C.14	0.004329
N	46	P46S	Ccc	Tcc	1	1	C.16	0.00106
N	46	P46P	ccC	ccT	1	1	C.35	0.000774
N	46	P46del	CCC	---	1	1	C.36.3	0.000567
N	46	P46P	ccC	ccT	1	1	C.37	0.000116
N	46	P46L	cCc	cTc	1	1	D.2	0.000075
N	46	P46A	Ccc	Gcc	1	1	D.2	0.000075
N	46	P46del	CCC	---	1	1	P.1	0.000016
N	46	P46T	Ccc	Acc	1	1	P.1	0.000016
N	46	P46P	ccC	ccA	1	1	P.1.1	0.000318
N	46	P46S	Ccc	Tcc	1	1	P.1.10	0.000269
N	46	P46L	cCc	cTc	1	1	P.1.10	0.000269
N	46	P46P	ccC	ccT	1	1	P.1.12	0.000484
N	46	P46P	ccC	ccT	1	1	P.1.14	0.000048
N	46	P46P	ccC	ccT	1	1	P.1.15	0.000232
N	46	P46P	ccC	ccT	1	1	P.1.17	0.000162
N	46	P46S	Ccc	Tcc	1	1	P.1.7	0.000319
N	46	P46L	cCc	cTc	1	1	Q.1	0.000126
N	46	P46S	Ccc	Tcc	1	1	Q.8	0.000165
N	46	P46L	cCc	cTc	1	1	R.1	0.00009
N	46	P46S	Ccc	Tcc	1	1	W.1	0.008696
N	46	P46L	cCc	cTc	1	1	W.4	0.001351

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.