CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 80

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	80	P80R		nonsyn	cCa	cGa	114785	114772	0.999887	28511-28513
N	80	P80R		nonsyn	cCA	cGC	114785	10	0.0000871194	28511-28513
N	80	P80R		nonsyn	cCA	cGG	114785	3	0.0000261358	28511-28513
N	80	P80S		nonsyn	Cca	Tca	1207	1204	0.997514	28511-28513
N	80	P80S		nonsyn	CcA	TcC	1207	1	0.0008285	28511-28513
N	80	P80S		nonsyn	CcA	TcG	1207	1	0.0008285	28511-28513
N	80	P80S		nonsyn	CcA	TcT	1207	1	0.0008285	28511-28513
N	80	P80Q		nonsyn	cCa	cAa	601	601	1	28511-28513
N	80	P80A		nonsyn	Cca	Gca	565	565	1	28511-28513
N	80	P80L		nonsyn	cCa	cTa	491	490	0.997963	28511-28513
N	80	P80L		nonsyn	cCA	cTC	491	1	0.00203666	28511-28513
N	80	P80P		syn	ccA	ccG	355	197	0.55493	28511-28513
N	80	P80P		syn	ccA	ccT	355	106	0.298592	28511-28513
N	80	P80P		syn	ccA	ccC	355	52	0.146479	28511-28513
N	80	P80T		nonsyn	Cca	Aca	75	74	0.986667	28511-28513
N	80	P80T		nonsyn	CcA	AcG	75	1	0.0133333	28511-28513
N	80	P80del		del	CCA	---	13	13	1	28511-28513
N	80	P80del1		del	ccA	cc-	6	2	0.333333	28511-28513
N	80	P80del1		del	Cca	-ca	6	2	0.333333	28511-28513
N	80	P80del1		del	CCa	-Ta	6	2	0.333333	28511-28513
N	80	P80V		nonsyn	CCa	GTa	4	4	1	28511-28513
N	80	P80del2		del	CCa	--a	3	3	1	28511-28513
N	80	P80X		nonsyn	CCA	TAG	2	1	0.5	28511-28513
N	80	P80X		nonsyn	CCa	TAa	2	1	0.5	28511-28513

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	80	P80R	cCa	cGa	114772	114785	All	0.021952
N	80	P80R	cCA	cGC	10	114785	All	0.000002
N	80	P80R	cCA	cGG	3	114785	All	0.000001
N	80	P80R	cCa	cGa	62802	62815	P.1	0.989382
N	80	P80R	cCA	cGC	10	62815	P.1	0.000158
N	80	P80R	cCA	cGG	3	62815	P.1	0.000047
N	80	P80R	cCa	cGa	20880	20880	P.1.14	0.998088
N	80	P80R	cCa	cGa	6154	6154	P.1.17	0.995471
N	80	P80R	cCa	cGa	4270	4270	P.1.15	0.9921
N	80	P80R	cCa	cGa	3683	3683	P.1.10	0.992455
N	80	P80R	cCa	cGa	3102	3102	P.1.7	0.990421
N	80	P80R	cCa	cGa	3048	3048	P.1.1	0.968234
N	80	P80R	cCa	cGa	2611	2611	P.1.16	0.976805
N	80	P80R	cCa	cGa	1918	1918	P.1.12	0.928364
N	80	P80S	Cca	Tca	1204	1207	All	0.00023
N	80	P80S	CcA	TcG	1	1207	All	0
N	80	P80S	CcA	TcT	1	1207	All	0
N	80	P80S	CcA	TcC	1	1207	All	0
N	80	P80R	cCa	cGa	1138	1138	P.1.17.1	0.995626
N	80	P80R	cCa	cGa	1105	1105	P.1.13	0.992812
N	80	P80R	cCa	cGa	1023	1023	P.1.4	0.999023
N	80	P80R	cCa	cGa	863	863	P.1.2	0.997688
N	80	P80Q	cCa	cAa	601	601	All	0.000115
N	80	P80A	Cca	Gca	565	565	All	0.000108
N	80	P80A	Cca	Gca	544	544	AY.4	0.000847
N	80	P80R	cCa	cGa	510	510	P.1.6	0.992218
N	80	P80L	cCa	cTa	490	491	All	0.000094
N	80	P80L	cCA	cTC	1	491	All	0
N	80	P80P	ccA	ccG	197	355	All	0.000038
N	80	P80P	ccA	ccT	106	355	All	0.00002
N	80	P80P	ccA	ccC	52	355	All	0.00001
N	80	P80S	Cca	Tca	305	305	B.1.621	0.026998
N	80	P80Q	cCa	cAa	210	210	B.1.617.2	0.000791
N	80	P80R	cCa	cGa	209	209	P.1.8	1
N	80	P80R	cCa	cGa	207	207	P.1.9	0.995192
N	80	P80R	cCa	cGa	189	189	B.1.630	0.989529
N	80	P80R	cCa	cGa	185	185	B.1	0.001695
N	80	P80R	cCa	cGa	163	163	B.1.1	0.002957
N	80	P80P	ccA	ccT	77	144	B.1.1.7	0.000069
N	80	P80P	ccA	ccC	35	144	B.1.1.7	0.000031
N	80	P80P	ccA	ccG	32	144	B.1.1.7	0.000029
N	80	P80R	cCa	cGa	112	112	P.1.10.1	0.910569
N	80	P80S	Cca	Tca	110	110	B.1.1.7	0.000098
N	80	P80S	Cca	Tca	105	105	B.1.617.2	0.000395
N	80	P80R	cCa	cGa	98	98	P.1.11	1
N	80	P80S	Cca	Tca	97	97	AY.3	0.000965
N	80	P80P	ccA	ccG	86	90	AY.4	0.000134
N	80	P80P	ccA	ccC	2	90	AY.4	0.000003
N	80	P80P	ccA	ccT	2	90	AY.4	0.000003
N	80	P80L	cCa	cTa	88	88	B.1.1.7	0.000079
N	80	P80S	Cca	Tca	80	80	AY.54	0.007628
N	80	P80S	Cca	Tca	78	78	AY.4	0.000121
N	80	P80T	Cca	Aca	74	75	All	0.000014
N	80	P80T	CcA	AcG	1	75	All	0
N	80	P80R	cCa	cGa	47	47	B.1.177.35	0.032481
N	80	P80Q	cCa	cAa	40	40	AY.43	0.000177
N	80	P80Q	cCa	cAa	40	40	AY.46.5	0.007937
N	80	P80S	Cca	Tca	39	39	AY.43	0.000173
N	80	P80R	cCa	cGa	37	37	B.1.1.528	0.177885
N	80	P80L	cCa	cTa	36	37	B.1.617.2	0.000136
N	80	P80L	cCA	cTC	1	37	B.1.617.2	0.000004
N	80	P80Q	cCa	cAa	35	35	B.1.1.7	0.000031
N	80	P80Q	cCa	cAa	33	33	AY.25	0.000198
N	80	P80L	cCa	cTa	30	30	AY.98	0.00237
N	80	P80L	cCa	cTa	30	30	B.1.177	0.000395
N	80	P80Q	cCa	cAa	29	29	AY.103	0.00018
N	80	P80Q	cCa	cAa	29	29	AY.4	0.000045
N	80	P80R	cCa	cGa	29	29	P.1.3	1
N	80	P80Q	cCa	cAa	27	27	AY.44	0.000164
N	80	P80R	cCa	cGa	27	27	C.37	0.003134
N	80	P80S	Cca	Tca	26	26	B.1.1.374	0.061758
N	80	P80R	cCa	cGa	25	25	C.1.2	0.106383
N	80	P80R	cCa	cGa	24	24	B.1.1.28	0.00747
N	80	P80R	cCa	cGa	24	24	P.1.10.2	1
N	80	P80S	Cca	Tca	21	21	B.1.177	0.000277
N	80	P80L	cCa	cTa	20	20	AY.4	0.000031
N	80	P80S	Cca	Tca	19	19	B.1.2	0.000167
N	80	P80L	cCa	cTa	18	18	AY.9	0.001217
N	80	P80R	cCa	cGa	17	17	B.1.160	0.00053
N	80	P80L	cCa	cTa	17	17	B.1.2	0.00015
N	80	P80P	ccA	ccG	12	17	B.1.617.2	0.000045
N	80	P80P	ccA	ccT	3	17	B.1.617.2	0.000011
N	80	P80P	ccA	ccC	2	17	B.1.617.2	0.000008
N	80	P80Q	cCa	cAa	17	17	C.35	0.013158
N	80	P80L	cCa	cTa	16	16	B.1.1	0.00029
N	80	P80Q	cCa	cAa	16	16	B.1.429	0.000376
N	80	P80S	Cca	Tca	15	15	AY.25	0.00009
N	80	P80L	cCa	cTa	15	15	B.1	0.000137
N	80	P80R	cCa	cGa	15	15	B.1.177	0.000198
N	80	P80S	Cca	Tca	14	14	B.1.177.60	0.003058
N	80	P80del	CCA	---	13	13	All	0.000002
N	80	P80S	Cca	Tca	13	13	AY.119	0.000459
N	80	P80S	Cca	Tca	12	13	AY.44	0.000073
N	80	P80S	CcA	TcG	1	13	AY.44	0.000006
N	80	P80S	Cca	Tca	13	13	B.1.1	0.000236
N	80	P80R	cCa	cGa	13	13	B.1.1.7	0.000012
N	80	P80R	cCa	cGa	13	13	P.1.5	1
N	80	P80R	cCa	cGa	12	12	B.1.1.519	0.000477
N	80	P80L	cCa	cTa	12	12	B.1.160	0.000374
N	80	P80T	Cca	Aca	12	12	B.1.2	0.000106
N	80	P80P	ccA	ccG	12	12	B.1.369	0.003423
N	80	P80S	Cca	Tca	12	12	B.1.587	0.02277
N	80	P80S	Cca	Tca	12	12	B.1.621.1	0.00607
N	80	P80T	Cca	Aca	11	11	AY.103	0.000068
N	80	P80R	cCa	cGa	11	11	AY.103	0.000068
N	80	P80Q	cCa	cAa	11	11	AY.5	0.000227
N	80	P80L	cCa	cTa	11	11	B.1.221	0.000781
N	80	P80R	cCa	cGa	11	11	B.1.429	0.000259
N	80	P80S	Cca	Tca	10	10	AY.103	0.000062
N	80	P80Q	cCa	cAa	10	10	AY.3	0.000099
N	80	P80L	cCa	cTa	10	10	B.1.1.214	0.000555
N	80	P80Q	cCa	cAa	10	10	B.1.177.81	0.001893
N	80	P80S	Cca	Tca	10	10	C.37	0.001161
N	80	P80S	Cca	Tca	9	9	AL.1	0.116883
N	80	P80S	Cca	Tca	9	9	AY.106	0.003014
N	80	P80Q	cCa	cAa	9	9	AY.120	0.000335
N	80	P80L	cCa	cTa	9	9	AY.44	0.000055
N	80	P80P	ccA	ccG	8	9	AY.44	0.000049
N	80	P80P	ccA	ccT	1	9	AY.44	0.000006
N	80	P80S	Cca	Tca	9	9	B.1	0.000082
N	80	P80R	cCa	cGa	9	9	B.1.214.2	0.005396
N	80	P80R	cCa	cGa	9	9	B.1.349	0.006433
N	80	P80L	cCa	cTa	9	9	B.1.396	0.006351
N	80	P80R	cCa	cGa	8	8	A.2.5	0.003992
N	80	P80S	Cca	Tca	8	8	AY.20	0.000311
N	80	P80S	Cca	Tca	8	8	AY.3.1	0.000682
N	80	P80T	Cca	Aca	8	8	AY.4	0.000012
N	80	P80S	Cca	Tca	8	8	AY.47	0.000249
N	80	P80T	Cca	Aca	7	8	B.1.1.7	0.000006
N	80	P80T	CcA	AcG	1	8	B.1.1.7	0.000001
N	80	P80L	cCa	cTa	7	7	B.1.1.519	0.000278
N	80	P80S	Cca	Tca	7	7	B.1.36	0.001021
N	80	P80S	Cca	Tca	7	7	B.1.427	0.000353
N	80	P80L	cCa	cTa	7	7	B.1.429	0.000165
N	80	P80del1	CCa	-Ta	2	6	All	0
N	80	P80del1	ccA	cc-	2	6	All	0
N	80	P80del1	Cca	-ca	2	6	All	0
N	80	P80Q	cCa	cAa	6	6	AY.100	0.000276
N	80	P80S	Cca	Tca	6	6	AY.14	0.000528
N	80	P80S	Cca	Tca	6	6	AY.23	0.000418
N	80	P80L	cCa	cTa	6	6	AY.25	0.000036
N	80	P80Q	cCa	cAa	6	6	AY.26	0.00017
N	80	P80R	cCa	cGa	6	6	AY.3	0.00006
N	80	P80L	cCa	cTa	6	6	AY.39.1	0.000238
N	80	P80Q	cCa	cAa	6	6	AY.4.4	0.002455
N	80	P80A	Cca	Gca	6	6	AY.4.5	0.000645
N	80	P80R	cCa	cGa	6	6	AY.43	0.000027
N	80	P80L	cCa	cTa	6	6	AY.43	0.000027
N	80	P80P	ccA	ccG	6	6	AY.96	0.012448
N	80	P80L	cCa	cTa	6	6	B.1.177.16	0.003987
N	80	P80R	cCa	cGa	6	6	B.1.351	0.000178
N	80	P80R	cCa	cGa	6	6	B.1.398	0.017857
N	80	P80R	cCa	cGa	6	6	B.1.617.2	0.000023
N	80	P80L	cCa	cTa	6	6	B.1.91	0.012448
N	80	P80S	Cca	Tca	5	5	AY.102	0.000133
N	80	P80P	ccA	ccT	5	5	AY.120	0.000186
N	80	P80L	cCa	cTa	5	5	AY.29	0.000079
N	80	P80S	Cca	Tca	4	5	AY.29	0.000063
N	80	P80S	CcA	TcT	1	5	AY.29	0.000016
N	80	P80R	cCa	cGa	5	5	AY.44	0.00003
N	80	P80S	Cca	Tca	5	5	AY.46.4	0.000823
N	80	P80P	ccA	ccT	3	5	B.1	0.000027
N	80	P80P	ccA	ccG	2	5	B.1	0.000018
N	80	P80A	Cca	Gca	5	5	B.1.1.7	0.000004
N	80	P80L	cCa	cTa	5	5	B.1.243	0.000348
N	80	P80Q	cCa	cAa	5	5	B.1.258	0.000333
N	80	P80S	Cca	Tca	5	5	B.1.258	0.000333
N	80	P80P	ccA	ccC	5	5	B.1.400	0.002145
N	80	P80S	Cca	Tca	5	5	B.1.425	0.01497
N	80	P80R	cCa	cGa	5	5	B.1.596	0.000436
N	80	P80A	Cca	Gca	5	5	B.1.617.2	0.000019
N	80	P80S	Cca	Tca	4	4	A.2	0.002647
N	80	P80V	CCa	GTa	4	4	All	0.000001
N	80	P80L	cCa	cTa	4	4	AY.103	0.000025
N	80	P80P	ccA	ccG	2	4	AY.103	0.000012
N	80	P80P	ccA	ccT	1	4	AY.103	0.000006
N	80	P80P	ccA	ccC	1	4	AY.103	0.000006
N	80	P80S	Cca	Tca	4	4	AY.26	0.000113
N	80	P80L	cCa	cTa	4	4	AY.4.2	0.000087
N	80	P80S	Cca	Tca	4	4	AY.5	0.000083
N	80	P80T	Cca	Aca	4	4	AY.54	0.000381
N	80	P80R	cCa	cGa	4	4	B	0.000511
N	80	P80S	Cca	Tca	4	4	B.1.1.519	0.000159
N	80	P80R	cCa	cGa	4	4	B.1.1.523	0.00625
N	80	P80L	cCa	cTa	4	4	B.1.351	0.000119
N	80	P80P	ccA	ccT	4	4	B.1.427	0.000202
N	80	P80R	cCa	cGa	4	4	B.1.526	0.000094
N	80	P80L	cCa	cTa	4	4	B.1.526	0.000094
N	80	P80Q	cCa	cAa	4	4	B.1.575	0.001214
N	80	P80R	cCa	cGa	4	4	B.1.621	0.000354
N	80	P80R	cCa	cGa	4	4	C.37.1	0.010471
N	80	P80L	cCa	cTa	4	4	P.1	0.000063
N	80	P80S	Cca	Tca	3	3	A.2.5	0.001497
N	80	P80del2	CCa	--a	3	3	All	0.000001
N	80	P80P	ccA	ccG	3	3	AY.102	0.00008
N	80	P80Q	cCa	cAa	3	3	AY.102	0.00008
N	80	P80T	Cca	Aca	3	3	AY.25	0.000018
N	80	P80T	Cca	Aca	3	3	AY.3	0.00003
N	80	P80P	ccA	ccG	3	3	AY.34	0.000291
N	80	P80S	Cca	Tca	3	3	AY.39	0.000074
N	80	P80S	Cca	Tca	3	3	AY.46	0.000312
N	80	P80P	ccA	ccG	3	3	AY.46.4	0.000494
N	80	P80S	Cca	Tca	3	3	AY.9	0.000203
N	80	P80Q	cCa	cAa	3	3	B.1	0.000027
N	80	P80R	cCa	cGa	3	3	B.1.1.161	0.010601
N	80	P80R	cCa	cGa	3	3	B.1.1.220	0.005576
N	80	P80S	Cca	Tca	3	3	B.1.1.241	0.006211
N	80	P80R	cCa	cGa	3	3	B.1.1.372	0.002066
N	80	P80R	cCa	cGa	3	3	B.1.1.507	0.026087
N	80	P80del	CCA	---	3	3	B.1.1.7	0.000003
N	80	P80P	ccA	ccG	3	3	B.1.177	0.00004
N	80	P80Q	cCa	cAa	3	3	B.1.177	0.00004
N	80	P80P	ccA	ccG	3	3	B.1.177.21	0.000229
N	80	P80L	cCa	cTa	3	3	B.1.177.32	0.004049
N	80	P80L	cCa	cTa	3	3	B.1.177.4	0.000633
N	80	P80Q	cCa	cAa	3	3	B.1.2	0.000026
N	80	P80R	cCa	cGa	3	3	B.1.221	0.000213
N	80	P80S	Cca	Tca	3	3	B.1.221	0.000213
N	80	P80R	cCa	cGa	3	3	B.1.234	0.000396
N	80	P80S	Cca	Tca	3	3	B.1.243	0.000209
N	80	P80P	ccA	ccC	3	3	B.1.36.1	0.003421
N	80	P80P	ccA	ccG	3	3	B.1.422	0.002437
N	80	P80L	cCa	cTa	3	3	B.1.564	0.001278
N	80	P80S	Cca	Tca	3	3	B.1.595.3	0.078947
N	80	P80S	Cca	Tca	3	3	B.1.596	0.000261
N	80	P80L	cCa	cTa	3	3	B.1.596	0.000261
N	80	P80T	Cca	Aca	3	3	B.1.617.2	0.000011
N	80	P80R	cCa	cGa	3	3	C.36.3.1	0.008152
N	80	P80R	cCa	cGa	3	3	P.2	0.00056
N	80	P80S	Cca	Tca	3	3	Q.1	0.000379
N	80	P80del1	CCa	-Ta	2	2		0.111111
N	80	P80T	Cca	Aca	2	2		0.111111
N	80	P80V	CCa	GTa	2	2		0.111111
N	80	P80del2	CCa	--a	2	2		0.111111
N	80	P80X	CCA	TAG	1	2	All	0
N	80	P80X	CCa	TAa	1	2	All	0
N	80	P80S	Cca	Tca	2	2	AY.100	0.000092
N	80	P80R	cCa	cGa	2	2	AY.101	0.000981
N	80	P80R	cCa	cGa	2	2	AY.102	0.000053
N	80	P80S	Cca	Tca	2	2	AY.110	0.000225
N	80	P80L	cCa	cTa	2	2	AY.111	0.000366
N	80	P80Q	cCa	cAa	2	2	AY.114	0.000462
N	80	P80S	Cca	Tca	2	2	AY.118	0.000125
N	80	P80Q	cCa	cAa	2	2	AY.119	0.000071
N	80	P80L	cCa	cTa	2	2	AY.120	0.000074
N	80	P80S	Cca	Tca	2	2	AY.120.2.1	0.000997
N	80	P80P	ccA	ccT	2	2	AY.16.1	0.00094
N	80	P80R	cCa	cGa	2	2	AY.20	0.000078
N	80	P80R	cCa	cGa	2	2	AY.23	0.000139
N	80	P80P	ccA	ccG	1	2	AY.26	0.000028
N	80	P80P	ccA	ccT	1	2	AY.26	0.000028
N	80	P80L	cCa	cTa	2	2	AY.3	0.00002
N	80	P80P	ccA	ccT	1	2	AY.3	0.00001
N	80	P80P	ccA	ccG	1	2	AY.3	0.00001
N	80	P80L	cCa	cTa	2	2	AY.39	0.000049
N	80	P80P	ccA	ccG	2	2	AY.39	0.000049
N	80	P80Q	cCa	cAa	2	2	AY.4.5	0.000215
N	80	P80Q	cCa	cAa	2	2	AY.42	0.00008
N	80	P80T	Cca	Aca	2	2	AY.44	0.000012
N	80	P80Q	cCa	cAa	2	2	AY.46	0.000208
N	80	P80Q	cCa	cAa	2	2	AY.46.6	0.000144
N	80	P80Q	cCa	cAa	2	2	AY.48	0.00093
N	80	P80R	cCa	cGa	2	2	AY.63	0.000774
N	80	P80L	cCa	cTa	2	2	AY.65	0.001066
N	80	P80T	Cca	Aca	2	2	AY.73	0.001331
N	80	P80L	cCa	cTa	2	2	AY.9.2	0.000073
N	80	P80R	cCa	cGa	2	2	AY.9.2	0.000073
N	80	P80R	cCa	cGa	2	2	AZ.1	0.001735
N	80	P80T	Cca	Aca	2	2	B	0.000256
N	80	P80L	cCa	cTa	2	2	B.1.1.1	0.000653
N	80	P80R	cCa	cGa	2	2	B.1.1.117	0.019417
N	80	P80A	Cca	Gca	2	2	B.1.1.348	0.001592
N	80	P80R	cCa	cGa	2	2	B.1.1.348	0.001592
N	80	P80L	cCa	cTa	2	2	B.1.1.37	0.000386
N	80	P80R	cCa	cGa	2	2	B.1.1.409	0.005666
N	80	P80S	Cca	Tca	2	2	B.1.1.464	0.002946
N	80	P80Q	cCa	cAa	2	2	B.1.1.519	0.000079
N	80	P80V	CCa	GTa	2	2	B.1.1.7	0.000002
N	80	P80L	cCa	cTa	2	2	B.1.139	0.001466
N	80	P80T	Cca	Aca	2	2	B.1.177	0.000026
N	80	P80S	Cca	Tca	2	2	B.1.177.2	0.009091
N	80	P80L	cCa	cTa	2	2	B.1.177.62	0.002384
N	80	P80R	cCa	cGa	2	2	B.1.177.7	0.00033
N	80	P80R	cCa	cGa	2	2	B.1.177.73	0.001133
N	80	P80R	cCa	cGa	2	2	B.1.2	0.000018
N	80	P80P	ccA	ccG	1	2	B.1.2	0.000009
N	80	P80P	ccA	ccC	1	2	B.1.2	0.000009
N	80	P80L	cCa	cTa	2	2	B.1.234	0.000264
N	80	P80S	Cca	Tca	2	2	B.1.240	0.000431
N	80	P80R	cCa	cGa	2	2	B.1.241	0.001623
N	80	P80L	cCa	cTa	2	2	B.1.258.17	0.000208
N	80	P80R	cCa	cGa	2	2	B.1.311	0.000549
N	80	P80R	cCa	cGa	2	2	B.1.324	0.00321
N	80	P80P	ccA	ccT	2	2	B.1.36.29	0.001035
N	80	P80R	cCa	cGa	2	2	B.1.369	0.00057
N	80	P80R	cCa	cGa	2	2	B.1.524	0.002813
N	80	P80S	Cca	Tca	2	2	B.1.526	0.000047
N	80	P80R	cCa	cGa	2	2	B.1.533	0.019231
N	80	P80Q	cCa	cAa	2	2	B.1.561	0.000794
N	80	P80R	cCa	cGa	2	2	B.1.623	0.001073
N	80	P80S	Cca	Tca	2	2	C.38	0.016129
N	80	P80S	Cca	Tca	2	2	D.2	0.00015
N	80	P80L	cCa	cTa	2	2	D.2	0.00015
N	80	P80P	ccA	ccG	1	1	A.1	0.000282
N	80	P80L	cCa	cTa	1	1	A.2.5	0.000499
N	80	P80L	cCa	cTa	1	1	A.23.1	0.000704
N	80	P80L	cCa	cTa	1	1	AA.3	0.027027
N	80	P80L	cCa	cTa	1	1	AU.3	0.00211
N	80	P80L	cCa	cTa	1	1	AY.100	0.000046
N	80	P80R	cCa	cGa	1	1	AY.108	0.001103
N	80	P80Q	cCa	cAa	1	1	AY.109	0.00074
N	80	P80L	cCa	cTa	1	1	AY.11	0.001339
N	80	P80Q	cCa	cAa	1	1	AY.11	0.001339
N	80	P80P	ccA	ccG	1	1	AY.110	0.000113
N	80	P80S	Cca	Tca	1	1	AY.111	0.000183
N	80	P80Q	cCa	cAa	1	1	AY.117	0.000085
N	80	P80P	ccA	ccG	1	1	AY.117	0.000085
N	80	P80Q	cCa	cAa	1	1	AY.118	0.000063
N	80	P80L	cCa	cTa	1	1	AY.119	0.000035
N	80	P80S	Cca	Tca	1	1	AY.120.1	0.000321
N	80	P80R	cCa	cGa	1	1	AY.120.2	0.001285
N	80	P80S	Cca	Tca	1	1	AY.121	0.000135
N	80	P80T	Cca	Aca	1	1	AY.121	0.000135
N	80	P80R	cCa	cGa	1	1	AY.13	0.000161
N	80	P80S	Cca	Tca	1	1	AY.13	0.000161
N	80	P80L	cCa	cTa	1	1	AY.14	0.000088
N	80	P80R	cCa	cGa	1	1	AY.16.1	0.00047
N	80	P80S	Cca	Tca	1	1	AY.17	0.008197
N	80	P80R	cCa	cGa	1	1	AY.2	0.000356
N	80	P80L	cCa	cTa	1	1	AY.20	0.000039
N	80	P80Q	cCa	cAa	1	1	AY.20	0.000039
N	80	P80P	ccA	ccC	1	1	AY.23	0.00007
N	80	P80S	Cca	Tca	1	1	AY.23.1	0.000417
N	80	P80R	cCa	cGa	1	1	AY.25	0.000006
N	80	P80L	cCa	cTa	1	1	AY.26	0.000028
N	80	P80Q	cCa	cAa	1	1	AY.27	0.000065
N	80	P80P	ccA	ccC	1	1	AY.29	0.000016
N	80	P80L	cCa	cTa	1	1	AY.29.1	0.000221
N	80	P80del	CCA	---	1	1	AY.3	0.00001
N	80	P80L	cCa	cTa	1	1	AY.3.1	0.000085
N	80	P80L	cCa	cTa	1	1	AY.34	0.000097
N	80	P80R	cCa	cGa	1	1	AY.35	0.000233
N	80	P80Q	cCa	cAa	1	1	AY.37	0.000316
N	80	P80T	Cca	Aca	1	1	AY.37	0.000316
N	80	P80A	Cca	Gca	1	1	AY.39	0.000025
N	80	P80Q	cCa	cAa	1	1	AY.39	0.000025
N	80	P80R	cCa	cGa	1	1	AY.39	0.000025
N	80	P80Q	cCa	cAa	1	1	AY.39.1	0.00004
N	80	P80R	cCa	cGa	1	1	AY.39.1	0.00004
N	80	P80P	ccA	ccT	1	1	AY.39.1	0.00004
N	80	P80R	cCa	cGa	1	1	AY.4	0.000002
N	80	P80Q	cCa	cAa	1	1	AY.4.2.1	0.000149
N	80	P80S	Cca	Tca	1	1	AY.4.5	0.000107
N	80	P80R	cCa	cGa	1	1	AY.4.5	0.000107
N	80	P80Q	cCa	cAa	1	1	AY.41	0.000294
N	80	P80L	cCa	cTa	1	1	AY.41	0.000294
N	80	P80T	Cca	Aca	1	1	AY.43	0.000004
N	80	P80P	ccA	ccC	1	1	AY.43	0.000004
N	80	P80A	Cca	Gca	1	1	AY.44	0.000006
N	80	P80del1	ccA	cc-	1	1	AY.44	0.000006
N	80	P80Q	cCa	cAa	1	1	AY.45	0.000122
N	80	P80S	Cca	Tca	1	1	AY.45	0.000122
N	80	P80P	ccA	ccG	1	1	AY.45	0.000122
N	80	P80P	ccA	ccG	1	1	AY.46	0.000104
N	80	P80R	cCa	cGa	1	1	AY.47	0.000031
N	80	P80Q	cCa	cAa	1	1	AY.47	0.000031
N	80	P80L	cCa	cTa	1	1	AY.47	0.000031
N	80	P80S	CcA	TcC	1	1	AY.48	0.000465
N	80	P80R	cCa	cGa	1	1	AY.5	0.000021
N	80	P80Q	cCa	cAa	1	1	AY.54	0.000095
N	80	P80Q	cCa	cAa	1	1	AY.56	0.001605
N	80	P80Q	cCa	cAa	1	1	AY.57	0.000656
N	80	P80Q	cCa	cAa	1	1	AY.6	0.000041
N	80	P80P	ccA	ccG	1	1	AY.6	0.000041
N	80	P80L	cCa	cTa	1	1	AY.6	0.000041
N	80	P80S	Cca	Tca	1	1	AY.61	0.000105
N	80	P80R	cCa	cGa	1	1	AY.61	0.000105
N	80	P80R	cCa	cGa	1	1	AY.62	0.000436
N	80	P80S	Cca	Tca	1	1	AY.62	0.000436
N	80	P80S	Cca	Tca	1	1	AY.63	0.000387
N	80	P80del	CCA	---	1	1	AY.67	0.000464
N	80	P80L	cCa	cTa	1	1	AY.67	0.000464
N	80	P80T	Cca	Aca	1	1	AY.7.1	0.000113
N	80	P80S	Cca	Tca	1	1	AY.75	0.000056
N	80	P80S	Cca	Tca	1	1	AY.75.1	0.00018
N	80	P80R	cCa	cGa	1	1	AY.75.1	0.00018
N	80	P80Q	cCa	cAa	1	1	AY.84	0.000437
N	80	P80T	Cca	Aca	1	1	AY.85	0.000427
N	80	P80T	Cca	Aca	1	1	AY.86	0.00083
N	80	P80P	ccA	ccG	1	1	AY.9.1	0.000084
N	80	P80del	CCA	---	1	1	AY.9.2	0.000037
N	80	P80S	Cca	Tca	1	1	AY.9.2	0.000037
N	80	P80S	Cca	Tca	1	1	AY.92	0.000287
N	80	P80Q	cCa	cAa	1	1	AY.98	0.000079
N	80	P80P	ccA	ccG	1	1	AY.98	0.000079
N	80	P80S	Cca	Tca	1	1	AY.98	0.000079
N	80	P80L	cCa	cTa	1	1	AY.98.1	0.000048
N	80	P80R	cCa	cGa	1	1	AY.99.2	0.000092
N	80	P80S	Cca	Tca	1	1	B	0.000128
N	80	P80del1	ccA	cc-	1	1	B.1	0.000009
N	80	P80X	CCA	TAG	1	1	B.1	0.000009
N	80	P80del	CCA	---	1	1	B.1	0.000009
N	80	P80del	CCA	---	1	1	B.1.1	0.000018
N	80	P80X	CCa	TAa	1	1	B.1.1	0.000018
N	80	P80S	Cca	Tca	1	1	B.1.1.113	0.006993
N	80	P80R	cCa	cGa	1	1	B.1.1.121	0.002427
N	80	P80S	Cca	Tca	1	1	B.1.1.15	0.013514
N	80	P80P	ccA	ccG	1	1	B.1.1.174	0.003378
N	80	P80T	Cca	Aca	1	1	B.1.1.189	0.001513
N	80	P80R	cCa	cGa	1	1	B.1.1.198	0.001468
N	80	P80S	Cca	Tca	1	1	B.1.1.222	0.000204
N	80	P80L	cCa	cTa	1	1	B.1.1.232	0.001815
N	80	P80R	cCa	cGa	1	1	B.1.1.236	0.006897
N	80	P80Q	cCa	cAa	1	1	B.1.1.255	0.00303
N	80	P80R	cCa	cGa	1	1	B.1.1.265	0.003155
N	80	P80L	cCa	cTa	1	1	B.1.1.284	0.000107
N	80	P80S	Cca	Tca	1	1	B.1.1.286	0.002899
N	80	P80R	cCa	cGa	1	1	B.1.1.294	0.001266
N	80	P80S	Cca	Tca	1	1	B.1.1.298	0.000862
N	80	P80R	cCa	cGa	1	1	B.1.1.306	0.000438
N	80	P80T	Cca	Aca	1	1	B.1.1.326	0.001761
N	80	P80R	cCa	cGa	1	1	B.1.1.33	0.000421
N	80	P80S	Cca	Tca	1	1	B.1.1.33	0.000421
N	80	P80T	Cca	Aca	1	1	B.1.1.377	0.001381
N	80	P80Q	cCa	cAa	1	1	B.1.1.420	0.001006
N	80	P80S	Cca	Tca	1	1	B.1.1.434	0.000349
N	80	P80L	cCa	cTa	1	1	B.1.1.486	0.001577
N	80	P80P	ccA	ccT	1	1	B.1.1.519	0.00004
N	80	P80R	cCa	cGa	1	1	B.1.1.54	0.003021
N	80	P80S	Cca	Tca	1	1	B.1.1.56	0.017857
N	80	P80del1	Cca	-ca	1	1	B.1.1.7	0.000001
N	80	P80del2	CCa	--a	1	1	B.1.1.7	0.000001
N	80	P80S	Cca	Tca	1	1	B.1.1.70	0.000341
N	80	P80R	cCa	cGa	1	1	B.1.1.99	0.02381
N	80	P80R	cCa	cGa	1	1	B.1.111	0.001175
N	80	P80P	ccA	ccG	1	1	B.1.158	0.02381
N	80	P80Q	cCa	cAa	1	1	B.1.160	0.000031
N	80	P80S	Cca	Tca	1	1	B.1.160	0.000031
N	80	P80L	cCa	cTa	1	1	B.1.160.22	0.006757
N	80	P80S	Cca	Tca	1	1	B.1.160.28	0.002924
N	80	P80L	cCa	cTa	1	1	B.1.160.32	0.004292
N	80	P80R	cCa	cGa	1	1	B.1.170	0.00431
N	80	P80Q	cCa	cAa	1	1	B.1.177.10	0.000878
N	80	P80L	cCa	cTa	1	1	B.1.177.21	0.000076
N	80	P80R	cCa	cGa	1	1	B.1.177.42	0.000894
N	80	P80L	cCa	cTa	1	1	B.1.177.6	0.000977
N	80	P80del	CCA	---	1	1	B.1.177.63	0.002703
N	80	P80S	Cca	Tca	1	1	B.1.177.7	0.000165
N	80	P80L	cCa	cTa	1	1	B.1.177.79	0.002342
N	80	P80L	cCa	cTa	1	1	B.1.177.8	0.000752
N	80	P80S	Cca	Tca	1	1	B.1.177.81	0.000189
N	80	P80R	cCa	cGa	1	1	B.1.179	0.003759
N	80	P80del1	Cca	-ca	1	1	B.1.2	0.000009
N	80	P80R	cCa	cGa	1	1	B.1.214	0.003663
N	80	P80S	Cca	Tca	1	1	B.1.223	0.002778
N	80	P80R	cCa	cGa	1	1	B.1.236	0.002053
N	80	P80S	Cca	Tca	1	1	B.1.241	0.000812
N	80	P80L	cCa	cTa	1	1	B.1.258	0.000067
N	80	P80L	cCa	cTa	1	1	B.1.258.11	0.000396
N	80	P80L	cCa	cTa	1	1	B.1.258.14	0.00098
N	80	P80S	Cca	Tca	1	1	B.1.258.14	0.00098
N	80	P80S	Cca	Tca	1	1	B.1.258.17	0.000104
N	80	P80L	cCa	cTa	1	1	B.1.258.22	0.002667
N	80	P80L	cCa	cTa	1	1	B.1.258.6	0.019608
N	80	P80P	ccA	ccG	1	1	B.1.280	0.007143
N	80	P80S	Cca	Tca	1	1	B.1.311	0.000275
N	80	P80Q	cCa	cAa	1	1	B.1.351	0.00003
N	80	P80L	cCa	cTa	1	1	B.1.351.5	0.0006
N	80	P80S	Cca	Tca	1	1	B.1.351.5	0.0006
N	80	P80P	ccA	ccG	1	1	B.1.36	0.000146
N	80	P80R	cCa	cGa	1	1	B.1.36	0.000146
N	80	P80A	Cca	Gca	1	1	B.1.36.16	0.001425
N	80	P80P	ccA	ccG	1	1	B.1.36.17	0.000494
N	80	P80L	cCa	cTa	1	1	B.1.36.29	0.000517
N	80	P80L	cCa	cTa	1	1	B.1.36.39	0.002217
N	80	P80S	Cca	Tca	1	1	B.1.367	0.000792
N	80	P80R	cCa	cGa	1	1	B.1.367	0.000792
N	80	P80P	ccA	ccT	1	1	B.1.375	0.00082
N	80	P80L	cCa	cTa	1	1	B.1.389	0.001002
N	80	P80S	Cca	Tca	1	1	B.1.400	0.000429
N	80	P80L	cCa	cTa	1	1	B.1.408	0.00369
N	80	P80R	cCa	cGa	1	1	B.1.415	0.014286
N	80	P80del	CCA	---	1	1	B.1.415	0.014286
N	80	P80del	CCA	---	1	1	B.1.427	0.00005
N	80	P80L	cCa	cTa	1	1	B.1.428	0.00102
N	80	P80L	cCa	cTa	1	1	B.1.433	0.003195
N	80	P80del	CCA	---	1	1	B.1.439	0.005917
N	80	P80S	Cca	Tca	1	1	B.1.466.2	0.000391
N	80	P80L	cCa	cTa	1	1	B.1.466.2	0.000391
N	80	P80T	Cca	Aca	1	1	B.1.466.2	0.000391
N	80	P80R	cCa	cGa	1	1	B.1.497	0.000315
N	80	P80T	Cca	Aca	1	1	B.1.517	0.000427
N	80	P80L	cCa	cTa	1	1	B.1.524	0.001406
N	80	P80L	cCa	cTa	1	1	B.1.525	0.000113
N	80	P80P	ccA	ccT	1	1	B.1.525	0.000113
N	80	P80T	Cca	Aca	1	1	B.1.526	0.000024
N	80	P80T	Cca	Aca	1	1	B.1.561	0.000397
N	80	P80R	cCa	cGa	1	1	B.1.575	0.000303
N	80	P80S	Cca	Tca	1	1	B.1.575	0.000303
N	80	P80L	cCa	cTa	1	1	B.1.576	0.000907
N	80	P80S	Cca	Tca	1	1	B.1.582	0.000491
N	80	P80Q	cCa	cAa	1	1	B.1.597	0.00463
N	80	P80Q	cCa	cAa	1	1	B.1.602	0.006536
N	80	P80L	cCa	cTa	1	1	B.1.609	0.000479
N	80	P80R	cCa	cGa	1	1	B.1.609	0.000479
N	80	P80L	cCa	cTa	1	1	B.1.619	0.000871
N	80	P80R	cCa	cGa	1	1	B.1.620	0.000946
N	80	P80L	cCa	cTa	1	1	B.1.621	0.000089
N	80	P80Q	cCa	cAa	1	1	B.1.621	0.000089
N	80	P80L	cCa	cTa	1	1	B.1.628	0.000352
N	80	P80R	cCa	cGa	1	1	B.1.636	0.006711
N	80	P80R	cCa	cGa	1	1	B.1.637	0.000073
N	80	P80L	cCa	cTa	1	1	B.1.637	0.000073
N	80	P80L	cCa	cTa	1	1	B.3	0.000831
N	80	P80L	cCa	cTa	1	1	B.35	0.007812
N	80	P80S	Cca	Tca	1	1	B.39	0.002331
N	80	P80L	cCa	cTa	1	1	B.6.6	0.000889
N	80	P80S	Cca	Tca	1	1	B.6.6	0.000889
N	80	P80R	cCa	cGa	1	1	C.13	0.025641
N	80	P80L	cCa	cTa	1	1	C.30	0.001727
N	80	P80L	cCa	cTa	1	1	C.37	0.000116
N	80	P80R	cCa	cGa	1	1	D.2	0.000075
N	80	P80P	ccA	ccG	1	1	D.2	0.000075
N	80	P80del	CCA	---	1	1	P.1	0.000016
N	80	P80Q	cCa	cAa	1	1	P.1.12	0.000484
N	80	P80L	cCa	cTa	1	1	P.1.17	0.000162
N	80	P80L	cCa	cTa	1	1	P.1.7	0.000319
N	80	P80S	Cca	Tca	1	1	P.2	0.000187
N	80	P80R	cCa	cGa	1	1	P.4	0.003802
N	80	P80R	cCa	cGa	1	1	P.7	0.004367
N	80	P80R	cCa	cGa	1	1	Q.1	0.000126
N	80	P80S	Cca	Tca	1	1	Q.8	0.000165
N	80	P80R	cCa	cGa	1	1	Q.8	0.000165
N	80	P80S	Cca	Tca	1	1	R.1	0.00009
N	80	P80L	cCa	cTa	1	1	R.1	0.00009
N	80	P80L	cCa	cTa	1	1	W.3	0.005263

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.