CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 16

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	16	T16T		syn	acG	acT	6743	4669	0.692422	28319-28321
N	16	T16T		syn	acG	acA	6743	2063	0.305947	28319-28321
N	16	T16T		syn	acG	acC	6743	11	0.00163132	28319-28321
N	16	T16M		nonsyn	aCg	aTg	2406	2406	1	28319-28321
N	16	T16A		nonsyn	Acg	Gcg	969	968	0.998968	28319-28321
N	16	T16A		nonsyn	AcG	GcT	969	1	0.00103199	28319-28321
N	16	T16del		del	ACG	---	48	48	1	28319-28321
N	16	T16K		nonsyn	aCg	aAg	31	31	1	28319-28321
N	16	T16S		nonsyn	Acg	Tcg	30	30	1	28319-28321
N	16	T16P		nonsyn	Acg	Ccg	6	6	1	28319-28321
N	16	T16L		nonsyn	ACg	CTg	3	2	0.666667	28319-28321
N	16	T16L		nonsyn	ACg	TTg	3	1	0.333333	28319-28321
N	16	T16I		nonsyn	aCG	aTA	2	1	0.5	28319-28321
N	16	T16I		nonsyn	aCG	aTT	2	1	0.5	28319-28321

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	16	T16T	acG	acT	4669	6743	All	0.000893
N	16	T16T	acG	acA	2063	6743	All	0.000395
N	16	T16T	acG	acC	11	6743	All	0.000002
N	16	T16M	aCg	aTg	2406	2406	All	0.00046
N	16	T16T	acG	acA	1132	1132	B.1.177.10	0.993854
N	16	T16T	acG	acT	1063	1130	B.1.1.7	0.000952
N	16	T16T	acG	acA	63	1130	B.1.1.7	0.000056
N	16	T16T	acG	acC	4	1130	B.1.1.7	0.000004
N	16	T16A	Acg	Gcg	968	969	All	0.000185
N	16	T16A	AcG	GcT	1	969	All	0
N	16	T16T	acG	acT	863	893	AY.4	0.001343
N	16	T16T	acG	acA	29	893	AY.4	0.000045
N	16	T16T	acG	acC	1	893	AY.4	0.000002
N	16	T16A	Acg	Gcg	846	846	AY.26	0.02395
N	16	T16M	aCg	aTg	377	377	B.1.1.7	0.000337
N	16	T16M	aCg	aTg	347	347	AY.44	0.002112
N	16	T16T	acG	acT	306	306	B.1.234	0.040375
N	16	T16M	aCg	aTg	240	240	B.1.2	0.002113
N	16	T16T	acG	acT	103	176	B.1.2	0.000907
N	16	T16T	acG	acA	72	176	B.1.2	0.000634
N	16	T16T	acG	acC	1	176	B.1.2	0.000009
N	16	T16T	acG	acT	121	175	B.1	0.001108
N	16	T16T	acG	acA	54	175	B.1	0.000495
N	16	T16T	acG	acT	138	146	B.1.617.2	0.00052
N	16	T16T	acG	acA	8	146	B.1.617.2	0.00003
N	16	T16T	acG	acT	141	141	B.1.177.12	0.02139
N	16	T16M	aCg	aTg	121	121	AY.4	0.000188
N	16	T16T	acG	acT	82	119	B.1.177	0.00108
N	16	T16T	acG	acA	37	119	B.1.177	0.000487
N	16	T16T	acG	acA	71	115	B.1.1	0.001288
N	16	T16T	acG	acT	44	115	B.1.1	0.000798
N	16	T16M	aCg	aTg	115	115	B.1.362	0.177196
N	16	T16T	acG	acT	113	114	AY.74	0.013068
N	16	T16T	acG	acA	1	114	AY.74	0.000116
N	16	T16T	acG	acA	79	105	B.1.429	0.001859
N	16	T16T	acG	acT	25	105	B.1.429	0.000588
N	16	T16T	acG	acC	1	105	B.1.429	0.000024
N	16	T16M	aCg	aTg	101	101	AY.43	0.000447
N	16	T16T	acG	acT	94	95	B.1.1.50	0.063815
N	16	T16T	acG	acA	1	95	B.1.1.50	0.000679
N	16	T16T	acG	acT	94	94	AY.42	0.003782
N	16	T16M	aCg	aTg	94	94	B.1.617.2	0.000354
N	16	T16T	acG	acT	77	87	AY.103	0.000478
N	16	T16T	acG	acA	10	87	AY.103	0.000062
N	16	T16T	acG	acT	82	82	B.1.1.266	1
N	16	T16T	acG	acT	67	77	AY.43	0.000297
N	16	T16T	acG	acA	8	77	AY.43	0.000035
N	16	T16T	acG	acC	2	77	AY.43	0.000009
N	16	T16M	aCg	aTg	72	72	B.1	0.000659
N	16	T16M	aCg	aTg	69	69	AY.103	0.000428
N	16	T16T	acG	acT	58	67	AY.3	0.000577
N	16	T16T	acG	acA	9	67	AY.3	0.00009
N	16	T16T	acG	acT	65	65	U.2	0.570175
N	16	T16T	acG	acT	53	64	P.1	0.000835
N	16	T16T	acG	acA	10	64	P.1	0.000158
N	16	T16T	acG	acC	1	64	P.1	0.000016
N	16	T16T	acG	acT	60	60	AY.4.5	0.00645
N	16	T16T	acG	acT	51	60	B.1.160	0.001591
N	16	T16T	acG	acA	9	60	B.1.160	0.000281
N	16	T16T	acG	acT	59	59	AY.54	0.005625
N	16	T16A	Acg	Gcg	58	58	B.1.1.7	0.000052
N	16	T16T	acG	acT	40	52	AY.25	0.000241
N	16	T16T	acG	acA	12	52	AY.25	0.000072
N	16	T16T	acG	acA	40	52	B.1.1.519	0.001588
N	16	T16T	acG	acT	12	52	B.1.1.519	0.000477
N	16	T16T	acG	acT	46	51	AY.44	0.00028
N	16	T16T	acG	acA	5	51	AY.44	0.00003
N	16	T16M	aCg	aTg	51	51	B.1.1	0.000925
N	16	T16T	acG	acT	49	49	B.1.177.81	0.009277
N	16	T16del	ACG	---	48	48	All	0.000009
N	16	T16T	acG	acA	34	39	B.1.1.1	0.011107
N	16	T16T	acG	acT	5	39	B.1.1.1	0.001633
N	16	T16M	aCg	aTg	39	39	B.1.177	0.000514
N	16	T16M	aCg	aTg	38	38	B.1.429	0.000894
N	16	T16M	aCg	aTg	36	36	AY.7.1	0.004057
N	16	T16T	acG	acT	30	32	AY.46.6	0.002166
N	16	T16T	acG	acA	2	32	AY.46.6	0.000144
N	16	T16K	aCg	aAg	31	31	All	0.000006
N	16	T16T	acG	acT	31	31	AY.102	0.000822
N	16	T16T	acG	acA	27	31	B.1.1.63	0.010417
N	16	T16T	acG	acT	4	31	B.1.1.63	0.001543
N	16	T16S	Acg	Tcg	30	30	All	0.000006
N	16	T16M	aCg	aTg	29	29	AY.47	0.000902
N	16	T16T	acG	acA	29	29	B.1.1.434	0.010108
N	16	T16T	acG	acA	28	29	B.1.466.2	0.010955
N	16	T16T	acG	acT	1	29	B.1.466.2	0.000391
N	16	T16T	acG	acT	28	28	AY.45	0.003407
N	16	T16T	acG	acT	22	27	B.1.351	0.000654
N	16	T16T	acG	acA	5	27	B.1.351	0.000149
N	16	T16M	aCg	aTg	25	25	AY.25	0.00015
N	16	T16T	acG	acT	25	25	B.1.1.47	0.13369
N	16	T16T	acG	acT	25	25	B.1.177.60	0.005461
N	16	T16M	aCg	aTg	24	24	AY.3	0.000239
N	16	T16T	acG	acA	24	24	B.1.1.70	0.008186
N	16	T16T	acG	acT	23	24	B.1.243	0.0016
N	16	T16T	acG	acA	1	24	B.1.243	0.00007
N	16	T16M	aCg	aTg	24	24	B.1.351	0.000713
N	16	T16M	aCg	aTg	23	23	AY.4.2	0.000499
N	16	T16T	acG	acT	20	21	AY.39	0.000494
N	16	T16T	acG	acC	1	21	AY.39	0.000025
N	16	T16T	acG	acT	21	21	AY.98.1	0.001017
N	16	T16T	acG	acA	14	21	B.1.1.216	0.012467
N	16	T16T	acG	acT	7	21	B.1.1.216	0.006233
N	16	T16M	aCg	aTg	21	21	B.1.1.284	0.002255
N	16	T16M	aCg	aTg	21	21	B.1.596	0.00183
N	16	T16T	acG	acA	13	20	B.1.258	0.000865
N	16	T16T	acG	acT	7	20	B.1.258	0.000466
N	16	T16M	aCg	aTg	20	20	B.1.311	0.005491
N	16	T16T	acG	acT	19	20	B.1.526	0.000447
N	16	T16T	acG	acA	1	20	B.1.526	0.000024
N	16	T16T	acG	acA	17	19	B.1.1.305	0.065637
N	16	T16T	acG	acT	2	19	B.1.1.305	0.007722
N	16	T16M	aCg	aTg	19	19	B.1.177.36	0.306452
N	16	T16T	acG	acT	18	18	AY.119	0.000636
N	16	T16M	aCg	aTg	18	18	B.1.160	0.000561
N	16	T16M	aCg	aTg	17	17	B.1.177.86	0.003119
N	16	T16M	aCg	aTg	17	17	P.1	0.000268
N	16	T16T	acG	acT	13	16	AY.121	0.001759
N	16	T16T	acG	acA	3	16	AY.121	0.000406
N	16	T16M	aCg	aTg	16	16	B.1.36.29	0.008277
N	16	T16T	acG	acT	15	15	B.1.499	0.015756
N	16	T16M	aCg	aTg	14	14	AY.111	0.002564
N	16	T16T	acG	acT	10	14	AY.4.2	0.000217
N	16	T16T	acG	acA	4	14	AY.4.2	0.000087
N	16	T16T	acG	acA	11	14	AY.98	0.000869
N	16	T16T	acG	acT	3	14	AY.98	0.000237
N	16	T16T	acG	acT	13	13	AY.3.1	0.001108
N	16	T16M	aCg	aTg	13	13	AY.35	0.00303
N	16	T16S	Acg	Tcg	13	13	B.1.1.7	0.000012
N	16	T16M	aCg	aTg	13	13	B.1.177.20	0.019727
N	16	T16T	acG	acT	13	13	B.1.36.17	0.006423
N	16	T16M	aCg	aTg	13	13	B.1.427	0.000656
N	16	T16T	acG	acA	10	13	P.1.14	0.000478
N	16	T16T	acG	acT	3	13	P.1.14	0.000143
N	16	T16T	acG	acT	12	12	AY.120	0.000446
N	16	T16M	aCg	aTg	12	12	AY.38	0.005991
N	16	T16T	acG	acT	9	11	AY.6	0.00037
N	16	T16T	acG	acA	2	11	AY.6	0.000082
N	16	T16M	aCg	aTg	11	11	B.1.177.43	0.016248
N	16	T16M	aCg	aTg	11	11	B.1.525	0.001245
N	16	T16T	acG	acA	11	11	B.1.527	0.040741
N	16	T16T	acG	acT	11	11	B.1.617.1	0.001419
N	16	T16M	aCg	aTg	10	10	AY.6	0.000411
N	16	T16M	aCg	aTg	10	10	B.1.1.214	0.000555
N	16	T16T	acG	acT	10	10	B.1.517	0.00427
N	16	T16T	acG	acT	10	10	B.1.523	0.02451
N	16	T16M	aCg	aTg	9	9	AY.118	0.000564
N	16	T16T	acG	acT	8	9	AY.118	0.000501
N	16	T16T	acG	acA	1	9	AY.118	0.000063
N	16	T16T	acG	acT	8	9	AY.29	0.000126
N	16	T16T	acG	acA	1	9	AY.29	0.000016
N	16	T16M	aCg	aTg	9	9	AY.39	0.000222
N	16	T16T	acG	acT	8	9	AY.75	0.000448
N	16	T16T	acG	acA	1	9	AY.75	0.000056
N	16	T16del	ACG	---	9	9	AY.99.2	0.000829
N	16	T16T	acG	acA	9	9	B.1.177.72	0.030508
N	16	T16T	acG	acT	8	9	B.1.396	0.005646
N	16	T16T	acG	acA	1	9	B.1.396	0.000706
N	16	T16A	Acg	Gcg	8	8	AY.3	0.00008
N	16	T16T	acG	acT	5	8	AY.9.2	0.000184
N	16	T16T	acG	acA	3	8	AY.9.2	0.00011
N	16	T16S	Acg	Tcg	8	8	B.1.1.214	0.000444
N	16	T16T	acG	acA	8	8	B.1.1.354	0.035088
N	16	T16M	aCg	aTg	8	8	B.1.36	0.001167
N	16	T16T	acG	acT	5	8	B.1.36	0.00073
N	16	T16T	acG	acA	3	8	B.1.36	0.000438
N	16	T16M	aCg	aTg	7	7	AY.100	0.000322
N	16	T16M	aCg	aTg	7	7	AY.102	0.000186
N	16	T16T	acG	acT	7	7	AY.26	0.000198
N	16	T16T	acG	acT	7	7	AY.36	0.001037
N	16	T16T	acG	acT	7	7	AY.41	0.002058
N	16	T16T	acG	acT	6	7	AY.48	0.002791
N	16	T16T	acG	acA	1	7	AY.48	0.000465
N	16	T16T	acG	acT	6	7	AY.61	0.000629
N	16	T16T	acG	acA	1	7	AY.61	0.000105
N	16	T16K	aCg	aAg	7	7	B.1.2	0.000062
N	16	T16P	Acg	Ccg	6	6	All	0.000001
N	16	T16T	acG	acT	5	6	AY.20	0.000194
N	16	T16T	acG	acA	1	6	AY.20	0.000039
N	16	T16M	aCg	aTg	6	6	AY.26	0.00017
N	16	T16M	aCg	aTg	6	6	AY.3.1	0.000512
N	16	T16A	Acg	Gcg	6	6	AY.46.6	0.000433
N	16	T16T	acG	acT	6	6	AY.5	0.000124
N	16	T16T	acG	acA	6	6	B.1.1.265	0.018927
N	16	T16T	acG	acA	6	6	B.1.1.291	0.004454
N	16	T16M	aCg	aTg	6	6	B.1.177.7	0.000989
N	16	T16T	acG	acA	6	6	B.1.36.26	0.017143
N	16	T16M	aCg	aTg	6	6	B.1.369	0.001711
N	16	T16T	acG	acT	6	6	B.1.499.1	0.666667
N	16	T16M	aCg	aTg	6	6	B.1.526	0.000141
N	16	T16M	aCg	aTg	6	6	B.1.595	0.001566
N	16	T16T	acG	acT	4	6	P.1.15	0.000929
N	16	T16T	acG	acA	2	6	P.1.15	0.000465
N	16	T16T	acG	acT	5	5	AY.100	0.00023
N	16	T16M	aCg	aTg	5	5	AY.119	0.000177
N	16	T16M	aCg	aTg	5	5	AY.121	0.000677
N	16	T16K	aCg	aAg	5	5	AY.4	0.000008
N	16	T16T	acG	acT	5	5	AY.4.2.1	0.000745
N	16	T16A	Acg	Gcg	5	5	AY.43	0.000022
N	16	T16del	ACG	---	5	5	AY.43	0.000022
N	16	T16M	aCg	aTg	5	5	AY.46	0.00052
N	16	T16M	aCg	aTg	5	5	AY.5	0.000103
N	16	T16T	acG	acA	4	5	B.1.1.25	0.002274
N	16	T16T	acG	acT	1	5	B.1.1.25	0.000569
N	16	T16A	Acg	Gcg	5	5	B.1.2	0.000044
N	16	T16A	Acg	Gcg	5	5	B.1.243	0.000348
N	16	T16M	aCg	aTg	5	5	B.1.258	0.000333
N	16	T16T	acG	acT	5	5	B.1.258.14	0.004902
N	16	T16T	acG	acT	3	5	B.1.525	0.000339
N	16	T16T	acG	acA	2	5	B.1.525	0.000226
N	16	T16T	acG	acT	5	5	B.1.619.1	0.003207
N	16	T16T	acG	acT	3	5	B.1.621	0.000266
N	16	T16T	acG	acA	2	5	B.1.621	0.000177
N	16	T16M	aCg	aTg	5	5	P.1.7	0.001596
N	16	T16T	acG	acT	5	5	P.2	0.000933
N	16	T16T	acG	acT	4	4	A.2	0.002647
N	16	T16T	acG	acA	4	4	AY.114	0.000924
N	16	T16T	acG	acT	4	4	AY.120.1	0.001284
N	16	T16T	acG	acT	4	4	AY.2	0.001425
N	16	T16M	aCg	aTg	4	4	AY.20	0.000155
N	16	T16T	acG	acT	3	4	AY.46	0.000312
N	16	T16T	acG	acA	1	4	AY.46	0.000104
N	16	T16T	acG	acT	3	4	AY.47	0.000093
N	16	T16T	acG	acA	1	4	AY.47	0.000031
N	16	T16T	acG	acA	3	4	AY.77	0.003382
N	16	T16T	acG	acT	1	4	AY.77	0.001127
N	16	T16A	Acg	Gcg	4	4	AY.98.1	0.000194
N	16	T16M	aCg	aTg	4	4	B.1.1.28	0.001245
N	16	T16T	acG	acA	4	4	B.1.1.28	0.001245
N	16	T16M	aCg	aTg	4	4	B.1.1.317	0.001647
N	16	T16T	acG	acT	3	4	B.1.1.448	0.006098
N	16	T16T	acG	acA	1	4	B.1.1.448	0.002033
N	16	T16T	acG	acA	4	4	B.1.1.526	0.014184
N	16	T16del	ACG	---	4	4	B.1.1.7	0.000004
N	16	T16T	acG	acA	4	4	B.1.111	0.0047
N	16	T16M	aCg	aTg	4	4	B.1.177.44	0.002076
N	16	T16M	aCg	aTg	4	4	B.1.177.56	0.00267
N	16	T16T	acG	acT	4	4	B.1.177.75	0.004162
N	16	T16T	acG	acT	3	4	B.1.36.29	0.001552
N	16	T16T	acG	acA	1	4	B.1.36.29	0.000517
N	16	T16T	acG	acA	4	4	B.1.36.9	0.012862
N	16	T16M	aCg	aTg	4	4	B.1.400	0.001716
N	16	T16T	acG	acA	2	4	B.1.582	0.000981
N	16	T16T	acG	acT	2	4	B.1.582	0.000981
N	16	T16T	acG	acT	4	4	B.1.596	0.000349
N	16	T16M	aCg	aTg	4	4	B.1.599	0.014599
N	16	T16M	aCg	aTg	4	4	B.1.600	0.023392
N	16	T16A	Acg	Gcg	4	4	B.1.617.2	0.000015
N	16	T16T	acG	acT	4	4	C.37	0.000464
N	16	T16T	acG	acT	4	4	Q.8	0.00066
N	16	T16T	acG	acA	2	3	A.23.1	0.001408
N	16	T16T	acG	acT	1	3	A.23.1	0.000704
N	16	T16L	ACg	CTg	2	3	All	0
N	16	T16L	ACg	TTg	1	3	All	0
N	16	T16T	acG	acA	2	3	AY.111	0.000366
N	16	T16T	acG	acT	1	3	AY.111	0.000183
N	16	T16A	Acg	Gcg	3	3	AY.113	0.000427
N	16	T16T	acG	acT	3	3	AY.117	0.000254
N	16	T16M	aCg	aTg	3	3	AY.29	0.000047
N	16	T16T	acG	acA	3	3	AY.29.1	0.000662
N	16	T16T	acG	acT	2	3	AY.34	0.000194
N	16	T16T	acG	acA	1	3	AY.34	0.000097
N	16	T16A	Acg	Gcg	2	3	AY.4	0.000003
N	16	T16A	AcG	GcT	1	3	AY.4	0.000002
N	16	T16T	acG	acT	3	3	AY.46.3	0.002801
N	16	T16T	acG	acT	3	3	AY.46.4	0.000494
N	16	T16M	aCg	aTg	3	3	AY.54	0.000286
N	16	T16T	acG	acA	3	3	AY.7.2	0.001678
N	16	T16M	aCg	aTg	3	3	AY.98	0.000237
N	16	T16K	aCg	aAg	3	3	B.1	0.000027
N	16	T16M	aCg	aTg	3	3	B.1.1.228	0.009146
N	16	T16T	acG	acA	2	3	B.1.1.277	0.001517
N	16	T16T	acG	acT	1	3	B.1.1.277	0.000759
N	16	T16T	acG	acT	2	3	B.1.1.317	0.000823
N	16	T16T	acG	acA	1	3	B.1.1.317	0.000412
N	16	T16del	ACG	---	3	3	B.1.1.368	0.009259
N	16	T16T	acG	acA	3	3	B.1.1.368	0.009259
N	16	T16T	acG	acT	3	3	B.1.1.397	0.006757
N	16	T16M	aCg	aTg	3	3	B.1.1.429	0.013825
N	16	T16M	aCg	aTg	3	3	B.1.1.519	0.000119
N	16	T16M	aCg	aTg	3	3	B.1.160.20	0.026786
N	16	T16M	aCg	aTg	3	3	B.1.160.26	0.007264
N	16	T16M	aCg	aTg	3	3	B.1.177.60	0.000655
N	16	T16T	acG	acA	2	3	B.1.177.73	0.001133
N	16	T16T	acG	acT	1	3	B.1.177.73	0.000566
N	16	T16M	aCg	aTg	3	3	B.1.177.75	0.003122
N	16	T16T	acG	acA	2	3	B.1.177.8	0.001505
N	16	T16T	acG	acT	1	3	B.1.177.8	0.000752
N	16	T16M	aCg	aTg	3	3	B.1.221	0.000213
N	16	T16T	acG	acT	3	3	B.1.239	0.003663
N	16	T16T	acG	acT	2	3	B.1.36.18	0.00084
N	16	T16T	acG	acA	1	3	B.1.36.18	0.00042
N	16	T16T	acG	acT	3	3	B.1.427	0.000151
N	16	T16T	acG	acT	3	3	B.1.470	0.004213
N	16	T16T	acG	acT	3	3	B.1.575	0.00091
N	16	T16T	acG	acT	2	3	B.1.595	0.000522
N	16	T16T	acG	acA	1	3	B.1.595	0.000261
N	16	T16M	aCg	aTg	3	3	B.1.597	0.013889
N	16	T16del	ACG	---	3	3	B.1.617.2	0.000011
N	16	T16K	aCg	aAg	3	3	B.1.617.2	0.000011
N	16	T16M	aCg	aTg	3	3	B.1.621	0.000266
N	16	T16M	aCg	aTg	3	3	B.1.621.1	0.001517
N	16	T16T	acG	acA	3	3	B.40	0.001093
N	16	T16T	acG	acT	3	3	C.18	0.007772
N	16	T16T	acG	acT	3	3	C.31	0.053571
N	16	T16T	acG	acA	2	3	C.36	0.001821
N	16	T16T	acG	acT	1	3	C.36	0.000911
N	16	T16K	aCg	aAg	3	3	P.1.16	0.001122
N	16	T16M	aCg	aTg	3	3	P.2	0.00056
N	16	T16M	aCg	aTg	2	2	A	0.000774
N	16	T16M	aCg	aTg	2	2	A.23.1	0.001408
N	16	T16A	Acg	Gcg	2	2	A.27	0.003311
N	16	T16I	aCG	aTT	1	2	All	0
N	16	T16I	aCG	aTA	1	2	All	0
N	16	T16M	aCg	aTg	2	2	AU.2	0.004843
N	16	T16M	aCg	aTg	2	2	AY.1	0.000791
N	16	T16K	aCg	aAg	2	2	AY.101	0.000981
N	16	T16T	acG	acT	2	2	AY.110	0.000225
N	16	T16T	acG	acT	2	2	AY.113	0.000285
N	16	T16del	ACG	---	2	2	AY.121	0.000271
N	16	T16T	acG	acT	2	2	AY.16.1	0.00094
N	16	T16T	acG	acT	2	2	AY.23	0.000139
N	16	T16del	ACG	---	2	2	AY.25	0.000012
N	16	T16T	acG	acT	2	2	AY.27	0.000129
N	16	T16S	Acg	Tcg	2	2	AY.3	0.00002
N	16	T16T	acG	acT	2	2	AY.33	0.000134
N	16	T16M	aCg	aTg	2	2	AY.34	0.000194
N	16	T16T	acG	acT	2	2	AY.35	0.000466
N	16	T16T	acG	acT	2	2	AY.37	0.000632
N	16	T16A	Acg	Gcg	2	2	AY.39	0.000049
N	16	T16K	aCg	aAg	2	2	AY.39	0.000049
N	16	T16T	acG	acA	2	2	AY.39.1	0.000079
N	16	T16M	aCg	aTg	2	2	AY.39.1	0.000079
N	16	T16P	Acg	Ccg	2	2	AY.4	0.000003
N	16	T16del	ACG	---	2	2	AY.46	0.000208
N	16	T16A	Acg	Gcg	2	2	AY.47	0.000062
N	16	T16M	aCg	aTg	2	2	AY.62	0.000871
N	16	T16M	aCg	aTg	2	2	AY.67	0.000929
N	16	T16T	acG	acT	2	2	AY.68	0.000547
N	16	T16T	acG	acT	1	2	AY.69	0.000187
N	16	T16T	acG	acA	1	2	AY.69	0.000187
N	16	T16M	aCg	aTg	2	2	AY.74	0.000231
N	16	T16T	acG	acT	1	2	AY.75.1	0.00018
N	16	T16T	acG	acA	1	2	AY.75.1	0.00018
N	16	T16T	acG	acT	2	2	AY.84	0.000875
N	16	T16T	acG	acT	2	2	AY.9.1	0.000167
N	16	T16T	acG	acT	2	2	AY.93	0.000546
N	16	T16M	aCg	aTg	2	2	AY.99.2	0.000184
N	16	T16T	acG	acT	2	2	AY.99.2	0.000184
N	16	T16A	Acg	Gcg	2	2	B.1.1	0.000036
N	16	T16P	Acg	Ccg	2	2	B.1.1	0.000036
N	16	T16del	ACG	---	2	2	B.1.1	0.000036
N	16	T16T	acG	acT	2	2	B.1.1.129	0.018349
N	16	T16T	acG	acA	1	2	B.1.1.141	0.002012
N	16	T16T	acG	acT	1	2	B.1.1.141	0.002012
N	16	T16T	acG	acA	2	2	B.1.1.159	0.009346
N	16	T16M	aCg	aTg	2	2	B.1.1.161	0.007067
N	16	T16M	aCg	aTg	2	2	B.1.1.189	0.003026
N	16	T16T	acG	acA	2	2	B.1.1.198	0.002937
N	16	T16T	acG	acT	2	2	B.1.1.207	0.002364
N	16	T16T	acG	acT	2	2	B.1.1.267	0.020202
N	16	T16M	aCg	aTg	2	2	B.1.1.27	0.011299
N	16	T16M	aCg	aTg	2	2	B.1.1.294	0.002532
N	16	T16T	acG	acT	2	2	B.1.1.297	0.004474
N	16	T16T	acG	acA	2	2	B.1.1.378	0.014599
N	16	T16M	aCg	aTg	2	2	B.1.1.39	0.001019
N	16	T16M	aCg	aTg	2	2	B.1.1.412	0.015267
N	16	T16T	acG	acA	2	2	B.1.1.432	0.002532
N	16	T16M	aCg	aTg	2	2	B.1.1.50	0.001358
N	16	T16A	Acg	Gcg	2	2	B.1.1.519	0.000079
N	16	T16M	aCg	aTg	2	2	B.1.1.63	0.000772
N	16	T16T	acG	acT	2	2	B.1.160.16	0.001859
N	16	T16T	acG	acT	2	2	B.1.177.4	0.000422
N	16	T16M	aCg	aTg	2	2	B.1.177.6	0.001953
N	16	T16T	acG	acT	2	2	B.1.177.7	0.00033
N	16	T16T	acG	acA	2	2	B.1.192	0.018519
N	16	T16T	acG	acA	2	2	B.1.201	0.011364
N	16	T16T	acG	acT	2	2	B.1.22	0.002635
N	16	T16M	aCg	aTg	2	2	B.1.243	0.000139
N	16	T16T	acG	acT	1	2	B.1.258.17	0.000104
N	16	T16T	acG	acA	1	2	B.1.258.17	0.000104
N	16	T16M	aCg	aTg	2	2	B.1.3	0.005236
N	16	T16K	aCg	aAg	2	2	B.1.351	0.000059
N	16	T16T	acG	acA	2	2	B.1.36.10	0.009569
N	16	T16T	acG	acT	2	2	B.1.36.22	0.002415
N	16	T16T	acG	acT	2	2	B.1.36.7	0.008
N	16	T16T	acG	acT	2	2	B.1.367	0.001585
N	16	T16T	acG	acT	2	2	B.1.369	0.00057
N	16	T16M	aCg	aTg	2	2	B.1.444	0.031746
N	16	T16T	acG	acA	2	2	B.1.466.1	0.014388
N	16	T16M	aCg	aTg	2	2	B.1.466.2	0.000782
N	16	T16M	aCg	aTg	2	2	B.1.517.1	0.010526
N	16	T16T	acG	acA	2	2	B.1.524	0.002813
N	16	T16T	acG	acT	2	2	B.1.561	0.000794
N	16	T16T	acG	acT	2	2	B.1.564	0.000852
N	16	T16M	aCg	aTg	2	2	B.1.580	0.00813
N	16	T16T	acG	acA	2	2	B.1.609	0.000959
N	16	T16S	Acg	Tcg	2	2	B.1.617.2	0.000008
N	16	T16M	aCg	aTg	2	2	B.1.619.1	0.001283
N	16	T16T	acG	acT	2	2	B.1.88.1	0.009615
N	16	T16M	aCg	aTg	2	2	B.23	0.005848
N	16	T16T	acG	acA	2	2	C.16	0.002121
N	16	T16T	acG	acA	2	2	C.23	0.011628
N	16	T16M	aCg	aTg	2	2	C.31	0.035714
N	16	T16T	acG	acT	2	2	K.2	0.08
N	16	T16M	aCg	aTg	2	2	P.1.15	0.000465
N	16	T16T	acG	acA	1	2	P.1.17	0.000162
N	16	T16T	acG	acT	1	2	P.1.17	0.000162
N	16	T16T	acG	acT	2	2	P.1.2	0.002312
N	16	T16T	acG	acT	1	2	Q.3	0.000145
N	16	T16T	acG	acA	1	2	Q.3	0.000145
N	16	T16M	aCg	aTg	2	2	Q.8	0.00033
N	16	T16M	aCg	aTg	2	2	R.1	0.00018
N	16	T16T	acG	acA	1	1	A.19	0.009434
N	16	T16T	acG	acT	1	1	A.2.5	0.000499
N	16	T16T	acG	acT	1	1	A.27	0.001656
N	16	T16M	aCg	aTg	1	1	A.3	0.002096
N	16	T16M	aCg	aTg	1	1	AB.1	0.008197
N	16	T16M	aCg	aTg	1	1	AQ.2	0.111111
N	16	T16T	acG	acT	1	1	AU.2	0.002421
N	16	T16T	acG	acT	1	1	AY.10	0.00053
N	16	T16del	ACG	---	1	1	AY.100	0.000046
N	16	T16T	acG	acT	1	1	AY.101	0.00049
N	16	T16del	ACG	---	1	1	AY.101	0.00049
N	16	T16M	aCg	aTg	1	1	AY.101	0.00049
N	16	T16A	Acg	Gcg	1	1	AY.102	0.000027
N	16	T16K	aCg	aAg	1	1	AY.102	0.000027
N	16	T16T	acG	acT	1	1	AY.106	0.000335
N	16	T16T	acG	acA	1	1	AY.108	0.001103
N	16	T16S	Acg	Tcg	1	1	AY.113	0.000142
N	16	T16T	acG	acT	1	1	AY.116	0.000287
N	16	T16T	acG	acT	1	1	AY.116.1	0.000311
N	16	T16A	Acg	Gcg	1	1	AY.118	0.000063
N	16	T16K	aCg	aAg	1	1	AY.120	0.000037
N	16	T16del	ACG	---	1	1	AY.120	0.000037
N	16	T16M	aCg	aTg	1	1	AY.120	0.000037
N	16	T16del	ACG	---	1	1	AY.120.1	0.000321
N	16	T16M	aCg	aTg	1	1	AY.16.1	0.00047
N	16	T16L	ACg	CTg	1	1	AY.18	0.010101
N	16	T16K	aCg	aAg	1	1	AY.23	0.00007
N	16	T16L	ACg	CTg	1	1	AY.23	0.00007
N	16	T16M	aCg	aTg	1	1	AY.23	0.00007
N	16	T16del	ACG	---	1	1	AY.23	0.00007
N	16	T16A	Acg	Gcg	1	1	AY.23	0.00007
N	16	T16A	Acg	Gcg	1	1	AY.25	0.000006
N	16	T16M	aCg	aTg	1	1	AY.27	0.000065
N	16	T16S	Acg	Tcg	1	1	AY.27	0.000065
N	16	T16S	Acg	Tcg	1	1	AY.30	0.000396
N	16	T16T	acG	acT	1	1	AY.31	0.018519
N	16	T16M	aCg	aTg	1	1	AY.33	0.000067
N	16	T16del	ACG	---	1	1	AY.33	0.000067
N	16	T16T	acG	acT	1	1	AY.38	0.000499
N	16	T16A	Acg	Gcg	1	1	AY.39.1	0.00004
N	16	T16del	ACG	---	1	1	AY.4	0.000002
N	16	T16T	acG	acA	1	1	AY.4.1	0.000737
N	16	T16T	acG	acT	1	1	AY.4.4	0.000409
N	16	T16del	ACG	---	1	1	AY.4.4	0.000409
N	16	T16T	acG	acT	1	1	AY.40	0.000964
N	16	T16M	aCg	aTg	1	1	AY.42	0.00004
N	16	T16S	Acg	Tcg	1	1	AY.43	0.000004
N	16	T16del	ACG	---	1	1	AY.44	0.000006
N	16	T16A	Acg	Gcg	1	1	AY.44	0.000006
N	16	T16M	aCg	aTg	1	1	AY.45	0.000122
N	16	T16T	acG	acT	1	1	AY.46.1	0.001027
N	16	T16del	ACG	---	1	1	AY.46.3	0.000934
N	16	T16del	ACG	---	1	1	AY.46.6	0.000072
N	16	T16M	aCg	aTg	1	1	AY.48	0.000465
N	16	T16K	aCg	aAg	1	1	AY.5	0.000021
N	16	T16del	ACG	---	1	1	AY.5	0.000021
N	16	T16del	ACG	---	1	1	AY.5.3	0.000337
N	16	T16T	acG	acA	1	1	AY.5.4	0.000277
N	16	T16T	acG	acT	1	1	AY.51	0.000909
N	16	T16T	acG	acT	1	1	AY.52	0.000814
N	16	T16T	acG	acT	1	1	AY.56	0.001605
N	16	T16T	acG	acT	1	1	AY.62	0.000436
N	16	T16T	acG	acT	1	1	AY.64	0.000595
N	16	T16M	aCg	aTg	1	1	AY.66	0.00107
N	16	T16T	acG	acT	1	1	AY.7	0.000196
N	16	T16M	aCg	aTg	1	1	AY.7	0.000196
N	16	T16T	acG	acT	1	1	AY.7.1	0.000113
N	16	T16T	acG	acT	1	1	AY.72	0.001361
N	16	T16T	acG	acT	1	1	AY.73	0.000665
N	16	T16A	Acg	Gcg	1	1	AY.75.1	0.00018
N	16	T16T	acG	acT	1	1	AY.78	0.001541
N	16	T16A	Acg	Gcg	1	1	AY.81	0.001992
N	16	T16M	aCg	aTg	1	1	AY.85	0.000427
N	16	T16T	acG	acT	1	1	AY.86	0.00083
N	16	T16T	acG	acT	1	1	AY.9	0.000068
N	16	T16M	aCg	aTg	1	1	AY.9.1	0.000084
N	16	T16M	aCg	aTg	1	1	AY.9.2	0.000037
N	16	T16T	acG	acT	1	1	AY.91	0.00073
N	16	T16M	aCg	aTg	1	1	AY.93	0.000273
N	16	T16T	acG	acA	1	1	B	0.000128
N	16	T16A	Acg	Gcg	1	1	B.1	0.000009
N	16	T16P	Acg	Ccg	1	1	B.1	0.000009
N	16	T16M	aCg	aTg	1	1	B.1.1.1	0.000327
N	16	T16M	aCg	aTg	1	1	B.1.1.117	0.009709
N	16	T16del	ACG	---	1	1	B.1.1.216	0.00089
N	16	T16M	aCg	aTg	1	1	B.1.1.219	0.005
N	16	T16T	acG	acA	1	1	B.1.1.220	0.001859
N	16	T16T	acG	acA	1	1	B.1.1.222	0.000204
N	16	T16T	acG	acT	1	1	B.1.1.231	0.003096
N	16	T16T	acG	acA	1	1	B.1.1.273	0.006757
N	16	T16M	aCg	aTg	1	1	B.1.1.282	0.011628
N	16	T16T	acG	acT	1	1	B.1.1.285	0.006536
N	16	T16M	aCg	aTg	1	1	B.1.1.298	0.000862
N	16	T16M	aCg	aTg	1	1	B.1.1.304	0.002809
N	16	T16T	acG	acA	1	1	B.1.1.306	0.000438
N	16	T16M	aCg	aTg	1	1	B.1.1.33	0.000421
N	16	T16T	acG	acA	1	1	B.1.1.369	0.000446
N	16	T16M	aCg	aTg	1	1	B.1.1.37	0.000193
N	16	T16T	acG	acA	1	1	B.1.1.37	0.000193
N	16	T16T	acG	acA	1	1	B.1.1.372	0.000689
N	16	T16T	acG	acT	1	1	B.1.1.409	0.002833
N	16	T16T	acG	acA	1	1	B.1.1.420	0.001006
N	16	T16M	aCg	aTg	1	1	B.1.1.435	0.034483
N	16	T16T	acG	acA	1	1	B.1.1.46	0.004367
N	16	T16M	aCg	aTg	1	1	B.1.1.461	0.012048
N	16	T16M	aCg	aTg	1	1	B.1.1.464	0.001473
N	16	T16T	acG	acT	1	1	B.1.1.483	0.038462
N	16	T16T	acG	acT	1	1	B.1.1.5	0.008333
N	16	T16T	acG	acT	1	1	B.1.1.518	0.006329
N	16	T16T	acG	acA	1	1	B.1.1.521	0.005348
N	16	T16M	aCg	aTg	1	1	B.1.1.523	0.001563
N	16	T16T	acG	acA	1	1	B.1.1.58	0.005376
N	16	T16P	Acg	Ccg	1	1	B.1.1.7	0.000001
N	16	T16M	aCg	aTg	1	1	B.1.1.70	0.000341
N	16	T16T	acG	acT	1	1	B.1.1.90	0.1
N	16	T16M	aCg	aTg	1	1	B.1.110	0.004525
N	16	T16M	aCg	aTg	1	1	B.1.120	0.007692
N	16	T16M	aCg	aTg	1	1	B.1.146	0.004237
N	16	T16I	aCG	aTT	1	1	B.1.160	0.000031
N	16	T16I	aCG	aTA	1	1	B.1.177.10	0.000878
N	16	T16M	aCg	aTg	1	1	B.1.177.11	0.001698
N	16	T16M	aCg	aTg	1	1	B.1.177.12	0.000152
N	16	T16M	aCg	aTg	1	1	B.1.177.16	0.000664
N	16	T16T	acG	acT	1	1	B.1.177.20	0.001517
N	16	T16T	acG	acA	1	1	B.1.177.23	0.003236
N	16	T16M	aCg	aTg	1	1	B.1.177.32	0.00135
N	16	T16T	acG	acT	1	1	B.1.177.33	0.001645
N	16	T16M	aCg	aTg	1	1	B.1.177.35	0.000691
N	16	T16M	aCg	aTg	1	1	B.1.177.4	0.000211
N	16	T16T	acG	acA	1	1	B.1.177.42	0.000894
N	16	T16T	acG	acT	1	1	B.1.177.44	0.000519
N	16	T16M	aCg	aTg	1	1	B.1.177.45	0.000381
N	16	T16T	acG	acT	1	1	B.1.177.45	0.000381
N	16	T16T	acG	acT	1	1	B.1.177.46	0.000918
N	16	T16M	aCg	aTg	1	1	B.1.177.5	0.001242
N	16	T16T	acG	acT	1	1	B.1.177.57	0.000281
N	16	T16M	aCg	aTg	1	1	B.1.177.57	0.000281
N	16	T16M	aCg	aTg	1	1	B.1.177.62	0.001192
N	16	T16L	ACg	TTg	1	1	B.1.177.63	0.002703
N	16	T16M	aCg	aTg	1	1	B.1.177.76	0.002494
N	16	T16M	aCg	aTg	1	1	B.1.177.77	0.000726
N	16	T16M	aCg	aTg	1	1	B.1.177.81	0.000189
N	16	T16T	acG	acT	1	1	B.1.177.82	0.000477
N	16	T16M	aCg	aTg	1	1	B.1.177.83	0.001481
N	16	T16M	aCg	aTg	1	1	B.1.177.87	0.000728
N	16	T16M	aCg	aTg	1	1	B.1.177.9	0.001332
N	16	T16M	aCg	aTg	1	1	B.1.199	0.004132
N	16	T16del	ACG	---	1	1	B.1.2	0.000009
N	16	T16T	acG	acT	1	1	B.1.206	0.000816
N	16	T16M	aCg	aTg	1	1	B.1.210	0.002132
N	16	T16M	aCg	aTg	1	1	B.1.214.2	0.0006
N	16	T16T	acG	acT	1	1	B.1.221	0.000071
N	16	T16A	Acg	Gcg	1	1	B.1.221	0.000071
N	16	T16T	acG	acT	1	1	B.1.232	0.000537
N	16	T16M	aCg	aTg	1	1	B.1.234	0.000132
N	16	T16T	acG	acT	1	1	B.1.237	0.004975
N	16	T16M	aCg	aTg	1	1	B.1.240	0.000216
N	16	T16M	aCg	aTg	1	1	B.1.258.5	0.008772
N	16	T16M	aCg	aTg	1	1	B.1.265	0.001271
N	16	T16T	acG	acA	1	1	B.1.314	0.007519
N	16	T16T	acG	acA	1	1	B.1.320	0.001245
N	16	T16T	acG	acT	1	1	B.1.332	0.003497
N	16	T16T	acG	acT	1	1	B.1.349	0.000715
N	16	T16T	acG	acT	1	1	B.1.351.2	0.000303
N	16	T16T	acG	acA	1	1	B.1.351.3	0.000876
N	16	T16T	acG	acT	1	1	B.1.36.16	0.001425
N	16	T16T	acG	acT	1	1	B.1.36.24	0.006173
N	16	T16T	acG	acT	1	1	B.1.36.35	0.002604
N	16	T16M	aCg	aTg	1	1	B.1.36.7	0.004
N	16	T16T	acG	acA	1	1	B.1.36.8	0.001
N	16	T16M	aCg	aTg	1	1	B.1.361	0.001289
N	16	T16T	acG	acA	1	1	B.1.381	0.007812
N	16	T16T	acG	acT	1	1	B.1.395	0.007042
N	16	T16T	acG	acT	1	1	B.1.400	0.000429
N	16	T16T	acG	acT	1	1	B.1.402	0.009804
N	16	T16M	aCg	aTg	1	1	B.1.416	0.001269
N	16	T16M	aCg	aTg	1	1	B.1.423	0.010204
N	16	T16T	acG	acA	1	1	B.1.425	0.002994
N	16	T16T	acG	acT	1	1	B.1.426	0.001009
N	16	T16M	aCg	aTg	1	1	B.1.438.1	0.000107
N	16	T16M	aCg	aTg	1	1	B.1.443	0.004673
N	16	T16T	acG	acT	1	1	B.1.443	0.004673
N	16	T16T	acG	acT	1	1	B.1.452	0.013699
N	16	T16T	acG	acT	1	1	B.1.467	0.04
N	16	T16T	acG	acA	1	1	B.1.497	0.000315
N	16	T16M	aCg	aTg	1	1	B.1.503	0.002488
N	16	T16M	aCg	aTg	1	1	B.1.504	0.03125
N	16	T16T	acG	acT	1	1	B.1.560	0.00463
N	16	T16M	aCg	aTg	1	1	B.1.561	0.000397
N	16	T16M	aCg	aTg	1	1	B.1.564	0.000426
N	16	T16S	Acg	Tcg	1	1	B.1.564	0.000426
N	16	T16T	acG	acT	1	1	B.1.570	0.002941
N	16	T16T	acG	acT	1	1	B.1.571	0.009709
N	16	T16M	aCg	aTg	1	1	B.1.575.1	0.002439
N	16	T16T	acG	acT	1	1	B.1.576	0.000907
N	16	T16T	acG	acT	1	1	B.1.577	0.000687
N	16	T16A	Acg	Gcg	1	1	B.1.595	0.000261
N	16	T16M	aCg	aTg	1	1	B.1.623	0.000536
N	16	T16M	aCg	aTg	1	1	B.1.627	0.00202
N	16	T16T	acG	acT	1	1	B.1.628	0.000352
N	16	T16T	acG	acT	1	1	B.1.637	0.000073
N	16	T16M	aCg	aTg	1	1	B.1.88.1	0.004808
N	16	T16T	acG	acA	1	1	B.1.9.4	0.006135
N	16	T16T	acG	acT	1	1	B.39	0.002331
N	16	T16T	acG	acT	1	1	B.4.5	0.011905
N	16	T16M	aCg	aTg	1	1	B.40	0.000364
N	16	T16M	aCg	aTg	1	1	B.6.6	0.000889
N	16	T16T	acG	acA	1	1	C.33	0.058824
N	16	T16T	acG	acT	1	1	C.36.3	0.000567
N	16	T16M	aCg	aTg	1	1	C.37	0.000116
N	16	T16T	acG	acA	1	1	C.9	0.030303
N	16	T16M	aCg	aTg	1	1	D.2	0.000075
N	16	T16T	acG	acA	1	1	N.6	0.007092
N	16	T16T	acG	acT	1	1	P.1.1	0.000318
N	16	T16T	acG	acA	1	1	P.1.12	0.000484
N	16	T16M	aCg	aTg	1	1	P.1.12	0.000484
N	16	T16M	aCg	aTg	1	1	P.1.14	0.000048
N	16	T16T	acG	acT	1	1	P.1.16	0.000374
N	16	T16M	aCg	aTg	1	1	P.1.17	0.000162
N	16	T16T	acG	acT	1	1	P.1.7	0.000319
N	16	T16del	ACG	---	1	1	P.1.7	0.000319
N	16	T16M	aCg	aTg	1	1	Q.1	0.000126
N	16	T16T	acG	acT	1	1	Q.1	0.000126
N	16	T16A	Acg	Gcg	1	1	Q.2	0.000613
N	16	T16M	aCg	aTg	1	1	Q.3	0.000145
N	16	T16T	acG	acT	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.