CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 146

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
S	146	H146H		syn	caC	caT	13133	13133	1	21998-22000
S	146	H146Y		nonsyn	Cac	Tac	3823	3822	0.999738	21998-22000
S	146	H146Y		nonsyn	CaC	TaT	3823	1	0.000261575	21998-22000
S	146	H146Q		nonsyn	caC	caA	1154	1101	0.954073	21998-22000
S	146	H146Q		nonsyn	caC	caG	1154	53	0.0459272	21998-22000
S	146	H146del		del	CAC	---	970	970	1	21998-22000
S	146	H146R		nonsyn	cAc	cGc	306	306	1	21998-22000
S	146	H146N		nonsyn	Cac	Aac	161	161	1	21998-22000
S	146	H146L		nonsyn	cAc	cTc	114	114	1	21998-22000
S	146	H146K		nonsyn	CaC	AaA	55	55	1	21998-22000
S	146	H146P		nonsyn	cAc	cCc	33	26	0.787879	21998-22000
S	146	H146P		nonsyn	cAC	cCA	33	7	0.212121	21998-22000
S	146	H146D		nonsyn	Cac	Gac	26	25	0.961538	21998-22000
S	146	H146D		nonsyn	CaC	GaT	26	1	0.0384615	21998-22000
S	146	H146T		nonsyn	CAC	ACA	23	22	0.956522	21998-22000
S	146	H146T		nonsyn	CAc	ACc	23	1	0.0434783	21998-22000
S	146	H146del1		del	Cac	-ac	13	8	0.615385	21998-22000
S	146	H146del1		del	caC	ca-	13	4	0.307692	21998-22000
S	146	H146del1		del	cAc	c-c	13	1	0.0769231	21998-22000
S	146	H146del2		del	CAc	--c	11	9	0.818182	21998-22000
S	146	H146del2		del	cAC	c--	11	2	0.181818	21998-22000
S	146	H146C		nonsyn	CAc	TGc	2	2	1	21998-22000
S	146	H146G		nonsyn	CAC	GGT	1	1	1	21998-22000
S	146	H146X		nonsyn	CaC	TaA	1	1	1	21998-22000

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
S	146	H146H	caC	caT	13133	13133	All	0.002512
S	146	H146H	caC	caT	3922	3922	AY.4	0.006104
S	146	H146Y	Cac	Tac	3822	3823	All	0.000731
S	146	H146Y	CaC	TaT	1	3823	All	0
S	146	H146H	caC	caT	2098	2098	AY.4.4	0.858429
S	146	H146H	caC	caT	1972	1972	B.1.1.7	0.001765
S	146	H146H	caC	caT	1368	1368	A.23.1	0.96338
S	146	H146Y	Cac	Tac	1360	1360	B.1.1.7	0.001218
S	146	H146Q	caC	caA	1101	1154	All	0.000211
S	146	H146Q	caC	caG	53	1154	All	0.00001
S	146	H146del	CAC	---	970	970	All	0.000186
S	146	H146Y	Cac	Tac	461	462	AY.4	0.000718
S	146	H146Y	CaC	TaT	1	462	AY.4	0.000002
S	146	H146Q	caC	caA	433	444	B.1.1.7	0.000388
S	146	H146Q	caC	caG	11	444	B.1.1.7	0.00001
S	146	H146H	caC	caT	390	390	AY.25	0.002346
S	146	H146H	caC	caT	308	308	B.1.617.2	0.00116
S	146	H146R	cAc	cGc	306	306	All	0.000059
S	146	H146Y	Cac	Tac	274	274	B.1.1.1	0.089513
S	146	H146Y	Cac	Tac	242	242	B.1.177	0.003187
S	146	H146H	caC	caT	201	201	B.1.2	0.00177
S	146	H146del	CAC	---	201	201	B.1.618	0.810484
S	146	H146H	caC	caT	192	192	AY.43	0.000851
S	146	H146del	CAC	---	173	173	B.1.1.7	0.000155
S	146	H146H	caC	caT	166	166	AY.44	0.00101
S	146	H146R	cAc	cGc	163	163	AY.3	0.001621
S	146	H146N	Cac	Aac	161	161	All	0.000031
S	146	H146Y	Cac	Tac	129	129	B.1.617.2	0.000486
S	146	H146H	caC	caT	121	121	AY.20	0.004703
S	146	H146Y	Cac	Tac	116	116	AY.3	0.001154
S	146	H146L	cAc	cTc	114	114	All	0.000022
S	146	H146H	caC	caT	110	110	AY.119	0.003884
S	146	H146Y	Cac	Tac	104	104	AY.43	0.000461
S	146	H146H	caC	caT	100	100	AY.6	0.004113
S	146	H146H	caC	caT	94	94	A.23	0.989474
S	146	H146H	caC	caT	93	93	AY.103	0.000577
S	146	H146H	caC	caT	84	84	B.1.131	0.736842
S	146	H146H	caC	caT	82	82	AY.3	0.000816
S	146	H146H	caC	caT	82	82	B.1	0.000751
S	146	H146Y	Cac	Tac	79	79	B.1	0.000724
S	146	H146H	caC	caT	79	79	B.1.177	0.00104
S	146	H146del	CAC	---	77	77	AY.4	0.00012
S	146	H146H	caC	caT	75	75	AY.9.2	0.002755
S	146	H146H	caC	caT	74	74	P.1	0.001166
S	146	H146Q	caC	caA	60	65	AY.4	0.000093
S	146	H146Q	caC	caG	5	65	AY.4	0.000008
S	146	H146Y	Cac	Tac	61	61	AY.9	0.004123
S	146	H146Y	Cac	Tac	59	59	AY.25	0.000355
S	146	H146Y	Cac	Tac	56	56	B.1.243	0.003897
S	146	H146K	CaC	AaA	55	55	All	0.000011
S	146	H146H	caC	caT	52	52	B.1.1	0.000943
S	146	H146del	CAC	---	50	50	AY.102	0.001326
S	146	H146del	CAC	---	50	50	AY.43	0.000222
S	146	H146H	caC	caT	49	49	B.1.369	0.013976
S	146	H146N	Cac	Aac	49	49	B.1.621	0.004337
S	146	H146Q	caC	caA	47	47	B.1.36	0.006857
S	146	H146Y	Cac	Tac	46	46	AY.103	0.000286
S	146	H146Y	Cac	Tac	45	45	AY.44	0.000274
S	146	H146del	CAC	---	44	44	C.37	0.005107
S	146	H146H	caC	caT	43	43	AY.102	0.00114
S	146	H146H	caC	caT	38	38	B.1.1.519	0.001509
S	146	H146R	cAc	cGc	38	38	B.1.1.7	0.000034
S	146	H146Y	Cac	Tac	38	38	B.1.264	0.469136
S	146	H146Y	Cac	Tac	37	37	AY.29	0.000584
S	146	H146H	caC	caT	37	37	AY.39	0.000914
S	146	H146Q	caC	caA	34	35	B.1.617.2	0.000128
S	146	H146Q	caC	caG	1	35	B.1.617.2	0.000004
S	146	H146Q	caC	caA	34	34	B.1.1.318	0.01026
S	146	H146H	caC	caT	34	34	P.2	0.006346
S	146	H146P	cAc	cCc	26	33	All	0.000005
S	146	H146P	cAC	cCA	7	33	All	0.000001
S	146	H146Y	Cac	Tac	33	33	B.1.1.519	0.00131
S	146	H146Q	caC	caA	30	33	B.1.177.81	0.00568
S	146	H146Q	caC	caG	3	33	B.1.177.81	0.000568
S	146	H146H	caC	caT	32	32	B.1.1.270	0.329897
S	146	H146Q	caC	caA	30	30	AY.103	0.000186
S	146	H146Y	Cac	Tac	30	30	AY.4.2	0.000651
S	146	H146Y	Cac	Tac	30	30	B.1.1	0.000544
S	146	H146H	caC	caT	30	30	B.1.1.70	0.010232
S	146	H146Y	Cac	Tac	29	29	AY.13	0.004668
S	146	H146Y	Cac	Tac	29	29	B.1.2	0.000255
S	146	H146H	caC	caT	29	29	B.1.526	0.000682
S	146	H146Q	caC	caA	28	28	AY.3	0.000278
S	146	H146H	caC	caT	28	28	AY.42	0.001126
S	146	H146H	caC	caT	27	27	AY.29	0.000426
S	146	H146D	Cac	Gac	25	26	All	0.000005
S	146	H146D	CaC	GaT	1	26	All	0
S	146	H146del	CAC	---	26	26	AY.25	0.000156
S	146	H146Y	Cac	Tac	26	26	AY.3.1	0.002217
S	146	H146Q	caC	caA	21	26	Q.1	0.002653
S	146	H146Q	caC	caG	5	26	Q.1	0.000632
S	146	H146H	caC	caT	25	25	AY.4.2	0.000542
S	146	H146H	caC	caT	25	25	B.1.258	0.001664
S	146	H146Q	caC	caA	24	24	B.1.2	0.000211
S	146	H146H	caC	caT	24	24	B.1.240	0.005174
S	146	H146H	caC	caT	24	24	B.1.429	0.000565
S	146	H146T	CAC	ACA	22	23	All	0.000004
S	146	H146T	CAc	ACc	1	23	All	0
S	146	H146Q	caC	caA	23	23	AY.23	0.001604
S	146	H146del	CAC	---	23	23	AY.44	0.00014
S	146	H146H	caC	caT	23	23	B.1.427	0.001161
S	146	H146H	caC	caT	23	23	B.1.617.1	0.002966
S	146	H146H	caC	caT	21	21	AY.5	0.000434
S	146	H146N	Cac	Aac	21	21	B.1.1.7	0.000019
S	146	H146del	CAC	---	21	21	B.1.2	0.000185
S	146	H146del	CAC	---	21	21	B.1.617.2	0.000079
S	146	H146Q	caC	caA	21	21	B.1.621	0.001859
S	146	H146H	caC	caT	20	20	AY.4.5	0.00215
S	146	H146Q	caC	caA	17	20	B.1	0.000156
S	146	H146Q	caC	caG	3	20	B.1	0.000027
S	146	H146K	CaC	AaA	20	20	B.1.1.7	0.000018
S	146	H146H	caC	caT	20	20	B.1.474	0.038023
S	146	H146H	caC	caT	19	19	AY.100	0.000874
S	146	H146H	caC	caT	19	19	AY.23	0.001325
S	146	H146Q	caC	caA	18	19	AY.25	0.000108
S	146	H146Q	caC	caG	1	19	AY.25	0.000006
S	146	H146H	caC	caT	19	19	B.1.1.111	0.279412
S	146	H146Q	caC	caA	19	19	B.1.177.63	0.051351
S	146	H146H	caC	caT	18	18	B.1.351	0.000535
S	146	H146H	caC	caT	17	17	AY.29.1	0.003749
S	146	H146L	cAc	cTc	17	17	B.1.1.7	0.000015
S	146	H146del	CAC	---	17	17	B.1.526	0.0004
S	146	H146K	CaC	AaA	17	17	B.1.621	0.001505
S	146	H146H	caC	caT	17	17	C.37	0.001973
S	146	H146Q	caC	caA	16	16	AY.14	0.001408
S	146	H146del	CAC	---	16	16	AY.4.2	0.000347
S	146	H146H	caC	caT	16	16	AY.47	0.000498
S	146	H146T	CAC	ACA	16	16	B.1.621	0.001416
S	146	H146L	cAc	cTc	15	15	AY.4	0.000023
S	146	H146H	caC	caT	15	15	AY.57	0.009843
S	146	H146Y	Cac	Tac	15	15	C.37	0.001741
S	146	H146H	caC	caT	14	14	AY.113	0.001993
S	146	H146Q	caC	caA	14	14	AY.44	0.000085
S	146	H146H	caC	caT	14	14	AY.54	0.001335
S	146	H146H	caC	caT	14	14	B.1.400	0.006006
S	146	H146del	CAC	---	14	14	B.1.582	0.006869
S	146	H146Y	Cac	Tac	14	14	B.1.596	0.00122
S	146	H146Y	Cac	Tac	14	14	P.1	0.000221
S	146	H146del1	Cac	-ac	8	13	All	0.000002
S	146	H146del1	caC	ca-	4	13	All	0.000001
S	146	H146del1	cAc	c-c	1	13	All	0
S	146	H146H	caC	caT	13	13	AY.26	0.000368
S	146	H146Y	Cac	Tac	13	13	AY.70	0.002711
S	146	H146Q	caC	caA	7	13	B.1.1	0.000127
S	146	H146Q	caC	caG	6	13	B.1.1	0.000109
S	146	H146H	caC	caT	13	13	B.1.1.222	0.002652
S	146	H146H	caC	caT	13	13	B.1.160	0.000405
S	146	H146Y	Cac	Tac	13	13	B.1.160	0.000405
S	146	H146H	caC	caT	13	13	B.1.234	0.001715
S	146	H146del	CAC	---	13	13	B.1.621	0.001151
S	146	H146Y	Cac	Tac	12	12	AY.119	0.000424
S	146	H146Y	Cac	Tac	12	12	AY.20	0.000466
S	146	H146R	cAc	cGc	12	12	AY.4	0.000019
S	146	H146L	cAc	cTc	12	12	AY.64	0.007143
S	146	H146del	CAC	---	12	12	B.1	0.00011
S	146	H146H	caC	caT	12	12	B.1.1.189	0.018154
S	146	H146H	caC	caT	12	12	B.1.1.214	0.000665
S	146	H146Y	Cac	Tac	12	12	B.1.177.44	0.006227
S	146	H146H	caC	caT	12	12	B.1.258.16	0.01964
S	146	H146H	caC	caT	12	12	C.36.3	0.006807
S	146	H146Q	caC	caA	11	12	P.1	0.000173
S	146	H146Q	caC	caG	1	12	P.1	0.000016
S	146	H146del2	CAc	--c	9	11	All	0.000002
S	146	H146del2	cAC	c--	2	11	All	0
S	146	H146N	Cac	Aac	11	11	B.1.351	0.000327
S	146	H146R	cAc	cGc	11	11	B.1.427	0.000555
S	146	H146R	cAc	cGc	11	11	B.1.617.2	0.000041
S	146	H146H	caC	caT	11	11	P.1.2	0.012717
S	146	H146H	caC	caT	10	10	A	0.00387
S	146	H146del	CAC	---	10	10	AY.116.1	0.003114
S	146	H146H	caC	caT	10	10	AY.120	0.000372
S	146	H146Y	Cac	Tac	10	10	AY.26	0.000283
S	146	H146Q	caC	caA	10	10	AY.4.2	0.000217
S	146	H146Q	caC	caA	10	10	AY.4.5	0.001075
S	146	H146del	CAC	---	10	10	AY.42	0.000402
S	146	H146P	cAc	cCc	10	10	B.1.1.7	0.000009
S	146	H146L	cAc	cTc	10	10	B.1.160	0.000312
S	146	H146H	caC	caT	10	10	B.1.36.24	0.061728
S	146	H146H	caC	caT	10	10	B.1.396	0.007057
S	146	H146H	caC	caT	10	10	B.1.525	0.001132
S	146	H146Q	caC	caA	10	10	B.1.526	0.000235
S	146	H146Y	Cac	Tac	10	10	B.1.619	0.008711
S	146	H146H	caC	caT	10	10	D.2	0.00075
S	146	H146del	CAC	---	10	10	P.1	0.000158
S	146	H146Y	Cac	Tac	9	9	AY.45	0.001095
S	146	H146R	cAc	cGc	9	9	AY.46.6	0.00065
S	146	H146H	caC	caT	9	9	AY.46.6	0.00065
S	146	H146Y	Cac	Tac	9	9	AY.47	0.00028
S	146	H146H	caC	caT	9	9	B.1.1.384	0.214286
S	146	H146H	caC	caT	9	9	B.1.1.50	0.00611
S	146	H146Y	Cac	Tac	9	9	B.1.36	0.001313
S	146	H146H	caC	caT	9	9	B.1.36	0.001313
S	146	H146Y	Cac	Tac	9	9	B.1.526	0.000212
S	146	H146H	caC	caT	9	9	P.1.15	0.002091
S	146	H146H	caC	caT	9	9	Q.1	0.001137
S	146	H146H	caC	caT	8	8	AY.111	0.001465
S	146	H146del	CAC	---	8	8	AY.39	0.000198
S	146	H146Y	Cac	Tac	8	8	AY.39	0.000198
S	146	H146Y	Cac	Tac	8	8	AY.5	0.000165
S	146	H146Y	Cac	Tac	8	8	AY.75	0.000448
S	146	H146H	caC	caT	8	8	AY.75.1	0.001442
S	146	H146Q	caC	caG	6	8	AY.9.2	0.00022
S	146	H146Q	caC	caA	2	8	AY.9.2	0.000073
S	146	H146H	caC	caT	8	8	B.1.346	0.010485
S	146	H146Y	Cac	Tac	8	8	B.1.351	0.000238
S	146	H146N	Cac	Aac	8	8	B.1.617.2	0.00003
S	146	H146Q	caC	caA	8	8	P.1.16	0.002993
S	146	H146H	caC	caT	8	8	Q.8	0.001319
S	146	H146L	cAc	cTc	7	7	AY.103	0.000043
S	146	H146L	cAc	cTc	7	7	AY.119	0.000247
S	146	H146Y	Cac	Tac	7	7	AY.120	0.00026
S	146	H146H	caC	caT	7	7	AY.23.1	0.002922
S	146	H146N	Cac	Aac	7	7	B.1	0.000064
S	146	H146Y	Cac	Tac	7	7	B.1.1.39	0.003568
S	146	H146H	caC	caT	7	7	B.1.1.417	0.018919
S	146	H146del1	Cac	-ac	7	7	B.1.1.7	0.000006
S	146	H146H	caC	caT	7	7	B.1.111	0.008226
S	146	H146del	CAC	---	7	7	B.1.160	0.000218
S	146	H146Q	caC	caA	7	7	B.1.177	0.000092
S	146	H146Q	caC	caA	7	7	B.1.351	0.000208
S	146	H146H	caC	caT	7	7	B.1.517	0.002989
S	146	H146H	caC	caT	7	7	B.1.621	0.00062
S	146	H146R	cAc	cGc	7	7	B.1.67	0.304348
S	146	H146N	Cac	Aac	7	7	P.1	0.00011
S	146	H146Y	Cac	Tac	6	6	AY.100	0.000276
S	146	H146Y	Cac	Tac	6	6	AY.102	0.000159
S	146	H146H	caC	caT	6	6	AY.33	0.000401
S	146	H146N	Cac	Aac	6	6	AY.4	0.000009
S	146	H146H	caC	caT	6	6	AY.45	0.00073
S	146	H146H	caC	caT	6	6	AY.46	0.000624
S	146	H146H	caC	caT	6	6	AY.58	0.005445
S	146	H146H	caC	caT	6	6	AY.75	0.000336
S	146	H146H	caC	caT	6	6	AY.99.2	0.000553
S	146	H146P	cAc	cCc	4	6	B.1	0.000037
S	146	H146P	cAC	cCA	2	6	B.1	0.000018
S	146	H146del	CAC	---	6	6	B.1.1	0.000109
S	146	H146H	caC	caT	6	6	B.1.1.33	0.002525
S	146	H146Y	Cac	Tac	6	6	B.1.1.416	0.00543
S	146	H146H	caC	caT	6	6	B.1.1.521	0.032086
S	146	H146Y	Cac	Tac	6	6	B.1.270	0.033708
S	146	H146Y	Cac	Tac	6	6	B.1.429	0.000141
S	146	H146Y	Cac	Tac	6	6	B.1.521	0.029851
S	146	H146H	caC	caT	6	6	B.1.596	0.000523
S	146	H146H	caC	caT	6	6	B.1.628	0.002114
S	146	H146Y	Cac	Tac	6	6	C.36	0.005464
S	146	H146H	caC	caT	6	6	P.1.14	0.000287
S	146	H146H	caC	caT	5	5	AY.118	0.000313
S	146	H146R	cAc	cGc	5	5	AY.25	0.00003
S	146	H146H	caC	caT	5	5	AY.30	0.001979
S	146	H146Y	Cac	Tac	5	5	AY.34	0.000485
S	146	H146del	CAC	---	5	5	AY.34.1	0.00255
S	146	H146D	Cac	Gac	5	5	AY.4	0.000008
S	146	H146del	CAC	---	5	5	AY.4.2.1	0.000745
S	146	H146Y	Cac	Tac	5	5	AY.42	0.000201
S	146	H146Q	caC	caA	5	5	AY.43	0.000022
S	146	H146Y	Cac	Tac	5	5	AY.46	0.00052
S	146	H146Y	Cac	Tac	5	5	AY.59	0.002648
S	146	H146H	caC	caT	5	5	AY.63	0.001934
S	146	H146H	caC	caT	5	5	AY.9	0.000338
S	146	H146H	caC	caT	5	5	AY.92	0.001436
S	146	H146Q	caC	caA	5	5	AY.98.1	0.000242
S	146	H146H	caC	caT	5	5	B.1.1.316	0.004625
S	146	H146Y	Cac	Tac	5	5	B.1.139	0.003666
S	146	H146Q	caC	caA	4	5	B.1.160	0.000125
S	146	H146Q	caC	caG	1	5	B.1.160	0.000031
S	146	H146H	caC	caT	5	5	B.1.177.4	0.001055
S	146	H146L	cAc	cTc	5	5	B.1.2	0.000044
S	146	H146H	caC	caT	5	5	B.1.243	0.000348
S	146	H146H	caC	caT	5	5	B.1.258.17	0.00052
S	146	H146del	CAC	---	5	5	B.1.351	0.000149
S	146	H146Y	Cac	Tac	5	5	B.1.36.18	0.002101
S	146	H146R	cAc	cGc	5	5	B.1.517	0.002135
S	146	H146H	caC	caT	5	5	B.1.524	0.007032
S	146	H146L	cAc	cTc	5	5	B.1.526	0.000118
S	146	H146H	caC	caT	5	5	B.1.561	0.001985
S	146	H146H	caC	caT	5	5	B.1.575	0.001517
S	146	H146Y	Cac	Tac	5	5	B.1.609	0.002397
S	146	H146del	CAC	---	5	5	B.1.617.1	0.000645
S	146	H146Y	Cac	Tac	5	5	B.1.617.1	0.000645
S	146	H146T	CAC	ACA	5	5	B.1.621.1	0.002529
S	146	H146H	caC	caT	5	5	C.16	0.005302
S	146	H146H	caC	caT	5	5	C.36	0.004554
S	146	H146Q	caC	caA	5	5	C.37	0.00058
S	146	H146H	caC	caT	5	5	P.1.1	0.001588
S	146	H146H	caC	caT	5	5	P.1.7	0.001596
S	146	H146Q	caC	caA	4	4	AY.100	0.000184
S	146	H146del	CAC	---	4	4	AY.100	0.000184
S	146	H146Q	caC	caA	4	4	AY.102	0.000106
S	146	H146del	CAC	---	4	4	AY.103	0.000025
S	146	H146Q	caC	caA	4	4	AY.116.1	0.001246
S	146	H146del	CAC	---	4	4	AY.119	0.000141
S	146	H146H	caC	caT	4	4	AY.12	0.001264
S	146	H146H	caC	caT	4	4	AY.121	0.000541
S	146	H146N	Cac	Aac	4	4	AY.29	0.000063
S	146	H146del	CAC	---	4	4	AY.29.1	0.000882
S	146	H146H	caC	caT	4	4	AY.36	0.000593
S	146	H146L	cAc	cTc	4	4	AY.39.1	0.000158
S	146	H146N	Cac	Aac	4	4	AY.44	0.000024
S	146	H146Q	caC	caA	4	4	AY.5	0.000083
S	146	H146Y	Cac	Tac	4	4	AY.54	0.000381
S	146	H146Y	Cac	Tac	4	4	AY.6	0.000165
S	146	H146R	cAc	cGc	4	4	AY.65	0.002132
S	146	H146H	caC	caT	4	4	AY.69	0.000747
S	146	H146del	CAC	---	4	4	AY.7	0.000784
S	146	H146Y	Cac	Tac	4	4	AY.74	0.000463
S	146	H146Y	Cac	Tac	4	4	AY.99.2	0.000369
S	146	H146H	caC	caT	4	4	B.1.1.141	0.008048
S	146	H146Y	Cac	Tac	4	4	B.1.1.25	0.002274
S	146	H146H	caC	caT	4	4	B.1.1.28	0.001245
S	146	H146H	caC	caT	4	4	B.1.1.294	0.005063
S	146	H146H	caC	caT	4	4	B.1.1.306	0.001754
S	146	H146H	caC	caT	4	4	B.1.1.317	0.001647
S	146	H146Q	caC	caG	4	4	B.1.1.416	0.00362
S	146	H146D	Cac	Gac	3	4	B.1.1.7	0.000003
S	146	H146D	CaC	GaT	1	4	B.1.1.7	0.000001
S	146	H146del	CAC	---	4	4	B.1.177	0.000053
S	146	H146H	caC	caT	4	4	B.1.177.60	0.000874
S	146	H146H	caC	caT	4	4	B.1.221	0.000284
S	146	H146Y	Cac	Tac	4	4	B.1.258	0.000266
S	146	H146Q	caC	caA	4	4	B.1.428	0.004082
S	146	H146H	caC	caT	4	4	B.1.509	0.003463
S	146	H146Y	Cac	Tac	4	4	B.1.525	0.000453
S	146	H146P	cAc	cCc	3	4	B.1.617.2	0.000011
S	146	H146P	cAC	cCA	1	4	B.1.617.2	0.000004
S	146	H146N	Cac	Aac	4	4	B.1.617.3	0.01194
S	146	H146Y	Cac	Tac	4	4	B.1.628	0.001409
S	146	H146Y	Cac	Tac	4	4	C.36.3	0.002269
S	146	H146H	caC	caT	4	4	Q.4	0.001819
S	146	H146Y	Cac	Tac	3	3	A	0.001161
S	146	H146H	caC	caT	3	3	A.2.5	0.001497
S	146	H146del	CAC	---	3	3	AY.101	0.001471
S	146	H146Y	Cac	Tac	3	3	AY.109	0.002219
S	146	H146Q	caC	caA	3	3	AY.111	0.000549
S	146	H146H	caC	caT	3	3	AY.116	0.00086
S	146	H146Y	Cac	Tac	3	3	AY.116	0.00086
S	146	H146del	CAC	---	3	3	AY.120	0.000112
S	146	H146Y	Cac	Tac	3	3	AY.14	0.000264
S	146	H146del	CAC	---	3	3	AY.20	0.000117
S	146	H146Y	Cac	Tac	3	3	AY.23	0.000209
S	146	H146Y	Cac	Tac	3	3	AY.24	0.001293
S	146	H146Y	Cac	Tac	3	3	AY.29.1	0.000662
S	146	H146D	Cac	Gac	3	3	AY.3	0.00003
S	146	H146Q	caC	caG	2	3	AY.37	0.000632
S	146	H146Q	caC	caA	1	3	AY.37	0.000316
S	146	H146H	caC	caT	3	3	AY.39.1	0.000119
S	146	H146H	caC	caT	3	3	AY.41	0.000882
S	146	H146N	Cac	Aac	3	3	AY.43	0.000013
S	146	H146H	caC	caT	3	3	AY.5.4	0.00083
S	146	H146Q	caC	caA	3	3	AY.54	0.000286
S	146	H146H	caC	caT	3	3	AY.61	0.000314
S	146	H146H	caC	caT	3	3	AY.62	0.001307
S	146	H146H	caC	caT	3	3	AY.7	0.000588
S	146	H146Y	Cac	Tac	3	3	AY.7.1	0.000338
S	146	H146H	caC	caT	3	3	AY.70	0.000626
S	146	H146Y	Cac	Tac	3	3	AY.75.1	0.000541
S	146	H146H	caC	caT	3	3	AY.89	0.014706
S	146	H146Y	Cac	Tac	3	3	AY.92	0.000862
S	146	H146Y	Cac	Tac	3	3	AY.98	0.000237
S	146	H146Y	Cac	Tac	3	3	AY.98.1	0.000145
S	146	H146H	caC	caT	3	3	B	0.000383
S	146	H146Y	Cac	Tac	3	3	B.1.1.10	0.003344
S	146	H146H	caC	caT	3	3	B.1.1.10	0.003344
S	146	H146Q	caC	caA	3	3	B.1.1.160	0.071429
S	146	H146H	caC	caT	3	3	B.1.1.176	0.001318
S	146	H146Y	Cac	Tac	3	3	B.1.1.214	0.000166
S	146	H146H	caC	caT	3	3	B.1.1.284	0.000322
S	146	H146del	CAC	---	3	3	B.1.1.284	0.000322
S	146	H146L	cAc	cTc	3	3	B.1.1.318	0.000905
S	146	H146Y	Cac	Tac	3	3	B.1.1.348	0.002389
S	146	H146H	caC	caT	3	3	B.1.1.348	0.002389
S	146	H146H	caC	caT	3	3	B.1.1.368	0.009259
S	146	H146del2	CAc	--c	3	3	B.1.1.7	0.000003
S	146	H146H	caC	caT	3	3	B.1.160.16	0.002788
S	146	H146Y	Cac	Tac	3	3	B.1.221	0.000213
S	146	H146K	CaC	AaA	3	3	B.1.239	0.003663
S	146	H146Q	caC	caA	3	3	B.1.243	0.000209
S	146	H146Q	caC	caA	3	3	B.1.258	0.0002
S	146	H146H	caC	caT	3	3	B.1.311	0.000824
S	146	H146del	CAC	---	3	3	B.1.311	0.000824
S	146	H146H	caC	caT	3	3	B.1.36.17	0.001482
S	146	H146H	caC	caT	3	3	B.1.438.1	0.000322
S	146	H146H	caC	caT	3	3	B.1.470	0.004213
S	146	H146H	caC	caT	3	3	B.1.637	0.000219
S	146	H146del	CAC	---	3	3	B.1.637	0.000219
S	146	H146Y	Cac	Tac	3	3	B.40	0.001093
S	146	H146R	cAc	cGc	3	3	P.1	0.000047
S	146	H146H	caC	caT	3	3	P.1.12	0.001452
S	146	H146del	CAC	---	3	3	P.1.15	0.000697
S	146	H146Y	Cac	Tac	3	3	Q.8	0.000495
S	146	H146Y	Cac	Tac	2	2		0.111111
S	146	H146del	CAC	---	2	2		0.111111
S	146	H146N	Cac	Aac	2	2	A.2.5.1	0.009615
S	146	H146del	CAC	---	2	2	A.27	0.003311
S	146	H146H	caC	caT	2	2	AD.1	0.00823
S	146	H146H	caC	caT	2	2	AE.8	0.000978
S	146	H146C	CAc	TGc	2	2	All	0
S	146	H146L	cAc	cTc	2	2	AY.102	0.000053
S	146	H146P	cAc	cCc	2	2	AY.103	0.000012
S	146	H146N	Cac	Aac	2	2	AY.103	0.000012
S	146	H146D	Cac	Gac	2	2	AY.103	0.000012
S	146	H146H	caC	caT	2	2	AY.106	0.00067
S	146	H146Y	Cac	Tac	2	2	AY.107	0.000932
S	146	H146del	CAC	---	2	2	AY.108	0.002205
S	146	H146H	caC	caT	2	2	AY.109	0.001479
S	146	H146Y	Cac	Tac	2	2	AY.111	0.000366
S	146	H146L	cAc	cTc	2	2	AY.113	0.000285
S	146	H146del	CAC	---	2	2	AY.116	0.000574
S	146	H146Y	Cac	Tac	2	2	AY.117	0.000169
S	146	H146R	cAc	cGc	2	2	AY.117	0.000169
S	146	H146H	caC	caT	2	2	AY.117	0.000169
S	146	H146R	cAc	cGc	2	2	AY.119	0.000071
S	146	H146H	caC	caT	2	2	AY.13	0.000322
S	146	H146H	caC	caT	2	2	AY.14	0.000176
S	146	H146Q	caC	caA	2	2	AY.2	0.000712
S	146	H146L	cAc	cTc	2	2	AY.20	0.000078
S	146	H146L	cAc	cTc	2	2	AY.25	0.000012
S	146	H146Q	caC	caA	2	2	AY.26	0.000057
S	146	H146del	CAC	---	2	2	AY.27	0.000129
S	146	H146del	CAC	---	2	2	AY.29	0.000032
S	146	H146del	CAC	---	2	2	AY.3	0.00002
S	146	H146N	Cac	Aac	2	2	AY.3	0.00002
S	146	H146H	caC	caT	2	2	AY.32	0.001065
S	146	H146del	CAC	---	2	2	AY.33	0.000134
S	146	H146del	CAC	---	2	2	AY.36	0.000296
S	146	H146Y	Cac	Tac	2	2	AY.36	0.000296
S	146	H146Y	Cac	Tac	2	2	AY.37	0.000632
S	146	H146N	Cac	Aac	2	2	AY.39	0.000049
S	146	H146Q	caC	caA	2	2	AY.39	0.000049
S	146	H146Y	Cac	Tac	2	2	AY.39.1	0.000079
S	146	H146del2	CAc	--c	2	2	AY.4	0.000003
S	146	H146K	CaC	AaA	2	2	AY.4	0.000003
S	146	H146del	CAC	---	2	2	AY.4.5	0.000215
S	146	H146Y	Cac	Tac	2	2	AY.41	0.000588
S	146	H146R	cAc	cGc	2	2	AY.42	0.00008
S	146	H146Q	caC	caG	1	2	AY.42	0.00004
S	146	H146Q	caC	caA	1	2	AY.42	0.00004
S	146	H146del2	CAc	--c	2	2	AY.43	0.000009
S	146	H146R	cAc	cGc	2	2	AY.43	0.000009
S	146	H146R	cAc	cGc	2	2	AY.44	0.000012
S	146	H146Q	caC	caA	2	2	AY.45	0.000243
S	146	H146del	CAC	---	2	2	AY.46	0.000208
S	146	H146Y	Cac	Tac	2	2	AY.46.6	0.000144
S	146	H146H	caC	caT	2	2	AY.53	0.000575
S	146	H146Q	caC	caA	2	2	AY.58	0.001815
S	146	H146Q	caC	caA	2	2	AY.6	0.000082
S	146	H146del	CAC	---	2	2	AY.62	0.000871
S	146	H146Y	Cac	Tac	2	2	AY.64	0.00119
S	146	H146Y	Cac	Tac	2	2	AY.65	0.001066
S	146	H146del	CAC	---	2	2	AY.65	0.001066
S	146	H146H	caC	caT	2	2	AY.66	0.002139
S	146	H146Y	Cac	Tac	2	2	AY.67	0.000929
S	146	H146Q	caC	caA	2	2	AY.68	0.000547
S	146	H146H	caC	caT	2	2	AY.68	0.000547
S	146	H146H	caC	caT	2	2	AY.7.1	0.000225
S	146	H146del	CAC	---	2	2	AY.7.2	0.001119
S	146	H146H	caC	caT	2	2	AY.74	0.000231
S	146	H146H	caC	caT	2	2	AY.85	0.000854
S	146	H146del	CAC	---	2	2	AY.9	0.000135
S	146	H146Y	Cac	Tac	2	2	AY.9.1	0.000167
S	146	H146Y	Cac	Tac	2	2	AY.93	0.000546
S	146	H146H	caC	caT	2	2	AY.98	0.000158
S	146	H146del	CAC	---	2	2	AY.98.1	0.000097
S	146	H146H	caC	caT	2	2	AY.98.1	0.000097
S	146	H146del	CAC	---	2	2	AY.99	0.002099
S	146	H146del	CAC	---	2	2	AZ.5	0.007018
S	146	H146Y	Cac	Tac	2	2	B	0.000256
S	146	H146L	cAc	cTc	2	2	B.1	0.000018
S	146	H146R	cAc	cGc	2	2	B.1.1	0.000036
S	146	H146H	caC	caT	2	2	B.1.1.157	0.001826
S	146	H146H	caC	caT	2	2	B.1.1.180	0.021505
S	146	H146H	caC	caT	2	2	B.1.1.192	0.004619
S	146	H146Y	Cac	Tac	2	2	B.1.1.207	0.002364
S	146	H146H	caC	caT	2	2	B.1.1.219	0.01
S	146	H146H	caC	caT	2	2	B.1.1.229	0.011494
S	146	H146H	caC	caT	2	2	B.1.1.241	0.004141
S	146	H146Y	Cac	Tac	2	2	B.1.1.284	0.000215
S	146	H146del	CAC	---	2	2	B.1.1.311	0.000716
S	146	H146del	CAC	---	2	2	B.1.1.318	0.000604
S	146	H146H	caC	caT	2	2	B.1.1.369	0.000892
S	146	H146H	caC	caT	2	2	B.1.1.37	0.000386
S	146	H146H	caC	caT	2	2	B.1.1.434	0.000697
S	146	H146H	caC	caT	2	2	B.1.1.453	0.016949
S	146	H146Y	Cac	Tac	2	2	B.1.1.525	0.010929
S	146	H146Y	Cac	Tac	2	2	B.1.1.526	0.007092
S	146	H146Y	Cac	Tac	2	2	B.1.111	0.00235
S	146	H146H	caC	caT	2	2	B.1.126	0.002551
S	146	H146Q	caC	caA	2	2	B.1.149	0.006849
S	146	H146H	caC	caT	2	2	B.1.160.25	0.022222
S	146	H146N	Cac	Aac	2	2	B.1.177	0.000026
S	146	H146Y	Cac	Tac	2	2	B.1.177.16	0.001329
S	146	H146H	caC	caT	2	2	B.1.177.40	0.010309
S	146	H146H	caC	caT	2	2	B.1.177.44	0.001038
S	146	H146Y	Cac	Tac	2	2	B.1.177.54	0.001213
S	146	H146Y	Cac	Tac	2	2	B.1.177.57	0.000562
S	146	H146Q	caC	caA	2	2	B.1.177.82	0.000955
S	146	H146H	caC	caT	2	2	B.1.177.86	0.000367
S	146	H146H	caC	caT	2	2	B.1.178	0.047619
S	146	H146R	cAc	cGc	2	2	B.1.2	0.000018
S	146	H146N	Cac	Aac	2	2	B.1.2	0.000018
S	146	H146H	caC	caT	2	2	B.1.214.2	0.001199
S	146	H146Y	Cac	Tac	2	2	B.1.234	0.000264
S	146	H146Q	caC	caA	2	2	B.1.240	0.000431
S	146	H146del	CAC	---	2	2	B.1.243	0.000139
S	146	H146R	cAc	cGc	2	2	B.1.258.17	0.000208
S	146	H146del	CAC	---	2	2	B.1.258.17	0.000208
S	146	H146H	caC	caT	2	2	B.1.265	0.002541
S	146	H146Q	caC	caA	2	2	B.1.265	0.002541
S	146	H146H	caC	caT	2	2	B.1.279	0.001027
S	146	H146K	CaC	AaA	2	2	B.1.344	0.016393
S	146	H146N	Cac	Aac	2	2	B.1.344	0.016393
S	146	H146Q	caC	caA	2	2	B.1.344	0.016393
S	146	H146Y	Cac	Tac	2	2	B.1.349	0.00143
S	146	H146L	cAc	cTc	2	2	B.1.351	0.000059
S	146	H146H	caC	caT	2	2	B.1.351.2	0.000605
S	146	H146Q	caC	caA	2	2	B.1.36.29	0.001035
S	146	H146Y	Cac	Tac	2	2	B.1.36.38	0.003284
S	146	H146Y	Cac	Tac	2	2	B.1.367	0.001585
S	146	H146H	caC	caT	2	2	B.1.371	0.002245
S	146	H146del	CAC	---	2	2	B.1.39	0.007812
S	146	H146Y	Cac	Tac	2	2	B.1.404	0.002604
S	146	H146del	CAC	---	2	2	B.1.409	0.001563
S	146	H146Q	caC	caA	2	2	B.1.427	0.000101
S	146	H146Q	caC	caA	2	2	B.1.429	0.000047
S	146	H146Q	caC	caA	2	2	B.1.466.2	0.000782
S	146	H146del	CAC	---	2	2	B.1.509	0.001732
S	146	H146Q	caC	caA	2	2	B.1.525	0.000226
S	146	H146R	cAc	cGc	2	2	B.1.526	0.000047
S	146	H146H	caC	caT	2	2	B.1.565	0.001621
S	146	H146del	CAC	---	2	2	B.1.596	0.000174
S	146	H146D	Cac	Gac	2	2	B.1.617.2	0.000008
S	146	H146L	cAc	cTc	2	2	B.1.617.2	0.000008
S	146	H146Y	Cac	Tac	2	2	B.1.621	0.000177
S	146	H146D	Cac	Gac	2	2	B.1.621	0.000177
S	146	H146P	cAC	cCA	2	2	B.1.621	0.000177
S	146	H146K	CaC	AaA	2	2	B.1.625	0.004706
S	146	H146Y	Cac	Tac	2	2	B.1.627	0.00404
S	146	H146Q	caC	caA	2	2	B.1.637	0.000146
S	146	H146Y	Cac	Tac	2	2	B.1.637	0.000146
S	146	H146P	cAc	cCc	1	2	B.1.637	0.000073
S	146	H146P	cAC	cCA	1	2	B.1.637	0.000073
S	146	H146Y	Cac	Tac	2	2	B.1.93	0.001867
S	146	H146H	caC	caT	2	2	B.40	0.000729
S	146	H146Q	caC	caA	2	2	D.2	0.00015
S	146	H146Y	Cac	Tac	2	2	D.2	0.00015
S	146	H146Q	caC	caA	2	2	L.3	0.007092
S	146	H146K	CaC	AaA	2	2	P.1	0.000032
S	146	H146H	caC	caT	2	2	P.1.10	0.000539
S	146	H146del	CAC	---	2	2	P.1.11	0.020408
S	146	H146H	caC	caT	2	2	P.1.4	0.001953
S	146	H146H	caC	caT	2	2	P.3	0.00319
S	146	H146Y	Cac	Tac	2	2	Q.1	0.000253
S	146	H146Y	Cac	Tac	2	2	Q.2	0.001227
S	146	H146Y	Cac	Tac	2	2	Q.3	0.00029
S	146	H146Q	caC	caA	2	2	R.1	0.00018
S	146	H146Q	caC	caA	1	1		0.055556
S	146	H146del	CAC	---	1	1	A	0.000387
S	146	H146Y	Cac	Tac	1	1	A.1	0.000282
S	146	H146H	caC	caT	1	1	A.1	0.000282
S	146	H146Q	caC	caA	1	1	A.1	0.000282
S	146	H146del	CAC	---	1	1	A.19	0.009434
S	146	H146R	cAc	cGc	1	1	A.2.3	0.004739
S	146	H146Q	caC	caA	1	1	A.2.4	0.003367
S	146	H146del	CAC	---	1	1	A.2.5	0.000499
S	146	H146N	Cac	Aac	1	1	A.2.5	0.000499
S	146	H146Y	Cac	Tac	1	1	A.2.5.2	0.001572
S	146	H146Q	caC	caA	1	1	A.21	0.00277
S	146	H146Y	Cac	Tac	1	1	A.3	0.002096
S	146	H146Y	Cac	Tac	1	1	A.30	0.142857
S	146	H146H	caC	caT	1	1	AD.2	0.000219
S	146	H146H	caC	caT	1	1	AE.1	0.011364
S	146	H146X	CaC	TaA	1	1	All	0
S	146	H146G	CAC	GGT	1	1	All	0
S	146	H146Y	Cac	Tac	1	1	AS.2	0.015625
S	146	H146Y	Cac	Tac	1	1	AU.3	0.00211
S	146	H146D	Cac	Gac	1	1	AY.100	0.000046
S	146	H146K	CaC	AaA	1	1	AY.100	0.000046
S	146	H146H	caC	caT	1	1	AY.101	0.00049
S	146	H146R	cAc	cGc	1	1	AY.102	0.000027
S	146	H146K	CaC	AaA	1	1	AY.102	0.000027
S	146	H146H	caC	caT	1	1	AY.104	0.001984
S	146	H146Q	caC	caA	1	1	AY.105	0.000643
S	146	H146N	Cac	Aac	1	1	AY.106	0.000335
S	146	H146del	CAC	---	1	1	AY.107	0.000466
S	146	H146H	caC	caT	1	1	AY.107	0.000466
S	146	H146del	CAC	---	1	1	AY.109	0.00074
S	146	H146R	cAc	cGc	1	1	AY.110	0.000113
S	146	H146N	Cac	Aac	1	1	AY.113	0.000142
S	146	H146Y	Cac	Tac	1	1	AY.113	0.000142
S	146	H146del	CAC	---	1	1	AY.117	0.000085
S	146	H146del	CAC	---	1	1	AY.118	0.000063
S	146	H146P	cAc	cCc	1	1	AY.118	0.000063
S	146	H146Y	Cac	Tac	1	1	AY.118	0.000063
S	146	H146Q	caC	caA	1	1	AY.119	0.000035
S	146	H146L	cAc	cTc	1	1	AY.12	0.000316
S	146	H146Q	caC	caA	1	1	AY.120	0.000037
S	146	H146H	caC	caT	1	1	AY.120.1	0.000321
S	146	H146Y	Cac	Tac	1	1	AY.120.1	0.000321
S	146	H146del	CAC	---	1	1	AY.120.2	0.001285
S	146	H146H	caC	caT	1	1	AY.120.2	0.001285
S	146	H146del	CAC	---	1	1	AY.121	0.000135
S	146	H146Y	Cac	Tac	1	1	AY.121	0.000135
S	146	H146H	caC	caT	1	1	AY.19	0.00114
S	146	H146Q	caC	caA	1	1	AY.20	0.000039
S	146	H146Y	Cac	Tac	1	1	AY.22	0.002092
S	146	H146P	cAC	cCA	1	1	AY.23	0.00007
S	146	H146R	cAc	cGc	1	1	AY.23.1	0.000417
S	146	H146Y	Cac	Tac	1	1	AY.23.1	0.000417
S	146	H146H	caC	caT	1	1	AY.24	0.000431
S	146	H146R	cAc	cGc	1	1	AY.26	0.000028
S	146	H146P	cAc	cCc	1	1	AY.26	0.000028
S	146	H146N	Cac	Aac	1	1	AY.27	0.000065
S	146	H146R	cAc	cGc	1	1	AY.29	0.000016
S	146	H146Q	caC	caG	1	1	AY.29	0.000016
S	146	H146K	CaC	AaA	1	1	AY.29.1	0.000221
S	146	H146L	cAc	cTc	1	1	AY.3	0.00001
S	146	H146H	caC	caT	1	1	AY.3.1	0.000085
S	146	H146Q	caC	caA	1	1	AY.3.1	0.000085
S	146	H146P	cAc	cCc	1	1	AY.32	0.000532
S	146	H146Y	Cac	Tac	1	1	AY.33	0.000067
S	146	H146Q	caC	caA	1	1	AY.33	0.000067
S	146	H146L	cAc	cTc	1	1	AY.34	0.000097
S	146	H146del1	caC	ca-	1	1	AY.34	0.000097
S	146	H146H	caC	caT	1	1	AY.34	0.000097
S	146	H146Q	caC	caA	1	1	AY.34	0.000097
S	146	H146del2	cAC	c--	1	1	AY.34.1	0.00051
S	146	H146H	caC	caT	1	1	AY.35	0.000233
S	146	H146H	caC	caT	1	1	AY.37	0.000316
S	146	H146H	caC	caT	1	1	AY.38	0.000499
S	146	H146Y	Cac	Tac	1	1	AY.38	0.000499
S	146	H146L	cAc	cTc	1	1	AY.39	0.000025
S	146	H146Q	caC	caA	1	1	AY.39.1	0.00004
S	146	H146P	cAc	cCc	1	1	AY.4	0.000002
S	146	H146del1	caC	ca-	1	1	AY.4	0.000002
S	146	H146L	cAc	cTc	1	1	AY.4.1	0.000737
S	146	H146del	CAC	---	1	1	AY.4.1	0.000737
S	146	H146R	cAc	cGc	1	1	AY.4.2	0.000022
S	146	H146H	caC	caT	1	1	AY.4.2.1	0.000149
S	146	H146N	Cac	Aac	1	1	AY.4.2.1	0.000149
S	146	H146N	Cac	Aac	1	1	AY.42	0.00004
S	146	H146K	CaC	AaA	1	1	AY.42	0.00004
S	146	H146D	Cac	Gac	1	1	AY.43	0.000004
S	146	H146X	CaC	TaA	1	1	AY.43	0.000004
S	146	H146L	cAc	cTc	1	1	AY.43	0.000004
S	146	H146L	cAc	cTc	1	1	AY.44	0.000006
S	146	H146D	Cac	Gac	1	1	AY.44	0.000006
S	146	H146N	Cac	Aac	1	1	AY.45	0.000122
S	146	H146del	CAC	---	1	1	AY.45	0.000122
S	146	H146Q	caC	caA	1	1	AY.46	0.000104
S	146	H146Q	caC	caA	1	1	AY.46.3	0.000934
S	146	H146Q	caC	caA	1	1	AY.46.4	0.000165
S	146	H146Q	caC	caA	1	1	AY.47	0.000031
S	146	H146del	CAC	---	1	1	AY.47	0.000031
S	146	H146del	CAC	---	1	1	AY.5	0.000021
S	146	H146del	CAC	---	1	1	AY.5.3	0.000337
S	146	H146Y	Cac	Tac	1	1	AY.52	0.000814
S	146	H146Y	Cac	Tac	1	1	AY.53	0.000288
S	146	H146L	cAc	cTc	1	1	AY.54	0.000095
S	146	H146del	CAC	---	1	1	AY.60	0.000938
S	146	H146Y	Cac	Tac	1	1	AY.61	0.000105
S	146	H146R	cAc	cGc	1	1	AY.62	0.000436
S	146	H146H	caC	caT	1	1	AY.64	0.000595
S	146	H146Y	Cac	Tac	1	1	AY.66	0.00107
S	146	H146K	CaC	AaA	1	1	AY.68	0.000274
S	146	H146Q	caC	caA	1	1	AY.69	0.000187
S	146	H146N	Cac	Aac	1	1	AY.69	0.000187
S	146	H146Y	Cac	Tac	1	1	AY.69	0.000187
S	146	H146Q	caC	caA	1	1	AY.71	0.000475
S	146	H146Y	Cac	Tac	1	1	AY.73	0.000665
S	146	H146del	CAC	---	1	1	AY.73	0.000665
S	146	H146del	CAC	---	1	1	AY.75	0.000056
S	146	H146Q	caC	caA	1	1	AY.75	0.000056
S	146	H146del	CAC	---	1	1	AY.78	0.001541
S	146	H146Y	Cac	Tac	1	1	AY.79	0.001211
S	146	H146Y	Cac	Tac	1	1	AY.8	0.000606
S	146	H146Y	Cac	Tac	1	1	AY.82	0.001357
S	146	H146Y	Cac	Tac	1	1	AY.83	0.001724
S	146	H146H	caC	caT	1	1	AY.84	0.000437
S	146	H146del	CAC	---	1	1	AY.84	0.000437
S	146	H146del	CAC	---	1	1	AY.85	0.000427
S	146	H146R	cAc	cGc	1	1	AY.85	0.000427
S	146	H146Y	Cac	Tac	1	1	AY.85	0.000427
S	146	H146N	Cac	Aac	1	1	AY.85	0.000427
S	146	H146Y	Cac	Tac	1	1	AY.86	0.00083
S	146	H146Y	Cac	Tac	1	1	AY.9.2	0.000037
S	146	H146del	CAC	---	1	1	AY.9.2	0.000037
S	146	H146Y	Cac	Tac	1	1	AY.96	0.002075
S	146	H146Q	caC	caA	1	1	AY.98	0.000079
S	146	H146Y	Cac	Tac	1	1	AY.99	0.001049
S	146	H146del	CAC	---	1	1	AY.99.1	0.001553
S	146	H146H	caC	caT	1	1	AZ.1	0.000867
S	146	H146del	CAC	---	1	1	AZ.2	0.000821
S	146	H146H	caC	caT	1	1	AZ.3	0.00152
S	146	H146N	Cac	Aac	1	1	B	0.000128
S	146	H146D	Cac	Gac	1	1	B	0.000128
S	146	H146R	cAc	cGc	1	1	B.1	0.000009
S	146	H146del2	CAc	--c	1	1	B.1	0.000009
S	146	H146N	Cac	Aac	1	1	B.1.1	0.000018
S	146	H146P	cAc	cCc	1	1	B.1.1	0.000018
S	146	H146del2	CAc	--c	1	1	B.1.1	0.000018
S	146	H146Q	caC	caA	1	1	B.1.1.1	0.000327
S	146	H146H	caC	caT	1	1	B.1.1.13	0.035714
S	146	H146H	caC	caT	1	1	B.1.1.135	0.004695
S	146	H146del	CAC	---	1	1	B.1.1.139	0.022727
S	146	H146N	Cac	Aac	1	1	B.1.1.153	0.001095
S	146	H146Q	caC	caA	1	1	B.1.1.157	0.000913
S	146	H146Y	Cac	Tac	1	1	B.1.1.157	0.000913
S	146	H146Y	Cac	Tac	1	1	B.1.1.158	0.012195
S	146	H146Q	caC	caA	1	1	B.1.1.176	0.000439
S	146	H146H	caC	caT	1	1	B.1.1.203	0.016949
S	146	H146H	caC	caT	1	1	B.1.1.207	0.001182
S	146	H146Y	Cac	Tac	1	1	B.1.1.222	0.000204
S	146	H146Y	Cac	Tac	1	1	B.1.1.227	0.004348
S	146	H146N	Cac	Aac	1	1	B.1.1.232	0.001815
S	146	H146Q	caC	caA	1	1	B.1.1.240	0.004695
S	146	H146R	cAc	cGc	1	1	B.1.1.271	0.055556
S	146	H146Q	caC	caA	1	1	B.1.1.284	0.000107
S	146	H146Y	Cac	Tac	1	1	B.1.1.286	0.002899
S	146	H146Y	Cac	Tac	1	1	B.1.1.29	0.010309
S	146	H146Y	Cac	Tac	1	1	B.1.1.294	0.001266
S	146	H146H	caC	caT	1	1	B.1.1.297	0.002237
S	146	H146Y	Cac	Tac	1	1	B.1.1.298	0.000862
S	146	H146Y	Cac	Tac	1	1	B.1.1.301	0.001179
S	146	H146H	caC	caT	1	1	B.1.1.302	0.002075
S	146	H146Y	Cac	Tac	1	1	B.1.1.304	0.002809
S	146	H146Q	caC	caA	1	1	B.1.1.306	0.000438
S	146	H146del1	caC	ca-	1	1	B.1.1.306	0.000438
S	146	H146H	caC	caT	1	1	B.1.1.312	0.001912
S	146	H146Q	caC	caA	1	1	B.1.1.315	0.008475
S	146	H146K	CaC	AaA	1	1	B.1.1.318	0.000302
S	146	H146D	Cac	Gac	1	1	B.1.1.318	0.000302
S	146	H146H	caC	caT	1	1	B.1.1.346	0.029412
S	146	H146Q	caC	caA	1	1	B.1.1.348	0.000796
S	146	H146H	caC	caT	1	1	B.1.1.349	0.010309
S	146	H146H	caC	caT	1	1	B.1.1.351	0.002793
S	146	H146Q	caC	caA	1	1	B.1.1.359	0.027778
S	146	H146H	caC	caT	1	1	B.1.1.372	0.000689
S	146	H146H	caC	caT	1	1	B.1.1.39	0.00051
S	146	H146Y	Cac	Tac	1	1	B.1.1.397	0.002252
S	146	H146H	caC	caT	1	1	B.1.1.398	0.003226
S	146	H146H	caC	caT	1	1	B.1.1.406	0.006494
S	146	H146H	caC	caT	1	1	B.1.1.413	0.006897
S	146	H146H	caC	caT	1	1	B.1.1.416	0.000905
S	146	H146L	cAc	cTc	1	1	B.1.1.416	0.000905
S	146	H146H	caC	caT	1	1	B.1.1.419	0.007407
S	146	H146H	caC	caT	1	1	B.1.1.420	0.001006
S	146	H146H	caC	caT	1	1	B.1.1.429	0.004608
S	146	H146Q	caC	caA	1	1	B.1.1.432	0.001266
S	146	H146H	caC	caT	1	1	B.1.1.445	0.037037
S	146	H146Q	caC	caA	1	1	B.1.1.46	0.004367
S	146	H146H	caC	caT	1	1	B.1.1.47	0.005348
S	146	H146H	caC	caT	1	1	B.1.1.485	0.016667
S	146	H146Q	caC	caG	1	1	B.1.1.50	0.000679
S	146	H146Y	Cac	Tac	1	1	B.1.1.50	0.000679
S	146	H146R	cAc	cGc	1	1	B.1.1.519	0.00004
S	146	H146Q	caC	caA	1	1	B.1.1.519	0.00004
S	146	H146H	caC	caT	1	1	B.1.1.63	0.000386
S	146	H146T	CAC	ACA	1	1	B.1.1.7	0.000001
S	146	H146H	caC	caT	1	1	B.1.112	0.005181
S	146	H146Y	Cac	Tac	1	1	B.1.127	0.002198
S	146	H146Y	Cac	Tac	1	1	B.1.128	0.000635
S	146	H146del	CAC	---	1	1	B.1.139	0.000733
S	146	H146L	cAc	cTc	1	1	B.1.139	0.000733
S	146	H146H	caC	caT	1	1	B.1.139	0.000733
S	146	H146Y	Cac	Tac	1	1	B.1.146	0.004237
S	146	H146N	Cac	Aac	1	1	B.1.160	0.000031
S	146	H146H	caC	caT	1	1	B.1.160.17	0.001701
S	146	H146del	CAC	---	1	1	B.1.160.23	0.004831
S	146	H146H	caC	caT	1	1	B.1.160.28	0.002924
S	146	H146del	CAC	---	1	1	B.1.160.30	0.002976
S	146	H146Y	Cac	Tac	1	1	B.1.160.9	0.007194
S	146	H146H	caC	caT	1	1	B.1.177.12	0.000152
S	146	H146H	caC	caT	1	1	B.1.177.16	0.000664
S	146	H146Y	Cac	Tac	1	1	B.1.177.17	0.000821
S	146	H146Y	Cac	Tac	1	1	B.1.177.21	0.000076
S	146	H146H	caC	caT	1	1	B.1.177.26	0.006993
S	146	H146Y	Cac	Tac	1	1	B.1.177.35	0.000691
S	146	H146del	CAC	---	1	1	B.1.177.4	0.000211
S	146	H146Q	caC	caA	1	1	B.1.177.4	0.000211
S	146	H146Y	Cac	Tac	1	1	B.1.177.43	0.001477
S	146	H146del1	caC	ca-	1	1	B.1.177.44	0.000519
S	146	H146N	Cac	Aac	1	1	B.1.177.45	0.000381
S	146	H146H	caC	caT	1	1	B.1.177.55	0.002331
S	146	H146H	caC	caT	1	1	B.1.177.58	0.001332
S	146	H146Q	caC	caA	1	1	B.1.177.6	0.000977
S	146	H146Y	Cac	Tac	1	1	B.1.177.60	0.000218
S	146	H146H	caC	caT	1	1	B.1.177.62	0.001192
S	146	H146Y	Cac	Tac	1	1	B.1.177.63	0.002703
S	146	H146H	caC	caT	1	1	B.1.177.65	0.000665
S	146	H146Y	Cac	Tac	1	1	B.1.177.68	0.015152
S	146	H146N	Cac	Aac	1	1	B.1.177.73	0.000566
S	146	H146Q	caC	caA	1	1	B.1.177.75	0.001041
S	146	H146Y	Cac	Tac	1	1	B.1.177.8	0.000752
S	146	H146Y	Cac	Tac	1	1	B.1.177.81	0.000189
S	146	H146H	caC	caT	1	1	B.1.177.81	0.000189
S	146	H146Y	Cac	Tac	1	1	B.1.177.82	0.000477
S	146	H146Y	Cac	Tac	1	1	B.1.177.84	0.006667
S	146	H146Q	caC	caA	1	1	B.1.177.86	0.000183
S	146	H146Q	caC	caA	1	1	B.1.177.87	0.000728
S	146	H146Y	Cac	Tac	1	1	B.1.177.87	0.000728
S	146	H146del	CAC	---	1	1	B.1.177.87	0.000728
S	146	H146Q	caC	caA	1	1	B.1.189	0.004292
S	146	H146Y	Cac	Tac	1	1	B.1.201	0.005682
S	146	H146R	cAc	cGc	1	1	B.1.210	0.002132
S	146	H146Y	Cac	Tac	1	1	B.1.214.2	0.0006
S	146	H146del	CAC	---	1	1	B.1.214.4	0.009091
S	146	H146L	cAc	cTc	1	1	B.1.221	0.000071
S	146	H146N	Cac	Aac	1	1	B.1.221.4	0.004167
S	146	H146Y	Cac	Tac	1	1	B.1.232	0.000537
S	146	H146H	caC	caT	1	1	B.1.232	0.000537
S	146	H146Q	caC	caA	1	1	B.1.239	0.001221
S	146	H146Y	Cac	Tac	1	1	B.1.240	0.000216
S	146	H146N	Cac	Aac	1	1	B.1.243	0.00007
S	146	H146H	caC	caT	1	1	B.1.258.11	0.000396
S	146	H146Q	caC	caA	1	1	B.1.258.6	0.019608
S	146	H146del	CAC	---	1	1	B.1.279	0.000514
S	146	H146Y	Cac	Tac	1	1	B.1.279	0.000514
S	146	H146R	cAc	cGc	1	1	B.1.279	0.000514
S	146	H146Y	Cac	Tac	1	1	B.1.311	0.000275
S	146	H146Y	Cac	Tac	1	1	B.1.320	0.001245
S	146	H146H	caC	caT	1	1	B.1.324	0.001605
S	146	H146Y	Cac	Tac	1	1	B.1.324	0.001605
S	146	H146Y	Cac	Tac	1	1	B.1.332	0.003497
S	146	H146H	caC	caT	1	1	B.1.336	0.002439
S	146	H146H	caC	caT	1	1	B.1.338	0.008621
S	146	H146H	caC	caT	1	1	B.1.340	0.004292
S	146	H146Q	caC	caA	1	1	B.1.351.2	0.000303
S	146	H146R	cAc	cGc	1	1	B.1.351.3	0.000876
S	146	H146H	caC	caT	1	1	B.1.36.18	0.00042
S	146	H146Q	caC	caA	1	1	B.1.36.24	0.006173
S	146	H146H	caC	caT	1	1	B.1.36.27	0.000763
S	146	H146H	caC	caT	1	1	B.1.36.29	0.000517
S	146	H146H	caC	caT	1	1	B.1.36.39	0.002217
S	146	H146R	cAc	cGc	1	1	B.1.36.8	0.001
S	146	H146H	caC	caT	1	1	B.1.36.8	0.001
S	146	H146H	caC	caT	1	1	B.1.362	0.001541
S	146	H146Y	Cac	Tac	1	1	B.1.369	0.000285
S	146	H146del	CAC	---	1	1	B.1.391	0.001127
S	146	H146Q	caC	caA	1	1	B.1.400	0.000429
S	146	H146H	caC	caT	1	1	B.1.403	0.003268
S	146	H146del	CAC	---	1	1	B.1.415	0.014286
S	146	H146Y	Cac	Tac	1	1	B.1.425	0.002994
S	146	H146N	Cac	Aac	1	1	B.1.427	0.00005
S	146	H146H	caC	caT	1	1	B.1.428	0.00102
S	146	H146L	cAc	cTc	1	1	B.1.429	0.000024
S	146	H146Y	Cac	Tac	1	1	B.1.438.1	0.000107
S	146	H146H	caC	caT	1	1	B.1.438.4	0.021277
S	146	H146Q	caC	caA	1	1	B.1.443	0.004673
S	146	H146H	caC	caT	1	1	B.1.456	0.003268
S	146	H146H	caC	caT	1	1	B.1.459	0.004082
S	146	H146H	caC	caT	1	1	B.1.466.1	0.007194
S	146	H146R	cAc	cGc	1	1	B.1.466.2	0.000391
S	146	H146Y	Cac	Tac	1	1	B.1.470	0.001404
S	146	H146H	caC	caT	1	1	B.1.471	0.002732
S	146	H146Y	Cac	Tac	1	1	B.1.471	0.002732
S	146	H146H	caC	caT	1	1	B.1.473	0.019231
S	146	H146H	caC	caT	1	1	B.1.497	0.000315
S	146	H146H	caC	caT	1	1	B.1.503	0.002488
S	146	H146K	CaC	AaA	1	1	B.1.525	0.000113
S	146	H146del2	cAC	c--	1	1	B.1.526	0.000024
S	146	H146Q	caC	caA	1	1	B.1.528	0.047619
S	146	H146Y	Cac	Tac	1	1	B.1.537	0.02
S	146	H146Q	caC	caA	1	1	B.1.549	0.007194
S	146	H146L	cAc	cTc	1	1	B.1.560	0.00463
S	146	H146H	caC	caT	1	1	B.1.560	0.00463
S	146	H146H	caC	caT	1	1	B.1.564	0.000426
S	146	H146Q	caC	caA	1	1	B.1.564	0.000426
S	146	H146del	CAC	---	1	1	B.1.565	0.00081
S	146	H146H	caC	caT	1	1	B.1.566	0.019231
S	146	H146Y	Cac	Tac	1	1	B.1.567	0.003333
S	146	H146Y	Cac	Tac	1	1	B.1.575	0.000303
S	146	H146Q	caC	caA	1	1	B.1.576	0.000907
S	146	H146T	CAc	ACc	1	1	B.1.576	0.000907
S	146	H146N	Cac	Aac	1	1	B.1.582	0.000491
S	146	H146del	CAC	---	1	1	B.1.585	0.027778
S	146	H146Y	Cac	Tac	1	1	B.1.587	0.001898
S	146	H146H	caC	caT	1	1	B.1.595	0.000261
S	146	H146D	Cac	Gac	1	1	B.1.596	0.000087
S	146	H146Q	caC	caA	1	1	B.1.596	0.000087
S	146	H146H	caC	caT	1	1	B.1.612	0.002653
S	146	H146R	cAc	cGc	1	1	B.1.617.1	0.000129
S	146	H146del1	cAc	c-c	1	1	B.1.617.1	0.000129
S	146	H146C	CAc	TGc	1	1	B.1.617.1	0.000129
S	146	H146Q	caC	caA	1	1	B.1.617.1	0.000129
S	146	H146C	CAc	TGc	1	1	B.1.617.2	0.000004
S	146	H146N	Cac	Aac	1	1	B.1.618	0.004032
S	146	H146H	caC	caT	1	1	B.1.619	0.000871
S	146	H146del	CAC	---	1	1	B.1.620	0.000946
S	146	H146del1	Cac	-ac	1	1	B.1.621	0.000089
S	146	H146Q	caC	caA	1	1	B.1.625	0.002353
S	146	H146N	Cac	Aac	1	1	B.1.625	0.002353
S	146	H146Y	Cac	Tac	1	1	B.1.88.1	0.004808
S	146	H146H	caC	caT	1	1	B.1.9.5	0.005682
S	146	H146H	caC	caT	1	1	B.1.93	0.000934
S	146	H146H	caC	caT	1	1	B.20	0.023256
S	146	H146H	caC	caT	1	1	B.27	0.015385
S	146	H146Q	caC	caG	1	1	B.28	0.003279
S	146	H146L	cAc	cTc	1	1	B.3	0.000831
S	146	H146H	caC	caT	1	1	B.3.1	0.001658
S	146	H146Q	caC	caA	1	1	B.40	0.000364
S	146	H146Q	caC	caA	1	1	B.55	0.00295
S	146	H146G	CAC	GGT	1	1	B.6	0.00091
S	146	H146R	cAc	cGc	1	1	B.6	0.00091
S	146	H146Y	Cac	Tac	1	1	C.14	0.004329
S	146	H146Y	Cac	Tac	1	1	C.17	0.055556
S	146	H146P	cAc	cCc	1	1	C.2	0.016129
S	146	H146H	caC	caT	1	1	C.23	0.005814
S	146	H146Q	caC	caA	1	1	C.30.1	0.006711
S	146	H146Y	Cac	Tac	1	1	C.35	0.000774
S	146	H146del	CAC	---	1	1	C.36	0.000911
S	146	H146R	cAc	cGc	1	1	C.37.1	0.002618
S	146	H146del	CAC	---	1	1	C.37.1	0.002618
S	146	H146Q	caC	caA	1	1	D.5	0.004975
S	146	H146Q	caC	caA	1	1	N.8	0.03125
S	146	H146H	caC	caT	1	1	N.9	0.005952
S	146	H146D	Cac	Gac	1	1	P.1	0.000016
S	146	H146Y	Cac	Tac	1	1	P.1.10	0.000269
S	146	H146Q	caC	caA	1	1	P.1.12	0.000484
S	146	H146Y	Cac	Tac	1	1	P.1.12	0.000484
S	146	H146N	Cac	Aac	1	1	P.1.14	0.000048
S	146	H146Y	Cac	Tac	1	1	P.1.14	0.000048
S	146	H146Q	caC	caA	1	1	P.1.14	0.000048
S	146	H146Q	caC	caA	1	1	P.1.15	0.000232
S	146	H146H	caC	caT	1	1	P.1.16	0.000374
S	146	H146H	caC	caT	1	1	P.1.17	0.000162
S	146	H146Q	caC	caA	1	1	P.1.17	0.000162
S	146	H146Y	Cac	Tac	1	1	P.1.17	0.000162
S	146	H146del	CAC	---	1	1	P.1.2	0.001156
S	146	H146Q	caC	caA	1	1	P.1.4	0.000977
S	146	H146Y	Cac	Tac	1	1	P.1.6	0.001946
S	146	H146Y	Cac	Tac	1	1	P.1.7	0.000319
S	146	H146Y	Cac	Tac	1	1	P.2	0.000187
S	146	H146del	CAC	---	1	1	P.2	0.000187
S	146	H146Q	caC	caA	1	1	P.2	0.000187
S	146	H146del	CAC	---	1	1	P.3	0.001595
S	146	H146H	caC	caT	1	1	P.7	0.004367
S	146	H146del	CAC	---	1	1	Q.2	0.000613
S	146	H146L	cAc	cTc	1	1	Q.3	0.000145
S	146	H146D	Cac	Gac	1	1	Q.8	0.000165
S	146	H146Y	Cac	Tac	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.