CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp1 : CodonNum = 27

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
ORF1ab/nsp1	27	L27L	L27L	syn	ctC	ctT	17503	17399	0.994058	344-346
ORF1ab/nsp1	27	L27L	L27L	syn	ctC	ctA	17503	55	0.00314232	344-346
ORF1ab/nsp1	27	L27L	L27L	syn	ctC	ctG	17503	47	0.00268525	344-346
ORF1ab/nsp1	27	L27L	L27L	syn	CtC	TtG	17503	2	0.000114266	344-346
ORF1ab/nsp1	27	L27F	L27F	nonsyn	Ctc	Ttc	2845	2839	0.997891	344-346
ORF1ab/nsp1	27	L27F	L27F	nonsyn	CtC	TtT	2845	6	0.00210896	344-346
ORF1ab/nsp1	27	L27I	L27I	nonsyn	Ctc	Atc	699	697	0.997139	344-346
ORF1ab/nsp1	27	L27I	L27I	nonsyn	CtC	AtT	699	2	0.00286123	344-346
ORF1ab/nsp1	27	L27H	L27H	nonsyn	cTc	cAc	227	227	1	344-346
ORF1ab/nsp1	27	L27del	L27del	del	CTC	---	144	144	1	344-346
ORF1ab/nsp1	27	L27P	L27P	nonsyn	cTc	cCc	58	57	0.982759	344-346
ORF1ab/nsp1	27	L27P	L27P	nonsyn	cTC	cCT	58	1	0.0172414	344-346
ORF1ab/nsp1	27	L27R	L27R	nonsyn	cTc	cGc	38	36	0.947368	344-346
ORF1ab/nsp1	27	L27R	L27R	nonsyn	cTC	cGA	38	2	0.0526316	344-346
ORF1ab/nsp1	27	L27V	L27V	nonsyn	Ctc	Gtc	15	15	1	344-346
ORF1ab/nsp1	27	L27del1	L27del1	del	ctC	ct-	3	3	1	344-346
ORF1ab/nsp1	27	L27Y	L27Y	nonsyn	CTc	TAc	2	2	1	344-346
ORF1ab/nsp1	27	L27del2	L27del2	del	CTc	--c	1	1	1	344-346
ORF1ab/nsp1	27	L27A	L27A	nonsyn	CTC	GCT	1	1	1	344-346

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
ORF1ab/nsp1	27	L27L	ctC	ctT	17399	17503	All	0.003328
ORF1ab/nsp1	27	L27L	ctC	ctA	55	17503	All	0.000011
ORF1ab/nsp1	27	L27L	ctC	ctG	47	17503	All	0.000009
ORF1ab/nsp1	27	L27L	CtC	TtG	2	17503	All	0
ORF1ab/nsp1	27	L27L	ctC	ctT	6114	6114	P.1.17	0.989
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2839	2845	All	0.000543
ORF1ab/nsp1	27	L27F	CtC	TtT	6	2845	All	0.000001
ORF1ab/nsp1	27	L27L	ctC	ctT	1481	1487	B.1.1.7	0.001326
ORF1ab/nsp1	27	L27L	ctC	ctA	5	1487	B.1.1.7	0.000004
ORF1ab/nsp1	27	L27L	ctC	ctG	1	1487	B.1.1.7	0.000001
ORF1ab/nsp1	27	L27L	ctC	ctT	1373	1373	AY.64	0.817262
ORF1ab/nsp1	27	L27L	ctC	ctT	1139	1139	P.1.17.1	0.9965
ORF1ab/nsp1	27	L27L	ctC	ctT	1016	1018	B.1.160	0.031687
ORF1ab/nsp1	27	L27L	ctC	ctA	2	1018	B.1.160	0.000062
ORF1ab/nsp1	27	L27F	Ctc	Ttc	740	740	B.1.1.7	0.000662
ORF1ab/nsp1	27	L27I	Ctc	Atc	697	699	All	0.000133
ORF1ab/nsp1	27	L27I	CtC	AtT	2	699	All	0
ORF1ab/nsp1	27	L27L	ctC	ctT	564	564	AY.43	0.002499
ORF1ab/nsp1	27	L27L	ctC	ctT	545	552	AY.103	0.003384
ORF1ab/nsp1	27	L27L	ctC	ctA	6	552	AY.103	0.000037
ORF1ab/nsp1	27	L27L	ctC	ctG	1	552	AY.103	0.000006
ORF1ab/nsp1	27	L27L	ctC	ctT	505	509	AY.4	0.000786
ORF1ab/nsp1	27	L27L	ctC	ctA	3	509	AY.4	0.000005
ORF1ab/nsp1	27	L27L	ctC	ctG	1	509	AY.4	0.000002
ORF1ab/nsp1	27	L27L	ctC	ctT	415	419	B.1	0.003801
ORF1ab/nsp1	27	L27L	ctC	ctA	2	419	B.1	0.000018
ORF1ab/nsp1	27	L27L	CtC	TtG	1	419	B.1	0.000009
ORF1ab/nsp1	27	L27L	ctC	ctG	1	419	B.1	0.000009
ORF1ab/nsp1	27	L27I	Ctc	Atc	418	418	B.1.1.374	0.992874
ORF1ab/nsp1	27	L27L	ctC	ctT	413	418	B.1.617.2	0.001555
ORF1ab/nsp1	27	L27L	ctC	ctG	3	418	B.1.617.2	0.000011
ORF1ab/nsp1	27	L27L	ctC	ctA	2	418	B.1.617.2	0.000008
ORF1ab/nsp1	27	L27L	ctC	ctT	265	265	B.1.243	0.01844
ORF1ab/nsp1	27	L27L	ctC	ctT	260	260	AY.44	0.001583
ORF1ab/nsp1	27	L27H	cTc	cAc	227	227	All	0.000043
ORF1ab/nsp1	27	L27F	Ctc	Ttc	220	220	AY.4	0.000342
ORF1ab/nsp1	27	L27L	ctC	ctT	215	217	B.1.2	0.001893
ORF1ab/nsp1	27	L27L	ctC	ctA	2	217	B.1.2	0.000018
ORF1ab/nsp1	27	L27L	ctC	ctT	194	197	P.1	0.003056
ORF1ab/nsp1	27	L27L	ctC	ctG	2	197	P.1	0.000032
ORF1ab/nsp1	27	L27L	ctC	ctA	1	197	P.1	0.000016
ORF1ab/nsp1	27	L27L	ctC	ctT	158	158	B.1.9.4	0.969325
ORF1ab/nsp1	27	L27F	Ctc	Ttc	156	156	AY.103	0.000969
ORF1ab/nsp1	27	L27del	CTC	---	144	144	All	0.000028
ORF1ab/nsp1	27	L27L	ctC	ctT	143	143	AY.62	0.062309
ORF1ab/nsp1	27	L27L	ctC	ctT	132	133	AY.39	0.003262
ORF1ab/nsp1	27	L27L	ctC	ctA	1	133	AY.39	0.000025
ORF1ab/nsp1	27	L27F	Ctc	Ttc	133	133	B.1.497	0.041863
ORF1ab/nsp1	27	L27F	Ctc	Ttc	127	127	B.1.617.2	0.000478
ORF1ab/nsp1	27	L27F	Ctc	Ttc	118	118	AZ.6	0.991597
ORF1ab/nsp1	27	L27F	Ctc	Ttc	107	107	AY.3	0.001064
ORF1ab/nsp1	27	L27L	ctC	ctT	103	103	B.1.427	0.005201
ORF1ab/nsp1	27	L27F	Ctc	Ttc	98	98	AY.25	0.000589
ORF1ab/nsp1	27	L27L	ctC	ctT	93	96	B.1.1	0.001687
ORF1ab/nsp1	27	L27L	ctC	ctA	3	96	B.1.1	0.000054
ORF1ab/nsp1	27	L27L	ctC	ctT	94	94	AY.3	0.000935
ORF1ab/nsp1	27	L27H	cTc	cAc	89	89	B.1.177.82	0.042482
ORF1ab/nsp1	27	L27H	cTc	cAc	84	84	B.1.617.2	0.000316
ORF1ab/nsp1	27	L27L	ctC	ctT	78	80	AY.25	0.000469
ORF1ab/nsp1	27	L27L	ctC	ctG	1	80	AY.25	0.000006
ORF1ab/nsp1	27	L27L	ctC	ctA	1	80	AY.25	0.000006
ORF1ab/nsp1	27	L27L	ctC	ctT	74	74	B.1.1.434	0.025793
ORF1ab/nsp1	27	L27L	ctC	ctT	72	72	AY.119	0.002542
ORF1ab/nsp1	27	L27L	ctC	ctT	69	69	AE.8	0.033741
ORF1ab/nsp1	27	L27F	Ctc	Ttc	65	65	AY.43	0.000288
ORF1ab/nsp1	27	L27F	Ctc	Ttc	63	63	B.1.558	0.287671
ORF1ab/nsp1	27	L27L	ctC	ctT	62	62	AY.26	0.001755
ORF1ab/nsp1	27	L27P	cTc	cCc	57	58	All	0.000011
ORF1ab/nsp1	27	L27P	cTC	cCT	1	58	All	0
ORF1ab/nsp1	27	L27F	Ctc	Ttc	57	57	AY.5	0.001177
ORF1ab/nsp1	27	L27L	ctC	ctT	57	57	B.1.234	0.007521
ORF1ab/nsp1	27	L27L	ctC	ctT	46	51	B.1.177	0.000606
ORF1ab/nsp1	27	L27L	ctC	ctA	5	51	B.1.177	0.000066
ORF1ab/nsp1	27	L27L	ctC	ctT	47	47	AY.102	0.001246
ORF1ab/nsp1	27	L27L	ctC	ctT	46	46	AY.9.1	0.003851
ORF1ab/nsp1	27	L27I	Ctc	Atc	46	46	B.1.1.7	0.000041
ORF1ab/nsp1	27	L27F	Ctc	Ttc	45	45	B.1.243	0.003131
ORF1ab/nsp1	27	L27L	ctC	ctT	43	43	AY.75	0.002409
ORF1ab/nsp1	27	L27L	ctC	ctT	41	41	AY.46.6	0.002961
ORF1ab/nsp1	27	L27F	Ctc	Ttc	41	41	B.1.2	0.000361
ORF1ab/nsp1	27	L27L	ctC	ctT	41	41	B.1.311	0.011258
ORF1ab/nsp1	27	L27F	Ctc	Ttc	41	41	P.1	0.000646
ORF1ab/nsp1	27	L27F	Ctc	Ttc	39	39	B.1	0.000357
ORF1ab/nsp1	27	L27L	ctC	ctT	39	39	B.1.429	0.000918
ORF1ab/nsp1	27	L27R	cTc	cGc	36	38	All	0.000007
ORF1ab/nsp1	27	L27R	cTC	cGA	2	38	All	0
ORF1ab/nsp1	27	L27L	ctC	ctT	38	38	AY.100	0.001748
ORF1ab/nsp1	27	L27L	ctC	ctT	38	38	AY.9.2	0.001396
ORF1ab/nsp1	27	L27I	Ctc	Atc	38	38	B.1.221	0.002699
ORF1ab/nsp1	27	L27F	Ctc	Ttc	37	37	AY.44	0.000225
ORF1ab/nsp1	27	L27F	Ctc	Ttc	36	36	B.1.177	0.000474
ORF1ab/nsp1	27	L27L	ctC	ctT	35	35	AY.118	0.002193
ORF1ab/nsp1	27	L27L	ctC	ctT	34	35	AY.29	0.000536
ORF1ab/nsp1	27	L27L	ctC	ctG	1	35	AY.29	0.000016
ORF1ab/nsp1	27	L27del	CTC	---	35	35	B.1.1.7	0.000031
ORF1ab/nsp1	27	L27L	ctC	ctT	34	34	AY.4.2	0.000737
ORF1ab/nsp1	27	L27L	ctC	ctG	27	29	AY.34	0.002618
ORF1ab/nsp1	27	L27L	ctC	ctT	1	29	AY.34	0.000097
ORF1ab/nsp1	27	L27L	ctC	ctA	1	29	AY.34	0.000097
ORF1ab/nsp1	27	L27L	ctC	ctT	29	29	P.4	0.110266
ORF1ab/nsp1	27	L27H	cTc	cAc	28	28	B.1.2	0.000247
ORF1ab/nsp1	27	L27L	ctC	ctT	24	27	AY.6	0.000987
ORF1ab/nsp1	27	L27L	ctC	ctA	3	27	AY.6	0.000123
ORF1ab/nsp1	27	L27I	Ctc	Atc	26	26	AY.44	0.000158
ORF1ab/nsp1	27	L27F	Ctc	Ttc	25	26	B.1.1	0.000454
ORF1ab/nsp1	27	L27F	CtC	TtT	1	26	B.1.1	0.000018
ORF1ab/nsp1	27	L27L	ctC	ctT	25	25	AY.121	0.003383
ORF1ab/nsp1	27	L27L	ctC	ctT	23	25	AY.5	0.000475
ORF1ab/nsp1	27	L27L	ctC	ctA	2	25	AY.5	0.000041
ORF1ab/nsp1	27	L27L	ctC	ctT	25	25	AY.98	0.001975
ORF1ab/nsp1	27	L27L	ctC	ctT	25	25	B.1.177.48	0.078125
ORF1ab/nsp1	27	L27L	ctC	ctT	23	25	B.1.351	0.000684
ORF1ab/nsp1	27	L27L	ctC	ctG	1	25	B.1.351	0.00003
ORF1ab/nsp1	27	L27L	ctC	ctA	1	25	B.1.351	0.00003
ORF1ab/nsp1	27	L27L	ctC	ctT	25	25	C.16	0.026511
ORF1ab/nsp1	27	L27L	ctC	ctT	24	24	C.36.3	0.013613
ORF1ab/nsp1	27	L27L	ctC	ctT	23	23	B.1.1.519	0.000913
ORF1ab/nsp1	27	L27F	Ctc	Ttc	23	23	B.1.160	0.000717
ORF1ab/nsp1	27	L27F	Ctc	Ttc	22	22	B.1.526	0.000517
ORF1ab/nsp1	27	L27L	ctC	ctT	22	22	P.1.16	0.00823
ORF1ab/nsp1	27	L27F	Ctc	Ttc	21	21	AY.47	0.000653
ORF1ab/nsp1	27	L27I	Ctc	Atc	21	21	B.1.617.2	0.000079
ORF1ab/nsp1	27	L27F	Ctc	Ttc	19	19	AY.102	0.000504
ORF1ab/nsp1	27	L27P	cTc	cCc	19	19	AY.3	0.000189
ORF1ab/nsp1	27	L27L	ctC	ctT	19	19	AZ.2	0.015599
ORF1ab/nsp1	27	L27L	ctC	ctT	19	19	B.1.1.67	0.086758
ORF1ab/nsp1	27	L27F	Ctc	Ttc	19	19	P.1.14	0.000908
ORF1ab/nsp1	27	L27L	ctC	ctT	18	18	AY.117	0.001521
ORF1ab/nsp1	27	L27F	Ctc	Ttc	18	18	B.1.177.6	0.017578
ORF1ab/nsp1	27	L27F	Ctc	Ttc	18	18	P.1.7	0.005747
ORF1ab/nsp1	27	L27L	ctC	ctT	17	17	B.1.526	0.0004
ORF1ab/nsp1	27	L27del	CTC	---	16	16	AY.4	0.000025
ORF1ab/nsp1	27	L27L	ctC	ctT	16	16	AY.42	0.000644
ORF1ab/nsp1	27	L27L	ctC	ctT	16	16	AY.65	0.008529
ORF1ab/nsp1	27	L27L	ctC	ctT	11	16	B.1.1.28	0.003424
ORF1ab/nsp1	27	L27L	ctC	ctA	5	16	B.1.1.28	0.001556
ORF1ab/nsp1	27	L27V	Ctc	Gtc	15	15	All	0.000003
ORF1ab/nsp1	27	L27I	Ctc	Atc	15	15	AY.9	0.001014
ORF1ab/nsp1	27	L27L	ctC	ctT	15	15	B.1.177.81	0.00284
ORF1ab/nsp1	27	L27L	ctC	ctT	15	15	B.1.36	0.002189
ORF1ab/nsp1	27	L27F	Ctc	Ttc	15	15	B.1.596	0.001307
ORF1ab/nsp1	27	L27L	ctC	ctT	14	14	AY.113	0.001993
ORF1ab/nsp1	27	L27I	Ctc	Atc	14	14	AY.20	0.000544
ORF1ab/nsp1	27	L27L	ctC	ctT	14	14	AY.20	0.000544
ORF1ab/nsp1	27	L27L	ctC	ctT	13	13	A.2.5	0.006487
ORF1ab/nsp1	27	L27L	ctC	ctT	12	13	AY.33	0.000801
ORF1ab/nsp1	27	L27L	ctC	ctG	1	13	AY.33	0.000067
ORF1ab/nsp1	27	L27L	ctC	ctT	13	13	AY.99.2	0.001198
ORF1ab/nsp1	27	L27L	ctC	ctT	13	13	B.1.1.214	0.000721
ORF1ab/nsp1	27	L27L	ctC	ctT	13	13	B.1.177.7	0.002143
ORF1ab/nsp1	27	L27L	ctC	ctT	13	13	B.1.621	0.001151
ORF1ab/nsp1	27	L27L	ctC	ctT	13	13	C.37	0.001509
ORF1ab/nsp1	27	L27L	ctC	ctT	12	12	A.2.4	0.040404
ORF1ab/nsp1	27	L27F	Ctc	Ttc	12	12	AY.100	0.000552
ORF1ab/nsp1	27	L27L	ctC	ctT	11	12	AY.23	0.000767
ORF1ab/nsp1	27	L27L	ctC	ctG	1	12	AY.23	0.00007
ORF1ab/nsp1	27	L27F	Ctc	Ttc	12	12	AY.26	0.00034
ORF1ab/nsp1	27	L27L	ctC	ctT	12	12	AY.61	0.001257
ORF1ab/nsp1	27	L27F	Ctc	Ttc	12	12	B.1.429	0.000282
ORF1ab/nsp1	27	L27L	ctC	ctT	12	12	B.1.525	0.001358
ORF1ab/nsp1	27	L27L	ctC	ctT	12	12	P.1.1	0.003812
ORF1ab/nsp1	27	L27L	ctC	ctT	11	11	AY.116	0.003155
ORF1ab/nsp1	27	L27L	ctC	ctT	11	11	AY.14	0.000968
ORF1ab/nsp1	27	L27F	Ctc	Ttc	11	11	AY.33	0.000735
ORF1ab/nsp1	27	L27L	ctC	ctT	11	11	AY.7.2	0.006152
ORF1ab/nsp1	27	L27L	ctC	ctT	11	11	B.1.1.222	0.002244
ORF1ab/nsp1	27	L27F	Ctc	Ttc	11	11	B.1.1.519	0.000437
ORF1ab/nsp1	27	L27L	ctC	ctT	11	11	B.1.177.86	0.002018
ORF1ab/nsp1	27	L27L	ctC	ctT	11	11	B.1.36.29	0.005691
ORF1ab/nsp1	27	L27F	Ctc	Ttc	10	10	A.2.5	0.00499
ORF1ab/nsp1	27	L27I	Ctc	Atc	10	10	AY.100	0.00046
ORF1ab/nsp1	27	L27I	Ctc	Atc	10	10	B.1	0.000092
ORF1ab/nsp1	27	L27I	Ctc	Atc	10	10	B.1.1	0.000181
ORF1ab/nsp1	27	L27F	Ctc	Ttc	10	10	B.1.258	0.000665
ORF1ab/nsp1	27	L27L	ctC	ctT	10	10	B.1.466.2	0.003912
ORF1ab/nsp1	27	L27L	ctC	ctT	10	10	Q.1	0.001263
ORF1ab/nsp1	27	L27F	Ctc	Ttc	9	9	AY.20	0.00035
ORF1ab/nsp1	27	L27del	CTC	---	9	9	AY.23	0.000628
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	AY.35	0.002097
ORF1ab/nsp1	27	L27F	Ctc	Ttc	9	9	AY.39	0.000222
ORF1ab/nsp1	27	L27F	Ctc	Ttc	9	9	AY.39.1	0.000357
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	AY.47	0.00028
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	AY.98.1	0.000436
ORF1ab/nsp1	27	L27I	Ctc	Atc	9	9	B.1.1.12	0.067164
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	B.1.111	0.010576
ORF1ab/nsp1	27	L27I	Ctc	Atc	9	9	B.1.3	0.02356
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	B.1.474	0.01711
ORF1ab/nsp1	27	L27F	Ctc	Ttc	9	9	B.1.637	0.000658
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	B.1.637	0.000658
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	D.2	0.000675
ORF1ab/nsp1	27	L27L	ctC	ctT	9	9	P.1.15	0.002091
ORF1ab/nsp1	27	L27I	Ctc	Atc	8	8	AY.120	0.000297
ORF1ab/nsp1	27	L27L	ctC	ctT	8	8	AY.13	0.001288
ORF1ab/nsp1	27	L27F	Ctc	Ttc	8	8	AY.29	0.000126
ORF1ab/nsp1	27	L27P	cTc	cCc	8	8	AY.4	0.000012
ORF1ab/nsp1	27	L27F	Ctc	Ttc	8	8	AY.4.2	0.000174
ORF1ab/nsp1	27	L27R	cTc	cGc	8	8	B.1.1.7	0.000007
ORF1ab/nsp1	27	L27L	ctC	ctT	8	8	B.1.221	0.000568
ORF1ab/nsp1	27	L27F	Ctc	Ttc	8	8	B.1.351	0.000238
ORF1ab/nsp1	27	L27L	ctC	ctT	8	8	B.1.9	0.049383
ORF1ab/nsp1	27	L27L	ctC	ctT	8	8	P.1.14	0.000382
ORF1ab/nsp1	27	L27L	ctC	ctT	8	8	P.1.6	0.015564
ORF1ab/nsp1	27	L27P	cTc	cCc	7	7	AY.25	0.000042
ORF1ab/nsp1	27	L27del	CTC	---	7	7	AY.43	0.000031
ORF1ab/nsp1	27	L27F	Ctc	Ttc	7	7	AY.9.2	0.000257
ORF1ab/nsp1	27	L27L	ctC	ctT	6	7	B	0.000767
ORF1ab/nsp1	27	L27L	ctC	ctA	1	7	B	0.000128
ORF1ab/nsp1	27	L27F	Ctc	Ttc	7	7	B.1.1.169	0.127273
ORF1ab/nsp1	27	L27F	Ctc	Ttc	7	7	B.1.1.284	0.000752
ORF1ab/nsp1	27	L27F	Ctc	Ttc	7	7	B.1.1.37	0.00135
ORF1ab/nsp1	27	L27H	cTc	cAc	7	7	B.1.1.7	0.000006
ORF1ab/nsp1	27	L27P	cTc	cCc	7	7	B.1.1.7	0.000006
ORF1ab/nsp1	27	L27F	Ctc	Ttc	7	7	B.1.110.3	0.005029
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	B.1.139	0.005132
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	B.1.177.54	0.004245
ORF1ab/nsp1	27	L27F	Ctc	Ttc	7	7	B.1.214.2	0.004197
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	B.1.241	0.005682
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	B.1.258	0.000466
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	B.1.349	0.005004
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	B.1.595	0.001827
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	B.1.596	0.00061
ORF1ab/nsp1	27	L27L	ctC	ctT	7	7	N.5	0.012367
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	AY.12	0.001896
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	AY.120.1	0.001926
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	AY.39.1	0.000238
ORF1ab/nsp1	27	L27I	Ctc	Atc	6	6	AY.4	0.000009
ORF1ab/nsp1	27	L27F	Ctc	Ttc	6	6	AY.46.6	0.000433
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	AY.5.3	0.002024
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	AY.54	0.000572
ORF1ab/nsp1	27	L27F	Ctc	Ttc	6	6	AY.75	0.000336
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	B.1.1.317	0.00247
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	B.1.1.397	0.013514
ORF1ab/nsp1	27	L27F	Ctc	Ttc	6	6	B.1.1.63	0.002315
ORF1ab/nsp1	27	L27del	CTC	---	6	6	B.1.177	0.000079
ORF1ab/nsp1	27	L27V	Ctc	Gtc	6	6	B.1.396	0.004234
ORF1ab/nsp1	27	L27F	Ctc	Ttc	6	6	B.1.400	0.002574
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	B.1.517	0.002562
ORF1ab/nsp1	27	L27F	Ctc	Ttc	6	6	B.1.621	0.000531
ORF1ab/nsp1	27	L27L	ctC	ctT	6	6	P.2	0.00112
ORF1ab/nsp1	27	L27F	Ctc	Ttc	6	6	R.1	0.00054
ORF1ab/nsp1	27	L27L	ctC	ctT	5	5	AD.2	0.001095
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	AY.23	0.000349
ORF1ab/nsp1	27	L27L	ctC	ctT	5	5	AY.24	0.002155
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	AY.42	0.000201
ORF1ab/nsp1	27	L27L	ctC	ctT	5	5	AY.85	0.002136
ORF1ab/nsp1	27	L27I	Ctc	Atc	5	5	B.1.1.192	0.011547
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.1.285	0.03268
ORF1ab/nsp1	27	L27L	ctC	ctT	5	5	B.1.1.294	0.006329
ORF1ab/nsp1	27	L27L	ctC	ctT	5	5	B.1.1.304	0.014045
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.1.318	0.001509
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.1.369	0.002231
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.177.54	0.003032
ORF1ab/nsp1	27	L27L	ctC	ctT	5	5	B.1.177.57	0.001405
ORF1ab/nsp1	27	L27L	ctC	ctA	3	5	B.1.177.73	0.001699
ORF1ab/nsp1	27	L27L	ctC	ctT	2	5	B.1.177.73	0.001133
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.177.83	0.007407
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.234	0.00066
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.311	0.001373
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.391	0.005637
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	B.1.425	0.01497
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	P.1.13	0.004492
ORF1ab/nsp1	27	L27F	Ctc	Ttc	5	5	Q.1	0.000632
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	A.21	0.01108
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	A.29	0.021277
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	AY.113	0.00057
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	AY.120	0.000149
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	AY.16	0.001519
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	AY.22	0.008368
ORF1ab/nsp1	27	L27R	cTc	cGc	4	4	AY.25	0.000024
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	AY.3.1	0.000341
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	AY.3.1	0.000341
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	AY.34.1	0.00204
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	AY.59	0.002119
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	AY.6	0.000165
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	AY.75.1	0.000721
ORF1ab/nsp1	27	L27R	cTc	cGc	4	4	AZ.2	0.003284
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.1.153	0.004381
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.1.201	0.097561
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.1.284	0.00043
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.1.285	0.026144
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.1.318	0.001207
ORF1ab/nsp1	27	L27del	CTC	---	4	4	B.1.1.33	0.001684
ORF1ab/nsp1	27	L27del	CTC	---	4	4	B.1.1.348	0.003185
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	B.1.1.348	0.003185
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	B.1.1.432	0.005063
ORF1ab/nsp1	27	L27I	Ctc	Atc	4	4	B.1.1.462	0.034483
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.1.464	0.005891
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.1.526	0.014184
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.177.45	0.001525
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.177.79	0.009368
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.240	0.000862
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.36.17	0.001976
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.36.36	0.002408
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.367	0.00317
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.425	0.011976
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	B.1.427	0.000202
ORF1ab/nsp1	27	L27V	Ctc	Gtc	4	4	B.1.558	0.018265
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	B.1.575	0.001214
ORF1ab/nsp1	27	L27F	Ctc	Ttc	4	4	B.6	0.00364
ORF1ab/nsp1	27	L27L	ctC	ctT	3	4	P.1.13	0.002695
ORF1ab/nsp1	27	L27L	ctC	ctA	1	4	P.1.13	0.000898
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	Q.8	0.00066
ORF1ab/nsp1	27	L27L	ctC	ctT	4	4	R.1	0.00036
ORF1ab/nsp1	27	L27del1	ctC	ct-	3	3	All	0.000001
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.105	0.001929
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.118	0.000188
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.119	0.000106
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.120	0.000112
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.121	0.000406
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.14	0.000264
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.16	0.001139
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.22	0.006276
ORF1ab/nsp1	27	L27del	CTC	---	3	3	AY.25	0.000018
ORF1ab/nsp1	27	L27R	cTc	cGc	3	3	AY.26	0.000085
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.35	0.000699
ORF1ab/nsp1	27	L27R	cTc	cGc	3	3	AY.4	0.000005
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.4.5	0.000322
ORF1ab/nsp1	27	L27del	CTC	---	3	3	AY.4.5	0.000322
ORF1ab/nsp1	27	L27I	Ctc	Atc	3	3	AY.43	0.000013
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.45	0.000365
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.45	0.000365
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.46	0.000312
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.46.4	0.000494
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.57	0.001969
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.67	0.001393
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.7	0.000588
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.7.1	0.000338
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.74	0.000347
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	AY.76	0.014493
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	AY.9	0.000203
ORF1ab/nsp1	27	L27I	Ctc	Atc	3	3	B.1.1.134	0.034091
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.1.207	0.003546
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	3	B.1.1.317	0.000823
ORF1ab/nsp1	27	L27F	CtC	TtT	1	3	B.1.1.317	0.000412
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.1.416	0.002715
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.1.453	0.025424
ORF1ab/nsp1	27	L27I	Ctc	Atc	3	3	B.1.177	0.00004
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.1.177.10	0.002634
ORF1ab/nsp1	27	L27L	ctC	ctG	3	3	B.1.177.12	0.000455
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.177.4	0.000633
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.177.60	0.000655
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.1.235	0.007557
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.324	0.004815
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.1.36.18	0.001261
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.409	0.002344
ORF1ab/nsp1	27	L27L	ctC	ctT	2	3	B.1.538	0.016129
ORF1ab/nsp1	27	L27L	CtC	TtG	1	3	B.1.538	0.008065
ORF1ab/nsp1	27	L27L	ctC	ctT	2	3	B.1.564	0.000852
ORF1ab/nsp1	27	L27L	ctC	ctG	1	3	B.1.564	0.000426
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.1.565	0.002431
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.1.575	0.00091
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.1.625	0.007059
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.1.628	0.001057
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	B.1.9.5	0.017045
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	B.40	0.001093
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	C.37	0.000348
ORF1ab/nsp1	27	L27F	Ctc	Ttc	3	3	D.2	0.000225
ORF1ab/nsp1	27	L27L	ctC	ctT	3	3	P.1.10	0.000808
ORF1ab/nsp1	27	L27F	CtC	TtT	3	3	P.1.17.1	0.002625
ORF1ab/nsp1	27	L27I	Ctc	Atc	3	3	Q.1	0.000379
ORF1ab/nsp1	27	L27L	ctC	ctA	1	2	A	0.000387
ORF1ab/nsp1	27	L27L	ctC	ctT	1	2	A	0.000387
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	A.21	0.00554
ORF1ab/nsp1	27	L27Y	CTc	TAc	2	2	All	0
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.101	0.000981
ORF1ab/nsp1	27	L27I	Ctc	Atc	2	2	AY.103	0.000012
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.107	0.000932
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.11	0.002677
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.111	0.000366
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.116	0.000574
ORF1ab/nsp1	27	L27L	ctC	ctA	1	2	AY.116.1	0.000311
ORF1ab/nsp1	27	L27L	ctC	ctT	1	2	AY.116.1	0.000311
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.117	0.000169
ORF1ab/nsp1	27	L27R	cTc	cGc	2	2	AY.16	0.000759
ORF1ab/nsp1	27	L27H	cTc	cAc	2	2	AY.23	0.000139
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.27	0.000129
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.30	0.000791
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.34.1	0.00102
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.37	0.000632
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.37	0.000632
ORF1ab/nsp1	27	L27H	cTc	cAc	2	2	AY.39	0.000049
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.4.2.1	0.000298
ORF1ab/nsp1	27	L27Y	CTc	TAc	2	2	AY.43	0.000009
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.46	0.000208
ORF1ab/nsp1	27	L27V	Ctc	Gtc	2	2	AY.46	0.000208
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.46.5	0.000397
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.54	0.000191
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.55	0.001835
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.60	0.001876
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.61	0.00021
ORF1ab/nsp1	27	L27P	cTc	cCc	2	2	AY.62	0.000871
ORF1ab/nsp1	27	L27I	CtC	AtT	2	2	AY.64	0.00119
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.71	0.00095
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.74	0.000231
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.84	0.000875
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.9	0.000135
ORF1ab/nsp1	27	L27I	Ctc	Atc	2	2	AY.9.2	0.000073
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.90	0.001369
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	AY.91	0.001461
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.93	0.000546
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	AY.99	0.002099
ORF1ab/nsp1	27	L27R	cTC	cGA	1	2	B.1	0.000009
ORF1ab/nsp1	27	L27R	cTc	cGc	1	2	B.1	0.000009
ORF1ab/nsp1	27	L27R	cTc	cGc	2	2	B.1.1	0.000036
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.1	0.000653
ORF1ab/nsp1	27	L27I	Ctc	Atc	2	2	B.1.1.161	0.007067
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.205	0.007435
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.1.214	0.000111
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.1.241	0.004141
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.25	0.001137
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.1.258	0.006515
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.1.28	0.000622
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.306	0.000877
ORF1ab/nsp1	27	L27del	CTC	---	2	2	B.1.1.311	0.000716
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.368	0.006173
ORF1ab/nsp1	27	L27L	ctC	ctT	1	2	B.1.1.37	0.000193
ORF1ab/nsp1	27	L27L	ctC	ctA	1	2	B.1.1.37	0.000193
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.372	0.001377
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.1.406	0.012987
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.50	0.001358
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.1.63	0.000772
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.147	0.001512
ORF1ab/nsp1	27	L27P	cTc	cCc	2	2	B.1.177	0.000026
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.177.12	0.000303
ORF1ab/nsp1	27	L27del	CTC	---	2	2	B.1.177.18	0.00232
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.177.21	0.000153
ORF1ab/nsp1	27	L27L	ctC	ctG	1	2	B.1.177.21	0.000076
ORF1ab/nsp1	27	L27L	ctC	ctT	1	2	B.1.177.21	0.000076
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.177.5	0.002484
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.177.77	0.001452
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.199	0.008264
ORF1ab/nsp1	27	L27R	cTc	cGc	2	2	B.1.2	0.000018
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.221	0.000142
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.241	0.001623
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.258.14	0.001961
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.258.18	0.2
ORF1ab/nsp1	27	L27H	cTc	cAc	2	2	B.1.311	0.000549
ORF1ab/nsp1	27	L27I	Ctc	Atc	2	2	B.1.351.3	0.001753
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.36.31	0.003503
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.36.8	0.002
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.362	0.003082
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.369	0.00057
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.396	0.001411
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.399	0.003868
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.420	0.020833
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.438.1	0.000215
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.466.2	0.000782
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.525	0.000226
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.577	0.001375
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.582	0.000981
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.595	0.000522
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.617.1	0.000258
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	B.1.617.1	0.000258
ORF1ab/nsp1	27	L27del	CTC	---	2	2	B.1.617.2	0.000008
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.1.638	0.105263
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	B.3	0.001661
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	C.1.2	0.008511
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	C.26	0.014706
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	C.36.3	0.001134
ORF1ab/nsp1	27	L27I	Ctc	Atc	2	2	C.37	0.000232
ORF1ab/nsp1	27	L27L	ctC	ctT	2	2	C.4	0.02
ORF1ab/nsp1	27	L27del	CTC	---	2	2	N.4	0.008511
ORF1ab/nsp1	27	L27del	CTC	---	2	2	N.6	0.014184
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	P.1.1	0.000635
ORF1ab/nsp1	27	L27F	Ctc	Ttc	2	2	P.1.16	0.000748
ORF1ab/nsp1	27	L27L	ctC	ctT	1	2	P.1.7	0.000319
ORF1ab/nsp1	27	L27L	ctC	ctG	1	2	P.1.7	0.000319
ORF1ab/nsp1	27	L27del	CTC	---	2	2	P.2	0.000373
ORF1ab/nsp1	27	L27P	cTC	cCT	1	1	A	0.000387
ORF1ab/nsp1	27	L27del1	ctC	ct-	1	1	A	0.000387
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	A.1	0.000282
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	A.1	0.000282
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	A.2.5.2	0.001572
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AD.2	0.000219
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AD.2	0.000219
ORF1ab/nsp1	27	L27A	CTC	GCT	1	1	All	0
ORF1ab/nsp1	27	L27del2	CTc	--c	1	1	All	0
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AU.3	0.00211
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AW.1	0.003049
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.10	0.00053
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	AY.102	0.000027
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	AY.103	0.000006
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.106	0.000335
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.106	0.000335
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.108	0.001103
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.109	0.00074
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.110	0.000113
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.111	0.000183
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.111	0.000183
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.114	0.000231
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.116	0.000287
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	AY.118	0.000063
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.12	0.000316
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	AY.120	0.000037
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.120	0.000037
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.120.2	0.001285
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.120.2.1	0.000498
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.16.1	0.00047
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.16.1	0.00047
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.25	0.000006
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	AY.25	0.000006
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.27	0.000065
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.29	0.000016
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.29.1	0.000221
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.3	0.00001
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.30	0.000396
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.32	0.000532
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.32	0.000532
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.33	0.000067
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.34	0.000097
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.36	0.000148
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.36	0.000148
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	AY.36	0.000148
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.37	0.000316
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.38	0.000499
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.38	0.000499
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.39	0.000025
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	AY.39	0.000025
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	AY.39.1	0.00004
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	AY.4.2	0.000022
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.4.4	0.000409
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.4.5	0.000107
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.4.5	0.000107
ORF1ab/nsp1	27	L27R	cTc	cGc	1	1	AY.4.5	0.000107
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.40	0.000964
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.41	0.000294
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.41	0.000294
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.41	0.000294
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	AY.43	0.000004
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	AY.43	0.000004
ORF1ab/nsp1	27	L27R	cTc	cGc	1	1	AY.44	0.000006
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.45	0.000122
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	AY.45	0.000122
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.46	0.000104
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.46.2	0.000635
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.48	0.000465
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.5	0.000021
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.5.1	0.003759
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.5.3	0.000337
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.5.4	0.000277
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.5.4	0.000277
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.53	0.000288
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.53	0.000288
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.54	0.000095
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.56	0.001605
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.58	0.000907
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	AY.6	0.000041
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.6	0.000041
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.6	0.000041
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.60	0.000938
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.68	0.000274
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.68	0.000274
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.7	0.000196
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.70	0.000209
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.72	0.001361
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	AY.73	0.000665
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.73	0.000665
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.75.1	0.00018
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.78	0.001541
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.79	0.001211
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.83	0.001724
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.84	0.000437
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.85	0.000427
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	AY.87	0.000833
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.87	0.000833
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.9	0.000068
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.9.1	0.000084
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.9.1	0.000084
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.9.2	0.000037
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.91	0.00073
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.92	0.000287
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.93	0.000273
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.94	0.000443
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.95	0.000761
ORF1ab/nsp1	27	L27del	CTC	---	1	1	AY.95	0.000761
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.95	0.000761
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	AY.96	0.002075
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AY.98	0.000079
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	AZ.1	0.000867
ORF1ab/nsp1	27	L27V	Ctc	Gtc	1	1	B.1	0.000009
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1	0.000009
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.1	0.000018
ORF1ab/nsp1	27	L27del1	ctC	ct-	1	1	B.1.1	0.000018
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.1	0.000327
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.161	0.003534
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.170	0.001247
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.176	0.000439
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.189	0.001513
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.198	0.001468
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.200	0.007463
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.216	0.00089
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.216	0.00089
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.220	0.001859
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.222	0.000204
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.229	0.005747
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.231	0.003096
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.1.232	0.001815
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.1.236	0.006897
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.242	0.043478
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.243	0.004082
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	B.1.1.258	0.003257
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	B.1.1.273	0.006757
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.274	0.005051
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.275	0.011236
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.277	0.000759
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.288	0.001916
ORF1ab/nsp1	27	L27R	cTc	cGc	1	1	B.1.1.291	0.000742
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.311	0.000358
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.316	0.000925
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.1.322	0.008772
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.326	0.001761
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.326	0.001761
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.328	0.016949
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.329	0.003846
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.33	0.000421
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.344	0.010753
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	B.1.1.350	0.04
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.363	0.005988
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.37	0.000193
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.370	0.012658
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.372	0.000689
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.373	0.02381
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.389	0.006061
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.39	0.00051
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.1.39	0.00051
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.398	0.003226
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.404	0.015873
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.409	0.002833
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.411	0.014706
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.416	0.000905
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.420	0.001006
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.434	0.000349
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.437	0.010417
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.466	0.008696
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.486	0.001577
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.507	0.008696
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.1.51	0.001718
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.523	0.001563
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.1.56	0.017857
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.59	0.006494
ORF1ab/nsp1	27	L27V	Ctc	Gtc	1	1	B.1.1.7	0.000001
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.1.8	0.003584
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.110	0.004525
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.111	0.001175
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.142	0.002899
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.160	0.000031
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.160.12	0.00641
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.160.15	0.00495
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.160.20	0.008929
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.160.21	0.020408
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.160.28	0.002924
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.169	0.014925
ORF1ab/nsp1	27	L27R	cTc	cGc	1	1	B.1.177	0.000013
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	B.1.177	0.000013
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.11	0.001698
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.177.18	0.00116
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.177.23	0.003236
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.177.28	0.007407
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.177.35	0.000691
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.177.4	0.000211
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	B.1.177.44	0.000519
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.177.56	0.000668
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.177.57	0.000281
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.177.6	0.000977
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.177.60	0.000218
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.177.63	0.002703
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.69	0.001484
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.177.70	0.005917
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.177.75	0.001041
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.177.87	0.000728
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.179	0.003759
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.181	0.019608
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.190	0.01
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.2	0.000009
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.206	0.000816
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.211	0.025
ORF1ab/nsp1	27	L27del2	CTc	--c	1	1	B.1.221.1	0.002907
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.221.4	0.004167
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.23	0.006061
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.236	0.002053
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.245	0.03125
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.258	0.000067
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	B.1.258	0.000067
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.258.17	0.000104
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.258.21	0.007752
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.265	0.001271
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.279	0.000514
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.298	0.002114
ORF1ab/nsp1	27	L27L	ctC	ctA	1	1	B.1.301	0.005917
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.305	0.002151
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.344	0.008197
ORF1ab/nsp1	27	L27R	cTc	cGc	1	1	B.1.351	0.00003
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.351.2	0.000303
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.351.2	0.000303
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.351.3	0.000876
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.356	0.001727
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.36.1	0.00114
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.36.1	0.00114
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.36.17	0.000494
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.36.18	0.00042
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.36.22	0.001208
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.36.29	0.000517
ORF1ab/nsp1	27	L27A	CTC	GCT	1	1	B.1.375	0.00082
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.390	0.010638
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.396	0.000706
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.398	0.002976
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.399	0.001934
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.400	0.000429
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.427	0.00005
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.428	0.00102
ORF1ab/nsp1	27	L27del	CTC	---	1	1	B.1.429	0.000024
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.433	0.003195
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.437	0.020833
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.453	0.003236
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.466	0.023256
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.497	0.000315
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.499	0.00105
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.509	0.000866
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.515	0.014493
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.521	0.004975
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.523	0.002451
ORF1ab/nsp1	27	L27I	Ctc	Atc	1	1	B.1.525	0.000113
ORF1ab/nsp1	27	L27R	cTc	cGc	1	1	B.1.526	0.000024
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.537	0.02
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.551	0.00129
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.561	0.000397
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.575.1	0.002439
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.576	0.000907
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.576	0.000907
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.580	0.004065
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.582	0.000491
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.587	0.001898
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.595.1	0.005848
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.602	0.006536
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.609	0.000479
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	B.1.617.1	0.000129
ORF1ab/nsp1	27	L27R	cTC	cGA	1	1	B.1.617.1	0.000129
ORF1ab/nsp1	27	L27R	cTc	cGc	1	1	B.1.617.2	0.000004
ORF1ab/nsp1	27	L27P	cTc	cCc	1	1	B.1.617.2	0.000004
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.621.1	0.000506
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.625	0.002353
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.1.628	0.000352
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	B.1.637	0.000073
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.1.8	0.001972
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.38	0.02381
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.4.8	0.071429
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	B.40	0.000364
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	B.6.6	0.000889
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	C.18	0.002591
ORF1ab/nsp1	27	L27V	Ctc	Gtc	1	1	C.26	0.007353
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	C.35	0.000774
ORF1ab/nsp1	27	L27del	CTC	---	1	1	C.35	0.000774
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	C.35	0.000774
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	C.36	0.000911
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	C.37.1	0.002618
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	N.10	0.029412
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	N.5	0.001767
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	P.1.14	0.000048
ORF1ab/nsp1	27	L27H	cTc	cAc	1	1	P.1.15	0.000232
ORF1ab/nsp1	27	L27F	CtC	TtT	1	1	P.1.17	0.000162
ORF1ab/nsp1	27	L27del1	ctC	ct-	1	1	P.1.17	0.000162
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	P.1.8	0.004785
ORF1ab/nsp1	27	L27F	Ctc	Ttc	1	1	P.2	0.000187
ORF1ab/nsp1	27	L27L	ctC	ctA	1	1	Q.2	0.000613
ORF1ab/nsp1	27	L27L	ctC	ctT	1	1	Q.7	0.001111
ORF1ab/nsp1	27	L27del	CTC	---	1	1	U.3	0.003861

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.