CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1381

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/nsp3	1381	A1381V	A2199V	nonsyn	gCa	gTa	849	840	0.989399	6860-6862
ORF1ab/nsp3	1381	A1381V	A2199V	nonsyn	gCA	gTT	849	8	0.00942285	6860-6862
ORF1ab/nsp3	1381	A1381V	A2199V	nonsyn	gCA	gTG	849	1	0.00117786	6860-6862
ORF1ab/nsp3	1381	A1381T	A2199T	nonsyn	Gca	Aca	391	385	0.984655	6860-6862
ORF1ab/nsp3	1381	A1381T	A2199T	nonsyn	GcA	AcT	391	4	0.0102302	6860-6862
ORF1ab/nsp3	1381	A1381T	A2199T	nonsyn	GcA	AcG	391	1	0.00255754	6860-6862
ORF1ab/nsp3	1381	A1381T	A2199T	nonsyn	GcA	AcC	391	1	0.00255754	6860-6862
ORF1ab/nsp3	1381	A1381A	A2199A	syn	gcA	gcG	251	180	0.717131	6860-6862
ORF1ab/nsp3	1381	A1381A	A2199A	syn	gcA	gcT	251	64	0.25498	6860-6862
ORF1ab/nsp3	1381	A1381A	A2199A	syn	gcA	gcC	251	7	0.0278884	6860-6862
ORF1ab/nsp3	1381	A1381del	A2199del	del	GCA	---	230	230	1	6860-6862
ORF1ab/nsp3	1381	A1381I	A2199I	nonsyn	GCa	ATa	158	101	0.639241	6860-6862
ORF1ab/nsp3	1381	A1381I	A2199I	nonsyn	GCA	ATT	158	57	0.360759	6860-6862
ORF1ab/nsp3	1381	A1381K	A2199K	nonsyn	GCa	AAa	155	155	1	6860-6862
ORF1ab/nsp3	1381	A1381E	A2199E	nonsyn	gCa	gAa	93	92	0.989247	6860-6862
ORF1ab/nsp3	1381	A1381E	A2199E	nonsyn	gCA	gAG	93	1	0.0107527	6860-6862
ORF1ab/nsp3	1381	A1381L	A2199L	nonsyn	GCa	TTa	90	88	0.977778	6860-6862
ORF1ab/nsp3	1381	A1381L	A2199L	nonsyn	GCA	TTG	90	2	0.0222222	6860-6862
ORF1ab/nsp3	1381	A1381S	A2199S	nonsyn	Gca	Tca	87	76	0.873563	6860-6862
ORF1ab/nsp3	1381	A1381S	A2199S	nonsyn	GcA	TcT	87	9	0.103448	6860-6862
ORF1ab/nsp3	1381	A1381S	A2199S	nonsyn	GCA	AGT	87	1	0.0114943	6860-6862
ORF1ab/nsp3	1381	A1381S	A2199S	nonsyn	GCA	AGC	87	1	0.0114943	6860-6862
ORF1ab/nsp3	1381	A1381X	A2199X	nonsyn	GCa	TAa	86	84	0.976744	6860-6862
ORF1ab/nsp3	1381	A1381X	A2199X	nonsyn	GCA	TAG	86	1	0.0116279	6860-6862
ORF1ab/nsp3	1381	A1381X	A2199X	nonsyn	GCa	TGa	86	1	0.0116279	6860-6862
ORF1ab/nsp3	1381	A1381N	A2199N	nonsyn	GCA	AAT	63	63	1	6860-6862
ORF1ab/nsp3	1381	A1381F	A2199F	nonsyn	GCA	TTT	59	59	1	6860-6862
ORF1ab/nsp3	1381	A1381Y	A2199Y	nonsyn	GCA	TAT	56	56	1	6860-6862
ORF1ab/nsp3	1381	A1381del1	A2199del1	del	gcA	gc-	14	10	0.714286	6860-6862
ORF1ab/nsp3	1381	A1381del1	A2199del1	del	GCa	-Ta	14	2	0.142857	6860-6862
ORF1ab/nsp3	1381	A1381del1	A2199del1	del	Gca	-ca	14	1	0.0714286	6860-6862
ORF1ab/nsp3	1381	A1381del1	A2199del1	del	gCA	g-N	14	1	0.0714286	6860-6862
ORF1ab/nsp3	1381	A1381P	A2199P	nonsyn	Gca	Cca	12	10	0.833333	6860-6862
ORF1ab/nsp3	1381	A1381P	A2199P	nonsyn	GcA	CcC	12	1	0.0833333	6860-6862
ORF1ab/nsp3	1381	A1381P	A2199P	nonsyn	GcA	CcG	12	1	0.0833333	6860-6862
ORF1ab/nsp3	1381	A1381R	A2199R	nonsyn	GCa	AGa	6	5	0.833333	6860-6862
ORF1ab/nsp3	1381	A1381D	A2199D	nonsyn	gCA	gAC	6	4	0.666667	6860-6862
ORF1ab/nsp3	1381	A1381G	A2199G	nonsyn	gCa	gGa	6	4	0.666667	6860-6862
ORF1ab/nsp3	1381	A1381D	A2199D	nonsyn	gCA	gAT	6	2	0.333333	6860-6862
ORF1ab/nsp3	1381	A1381G	A2199G	nonsyn	gCA	gGG	6	1	0.166667	6860-6862
ORF1ab/nsp3	1381	A1381G	A2199G	nonsyn	gCA	gGC	6	1	0.166667	6860-6862
ORF1ab/nsp3	1381	A1381R	A2199R	nonsyn	GCA	AGG	6	1	0.166667	6860-6862
ORF1ab/nsp3	1381	A1381del2	A2199del2	del	gCA	g--	5	3	0.6	6860-6862
ORF1ab/nsp3	1381	A1381del2	A2199del2	del	GCa	--a	5	1	0.2	6860-6862
ORF1ab/nsp3	1381	A1381del2	A2199del2	del	GCA	A--	5	1	0.2	6860-6862
ORF1ab/nsp3	1381	A1381Q	A2199Q	nonsyn	GCa	CAa	2	1	0.5	6860-6862
ORF1ab/nsp3	1381	A1381Q	A2199Q	nonsyn	GCA	CAG	2	1	0.5	6860-6862
ORF1ab/nsp3	1381	A1381C	A2199C	nonsyn	GCA	TGT	1	1	1	6860-6862

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/nsp3	1381	A1381V	gCa	gTa	840	849	All	0.000161
ORF1ab/nsp3	1381	A1381V	gCA	gTT	8	849	All	0.000002
ORF1ab/nsp3	1381	A1381V	gCA	gTG	1	849	All	0
ORF1ab/nsp3	1381	A1381T	Gca	Aca	385	391	All	0.000074
ORF1ab/nsp3	1381	A1381T	GcA	AcT	4	391	All	0.000001
ORF1ab/nsp3	1381	A1381T	GcA	AcG	1	391	All	0
ORF1ab/nsp3	1381	A1381T	GcA	AcC	1	391	All	0
ORF1ab/nsp3	1381	A1381A	gcA	gcG	180	251	All	0.000034
ORF1ab/nsp3	1381	A1381A	gcA	gcT	64	251	All	0.000012
ORF1ab/nsp3	1381	A1381A	gcA	gcC	7	251	All	0.000001
ORF1ab/nsp3	1381	A1381del	GCA	---	230	230	All	0.000044
ORF1ab/nsp3	1381	A1381I	GCa	ATa	101	158	All	0.000019
ORF1ab/nsp3	1381	A1381I	GCA	ATT	57	158	All	0.000011
ORF1ab/nsp3	1381	A1381K	GCa	AAa	155	155	All	0.00003
ORF1ab/nsp3	1381	A1381V	gCa	gTa	146	153	B.1.1.7	0.000131
ORF1ab/nsp3	1381	A1381V	gCA	gTT	7	153	B.1.1.7	0.000006
ORF1ab/nsp3	1381	A1381T	Gca	Aca	100	100	B.1.617.2	0.000377
ORF1ab/nsp3	1381	A1381E	gCa	gAa	92	93	All	0.000018
ORF1ab/nsp3	1381	A1381E	gCA	gAG	1	93	All	0
ORF1ab/nsp3	1381	A1381I	GCa	ATa	62	93	AY.25	0.000373
ORF1ab/nsp3	1381	A1381I	GCA	ATT	31	93	AY.25	0.000186
ORF1ab/nsp3	1381	A1381L	GCa	TTa	88	90	All	0.000017
ORF1ab/nsp3	1381	A1381L	GCA	TTG	2	90	All	0
ORF1ab/nsp3	1381	A1381S	Gca	Tca	76	87	All	0.000015
ORF1ab/nsp3	1381	A1381S	GcA	TcT	9	87	All	0.000002
ORF1ab/nsp3	1381	A1381S	GCA	AGT	1	87	All	0
ORF1ab/nsp3	1381	A1381S	GCA	AGC	1	87	All	0
ORF1ab/nsp3	1381	A1381X	GCa	TAa	84	86	All	0.000016
ORF1ab/nsp3	1381	A1381X	GCA	TAG	1	86	All	0
ORF1ab/nsp3	1381	A1381X	GCa	TGa	1	86	All	0
ORF1ab/nsp3	1381	A1381K	GCa	AAa	85	85	AY.25	0.000511
ORF1ab/nsp3	1381	A1381del	GCA	---	84	84	B.1.1.7	0.000075
ORF1ab/nsp3	1381	A1381V	gCa	gTa	80	80	AY.42	0.003218
ORF1ab/nsp3	1381	A1381V	gCa	gTa	73	73	B.1.1.329	0.280769
ORF1ab/nsp3	1381	A1381V	gCa	gTa	68	68	B.1.1.10	0.075808
ORF1ab/nsp3	1381	A1381V	gCa	gTa	67	67	AY.3	0.000666
ORF1ab/nsp3	1381	A1381N	GCA	AAT	63	63	All	0.000012
ORF1ab/nsp3	1381	A1381T	Gca	Aca	59	60	B.1.1.7	0.000053
ORF1ab/nsp3	1381	A1381T	GcA	AcT	1	60	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381F	GCA	TTT	59	59	All	0.000011
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	56	56	All	0.000011
ORF1ab/nsp3	1381	A1381X	GCa	TAa	53	53	AY.25	0.000319
ORF1ab/nsp3	1381	A1381T	Gca	Aca	50	50	AY.4	0.000078
ORF1ab/nsp3	1381	A1381A	gcA	gcG	50	50	AY.43	0.000222
ORF1ab/nsp3	1381	A1381L	GCa	TTa	48	48	AY.25	0.000289
ORF1ab/nsp3	1381	A1381T	Gca	Aca	44	46	AY.25	0.000265
ORF1ab/nsp3	1381	A1381T	GcA	AcT	2	46	AY.25	0.000012
ORF1ab/nsp3	1381	A1381S	Gca	Tca	35	42	B.1.1.7	0.000031
ORF1ab/nsp3	1381	A1381S	GcA	TcT	7	42	B.1.1.7	0.000006
ORF1ab/nsp3	1381	A1381A	gcA	gcT	34	40	B.1.1.7	0.00003
ORF1ab/nsp3	1381	A1381A	gcA	gcG	5	40	B.1.1.7	0.000004
ORF1ab/nsp3	1381	A1381A	gcA	gcC	1	40	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381N	GCA	AAT	35	35	AY.25	0.000211
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	33	33	AY.25	0.000198
ORF1ab/nsp3	1381	A1381E	gCa	gAa	32	32	AY.25	0.000192
ORF1ab/nsp3	1381	A1381V	gCa	gTa	31	31	AY.4	0.000048
ORF1ab/nsp3	1381	A1381F	GCA	TTT	29	29	AY.25	0.000174
ORF1ab/nsp3	1381	A1381V	gCa	gTa	29	29	B.1.177.60	0.006335
ORF1ab/nsp3	1381	A1381A	gcA	gcG	26	27	B.1.427	0.001313
ORF1ab/nsp3	1381	A1381A	gcA	gcC	1	27	B.1.427	0.00005
ORF1ab/nsp3	1381	A1381V	gCa	gTa	23	23	AY.44	0.00014
ORF1ab/nsp3	1381	A1381K	GCa	AAa	23	23	B.1.1.7	0.000021
ORF1ab/nsp3	1381	A1381V	gCa	gTa	22	22	AY.111	0.004029
ORF1ab/nsp3	1381	A1381I	GCa	ATa	12	21	B.1.1.7	0.000011
ORF1ab/nsp3	1381	A1381I	GCA	ATT	9	21	B.1.1.7	0.000008
ORF1ab/nsp3	1381	A1381V	gCa	gTa	19	19	AY.103	0.000118
ORF1ab/nsp3	1381	A1381L	GCa	TTa	18	19	B.1.1.7	0.000016
ORF1ab/nsp3	1381	A1381L	GCA	TTG	1	19	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381V	gCa	gTa	18	18	L.4	0.9
ORF1ab/nsp3	1381	A1381V	gCa	gTa	17	17	AY.25	0.000102
ORF1ab/nsp3	1381	A1381del	GCA	---	17	17	AY.4	0.000026
ORF1ab/nsp3	1381	A1381del	GCA	---	17	17	B.1.177	0.000224
ORF1ab/nsp3	1381	A1381E	gCa	gAa	15	16	B.1.1.7	0.000013
ORF1ab/nsp3	1381	A1381E	gCA	gAG	1	16	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381T	Gca	Aca	16	16	B.1.2	0.000141
ORF1ab/nsp3	1381	A1381V	gCa	gTa	16	16	P.1	0.000252
ORF1ab/nsp3	1381	A1381A	gcA	gcG	15	15	AY.3	0.000149
ORF1ab/nsp3	1381	A1381A	gcA	gcG	14	15	AY.44	0.000085
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	15	AY.44	0.000006
ORF1ab/nsp3	1381	A1381V	gCa	gTa	15	15	B.1	0.000137
ORF1ab/nsp3	1381	A1381V	gCa	gTa	15	15	B.1.617.2	0.000056
ORF1ab/nsp3	1381	A1381del1	gcA	gc-	10	14	All	0.000002
ORF1ab/nsp3	1381	A1381del1	GCa	-Ta	2	14	All	0
ORF1ab/nsp3	1381	A1381del1	Gca	-ca	1	14	All	0
ORF1ab/nsp3	1381	A1381del1	gCA	g-N	1	14	All	0
ORF1ab/nsp3	1381	A1381V	gCa	gTa	14	14	AY.43	0.000062
ORF1ab/nsp3	1381	A1381F	GCA	TTT	14	14	B.1.1.7	0.000013
ORF1ab/nsp3	1381	A1381V	gCa	gTa	14	14	B.1.2	0.000123
ORF1ab/nsp3	1381	A1381V	gCa	gTa	14	14	B.1.243	0.000974
ORF1ab/nsp3	1381	A1381V	gCa	gTa	12	13	B.1.1	0.000218
ORF1ab/nsp3	1381	A1381V	gCA	gTT	1	13	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381P	Gca	Cca	10	12	All	0.000002
ORF1ab/nsp3	1381	A1381P	GcA	CcG	1	12	All	0
ORF1ab/nsp3	1381	A1381P	GcA	CcC	1	12	All	0
ORF1ab/nsp3	1381	A1381I	GCa	ATa	6	11	AY.103	0.000037
ORF1ab/nsp3	1381	A1381I	GCA	ATT	5	11	AY.103	0.000031
ORF1ab/nsp3	1381	A1381T	Gca	Aca	11	11	AY.3	0.000109
ORF1ab/nsp3	1381	A1381K	GCa	AAa	11	11	AY.3	0.000109
ORF1ab/nsp3	1381	A1381A	gcA	gcG	10	11	AY.4	0.000016
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	11	AY.4	0.000002
ORF1ab/nsp3	1381	A1381N	GCA	AAT	11	11	B.1.1.7	0.00001
ORF1ab/nsp3	1381	A1381V	gCa	gTa	10	10	AY.20	0.000389
ORF1ab/nsp3	1381	A1381del	GCA	---	10	10	B.1	0.000092
ORF1ab/nsp3	1381	A1381X	GCa	TAa	10	10	B.1.1.7	0.000009
ORF1ab/nsp3	1381	A1381V	gCa	gTa	9	9	P.1.15	0.002091
ORF1ab/nsp3	1381	A1381E	gCa	gAa	8	8	AY.3	0.00008
ORF1ab/nsp3	1381	A1381V	gCa	gTa	8	8	AY.85	0.003417
ORF1ab/nsp3	1381	A1381V	gCa	gTa	8	8	AY.99.2	0.000737
ORF1ab/nsp3	1381	A1381del	GCA	---	8	8	B.1.1	0.000145
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	8	8	B.1.1.7	0.000007
ORF1ab/nsp3	1381	A1381del	GCA	---	8	8	B.1.617.2	0.00003
ORF1ab/nsp3	1381	A1381A	gcA	gcG	8	8	P.1.15	0.001859
ORF1ab/nsp3	1381	A1381V	gCa	gTa	7	7	B.1.97	0.179487
ORF1ab/nsp3	1381	A1381R	GCa	AGa	5	6	All	0.000001
ORF1ab/nsp3	1381	A1381G	gCa	gGa	4	6	All	0.000001
ORF1ab/nsp3	1381	A1381D	gCA	gAC	4	6	All	0.000001
ORF1ab/nsp3	1381	A1381D	gCA	gAT	2	6	All	0
ORF1ab/nsp3	1381	A1381R	GCA	AGG	1	6	All	0
ORF1ab/nsp3	1381	A1381G	gCA	gGC	1	6	All	0
ORF1ab/nsp3	1381	A1381G	gCA	gGG	1	6	All	0
ORF1ab/nsp3	1381	A1381A	gcA	gcG	5	6	AY.103	0.000031
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	6	AY.103	0.000006
ORF1ab/nsp3	1381	A1381S	Gca	Tca	4	6	AY.25	0.000024
ORF1ab/nsp3	1381	A1381S	GcA	TcT	2	6	AY.25	0.000012
ORF1ab/nsp3	1381	A1381S	Gca	Tca	6	6	AY.4	0.000009
ORF1ab/nsp3	1381	A1381K	GCa	AAa	6	6	AY.44	0.000037
ORF1ab/nsp3	1381	A1381T	Gca	Aca	6	6	AY.44	0.000037
ORF1ab/nsp3	1381	A1381A	gcA	gcG	6	6	B.1.2	0.000053
ORF1ab/nsp3	1381	A1381T	Gca	Aca	4	6	B.1.221	0.000284
ORF1ab/nsp3	1381	A1381T	GcA	AcC	1	6	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381T	GcA	AcG	1	6	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381del	GCA	---	6	6	B.1.258	0.000399
ORF1ab/nsp3	1381	A1381A	gcA	gcG	4	6	B.1.617.2	0.000015
ORF1ab/nsp3	1381	A1381A	gcA	gcT	2	6	B.1.617.2	0.000008
ORF1ab/nsp3	1381	A1381A	gcA	gcG	6	6	P.1	0.000095
ORF1ab/nsp3	1381	A1381del2	gCA	g--	3	5	All	0.000001
ORF1ab/nsp3	1381	A1381del2	GCA	A--	1	5	All	0
ORF1ab/nsp3	1381	A1381del2	GCa	--a	1	5	All	0
ORF1ab/nsp3	1381	A1381F	GCA	TTT	5	5	AY.103	0.000031
ORF1ab/nsp3	1381	A1381K	GCa	AAa	5	5	AY.103	0.000031
ORF1ab/nsp3	1381	A1381X	GCa	TAa	5	5	AY.103	0.000031
ORF1ab/nsp3	1381	A1381N	GCA	AAT	5	5	AY.103	0.000031
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	5	5	AY.103	0.000031
ORF1ab/nsp3	1381	A1381L	GCa	TTa	5	5	AY.103	0.000031
ORF1ab/nsp3	1381	A1381T	Gca	Aca	5	5	AY.119	0.000177
ORF1ab/nsp3	1381	A1381K	GCa	AAa	5	5	AY.26	0.000142
ORF1ab/nsp3	1381	A1381I	GCa	ATa	3	5	AY.26	0.000085
ORF1ab/nsp3	1381	A1381I	GCA	ATT	2	5	AY.26	0.000057
ORF1ab/nsp3	1381	A1381I	GCa	ATa	3	5	AY.44	0.000018
ORF1ab/nsp3	1381	A1381I	GCA	ATT	2	5	AY.44	0.000012
ORF1ab/nsp3	1381	A1381E	gCa	gAa	5	5	AY.74	0.000578
ORF1ab/nsp3	1381	A1381V	gCa	gTa	5	5	AY.9.2	0.000184
ORF1ab/nsp3	1381	A1381A	gcA	gcT	3	5	AY.99.2	0.000276
ORF1ab/nsp3	1381	A1381A	gcA	gcG	2	5	AY.99.2	0.000184
ORF1ab/nsp3	1381	A1381V	gCa	gTa	5	5	B.1.1.519	0.000199
ORF1ab/nsp3	1381	A1381del	GCA	---	5	5	B.1.221	0.000355
ORF1ab/nsp3	1381	A1381V	gCa	gTa	5	5	B.1.526	0.000118
ORF1ab/nsp3	1381	A1381V	gCa	gTa	4	4	AY.102	0.000106
ORF1ab/nsp3	1381	A1381V	gCa	gTa	4	4	AY.117	0.000338
ORF1ab/nsp3	1381	A1381T	Gca	Aca	4	4	AY.27	0.000259
ORF1ab/nsp3	1381	A1381I	GCa	ATa	3	4	AY.3	0.00003
ORF1ab/nsp3	1381	A1381I	GCA	ATT	1	4	AY.3	0.00001
ORF1ab/nsp3	1381	A1381T	Gca	Aca	4	4	AY.4.2	0.000087
ORF1ab/nsp3	1381	A1381del	GCA	---	4	4	AY.4.5	0.00043
ORF1ab/nsp3	1381	A1381T	Gca	Aca	4	4	AY.47	0.000124
ORF1ab/nsp3	1381	A1381T	Gca	Aca	4	4	AY.9.2	0.000147
ORF1ab/nsp3	1381	A1381A	gcA	gcG	4	4	B.1	0.000037
ORF1ab/nsp3	1381	A1381S	Gca	Tca	4	4	B.1	0.000037
ORF1ab/nsp3	1381	A1381V	gCa	gTa	4	4	B.1.1.1	0.001307
ORF1ab/nsp3	1381	A1381V	gCa	gTa	4	4	B.1.1.432	0.005063
ORF1ab/nsp3	1381	A1381P	Gca	Cca	3	4	B.1.1.7	0.000003
ORF1ab/nsp3	1381	A1381P	GcA	CcG	1	4	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381T	Gca	Aca	4	4	B.1.177	0.000053
ORF1ab/nsp3	1381	A1381A	gcA	gcG	2	4	B.1.177	0.000026
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	4	B.1.177	0.000013
ORF1ab/nsp3	1381	A1381A	gcA	gcC	1	4	B.1.177	0.000013
ORF1ab/nsp3	1381	A1381G	gCa	gGa	2	4	B.1.221	0.000142
ORF1ab/nsp3	1381	A1381G	gCA	gGC	1	4	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381G	gCA	gGG	1	4	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381S	Gca	Tca	4	4	B.1.258	0.000266
ORF1ab/nsp3	1381	A1381V	gCa	gTa	4	4	B.1.525	0.000453
ORF1ab/nsp3	1381	A1381I	GCa	ATa	2	4	P.1	0.000032
ORF1ab/nsp3	1381	A1381I	GCA	ATT	2	4	P.1	0.000032
ORF1ab/nsp3	1381	A1381T	Gca	Aca	3	3	AY.100	0.000138
ORF1ab/nsp3	1381	A1381S	Gca	Tca	3	3	AY.117	0.000254
ORF1ab/nsp3	1381	A1381L	GCa	TTa	3	3	AY.26	0.000085
ORF1ab/nsp3	1381	A1381X	GCa	TAa	3	3	AY.26	0.000085
ORF1ab/nsp3	1381	A1381L	GCa	TTa	3	3	AY.3	0.00003
ORF1ab/nsp3	1381	A1381X	GCa	TAa	3	3	AY.3	0.00003
ORF1ab/nsp3	1381	A1381A	gcA	gcG	3	3	AY.34	0.000291
ORF1ab/nsp3	1381	A1381T	Gca	Aca	3	3	AY.35	0.000699
ORF1ab/nsp3	1381	A1381T	Gca	Aca	3	3	AY.39	0.000074
ORF1ab/nsp3	1381	A1381T	Gca	Aca	3	3	AY.43	0.000013
ORF1ab/nsp3	1381	A1381del	GCA	---	3	3	AY.43	0.000013
ORF1ab/nsp3	1381	A1381L	GCa	TTa	3	3	AY.44	0.000018
ORF1ab/nsp3	1381	A1381X	GCa	TAa	3	3	AY.44	0.000018
ORF1ab/nsp3	1381	A1381E	gCa	gAa	3	3	AY.44	0.000018
ORF1ab/nsp3	1381	A1381I	GCa	ATa	2	3	AY.47	0.000062
ORF1ab/nsp3	1381	A1381I	GCA	ATT	1	3	AY.47	0.000031
ORF1ab/nsp3	1381	A1381T	Gca	Aca	3	3	B.1	0.000027
ORF1ab/nsp3	1381	A1381del1	gcA	gc-	2	3	B.1	0.000018
ORF1ab/nsp3	1381	A1381del1	gCA	g-N	1	3	B.1	0.000009
ORF1ab/nsp3	1381	A1381T	Gca	Aca	3	3	B.1.1	0.000054
ORF1ab/nsp3	1381	A1381E	gCa	gAa	3	3	B.1.1	0.000054
ORF1ab/nsp3	1381	A1381T	Gca	Aca	3	3	B.1.1.306	0.001315
ORF1ab/nsp3	1381	A1381A	gcA	gcT	3	3	B.1.1.317	0.001235
ORF1ab/nsp3	1381	A1381A	gcA	gcG	2	3	B.1.1.519	0.000079
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	3	B.1.1.519	0.00004
ORF1ab/nsp3	1381	A1381del1	gcA	gc-	3	3	B.1.1.7	0.000003
ORF1ab/nsp3	1381	A1381del2	gCA	g--	1	3	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381del2	GCA	A--	1	3	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381del2	GCa	--a	1	3	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381del	GCA	---	3	3	B.1.2	0.000026
ORF1ab/nsp3	1381	A1381V	gCa	gTa	3	3	B.1.221	0.000213
ORF1ab/nsp3	1381	A1381R	GCa	AGa	2	3	B.1.221	0.000142
ORF1ab/nsp3	1381	A1381R	GCA	AGG	1	3	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381A	gcA	gcT	3	3	B.1.258	0.0002
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	3	B.1.258	0.000133
ORF1ab/nsp3	1381	A1381T	GcA	AcT	1	3	B.1.258	0.000067
ORF1ab/nsp3	1381	A1381D	gCA	gAC	3	3	B.1.351	0.000089
ORF1ab/nsp3	1381	A1381E	gCa	gAa	3	3	B.1.525	0.000339
ORF1ab/nsp3	1381	A1381del	GCA	---	3	3	B.1.525	0.000339
ORF1ab/nsp3	1381	A1381del1	gcA	gc-	2	3	B.1.617.2	0.000008
ORF1ab/nsp3	1381	A1381del1	Gca	-ca	1	3	B.1.617.2	0.000004
ORF1ab/nsp3	1381	A1381V	gCa	gTa	3	3	C.37	0.000348
ORF1ab/nsp3	1381	A1381V	gCa	gTa	3	3	D.2	0.000225
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2		0.111111
ORF1ab/nsp3	1381	A1381del	GCA	---	2	2		0.111111
ORF1ab/nsp3	1381	A1381del1	GCa	-Ta	2	2		0.111111
ORF1ab/nsp3	1381	A1381A	gcA	gcT	2	2	A.27	0.003311
ORF1ab/nsp3	1381	A1381Q	GCa	CAa	1	2	All	0
ORF1ab/nsp3	1381	A1381Q	GCA	CAG	1	2	All	0
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	AY.100	0.000092
ORF1ab/nsp3	1381	A1381S	Gca	Tca	2	2	AY.102	0.000053
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	AY.103	0.000012
ORF1ab/nsp3	1381	A1381A	gcA	gcG	2	2	AY.110	0.000225
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	AY.111	0.000366
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	AY.118	0.000125
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	AY.119	0.000071
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	AY.120	0.000074
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	AY.120	0.000074
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	AY.19	0.002281
ORF1ab/nsp3	1381	A1381A	gcA	gcG	2	2	AY.20	0.000078
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	2	AY.20	0.000039
ORF1ab/nsp3	1381	A1381I	GCA	ATT	1	2	AY.20	0.000039
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	AY.23	0.000139
ORF1ab/nsp3	1381	A1381I	GCA	ATT	1	2	AY.23	0.00007
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	2	AY.23	0.00007
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	2	AY.25	0.000006
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	2	AY.25	0.000006
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	2	2	AY.26	0.000057
ORF1ab/nsp3	1381	A1381E	gCa	gAa	2	2	AY.26	0.000057
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	AY.26	0.000057
ORF1ab/nsp3	1381	A1381F	GCA	TTT	2	2	AY.26	0.000057
ORF1ab/nsp3	1381	A1381N	GCA	AAT	2	2	AY.26	0.000057
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	AY.27	0.000129
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	AY.39	0.000049
ORF1ab/nsp3	1381	A1381E	gCa	gAa	2	2	AY.4	0.000003
ORF1ab/nsp3	1381	A1381del1	gcA	gc-	2	2	AY.44	0.000012
ORF1ab/nsp3	1381	A1381N	GCA	AAT	2	2	AY.44	0.000012
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	2	2	AY.44	0.000012
ORF1ab/nsp3	1381	A1381F	GCA	TTT	2	2	AY.44	0.000012
ORF1ab/nsp3	1381	A1381A	gcA	gcG	2	2	AY.46	0.000208
ORF1ab/nsp3	1381	A1381X	GCa	TAa	2	2	AY.47	0.000062
ORF1ab/nsp3	1381	A1381K	GCa	AAa	2	2	AY.47	0.000062
ORF1ab/nsp3	1381	A1381L	GCa	TTa	2	2	AY.47	0.000062
ORF1ab/nsp3	1381	A1381del	GCA	---	2	2	AY.5	0.000041
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	2	AY.5.4	0.000277
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	2	AY.5.4	0.000277
ORF1ab/nsp3	1381	A1381E	gCa	gAa	2	2	B.1	0.000018
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	B.1.1.214	0.000111
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	B.1.1.39	0.001019
ORF1ab/nsp3	1381	A1381Q	GCa	CAa	1	2	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381Q	GCA	CAG	1	2	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381del	GCA	---	2	2	B.1.177.18	0.00232
ORF1ab/nsp3	1381	A1381del	GCA	---	2	2	B.1.177.7	0.00033
ORF1ab/nsp3	1381	A1381A	gcA	gcC	1	2	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	2	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	B.1.241	0.001623
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	B.1.258	0.000133
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	B.1.258.17	0.000208
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	2	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381I	GCA	ATT	1	2	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	B.1.596	0.000174
ORF1ab/nsp3	1381	A1381V	gCa	gTa	2	2	B.1.596	0.000174
ORF1ab/nsp3	1381	A1381I	GCA	ATT	1	2	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	2	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381T	Gca	Aca	2	2	B.1.637	0.000146
ORF1ab/nsp3	1381	A1381E	gCa	gAa	2	2	C.37	0.000232
ORF1ab/nsp3	1381	A1381K	GCa	AAa	2	2	C.37	0.000232
ORF1ab/nsp3	1381	A1381X	GCa	TAa	2	2	P.1	0.000032
ORF1ab/nsp3	1381	A1381del	GCA	---	2	2	P.1	0.000032
ORF1ab/nsp3	1381	A1381N	GCA	AAT	2	2	P.1	0.000032
ORF1ab/nsp3	1381	A1381L	GCa	TTa	2	2	P.1	0.000032
ORF1ab/nsp3	1381	A1381F	GCA	TTT	2	2	P.1	0.000032
ORF1ab/nsp3	1381	A1381K	GCa	AAa	2	2	P.1	0.000032
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	2	2	P.1	0.000032
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	2	R.1	0.00009
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	2	R.1	0.00009
ORF1ab/nsp3	1381	A1381P	Gca	Cca	1	1		0.055556
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1		0.055556
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1		0.055556
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1		0.055556
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	A	0.000387
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	A.2	0.000662
ORF1ab/nsp3	1381	A1381del2	gCA	g--	1	1	A.2.4	0.003367
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	A.2.4	0.003367
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	A.28	0.002646
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AD.2	0.000219
ORF1ab/nsp3	1381	A1381C	GCA	TGT	1	1	All	0
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AV.1	0.005051
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	AY.100	0.000046
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	AY.100	0.000046
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.100	0.000046
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.102	0.000027
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	AY.103	0.000006
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	AY.105	0.000643
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.105	0.000643
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	AY.105	0.000643
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.106	0.000335
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.107	0.000466
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.109	0.00074
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	AY.118	0.000063
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.120.1	0.000321
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	AY.13	0.000161
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.13	0.000161
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	AY.2	0.000356
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.2	0.000356
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	AY.2	0.000356
ORF1ab/nsp3	1381	A1381N	GCA	AAT	1	1	AY.20	0.000039
ORF1ab/nsp3	1381	A1381L	GCa	TTa	1	1	AY.20	0.000039
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	AY.20	0.000039
ORF1ab/nsp3	1381	A1381F	GCA	TTT	1	1	AY.20	0.000039
ORF1ab/nsp3	1381	A1381X	GCa	TAa	1	1	AY.20	0.000039
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	1	1	AY.20	0.000039
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	AY.20	0.000039
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.23	0.00007
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	AY.23	0.00007
ORF1ab/nsp3	1381	A1381N	GCA	AAT	1	1	AY.23	0.00007
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	AY.23.1	0.000417
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	AY.24	0.000431
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.29	0.000016
ORF1ab/nsp3	1381	A1381N	GCA	AAT	1	1	AY.3	0.00001
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	1	1	AY.3	0.00001
ORF1ab/nsp3	1381	A1381F	GCA	TTT	1	1	AY.3	0.00001
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	AY.3.1	0.000085
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.3.1	0.000085
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	AY.3.1	0.000085
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.32	0.000532
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	AY.33	0.000067
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.34	0.000097
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.36	0.000148
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.39	0.000025
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	AY.39	0.000025
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	AY.39	0.000025
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	AY.43	0.000004
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	AY.45	0.000122
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.46	0.000104
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.47	0.000031
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	AY.47	0.000031
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	AY.47	0.000031
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	1	1	AY.47	0.000031
ORF1ab/nsp3	1381	A1381N	GCA	AAT	1	1	AY.47	0.000031
ORF1ab/nsp3	1381	A1381F	GCA	TTT	1	1	AY.47	0.000031
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.48	0.000465
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.5	0.000021
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	AY.5	0.000021
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.5	0.000021
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.5.2	0.002463
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.52	0.000814
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.55	0.000917
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.60	0.000938
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.65	0.000533
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	AY.71	0.000475
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.73	0.000665
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.74	0.000116
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	AY.75	0.000056
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.75.1	0.00018
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.79	0.001211
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.84	0.000437
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	AY.9	0.000068
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	AY.9.2	0.000037
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	AY.93	0.000273
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B	0.000128
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B	0.000128
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	B.1	0.000009
ORF1ab/nsp3	1381	A1381del2	gCA	g--	1	1	B.1	0.000009
ORF1ab/nsp3	1381	A1381L	GCa	TTa	1	1	B.1	0.000009
ORF1ab/nsp3	1381	A1381P	Gca	Cca	1	1	B.1	0.000009
ORF1ab/nsp3	1381	A1381G	gCa	gGa	1	1	B.1	0.000009
ORF1ab/nsp3	1381	A1381R	GCa	AGa	1	1	B.1	0.000009
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381G	gCa	gGa	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381P	Gca	Cca	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381X	GCa	TAa	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381del1	gcA	gc-	1	1	B.1.1	0.000018
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.170	0.001247
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.218	0.007692
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.232	0.001815
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	1381	A1381P	Gca	Cca	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.315	0.008475
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.1.381	0.04
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	B.1.1.432	0.001266
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.1.432	0.001266
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.1.442	0.018519
ORF1ab/nsp3	1381	A1381D	gCA	gAC	1	1	B.1.1.459	0.015385
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	B.1.1.47	0.005348
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.1.486	0.001577
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1381	A1381P	Gca	Cca	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1381	A1381D	gCA	gAT	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.110.3	0.000718
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	1381	A1381A	gcA	gcC	1	1	B.1.160	0.000031
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.161	0.017241
ORF1ab/nsp3	1381	A1381P	Gca	Cca	1	1	B.1.177	0.000013
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1381	A1381P	Gca	Cca	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.50	0.004695
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.56	0.000668
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.6	0.000977
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.62	0.001192
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.68	0.015152
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.177.8	0.000752
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.201	0.005682
ORF1ab/nsp3	1381	A1381P	GcA	CcC	1	1	B.1.214.2	0.0006
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	1	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381S	GCA	AGC	1	1	B.1.221	0.000071
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.235	0.002519
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.240	0.000216
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.243	0.00007
ORF1ab/nsp3	1381	A1381D	gCA	gAT	1	1	B.1.258	0.000067
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	1	B.1.258	0.000067
ORF1ab/nsp3	1381	A1381N	GCA	AAT	1	1	B.1.258	0.000067
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	B.1.258	0.000067
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.1.258	0.000067
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.258.16	0.001637
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.258.3	0.001675
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.325	0.006897
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.349	0.000715
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.351	0.00003
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	B.1.351	0.00003
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.36	0.000146
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	B.1.36.22	0.001208
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.36.38	0.001642
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.363	0.012987
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.369	0.000285
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.396	0.000706
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.399	0.001934
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.400	0.000429
ORF1ab/nsp3	1381	A1381R	GCa	AGa	1	1	B.1.415	0.014286
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.427	0.00005
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.427	0.00005
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.1.428	0.00102
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.429	0.000024
ORF1ab/nsp3	1381	A1381A	gcA	gcT	1	1	B.1.429	0.000024
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.429	0.000024
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.469	0.00361
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.517	0.000427
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	B.1.524	0.001406
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.1.526	0.000024
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.564	0.000426
ORF1ab/nsp3	1381	A1381A	gcA	gcC	1	1	B.1.575	0.000303
ORF1ab/nsp3	1381	A1381L	GCa	TTa	1	1	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381C	GCA	TGT	1	1	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381X	GCa	TGa	1	1	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381S	GCA	AGT	1	1	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381F	GCA	TTT	1	1	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381R	GCa	AGa	1	1	B.1.576	0.000907
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.1.582	0.000491
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.588	0.00091
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.589	0.007576
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.596	0.000087
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.1.596	0.000087
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.612	0.002653
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1381	A1381V	gCA	gTG	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1381	A1381X	GCA	TAG	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1381	A1381S	Gca	Tca	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	1381	A1381F	GCA	TTT	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381Y	GCA	TAT	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381K	GCa	AAa	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381L	GCa	TTa	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381N	GCA	AAT	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381X	GCa	TAa	1	1	B.1.621	0.000089
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	B.1.621.1	0.000506
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.1.630	0.005236
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.34	0.013699
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.4.4	0.018868
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	B.40	0.000364
ORF1ab/nsp3	1381	A1381E	gCa	gAa	1	1	B.6	0.00091
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	C.36	0.000911
ORF1ab/nsp3	1381	A1381I	GCa	ATa	1	1	C.37	0.000116
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	C.37	0.000116
ORF1ab/nsp3	1381	A1381A	gcA	gcC	1	1	C.37	0.000116
ORF1ab/nsp3	1381	A1381L	GCA	TTG	1	1	P.1.10	0.000269
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	P.1.13	0.000898
ORF1ab/nsp3	1381	A1381A	gcA	gcG	1	1	P.1.14	0.000048
ORF1ab/nsp3	1381	A1381T	Gca	Aca	1	1	P.1.17	0.000162
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	Q.1	0.000126
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	Q.4	0.000455
ORF1ab/nsp3	1381	A1381V	gCa	gTa	1	1	Q.8	0.000165
ORF1ab/nsp3	1381	A1381del	GCA	---	1	1	Q.8	0.000165
ORF1ab/nsp3	1381	A1381T	Gca	Aca	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.