CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 5

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
ORF7a	5	L5del		del	CTT	---	6407	6407	1	27406-27408
ORF7a	5	L5P		nonsyn	cTt	cCt	2974	2871	0.965366	27406-27408
ORF7a	5	L5P		nonsyn	cTT	cCG	2974	101	0.033961	27406-27408
ORF7a	5	L5P		nonsyn	cTT	cCC	2974	2	0.000672495	27406-27408
ORF7a	5	L5F		nonsyn	Ctt	Ttt	2227	2226	0.999551	27406-27408
ORF7a	5	L5F		nonsyn	CtT	TtC	2227	1	0.000449035	27406-27408
ORF7a	5	L5L		syn	ctT	ctC	778	370	0.475578	27406-27408
ORF7a	5	L5L		syn	ctT	ctA	778	271	0.348329	27406-27408
ORF7a	5	L5L		syn	ctT	ctG	778	137	0.176093	27406-27408
ORF7a	5	L5I		nonsyn	Ctt	Att	506	504	0.996047	27406-27408
ORF7a	5	L5I		nonsyn	CtT	AtC	506	2	0.00395257	27406-27408
ORF7a	5	L5V		nonsyn	Ctt	Gtt	145	142	0.97931	27406-27408
ORF7a	5	L5V		nonsyn	CtT	GtC	145	2	0.0137931	27406-27408
ORF7a	5	L5V		nonsyn	CtT	GtA	145	1	0.00689655	27406-27408
ORF7a	5	L5R		nonsyn	cTt	cGt	126	123	0.97619	27406-27408
ORF7a	5	L5R		nonsyn	cTT	cGG	126	2	0.015873	27406-27408
ORF7a	5	L5R		nonsyn	cTT	cGA	126	1	0.00793651	27406-27408
ORF7a	5	L5del1		del	cTt	c-t	67	45	0.671642	27406-27408
ORF7a	5	L5del1		del	Ctt	-tt	67	16	0.238806	27406-27408
ORF7a	5	L5del1		del	ctT	ct-	67	2	0.0298507	27406-27408
ORF7a	5	L5del1		del	CtT	-tN	67	2	0.0298507	27406-27408
ORF7a	5	L5del1		del	CtT	-tC	67	1	0.0149254	27406-27408
ORF7a	5	L5del1		del	CTT	-NN	67	1	0.0149254	27406-27408
ORF7a	5	L5H		nonsyn	cTt	cAt	40	39	0.975	27406-27408
ORF7a	5	L5H		nonsyn	cTT	cAC	40	1	0.025	27406-27408
ORF7a	5	L5del2		del	cTT	c--	19	16	0.842105	27406-27408
ORF7a	5	L5del2		del	CTT	--N	19	3	0.157895	27406-27408
ORF7a	5	L5S		nonsyn	CTt	TCt	12	10	0.833333	27406-27408
ORF7a	5	L5S		nonsyn	CTt	AGt	12	2	0.166667	27406-27408
ORF7a	5	L5T		nonsyn	CTT	ACG	5	4	0.8	27406-27408
ORF7a	5	L5T		nonsyn	CTT	ACC	5	1	0.2	27406-27408
ORF7a	5	L5C		nonsyn	CTt	TGt	3	3	1	27406-27408
ORF7a	5	L5G		nonsyn	CTt	GGt	3	2	0.666667	27406-27408
ORF7a	5	L5G		nonsyn	CTT	GGG	3	1	0.333333	27406-27408
ORF7a	5	L5D		nonsyn	CTt	GAt	2	2	1	27406-27408
ORF7a	5	L5N		nonsyn	CTt	AAt	2	2	1	27406-27408
ORF7a	5	L5M		nonsyn	CtT	AtG	1	1	1	27406-27408
ORF7a	5	L5K		nonsyn	CTT	AAG	1	1	1	27406-27408

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
ORF7a	5	L5del	CTT	---	6407	6407	All	0.001225
ORF7a	5	L5del	CTT	---	5768	5768	B.1.1.7	0.005164
ORF7a	5	L5P	cTt	cCt	2871	2974	All	0.000549
ORF7a	5	L5P	cTT	cCG	101	2974	All	0.000019
ORF7a	5	L5P	cTT	cCC	2	2974	All	0
ORF7a	5	L5P	cTt	cCt	2536	2536	AY.4	0.003947
ORF7a	5	L5F	Ctt	Ttt	2226	2227	All	0.000426
ORF7a	5	L5F	CtT	TtC	1	2227	All	0
ORF7a	5	L5L	ctT	ctC	370	778	All	0.000071
ORF7a	5	L5L	ctT	ctA	271	778	All	0.000052
ORF7a	5	L5L	ctT	ctG	137	778	All	0.000026
ORF7a	5	L5F	Ctt	Ttt	750	750	B.1.1.7	0.000671
ORF7a	5	L5I	Ctt	Att	504	506	All	0.000096
ORF7a	5	L5I	CtT	AtC	2	506	All	0
ORF7a	5	L5I	Ctt	Att	377	377	AY.4	0.000587
ORF7a	5	L5L	ctT	ctC	144	187	B.1.1.7	0.000129
ORF7a	5	L5L	ctT	ctA	30	187	B.1.1.7	0.000027
ORF7a	5	L5L	ctT	ctG	13	187	B.1.1.7	0.000012
ORF7a	5	L5del	CTT	---	179	179	B.1.177.21	0.013688
ORF7a	5	L5F	Ctt	Ttt	169	169	AY.4	0.000263
ORF7a	5	L5V	Ctt	Gtt	142	145	All	0.000027
ORF7a	5	L5V	CtT	GtC	2	145	All	0
ORF7a	5	L5V	CtT	GtA	1	145	All	0
ORF7a	5	L5L	ctT	ctA	132	138	AY.5	0.002726
ORF7a	5	L5L	ctT	ctG	5	138	AY.5	0.000103
ORF7a	5	L5L	ctT	ctC	1	138	AY.5	0.000021
ORF7a	5	L5del	CTT	---	135	135	AY.4	0.00021
ORF7a	5	L5R	cTt	cGt	123	126	All	0.000024
ORF7a	5	L5R	cTT	cGG	2	126	All	0
ORF7a	5	L5R	cTT	cGA	1	126	All	0
ORF7a	5	L5R	cTt	cGt	99	101	B.1.1.7	0.000089
ORF7a	5	L5R	cTT	cGG	2	101	B.1.1.7	0.000002
ORF7a	5	L5F	Ctt	Ttt	83	83	AY.103	0.000515
ORF7a	5	L5del1	cTt	c-t	45	67	All	0.000009
ORF7a	5	L5del1	Ctt	-tt	16	67	All	0.000003
ORF7a	5	L5del1	ctT	ct-	2	67	All	0
ORF7a	5	L5del1	CtT	-tN	2	67	All	0
ORF7a	5	L5del1	CTT	-NN	1	67	All	0
ORF7a	5	L5del1	CtT	-tC	1	67	All	0
ORF7a	5	L5P	cTT	cCG	36	63	AY.85	0.015378
ORF7a	5	L5P	cTt	cCt	27	63	AY.85	0.011534
ORF7a	5	L5F	Ctt	Ttt	63	63	B.1.617.2	0.000237
ORF7a	5	L5F	Ctt	Ttt	61	61	B.1.2	0.000537
ORF7a	5	L5L	ctT	ctC	57	60	AY.4	0.000089
ORF7a	5	L5L	ctT	ctA	3	60	AY.4	0.000005
ORF7a	5	L5V	Ctt	Gtt	58	59	B.1.1.7	0.000052
ORF7a	5	L5V	CtT	GtA	1	59	B.1.1.7	0.000001
ORF7a	5	L5P	cTt	cCt	50	55	B.1.617.2	0.000188
ORF7a	5	L5P	cTT	cCG	5	55	B.1.617.2	0.000019
ORF7a	5	L5F	Ctt	Ttt	46	46	AY.102	0.00122
ORF7a	5	L5F	Ctt	Ttt	45	45	B.1	0.000412
ORF7a	5	L5F	Ctt	Ttt	44	44	B.1.427	0.002222
ORF7a	5	L5L	ctT	ctC	29	44	B.1.617.2	0.000109
ORF7a	5	L5L	ctT	ctG	13	44	B.1.617.2	0.000049
ORF7a	5	L5L	ctT	ctA	2	44	B.1.617.2	0.000008
ORF7a	5	L5L	ctT	ctA	40	41	AY.103	0.000248
ORF7a	5	L5L	ctT	ctC	1	41	AY.103	0.000006
ORF7a	5	L5H	cTt	cAt	39	40	All	0.000007
ORF7a	5	L5H	cTT	cAC	1	40	All	0
ORF7a	5	L5P	cTt	cCt	35	40	B.1.1.7	0.000031
ORF7a	5	L5P	cTT	cCG	5	40	B.1.1.7	0.000004
ORF7a	5	L5F	Ctt	Ttt	40	40	B.1.429	0.000941
ORF7a	5	L5F	Ctt	Ttt	39	39	B.1.526	0.000917
ORF7a	5	L5F	Ctt	Ttt	34	34	AY.3	0.000338
ORF7a	5	L5P	cTt	cCt	34	34	R.1	0.00306
ORF7a	5	L5F	Ctt	Ttt	32	32	AY.26	0.000906
ORF7a	5	L5F	Ctt	Ttt	32	32	B.1.396	0.022583
ORF7a	5	L5F	Ctt	Ttt	30	30	P.1	0.000473
ORF7a	5	L5F	Ctt	Ttt	29	29	AY.75	0.001625
ORF7a	5	L5L	ctT	ctG	28	28	AY.85	0.011961
ORF7a	5	L5L	ctT	ctA	20	28	B.1.429	0.000471
ORF7a	5	L5L	ctT	ctC	8	28	B.1.429	0.000188
ORF7a	5	L5F	Ctt	Ttt	27	27	AY.25	0.000162
ORF7a	5	L5F	Ctt	Ttt	27	27	AY.36	0.004002
ORF7a	5	L5P	cTt	cCt	15	27	P.1	0.000236
ORF7a	5	L5P	cTT	cCG	11	27	P.1	0.000173
ORF7a	5	L5P	cTT	cCC	1	27	P.1	0.000016
ORF7a	5	L5L	ctT	ctA	25	25	AY.33	0.001669
ORF7a	5	L5F	Ctt	Ttt	25	25	AY.44	0.000152
ORF7a	5	L5F	Ctt	Ttt	25	25	AZ.1	0.021683
ORF7a	5	L5F	Ctt	Ttt	24	24	B.1.177	0.000316
ORF7a	5	L5F	Ctt	Ttt	23	23	B.1.1	0.000417
ORF7a	5	L5F	Ctt	Ttt	23	23	B.1.351	0.000684
ORF7a	5	L5I	Ctt	Att	22	22	B.1.617.2	0.000083
ORF7a	5	L5del	CTT	---	21	21	AY.29	0.000331
ORF7a	5	L5F	Ctt	Ttt	21	21	B.1.1.189	0.03177
ORF7a	5	L5I	Ctt	Att	21	21	B.1.1.7	0.000019
ORF7a	5	L5F	Ctt	Ttt	20	20	B.1.1.519	0.000794
ORF7a	5	L5del2	cTT	c--	16	19	All	0.000003
ORF7a	5	L5del2	CTT	--N	3	19	All	0.000001
ORF7a	5	L5F	Ctt	Ttt	19	19	AY.100	0.000874
ORF7a	5	L5V	Ctt	Gtt	19	19	AY.23	0.001325
ORF7a	5	L5F	Ctt	Ttt	19	19	B.1.324	0.030498
ORF7a	5	L5L	ctT	ctG	19	19	B.1.565	0.015397
ORF7a	5	L5del	CTT	---	18	18	AY.3	0.000179
ORF7a	5	L5F	Ctt	Ttt	18	18	AY.43	0.00008
ORF7a	5	L5L	ctT	ctC	17	18	B.1.596	0.001481
ORF7a	5	L5L	ctT	ctA	1	18	B.1.596	0.000087
ORF7a	5	L5L	ctT	ctG	14	18	P.1	0.000221
ORF7a	5	L5L	ctT	ctC	4	18	P.1	0.000063
ORF7a	5	L5del	CTT	---	16	16	AY.25	0.000096
ORF7a	5	L5P	cTT	cCG	12	16	AY.30	0.004749
ORF7a	5	L5P	cTt	cCt	4	16	AY.30	0.001583
ORF7a	5	L5P	cTt	cCt	16	16	B.1.1.332	0.5
ORF7a	5	L5F	Ctt	Ttt	16	16	B.1.243	0.001113
ORF7a	5	L5F	Ctt	Ttt	15	15	AY.23	0.001046
ORF7a	5	L5I	Ctt	Att	14	14	AY.103	0.000087
ORF7a	5	L5del	CTT	---	14	14	AY.103	0.000087
ORF7a	5	L5del	CTT	---	14	14	AY.43	0.000062
ORF7a	5	L5F	Ctt	Ttt	14	14	AY.5	0.000289
ORF7a	5	L5del	CTT	---	14	14	B.1	0.000128
ORF7a	5	L5F	Ctt	Ttt	14	14	B.1.1.230	0.12844
ORF7a	5	L5F	Ctt	Ttt	14	14	B.1.258	0.000932
ORF7a	5	L5del	CTT	---	14	14	B.1.617.2	0.000053
ORF7a	5	L5F	Ctt	Ttt	14	14	C.37	0.001625
ORF7a	5	L5del1	cTt	c-t	9	13	AY.103	0.000056
ORF7a	5	L5del1	Ctt	-tt	4	13	AY.103	0.000025
ORF7a	5	L5P	cTt	cCt	11	13	AY.43	0.000049
ORF7a	5	L5P	cTT	cCG	2	13	AY.43	0.000009
ORF7a	5	L5L	ctT	ctC	10	13	AY.44	0.000061
ORF7a	5	L5L	ctT	ctG	2	13	AY.44	0.000012
ORF7a	5	L5L	ctT	ctA	1	13	AY.44	0.000006
ORF7a	5	L5S	CTt	TCt	10	12	All	0.000002
ORF7a	5	L5S	CTt	AGt	2	12	All	0
ORF7a	5	L5L	ctT	ctC	8	12	AY.25	0.000048
ORF7a	5	L5L	ctT	ctA	4	12	AY.25	0.000024
ORF7a	5	L5del	CTT	---	12	12	AY.39	0.000297
ORF7a	5	L5del	CTT	---	12	12	AY.44	0.000073
ORF7a	5	L5F	Ctt	Ttt	12	12	B.1.177.43	0.017725
ORF7a	5	L5L	ctT	ctC	10	12	B.1.2	0.000088
ORF7a	5	L5L	ctT	ctG	2	12	B.1.2	0.000018
ORF7a	5	L5F	Ctt	Ttt	11	11	AY.20	0.000428
ORF7a	5	L5L	ctT	ctG	9	11	AY.43	0.00004
ORF7a	5	L5L	ctT	ctC	1	11	AY.43	0.000004
ORF7a	5	L5L	ctT	ctA	1	11	AY.43	0.000004
ORF7a	5	L5F	Ctt	Ttt	11	11	AY.46.4	0.00181
ORF7a	5	L5P	cTt	cCt	11	11	B.1	0.000101
ORF7a	5	L5P	cTT	cCG	6	10	AY.39	0.000148
ORF7a	5	L5P	cTt	cCt	4	10	AY.39	0.000099
ORF7a	5	L5P	cTt	cCt	10	10	B.1.177	0.000132
ORF7a	5	L5F	Ctt	Ttt	10	10	B.1.177.81	0.001893
ORF7a	5	L5del1	cTt	c-t	9	10	B.1.617.2	0.000034
ORF7a	5	L5del1	Ctt	-tt	1	10	B.1.617.2	0.000004
ORF7a	5	L5L	ctT	ctC	10	10	C.37	0.001161
ORF7a	5	L5L	ctT	ctC	9	9	AY.120	0.000335
ORF7a	5	L5del	CTT	---	9	9	B.1.1.284	0.000967
ORF7a	5	L5F	Ctt	Ttt	9	9	B.1.1.434	0.003137
ORF7a	5	L5F	Ctt	Ttt	9	9	B.1.177.5	0.01118
ORF7a	5	L5del	CTT	---	9	9	C.8	0.040179
ORF7a	5	L5del1	cTt	c-t	8	8	AY.102	0.000212
ORF7a	5	L5F	Ctt	Ttt	8	8	AY.119	0.000282
ORF7a	5	L5P	cTt	cCt	8	8	AY.25	0.000048
ORF7a	5	L5F	Ctt	Ttt	8	8	AY.29	0.000126
ORF7a	5	L5F	Ctt	Ttt	8	8	AY.3.1	0.000682
ORF7a	5	L5F	Ctt	Ttt	8	8	AY.39	0.000198
ORF7a	5	L5I	Ctt	Att	8	8	AY.44	0.000049
ORF7a	5	L5F	Ctt	Ttt	8	8	AY.47	0.000249
ORF7a	5	L5del1	cTt	c-t	5	8	B.1.1.7	0.000004
ORF7a	5	L5del1	CtT	-tN	2	8	B.1.1.7	0.000002
ORF7a	5	L5del1	CTT	-NN	1	8	B.1.1.7	0.000001
ORF7a	5	L5H	cTt	cAt	8	8	B.1.160	0.00025
ORF7a	5	L5F	Ctt	Ttt	8	8	B.1.160	0.00025
ORF7a	5	L5V	Ctt	Gtt	8	8	B.1.258	0.000532
ORF7a	5	L5F	Ctt	Ttt	8	8	B.1.369	0.002282
ORF7a	5	L5V	Ctt	Gtt	8	8	B.1.525	0.000905
ORF7a	5	L5F	Ctt	Ttt	8	8	B.40	0.002914
ORF7a	5	L5P	cTt	cCt	6	7	AY.102	0.000159
ORF7a	5	L5P	cTT	cCG	1	7	AY.102	0.000027
ORF7a	5	L5del	CTT	---	7	7	AY.118	0.000439
ORF7a	5	L5P	cTT	cCG	4	7	AY.39.1	0.000158
ORF7a	5	L5P	cTt	cCt	3	7	AY.39.1	0.000119
ORF7a	5	L5S	CTt	TCt	7	7	AY.4	0.000011
ORF7a	5	L5del	CTT	---	7	7	B.1.1.214	0.000388
ORF7a	5	L5del	CTT	---	7	7	B.1.177	0.000092
ORF7a	5	L5P	cTt	cCt	7	7	B.1.2	0.000062
ORF7a	5	L5P	cTt	cCt	7	7	B.1.409	0.005469
ORF7a	5	L5V	Ctt	Gtt	7	7	B.1.429	0.000165
ORF7a	5	L5del	CTT	---	7	7	C.37	0.000812
ORF7a	5	L5del	CTT	---	7	7	P.1	0.00011
ORF7a	5	L5I	Ctt	Att	6	6	AY.25	0.000036
ORF7a	5	L5P	cTt	cCt	6	6	AY.3	0.00006
ORF7a	5	L5V	Ctt	Gtt	6	6	AY.39	0.000148
ORF7a	5	L5del	CTT	---	6	6	AY.47	0.000187
ORF7a	5	L5F	Ctt	Ttt	6	6	AY.57	0.003937
ORF7a	5	L5F	Ctt	Ttt	6	6	B.1.1.196	0.034286
ORF7a	5	L5F	Ctt	Ttt	6	6	B.1.177.60	0.001311
ORF7a	5	L5del	CTT	---	6	6	B.1.2	0.000053
ORF7a	5	L5F	Ctt	Ttt	6	6	B.1.258.17	0.000624
ORF7a	5	L5F	Ctt	Ttt	6	6	B.1.351.2	0.001815
ORF7a	5	L5del	CTT	---	6	6	B.1.526	0.000141
ORF7a	5	L5F	Ctt	Ttt	6	6	B.1.596	0.000523
ORF7a	5	L5F	Ctt	Ttt	6	6	R.1	0.00054
ORF7a	5	L5T	CTT	ACG	4	5	All	0.000001
ORF7a	5	L5T	CTT	ACC	1	5	All	0
ORF7a	5	L5P	cTT	cCG	3	5	AY.101	0.001471
ORF7a	5	L5P	cTt	cCt	2	5	AY.101	0.000981
ORF7a	5	L5F	Ctt	Ttt	5	5	AY.106	0.001674
ORF7a	5	L5P	cTt	cCt	5	5	AY.116	0.001434
ORF7a	5	L5del	CTT	---	5	5	AY.26	0.000142
ORF7a	5	L5F	Ctt	Ttt	4	5	AY.33	0.000267
ORF7a	5	L5F	CtT	TtC	1	5	AY.33	0.000067
ORF7a	5	L5F	Ctt	Ttt	5	5	AY.4.2.1	0.000745
ORF7a	5	L5F	Ctt	Ttt	5	5	AY.42	0.000201
ORF7a	5	L5F	Ctt	Ttt	5	5	AY.98	0.000395
ORF7a	5	L5del	CTT	---	5	5	AY.98.1	0.000242
ORF7a	5	L5F	Ctt	Ttt	5	5	B.1.1.153	0.005476
ORF7a	5	L5F	Ctt	Ttt	5	5	B.1.177.17	0.004105
ORF7a	5	L5del	CTT	---	5	5	B.1.177.44	0.002595
ORF7a	5	L5P	cTt	cCt	5	5	B.1.526	0.000118
ORF7a	5	L5P	cTT	cCG	3	5	P.2	0.00056
ORF7a	5	L5P	cTt	cCt	2	5	P.2	0.000373
ORF7a	5	L5del	CTT	---	5	5	Q.8	0.000825
ORF7a	5	L5H	cTt	cAt	4	4		0.222222
ORF7a	5	L5del	CTT	---	4	4	AY.106	0.00134
ORF7a	5	L5F	Ctt	Ttt	4	4	AY.118	0.000251
ORF7a	5	L5L	ctT	ctG	4	4	AY.30	0.001583
ORF7a	5	L5F	Ctt	Ttt	4	4	AY.35	0.000932
ORF7a	5	L5I	Ctt	Att	4	4	AY.39	0.000099
ORF7a	5	L5V	CtT	GtC	2	4	AY.4	0.000003
ORF7a	5	L5V	Ctt	Gtt	2	4	AY.4	0.000003
ORF7a	5	L5P	cTt	cCt	4	4	AY.42	0.000161
ORF7a	5	L5V	Ctt	Gtt	4	4	AY.43	0.000018
ORF7a	5	L5L	ctT	ctA	3	4	AY.6	0.000123
ORF7a	5	L5L	ctT	ctC	1	4	AY.6	0.000041
ORF7a	5	L5P	cTT	cCG	2	4	AY.62	0.000871
ORF7a	5	L5P	cTt	cCt	2	4	AY.62	0.000871
ORF7a	5	L5P	cTT	cCG	2	4	AY.67	0.000929
ORF7a	5	L5P	cTt	cCt	2	4	AY.67	0.000929
ORF7a	5	L5L	ctT	ctC	3	4	AY.99.2	0.000276
ORF7a	5	L5L	ctT	ctG	1	4	AY.99.2	0.000092
ORF7a	5	L5P	cTt	cCt	4	4	B.1.1	0.000073
ORF7a	5	L5del	CTT	---	4	4	B.1.1	0.000073
ORF7a	5	L5L	ctT	ctC	3	4	B.1.177	0.00004
ORF7a	5	L5L	ctT	ctG	1	4	B.1.177	0.000013
ORF7a	5	L5V	Ctt	Gtt	4	4	B.1.2	0.000035
ORF7a	5	L5del	CTT	---	4	4	B.1.429	0.000094
ORF7a	5	L5F	Ctt	Ttt	4	4	B.1.9.4	0.02454
ORF7a	5	L5F	Ctt	Ttt	4	4	D.2	0.0003
ORF7a	5	L5F	Ctt	Ttt	4	4	P.1.14	0.000191
ORF7a	5	L5del	CTT	---	4	4	P.1.16	0.001496
ORF7a	5	L5C	CTt	TGt	3	3	All	0.000001
ORF7a	5	L5G	CTt	GGt	2	3	All	0
ORF7a	5	L5G	CTT	GGG	1	3	All	0
ORF7a	5	L5L	ctT	ctG	3	3	AY.101	0.001471
ORF7a	5	L5L	ctT	ctA	2	3	AY.102	0.000053
ORF7a	5	L5L	ctT	ctG	1	3	AY.102	0.000027
ORF7a	5	L5del1	Ctt	-tt	3	3	AY.110	0.000338
ORF7a	5	L5F	Ctt	Ttt	3	3	AY.16.1	0.00141
ORF7a	5	L5R	cTt	cGt	3	3	AY.26	0.000085
ORF7a	5	L5L	ctT	ctC	3	3	AY.27	0.000194
ORF7a	5	L5del1	Ctt	-tt	3	3	AY.29	0.000047
ORF7a	5	L5F	Ctt	Ttt	3	3	AY.37	0.000948
ORF7a	5	L5L	ctT	ctC	2	3	AY.39	0.000049
ORF7a	5	L5L	ctT	ctG	1	3	AY.39	0.000025
ORF7a	5	L5I	Ctt	Att	3	3	AY.43	0.000013
ORF7a	5	L5P	cTt	cCt	2	3	AY.47	0.000062
ORF7a	5	L5P	cTT	cCG	1	3	AY.47	0.000031
ORF7a	5	L5I	Ctt	Att	3	3	AY.7.2	0.001678
ORF7a	5	L5L	ctT	ctG	3	3	AY.94	0.001328
ORF7a	5	L5P	cTt	cCt	2	3	AY.99.2	0.000184
ORF7a	5	L5P	cTT	cCG	1	3	AY.99.2	0.000092
ORF7a	5	L5H	cTt	cAt	3	3	B.1.1	0.000054
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.1.1	0.00098
ORF7a	5	L5L	ctT	ctC	3	3	B.1.1.189	0.004539
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.1.305	0.011583
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.1.412	0.022901
ORF7a	5	L5I	Ctt	Att	3	3	B.1.1.429	0.013825
ORF7a	5	L5del2	cTT	c--	3	3	B.1.1.7	0.000003
ORF7a	5	L5I	Ctt	Att	3	3	B.1.177	0.00004
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.177.57	0.000843
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.177.7	0.000495
ORF7a	5	L5del2	cTT	c--	3	3	B.1.2	0.000026
ORF7a	5	L5del	CTT	---	3	3	B.1.234	0.000396
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.234	0.000396
ORF7a	5	L5H	cTt	cAt	3	3	B.1.240	0.000647
ORF7a	5	L5L	ctT	ctC	3	3	B.1.258.14	0.002941
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.36.29	0.001552
ORF7a	5	L5V	Ctt	Gtt	3	3	B.1.427	0.000151
ORF7a	5	L5I	Ctt	Att	3	3	B.1.429	0.000071
ORF7a	5	L5del2	CTT	--N	3	3	B.1.438.1	0.000322
ORF7a	5	L5I	Ctt	Att	3	3	B.1.438.1	0.000322
ORF7a	5	L5F	Ctt	Ttt	3	3	B.1.617.1	0.000387
ORF7a	5	L5R	cTt	cGt	3	3	B.1.617.2	0.000011
ORF7a	5	L5L	ctT	ctC	3	3	B.1.621	0.000266
ORF7a	5	L5P	cTt	cCt	3	3	B.1.621	0.000266
ORF7a	5	L5del	CTT	---	3	3	B.1.626	0.017143
ORF7a	5	L5R	cTt	cGt	2	2		0.111111
ORF7a	5	L5G	CTt	GGt	2	2		0.111111
ORF7a	5	L5I	Ctt	Att	2	2		0.111111
ORF7a	5	L5V	Ctt	Gtt	2	2		0.111111
ORF7a	5	L5S	CTt	AGt	2	2		0.111111
ORF7a	5	L5N	CTt	AAt	2	2		0.111111
ORF7a	5	L5C	CTt	TGt	2	2		0.111111
ORF7a	5	L5D	CTt	GAt	2	2		0.111111
ORF7a	5	L5del	CTT	---	2	2	A.28	0.005291
ORF7a	5	L5N	CTt	AAt	2	2	All	0
ORF7a	5	L5D	CTt	GAt	2	2	All	0
ORF7a	5	L5del	CTT	---	2	2	AY.100	0.000092
ORF7a	5	L5P	cTT	cCG	1	2	AY.103	0.000006
ORF7a	5	L5P	cTt	cCt	1	2	AY.103	0.000006
ORF7a	5	L5H	cTt	cAt	2	2	AY.116.1	0.000623
ORF7a	5	L5P	cTt	cCt	2	2	AY.117	0.000169
ORF7a	5	L5V	Ctt	Gtt	2	2	AY.119	0.000071
ORF7a	5	L5del	CTT	---	2	2	AY.119	0.000071
ORF7a	5	L5I	Ctt	Att	2	2	AY.12	0.000632
ORF7a	5	L5del	CTT	---	2	2	AY.20	0.000078
ORF7a	5	L5del	CTT	---	2	2	AY.29.1	0.000441
ORF7a	5	L5L	ctT	ctC	2	2	AY.3	0.00002
ORF7a	5	L5del	CTT	---	2	2	AY.3.1	0.000171
ORF7a	5	L5del	CTT	---	2	2	AY.33	0.000134
ORF7a	5	L5L	ctT	ctG	2	2	AY.39.1	0.000079
ORF7a	5	L5R	cTt	cGt	2	2	AY.4	0.000003
ORF7a	5	L5del2	cTT	c--	2	2	AY.4	0.000003
ORF7a	5	L5del	CTT	---	2	2	AY.42	0.00008
ORF7a	5	L5del1	Ctt	-tt	2	2	AY.44	0.000012
ORF7a	5	L5P	cTt	cCt	2	2	AY.44	0.000012
ORF7a	5	L5S	CTt	TCt	2	2	AY.44	0.000012
ORF7a	5	L5P	cTt	cCt	1	2	AY.46	0.000104
ORF7a	5	L5P	cTT	cCG	1	2	AY.46	0.000104
ORF7a	5	L5F	Ctt	Ttt	2	2	AY.54	0.000191
ORF7a	5	L5F	Ctt	Ttt	2	2	AY.59	0.001059
ORF7a	5	L5F	Ctt	Ttt	2	2	AY.6	0.000082
ORF7a	5	L5L	ctT	ctG	2	2	AY.62	0.000871
ORF7a	5	L5F	Ctt	Ttt	2	2	AY.62	0.000871
ORF7a	5	L5L	ctT	ctG	2	2	AY.67	0.000929
ORF7a	5	L5F	Ctt	Ttt	2	2	AY.74	0.000231
ORF7a	5	L5del	CTT	---	2	2	AY.75	0.000112
ORF7a	5	L5I	Ctt	Att	2	2	AY.75.1	0.000361
ORF7a	5	L5L	ctT	ctA	2	2	AY.84	0.000875
ORF7a	5	L5P	cTt	cCt	2	2	AY.9.2	0.000073
ORF7a	5	L5V	Ctt	Gtt	2	2	AY.94	0.000885
ORF7a	5	L5F	Ctt	Ttt	2	2	AY.99.2	0.000184
ORF7a	5	L5I	Ctt	Att	2	2	B.1	0.000018
ORF7a	5	L5L	ctT	ctC	2	2	B.1.1	0.000036
ORF7a	5	L5R	cTt	cGt	2	2	B.1.1	0.000036
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.1.141	0.004024
ORF7a	5	L5L	ctT	ctG	2	2	B.1.1.207	0.002364
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.1.214	0.000111
ORF7a	5	L5H	cTt	cAt	2	2	B.1.1.222	0.000408
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.1.284	0.000215
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.1.317	0.000823
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.1.39	0.001019
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.1.432	0.002532
ORF7a	5	L5H	cTT	cAC	1	2	B.1.1.7	0.000001
ORF7a	5	L5H	cTt	cAt	1	2	B.1.1.7	0.000001
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.110.3	0.001437
ORF7a	5	L5del	CTT	---	2	2	B.1.160	0.000062
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.160.14	0.004237
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.160.23	0.009662
ORF7a	5	L5R	cTt	cGt	2	2	B.1.177.57	0.000562
ORF7a	5	L5del	CTT	---	2	2	B.1.177.86	0.000367
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.177.86	0.000367
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.177.9	0.002663
ORF7a	5	L5I	Ctt	Att	2	2	B.1.2	0.000018
ORF7a	5	L5R	cTt	cGt	2	2	B.1.2	0.000018
ORF7a	5	L5del1	cTt	c-t	1	2	B.1.2	0.000009
ORF7a	5	L5del1	Ctt	-tt	1	2	B.1.2	0.000009
ORF7a	5	L5I	Ctt	Att	2	2	B.1.218	0.010309
ORF7a	5	L5P	cTt	cCt	2	2	B.1.221	0.000142
ORF7a	5	L5P	cTt	cCt	2	2	B.1.243	0.000139
ORF7a	5	L5del	CTT	---	2	2	B.1.258.11	0.000793
ORF7a	5	L5L	ctT	ctG	2	2	B.1.258.3	0.00335
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.311	0.000549
ORF7a	5	L5del	CTT	---	2	2	B.1.351	0.000059
ORF7a	5	L5L	ctT	ctC	2	2	B.1.351	0.000059
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.36	0.000292
ORF7a	5	L5del	CTT	---	2	2	B.1.36	0.000292
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.36.18	0.00084
ORF7a	5	L5R	cTt	cGt	2	2	B.1.36.38	0.003284
ORF7a	5	L5L	ctT	ctC	1	2	B.1.427	0.00005
ORF7a	5	L5L	ctT	ctG	1	2	B.1.427	0.00005
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.516	0.003914
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.589	0.015152
ORF7a	5	L5del	CTT	---	2	2	B.1.596	0.000174
ORF7a	5	L5V	Ctt	Gtt	2	2	B.1.596	0.000174
ORF7a	5	L5L	ctT	ctC	2	2	B.1.617.1	0.000258
ORF7a	5	L5P	cTt	cCt	2	2	B.1.617.1	0.000258
ORF7a	5	L5H	cTt	cAt	2	2	B.1.617.2	0.000008
ORF7a	5	L5del2	cTT	c--	2	2	B.1.617.2	0.000008
ORF7a	5	L5del	CTT	---	2	2	B.1.621	0.000177
ORF7a	5	L5F	Ctt	Ttt	2	2	B.1.621	0.000177
ORF7a	5	L5del	CTT	---	2	2	B.1.637	0.000146
ORF7a	5	L5L	ctT	ctC	2	2	B.15	0.035088
ORF7a	5	L5F	Ctt	Ttt	2	2	C.36.3	0.001134
ORF7a	5	L5P	cTt	cCt	1	2	P.1.12	0.000484
ORF7a	5	L5L	ctT	ctC	1	2	P.1.12	0.000484
ORF7a	5	L5L	ctT	ctG	1	2	P.1.12	0.000484
ORF7a	5	L5P	cTT	cCG	1	2	P.1.12	0.000484
ORF7a	5	L5L	ctT	ctC	2	2	P.1.14	0.000096
ORF7a	5	L5V	Ctt	Gtt	2	2	P.1.17	0.000324
ORF7a	5	L5T	CTT	ACC	1	2	P.1.2	0.001156
ORF7a	5	L5L	ctT	ctG	1	2	P.1.2	0.001156
ORF7a	5	L5P	cTT	cCC	1	2	P.1.2	0.001156
ORF7a	5	L5L	ctT	ctC	1	2	P.1.2	0.001156
ORF7a	5	L5T	CTT	ACG	1	2	P.1.2	0.001156
ORF7a	5	L5P	cTT	cCG	1	2	P.1.2	0.001156
ORF7a	5	L5P	cTt	cCt	1	2	P.7	0.004367
ORF7a	5	L5P	cTT	cCG	1	2	P.7	0.004367
ORF7a	5	L5del	CTT	---	2	2	Q.1	0.000253
ORF7a	5	L5F	Ctt	Ttt	2	2	Q.8	0.00033
ORF7a	5	L5del	CTT	---	1	1	A	0.000387
ORF7a	5	L5L	ctT	ctC	1	1	A.1	0.000282
ORF7a	5	L5F	Ctt	Ttt	1	1	A.2.5	0.000499
ORF7a	5	L5F	Ctt	Ttt	1	1	A.23.1	0.000704
ORF7a	5	L5P	cTt	cCt	1	1	AD.2	0.000219
ORF7a	5	L5M	CtT	AtG	1	1	All	0
ORF7a	5	L5K	CTT	AAG	1	1	All	0
ORF7a	5	L5F	Ctt	Ttt	1	1	AU.1	0.001266
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.10	0.00053
ORF7a	5	L5T	CTT	ACG	1	1	AY.101	0.00049
ORF7a	5	L5I	CtT	AtC	1	1	AY.101	0.00049
ORF7a	5	L5I	Ctt	Att	1	1	AY.102	0.000027
ORF7a	5	L5del1	cTt	c-t	1	1	AY.105	0.000643
ORF7a	5	L5P	cTt	cCt	1	1	AY.105	0.000643
ORF7a	5	L5del	CTT	---	1	1	AY.107	0.000466
ORF7a	5	L5L	ctT	ctC	1	1	AY.107	0.000466
ORF7a	5	L5del	CTT	---	1	1	AY.108	0.001103
ORF7a	5	L5del	CTT	---	1	1	AY.109	0.00074
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.110	0.000113
ORF7a	5	L5P	cTt	cCt	1	1	AY.111	0.000183
ORF7a	5	L5L	ctT	ctA	1	1	AY.111	0.000183
ORF7a	5	L5del1	cTt	c-t	1	1	AY.113	0.000142
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.113	0.000142
ORF7a	5	L5L	ctT	ctC	1	1	AY.114	0.000231
ORF7a	5	L5L	ctT	ctC	1	1	AY.115	0.005208
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.116	0.000287
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.117	0.000085
ORF7a	5	L5L	ctT	ctC	1	1	AY.117	0.000085
ORF7a	5	L5I	Ctt	Att	1	1	AY.117	0.000085
ORF7a	5	L5del1	CtT	-tC	1	1	AY.117	0.000085
ORF7a	5	L5I	Ctt	Att	1	1	AY.119	0.000035
ORF7a	5	L5P	cTt	cCt	1	1	AY.119	0.000035
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.12	0.000316
ORF7a	5	L5del	CTT	---	1	1	AY.120	0.000037
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.120	0.000037
ORF7a	5	L5del1	cTt	c-t	1	1	AY.120	0.000037
ORF7a	5	L5H	cTt	cAt	1	1	AY.120.1	0.000321
ORF7a	5	L5del	CTT	---	1	1	AY.120.1	0.000321
ORF7a	5	L5V	Ctt	Gtt	1	1	AY.120.2	0.001285
ORF7a	5	L5L	ctT	ctC	1	1	AY.120.2.1	0.000498
ORF7a	5	L5del1	cTt	c-t	1	1	AY.121	0.000135
ORF7a	5	L5del	CTT	---	1	1	AY.121	0.000135
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.13	0.000161
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.22	0.002092
ORF7a	5	L5L	ctT	ctC	1	1	AY.23	0.00007
ORF7a	5	L5del1	cTt	c-t	1	1	AY.23	0.00007
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.23.1	0.000417
ORF7a	5	L5P	cTt	cCt	1	1	AY.23.1	0.000417
ORF7a	5	L5V	Ctt	Gtt	1	1	AY.25	0.000006
ORF7a	5	L5L	ctT	ctG	1	1	AY.26	0.000028
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.27	0.000065
ORF7a	5	L5P	cTt	cCt	1	1	AY.27	0.000065
ORF7a	5	L5G	CTT	GGG	1	1	AY.29	0.000016
ORF7a	5	L5del2	cTT	c--	1	1	AY.29	0.000016
ORF7a	5	L5I	Ctt	Att	1	1	AY.29	0.000016
ORF7a	5	L5P	cTt	cCt	1	1	AY.29	0.000016
ORF7a	5	L5I	Ctt	Att	1	1	AY.3	0.00001
ORF7a	5	L5del	CTT	---	1	1	AY.32	0.000532
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.32	0.000532
ORF7a	5	L5P	cTt	cCt	1	1	AY.33	0.000067
ORF7a	5	L5H	cTt	cAt	1	1	AY.33	0.000067
ORF7a	5	L5I	Ctt	Att	1	1	AY.33	0.000067
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.34	0.000097
ORF7a	5	L5L	ctT	ctC	1	1	AY.34	0.000097
ORF7a	5	L5del	CTT	---	1	1	AY.34	0.000097
ORF7a	5	L5V	Ctt	Gtt	1	1	AY.38	0.000499
ORF7a	5	L5del1	cTt	c-t	1	1	AY.39	0.000025
ORF7a	5	L5del1	ctT	ct-	1	1	AY.4	0.000002
ORF7a	5	L5H	cTt	cAt	1	1	AY.4	0.000002
ORF7a	5	L5del	CTT	---	1	1	AY.4.2	0.000022
ORF7a	5	L5L	ctT	ctC	1	1	AY.4.2	0.000022
ORF7a	5	L5R	cTt	cGt	1	1	AY.4.2	0.000022
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.4.2	0.000022
ORF7a	5	L5P	cTt	cCt	1	1	AY.4.5	0.000107
ORF7a	5	L5V	Ctt	Gtt	1	1	AY.42	0.00004
ORF7a	5	L5del	CTT	---	1	1	AY.45	0.000122
ORF7a	5	L5del1	cTt	c-t	1	1	AY.45	0.000122
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.46	0.000104
ORF7a	5	L5P	cTT	cCG	1	1	AY.46.1	0.001027
ORF7a	5	L5del1	cTt	c-t	1	1	AY.46.4	0.000165
ORF7a	5	L5L	ctT	ctC	1	1	AY.47	0.000031
ORF7a	5	L5I	Ctt	Att	1	1	AY.5.3	0.000337
ORF7a	5	L5del	CTT	---	1	1	AY.54	0.000095
ORF7a	5	L5L	ctT	ctA	1	1	AY.58	0.000907
ORF7a	5	L5H	cTt	cAt	1	1	AY.6	0.000041
ORF7a	5	L5V	Ctt	Gtt	1	1	AY.6	0.000041
ORF7a	5	L5I	Ctt	Att	1	1	AY.6	0.000041
ORF7a	5	L5I	Ctt	Att	1	1	AY.61	0.000105
ORF7a	5	L5del	CTT	---	1	1	AY.66	0.00107
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.68	0.000274
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.69	0.000187
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.70	0.000209
ORF7a	5	L5P	cTt	cCt	1	1	AY.73	0.000665
ORF7a	5	L5V	Ctt	Gtt	1	1	AY.74	0.000116
ORF7a	5	L5L	ctT	ctC	1	1	AY.75.1	0.00018
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.75.1	0.00018
ORF7a	5	L5del	CTT	---	1	1	AY.79	0.001211
ORF7a	5	L5P	cTT	cCG	1	1	AY.79	0.001211
ORF7a	5	L5H	cTt	cAt	1	1	AY.79	0.001211
ORF7a	5	L5del	CTT	---	1	1	AY.84	0.000437
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.85	0.000427
ORF7a	5	L5P	cTt	cCt	1	1	AY.9	0.000068
ORF7a	5	L5del	CTT	---	1	1	AY.9	0.000068
ORF7a	5	L5P	cTt	cCt	1	1	AY.9.1	0.000084
ORF7a	5	L5del1	cTt	c-t	1	1	AY.9.2	0.000037
ORF7a	5	L5del	CTT	---	1	1	AY.9.2	0.000037
ORF7a	5	L5del	CTT	---	1	1	AY.94	0.000443
ORF7a	5	L5L	ctT	ctC	1	1	AY.98	0.000079
ORF7a	5	L5del	CTT	---	1	1	AY.99	0.001049
ORF7a	5	L5F	Ctt	Ttt	1	1	AY.99	0.001049
ORF7a	5	L5I	Ctt	Att	1	1	B	0.000128
ORF7a	5	L5P	cTt	cCt	1	1	B	0.000128
ORF7a	5	L5del2	cTT	c--	1	1	B.1	0.000009
ORF7a	5	L5H	cTt	cAt	1	1	B.1	0.000009
ORF7a	5	L5del1	Ctt	-tt	1	1	B.1	0.000009
ORF7a	5	L5R	cTt	cGt	1	1	B.1	0.000009
ORF7a	5	L5I	Ctt	Att	1	1	B.1.1	0.000018
ORF7a	5	L5K	CTT	AAG	1	1	B.1.1	0.000018
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.1	0.000327
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.135	0.004695
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.198	0.001468
ORF7a	5	L5del	CTT	---	1	1	B.1.1.207	0.001182
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.216	0.00089
ORF7a	5	L5del	CTT	---	1	1	B.1.1.222	0.000204
ORF7a	5	L5P	cTt	cCt	1	1	B.1.1.222	0.000204
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.25	0.000569
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.256	0.013699
ORF7a	5	L5del	CTT	---	1	1	B.1.1.258	0.003257
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.273	0.006757
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.28	0.000311
ORF7a	5	L5P	cTt	cCt	1	1	B.1.1.28	0.000311
ORF7a	5	L5P	cTt	cCt	1	1	B.1.1.284	0.000107
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.294	0.001266
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.311	0.000358
ORF7a	5	L5L	ctT	ctA	1	1	B.1.1.33	0.000421
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.362	0.005618
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.37	0.000193
ORF7a	5	L5P	cTt	cCt	1	1	B.1.1.37	0.000193
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.372	0.000689
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.378	0.007299
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.41	0.006329
ORF7a	5	L5R	cTt	cGt	1	1	B.1.1.485	0.016667
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.1.50	0.000679
ORF7a	5	L5L	ctT	ctC	1	1	B.1.1.519	0.00004
ORF7a	5	L5del	CTT	---	1	1	B.1.1.519	0.00004
ORF7a	5	L5P	cTt	cCt	1	1	B.1.1.519	0.00004
ORF7a	5	L5L	ctT	ctG	1	1	B.1.1.521	0.005348
ORF7a	5	L5S	CTt	TCt	1	1	B.1.1.7	0.000001
ORF7a	5	L5C	CTt	TGt	1	1	B.1.1.7	0.000001
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.103	0.019231
ORF7a	5	L5del	CTT	---	1	1	B.1.115	0.021739
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.140	0.018868
ORF7a	5	L5H	cTt	cAt	1	1	B.1.147	0.000756
ORF7a	5	L5L	ctT	ctC	1	1	B.1.160	0.000031
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.160.10	0.008065
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.160.30	0.002976
ORF7a	5	L5del	CTT	---	1	1	B.1.161	0.017241
ORF7a	5	L5V	Ctt	Gtt	1	1	B.1.177	0.000013
ORF7a	5	L5H	cTt	cAt	1	1	B.1.177	0.000013
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.177.10	0.000878
ORF7a	5	L5del2	cTT	c--	1	1	B.1.177.12	0.000152
ORF7a	5	L5P	cTt	cCt	1	1	B.1.177.42	0.000894
ORF7a	5	L5P	cTt	cCt	1	1	B.1.177.60	0.000218
ORF7a	5	L5del	CTT	---	1	1	B.1.177.63	0.002703
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.177.73	0.000566
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.177.75	0.001041
ORF7a	5	L5del	CTT	---	1	1	B.1.177.81	0.000189
ORF7a	5	L5H	cTt	cAt	1	1	B.1.2	0.000009
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.214.2	0.0006
ORF7a	5	L5L	ctT	ctA	1	1	B.1.214.2	0.0006
ORF7a	5	L5del	CTT	---	1	1	B.1.221	0.000071
ORF7a	5	L5P	cTt	cCt	1	1	B.1.223	0.002778
ORF7a	5	L5L	ctT	ctC	1	1	B.1.234	0.000132
ORF7a	5	L5del2	cTT	c--	1	1	B.1.234	0.000132
ORF7a	5	L5H	cTt	cAt	1	1	B.1.234	0.000132
ORF7a	5	L5I	Ctt	Att	1	1	B.1.240	0.000216
ORF7a	5	L5del	CTT	---	1	1	B.1.240	0.000216
ORF7a	5	L5I	Ctt	Att	1	1	B.1.243	0.00007
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.256	0.017241
ORF7a	5	L5I	Ctt	Att	1	1	B.1.258	0.000067
ORF7a	5	L5I	Ctt	Att	1	1	B.1.258.17	0.000104
ORF7a	5	L5I	Ctt	Att	1	1	B.1.258.4	0.003448
ORF7a	5	L5H	cTt	cAt	1	1	B.1.258.7	0.001912
ORF7a	5	L5I	Ctt	Att	1	1	B.1.301	0.005917
ORF7a	5	L5V	Ctt	Gtt	1	1	B.1.311	0.000275
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.346	0.001311
ORF7a	5	L5P	cTt	cCt	1	1	B.1.349	0.000715
ORF7a	5	L5P	cTt	cCt	1	1	B.1.351	0.00003
ORF7a	5	L5del1	ctT	ct-	1	1	B.1.351	0.00003
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.36.17	0.000494
ORF7a	5	L5L	ctT	ctC	1	1	B.1.36.29	0.000517
ORF7a	5	L5del1	cTt	c-t	1	1	B.1.362	0.001541
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.375	0.00082
ORF7a	5	L5V	Ctt	Gtt	1	1	B.1.396	0.000706
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.398	0.002976
ORF7a	5	L5I	Ctt	Att	1	1	B.1.398	0.002976
ORF7a	5	L5L	ctT	ctC	1	1	B.1.404	0.001302
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.407	0.035714
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.413	0.004255
ORF7a	5	L5del	CTT	---	1	1	B.1.427	0.00005
ORF7a	5	L5P	cTt	cCt	1	1	B.1.427	0.00005
ORF7a	5	L5P	cTt	cCt	1	1	B.1.429	0.000024
ORF7a	5	L5P	cTt	cCt	1	1	B.1.438.1	0.000107
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.438.1	0.000107
ORF7a	5	L5L	ctT	ctG	1	1	B.1.462	0.007246
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.466.2	0.000391
ORF7a	5	L5del	CTT	---	1	1	B.1.466.2	0.000391
ORF7a	5	L5del	CTT	---	1	1	B.1.468	0.005714
ORF7a	5	L5P	cTt	cCt	1	1	B.1.469	0.00361
ORF7a	5	L5del	CTT	---	1	1	B.1.470	0.001404
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.470	0.001404
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.509	0.000866
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.517	0.000427
ORF7a	5	L5del	CTT	---	1	1	B.1.525	0.000113
ORF7a	5	L5I	Ctt	Att	1	1	B.1.526	0.000024
ORF7a	5	L5H	cTt	cAt	1	1	B.1.526	0.000024
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.540	0.009709
ORF7a	5	L5P	cTt	cCt	1	1	B.1.568	0.001111
ORF7a	5	L5del1	cTt	c-t	1	1	B.1.574	0.002151
ORF7a	5	L5R	cTT	cGA	1	1	B.1.576	0.000907
ORF7a	5	L5I	Ctt	Att	1	1	B.1.576	0.000907
ORF7a	5	L5L	ctT	ctC	1	1	B.1.582	0.000491
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.582	0.000491
ORF7a	5	L5L	ctT	ctC	1	1	B.1.595	0.000261
ORF7a	5	L5P	cTt	cCt	1	1	B.1.596	0.000087
ORF7a	5	L5I	Ctt	Att	1	1	B.1.596	0.000087
ORF7a	5	L5del1	cTt	c-t	1	1	B.1.596	0.000087
ORF7a	5	L5del1	cTt	c-t	1	1	B.1.606	0.006024
ORF7a	5	L5del	CTT	---	1	1	B.1.617.1	0.000129
ORF7a	5	L5del	CTT	---	1	1	B.1.617.3	0.002985
ORF7a	5	L5del	CTT	---	1	1	B.1.620	0.000946
ORF7a	5	L5V	Ctt	Gtt	1	1	B.1.621	0.000089
ORF7a	5	L5del	CTT	---	1	1	B.1.630	0.005236
ORF7a	5	L5F	Ctt	Ttt	1	1	B.1.634	0.003425
ORF7a	5	L5V	Ctt	Gtt	1	1	B.1.636	0.006711
ORF7a	5	L5F	Ctt	Ttt	1	1	B.3	0.000831
ORF7a	5	L5L	ctT	ctC	1	1	B.51	0.047619
ORF7a	5	L5V	Ctt	Gtt	1	1	C.14	0.004329
ORF7a	5	L5H	cTt	cAt	1	1	C.16	0.00106
ORF7a	5	L5F	Ctt	Ttt	1	1	C.16	0.00106
ORF7a	5	L5L	ctT	ctA	1	1	C.18	0.002591
ORF7a	5	L5F	Ctt	Ttt	1	1	C.23	0.005814
ORF7a	5	L5del	CTT	---	1	1	C.36.3	0.000567
ORF7a	5	L5del1	Ctt	-tt	1	1	C.37	0.000116
ORF7a	5	L5L	ctT	ctC	1	1	D.2	0.000075
ORF7a	5	L5P	cTt	cCt	1	1	D.2	0.000075
ORF7a	5	L5F	Ctt	Ttt	1	1	N.6	0.007092
ORF7a	5	L5I	Ctt	Att	1	1	P.1	0.000016
ORF7a	5	L5H	cTt	cAt	1	1	P.1	0.000016
ORF7a	5	L5V	Ctt	Gtt	1	1	P.1	0.000016
ORF7a	5	L5del2	cTT	c--	1	1	P.1	0.000016
ORF7a	5	L5T	CTT	ACG	1	1	P.1	0.000016
ORF7a	5	L5R	cTt	cGt	1	1	P.1	0.000016
ORF7a	5	L5F	Ctt	Ttt	1	1	P.1.1	0.000318
ORF7a	5	L5F	Ctt	Ttt	1	1	P.1.15	0.000232
ORF7a	5	L5T	CTT	ACG	1	1	P.1.15	0.000232
ORF7a	5	L5R	cTt	cGt	1	1	P.1.17	0.000162
ORF7a	5	L5F	Ctt	Ttt	1	1	P.1.17	0.000162
ORF7a	5	L5M	CtT	AtG	1	1	P.1.2	0.001156
ORF7a	5	L5I	CtT	AtC	1	1	P.1.2	0.001156
ORF7a	5	L5P	cTt	cCt	1	1	P.1.8	0.004785
ORF7a	5	L5L	ctT	ctG	1	1	P.2	0.000187
ORF7a	5	L5del	CTT	---	1	1	P.2	0.000187
ORF7a	5	L5F	Ctt	Ttt	1	1	P.5	0.013699
ORF7a	5	L5L	ctT	ctG	1	1	P.7	0.004367
ORF7a	5	L5del	CTT	---	1	1	Q.5	0.016949
ORF7a	5	L5F	Ctt	Ttt	1	1	Q.5	0.016949
ORF7a	5	L5R	cTt	cGt	1	1	Q.8	0.000165
ORF7a	5	L5L	ctT	ctC	1	1	Q.8	0.000165
ORF7a	5	L5P	cTt	cCt	1	1	U.3	0.003861
ORF7a	5	L5del2	cTT	c--	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.