CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 40

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	40	Y40Y		syn	taC	taT	21751	21751	1	27511-27513
ORF7a	40	Y40del		del	TAC	---	1921	1921	1	27511-27513
ORF7a	40	Y40H		nonsyn	Tac	Cac	1062	1058	0.996234	27511-27513
ORF7a	40	Y40H		nonsyn	TaC	CaT	1062	4	0.00376648	27511-27513
ORF7a	40	Y40X		nonsyn	taC	taA	232	163	0.702586	27511-27513
ORF7a	40	Y40X		nonsyn	taC	taG	232	64	0.275862	27511-27513
ORF7a	40	Y40X		nonsyn	tAC	tGA	232	5	0.0215517	27511-27513
ORF7a	40	Y40del2		del	tAC	t--	201	114	0.567164	27511-27513
ORF7a	40	Y40del2		del	TAc	--c	201	87	0.432836	27511-27513
ORF7a	40	Y40F		nonsyn	tAc	tTc	92	59	0.641304	27511-27513
ORF7a	40	Y40F		nonsyn	tAC	tTT	92	33	0.358696	27511-27513
ORF7a	40	Y40C		nonsyn	tAc	tGc	88	72	0.818182	27511-27513
ORF7a	40	Y40C		nonsyn	tAC	tGT	88	16	0.181818	27511-27513
ORF7a	40	Y40del1		del	Tac	-ac	73	56	0.767123	27511-27513
ORF7a	40	Y40del1		del	taC	ta-	73	10	0.136986	27511-27513
ORF7a	40	Y40del1		del	tAC	t-N	73	3	0.0410959	27511-27513
ORF7a	40	Y40del1		del	TaC	-aN	73	2	0.0273973	27511-27513
ORF7a	40	Y40del1		del	TaC	Ga-	73	2	0.0273973	27511-27513
ORF7a	40	Y40N		nonsyn	Tac	Aac	40	39	0.975	27511-27513
ORF7a	40	Y40L		nonsyn	tAC	tTA	40	29	0.725	27511-27513
ORF7a	40	Y40L		nonsyn	tAC	tTG	40	7	0.175	27511-27513
ORF7a	40	Y40L		nonsyn	TAc	CTc	40	4	0.1	27511-27513
ORF7a	40	Y40N		nonsyn	TaC	AaT	40	1	0.025	27511-27513
ORF7a	40	Y40S		nonsyn	tAc	tCc	31	18	0.580645	27511-27513
ORF7a	40	Y40S		nonsyn	tAC	tCT	31	7	0.225806	27511-27513
ORF7a	40	Y40S		nonsyn	tAC	tCA	31	6	0.193548	27511-27513
ORF7a	40	Y40D		nonsyn	Tac	Gac	13	13	1	27511-27513
ORF7a	40	Y40Q		nonsyn	TaC	CaA	5	4	0.8	27511-27513
ORF7a	40	Y40Q		nonsyn	TaC	CaG	5	1	0.2	27511-27513
ORF7a	40	Y40W		nonsyn	tAC	tGG	1	1	1	27511-27513
ORF7a	40	Y40E		nonsyn	TaC	GaA	1	1	1	27511-27513
ORF7a	40	Y40K		nonsyn	TaC	AaG	1	1	1	27511-27513

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	40	Y40Y	taC	taT	21751	21751	All	0.00416
ORF7a	40	Y40Y	taC	taT	10374	10374	B.1.1.7	0.009287
ORF7a	40	Y40Y	taC	taT	2792	2792	AY.4	0.004346
ORF7a	40	Y40del	TAC	---	1921	1921	All	0.000367
ORF7a	40	Y40Y	taC	taT	1274	1274	B.1.429	0.029976
ORF7a	40	Y40H	Tac	Cac	1058	1062	All	0.000202
ORF7a	40	Y40H	TaC	CaT	4	1062	All	0.000001
ORF7a	40	Y40Y	taC	taT	562	562	C.30	0.970639
ORF7a	40	Y40Y	taC	taT	423	423	AY.103	0.002626
ORF7a	40	Y40Y	taC	taT	422	422	B.1.617.2	0.001589
ORF7a	40	Y40Y	taC	taT	387	387	B.1.177.16	0.257143
ORF7a	40	Y40Y	taC	taT	378	378	AY.25	0.002274
ORF7a	40	Y40Y	taC	taT	364	364	B.1.1.1	0.118915
ORF7a	40	Y40del	TAC	---	352	352	B.1.1.7	0.000315
ORF7a	40	Y40H	Tac	Cac	334	334	B.1.1.7	0.000299
ORF7a	40	Y40Y	taC	taT	332	332	AY.43	0.001471
ORF7a	40	Y40Y	taC	taT	295	295	B.1.1.434	0.102823
ORF7a	40	Y40Y	taC	taT	289	289	B.1.2	0.002545
ORF7a	40	Y40H	Tac	Cac	287	287	AY.4	0.000447
ORF7a	40	Y40del	TAC	---	264	264	AY.4	0.000411
ORF7a	40	Y40Y	taC	taT	259	259	B.1.1.39	0.132008
ORF7a	40	Y40Y	taC	taT	250	250	AY.74	0.028912
ORF7a	40	Y40X	taC	taA	163	232	All	0.000031
ORF7a	40	Y40X	taC	taG	64	232	All	0.000012
ORF7a	40	Y40X	tAC	tGA	5	232	All	0.000001
ORF7a	40	Y40del	TAC	---	219	219	B.1.617.2	0.000825
ORF7a	40	Y40del2	tAC	t--	114	201	All	0.000022
ORF7a	40	Y40del2	TAc	--c	87	201	All	0.000017
ORF7a	40	Y40Y	taC	taT	198	198	B.1	0.001814
ORF7a	40	Y40del	TAC	---	179	179	B.1.177.21	0.013688
ORF7a	40	Y40Y	taC	taT	167	167	AY.44	0.001016
ORF7a	40	Y40del	TAC	---	158	158	AY.25	0.00095
ORF7a	40	Y40Y	taC	taT	147	147	C.30.1	0.986577
ORF7a	40	Y40Y	taC	taT	139	139	B.1.177.82	0.066348
ORF7a	40	Y40Y	taC	taT	124	124	AY.3	0.001233
ORF7a	40	Y40Y	taC	taT	115	115	AY.102	0.003049
ORF7a	40	Y40Y	taC	taT	114	114	Q.1	0.014401
ORF7a	40	Y40F	tAc	tTc	59	92	All	0.000011
ORF7a	40	Y40F	tAC	tTT	33	92	All	0.000006
ORF7a	40	Y40Y	taC	taT	91	91	B.1.1.519	0.003614
ORF7a	40	Y40C	tAc	tGc	72	88	All	0.000014
ORF7a	40	Y40C	tAC	tGT	16	88	All	0.000003
ORF7a	40	Y40Y	taC	taT	85	85	AY.120	0.00316
ORF7a	40	Y40Y	taC	taT	84	84	B.1.1	0.001524
ORF7a	40	Y40Y	taC	taT	81	81	P.1	0.001276
ORF7a	40	Y40del	TAC	---	75	75	AY.103	0.000466
ORF7a	40	Y40del1	Tac	-ac	56	73	All	0.000011
ORF7a	40	Y40del1	taC	ta-	10	73	All	0.000002
ORF7a	40	Y40del1	tAC	t-N	3	73	All	0.000001
ORF7a	40	Y40del1	TaC	Ga-	2	73	All	0
ORF7a	40	Y40del1	TaC	-aN	2	73	All	0
ORF7a	40	Y40Y	taC	taT	71	71	B.1.177	0.000935
ORF7a	40	Y40Y	taC	taT	67	67	AY.26	0.001897
ORF7a	40	Y40X	taC	taA	47	63	B.1.1.7	0.000042
ORF7a	40	Y40X	taC	taG	16	63	B.1.1.7	0.000014
ORF7a	40	Y40Y	taC	taT	61	61	AY.4.2	0.001323
ORF7a	40	Y40Y	taC	taT	57	57	AY.119	0.002013
ORF7a	40	Y40Y	taC	taT	56	56	P.1.13	0.050314
ORF7a	40	Y40del2	tAC	t--	55	55	AY.39.1	0.002179
ORF7a	40	Y40Y	taC	taT	53	53	AY.29	0.000836
ORF7a	40	Y40del2	TAc	--c	52	52	AY.4	0.000081
ORF7a	40	Y40del	TAC	---	49	49	AY.3	0.000487
ORF7a	40	Y40del	TAC	---	49	49	AY.3.1	0.004178
ORF7a	40	Y40Y	taC	taT	47	47	B.1.243	0.00327
ORF7a	40	Y40del	TAC	---	46	46	AY.29	0.000726
ORF7a	40	Y40H	Tac	Cac	46	46	AY.43	0.000204
ORF7a	40	Y40Y	taC	taT	46	46	B.1.160	0.001435
ORF7a	40	Y40del	TAC	---	45	45	AY.44	0.000274
ORF7a	40	Y40Y	taC	taT	41	41	B.1.258.22	0.109333
ORF7a	40	Y40N	Tac	Aac	39	40	All	0.000007
ORF7a	40	Y40L	tAC	tTA	29	40	All	0.000006
ORF7a	40	Y40L	tAC	tTG	7	40	All	0.000001
ORF7a	40	Y40L	TAc	CTc	4	40	All	0.000001
ORF7a	40	Y40N	TaC	AaT	1	40	All	0
ORF7a	40	Y40Y	taC	taT	40	40	B.1.1.318	0.01207
ORF7a	40	Y40Y	taC	taT	37	37	AY.100	0.001702
ORF7a	40	Y40X	taC	taA	36	37	AY.4	0.000056
ORF7a	40	Y40X	taC	taG	1	37	AY.4	0.000002
ORF7a	40	Y40Y	taC	taT	36	36	AY.114	0.00832
ORF7a	40	Y40del	TAC	---	36	36	B.1.1.284	0.003866
ORF7a	40	Y40H	Tac	Cac	35	35	AY.103	0.000217
ORF7a	40	Y40H	Tac	Cac	33	33	B.1.637	0.002411
ORF7a	40	Y40Y	taC	taT	32	32	AY.117	0.002705
ORF7a	40	Y40Y	taC	taT	32	32	AY.118	0.002005
ORF7a	40	Y40Y	taC	taT	32	32	B.1.221	0.002273
ORF7a	40	Y40Y	taC	taT	32	32	B.1.351	0.000951
ORF7a	40	Y40del	TAC	---	32	32	B.1.621	0.002833
ORF7a	40	Y40S	tAc	tCc	18	31	All	0.000003
ORF7a	40	Y40S	tAC	tCT	7	31	All	0.000001
ORF7a	40	Y40S	tAC	tCA	6	31	All	0.000001
ORF7a	40	Y40del2	tAC	t--	19	31	AY.39	0.00047
ORF7a	40	Y40del2	TAc	--c	12	31	AY.39	0.000297
ORF7a	40	Y40Y	taC	taT	31	31	B.1.110.3	0.02227
ORF7a	40	Y40del	TAC	---	30	30	AY.43	0.000133
ORF7a	40	Y40C	tAc	tGc	18	30	B.1.1.7	0.000016
ORF7a	40	Y40C	tAC	tGT	12	30	B.1.1.7	0.000011
ORF7a	40	Y40Y	taC	taT	29	29	AY.27	0.001877
ORF7a	40	Y40Y	taC	taT	29	29	AY.42	0.001167
ORF7a	40	Y40Y	taC	taT	29	29	B.1.177.57	0.008148
ORF7a	40	Y40Y	taC	taT	28	28	B.1.575	0.008495
ORF7a	40	Y40Y	taC	taT	27	27	AY.30	0.010685
ORF7a	40	Y40del	TAC	---	27	27	B.1	0.000247
ORF7a	40	Y40Y	taC	taT	27	27	B.1.258.17	0.002807
ORF7a	40	Y40Y	taC	taT	26	26	AF.1	0.962963
ORF7a	40	Y40H	Tac	Cac	26	26	B.1.617.2	0.000098
ORF7a	40	Y40Y	taC	taT	26	26	B.1.637	0.0019
ORF7a	40	Y40Y	taC	taT	26	26	D.2	0.001951
ORF7a	40	Y40Y	taC	taT	25	25	B.1.621	0.002213
ORF7a	40	Y40Y	taC	taT	24	24	AY.11	0.032129
ORF7a	40	Y40H	Tac	Cac	24	24	AY.25	0.000144
ORF7a	40	Y40X	taC	taG	21	24	B.1.160	0.000655
ORF7a	40	Y40X	taC	taA	2	24	B.1.160	0.000062
ORF7a	40	Y40X	tAC	tGA	1	24	B.1.160	0.000031
ORF7a	40	Y40Y	taC	taT	24	24	R.1	0.00216
ORF7a	40	Y40Y	taC	taT	23	23	AY.39	0.000568
ORF7a	40	Y40del	TAC	---	23	23	B.1.1.214	0.001276
ORF7a	40	Y40Y	taC	taT	23	23	B.1.427	0.001161
ORF7a	40	Y40Y	taC	taT	22	22	AY.23	0.001534
ORF7a	40	Y40F	tAc	tTc	17	22	B.1	0.000156
ORF7a	40	Y40F	tAC	tTT	5	22	B.1	0.000046
ORF7a	40	Y40Y	taC	taT	22	22	B.1.576	0.019946
ORF7a	40	Y40H	Tac	Cac	22	22	P.1	0.000347
ORF7a	40	Y40X	taC	taG	13	21	B.1.617.2	0.000049
ORF7a	40	Y40X	taC	taA	6	21	B.1.617.2	0.000023
ORF7a	40	Y40X	tAC	tGA	2	21	B.1.617.2	0.000008
ORF7a	40	Y40Y	taC	taT	20	20	AY.5	0.000413
ORF7a	40	Y40Y	taC	taT	20	20	AY.98.1	0.000969
ORF7a	40	Y40del	TAC	---	19	19	AY.7.2	0.010626
ORF7a	40	Y40H	Tac	Cac	19	19	B.1	0.000174
ORF7a	40	Y40H	Tac	Cac	18	18	AY.27	0.001165
ORF7a	40	Y40Y	taC	taT	17	17	AY.20	0.000661
ORF7a	40	Y40Y	taC	taT	17	17	AY.75	0.000952
ORF7a	40	Y40Y	taC	taT	17	17	B.1.240	0.003665
ORF7a	40	Y40Y	taC	taT	16	16	AY.33	0.001068
ORF7a	40	Y40Y	taC	taT	16	16	AY.45	0.001947
ORF7a	40	Y40Y	taC	taT	16	16	B.1.1.372	0.011019
ORF7a	40	Y40del	TAC	---	15	15	AY.39	0.000371
ORF7a	40	Y40H	Tac	Cac	14	14	AY.106	0.004689
ORF7a	40	Y40D	Tac	Gac	13	13	All	0.000002
ORF7a	40	Y40H	Tac	Cac	12	13	AY.3	0.000119
ORF7a	40	Y40H	TaC	CaT	1	13	AY.3	0.00001
ORF7a	40	Y40Y	taC	taT	13	13	AY.39.1	0.000515
ORF7a	40	Y40H	Tac	Cac	13	13	AY.44	0.000079
ORF7a	40	Y40Y	taC	taT	13	13	AY.91	0.009496
ORF7a	40	Y40del2	TAc	--c	8	13	B.1.617.2	0.00003
ORF7a	40	Y40del2	tAC	t--	5	13	B.1.617.2	0.000019
ORF7a	40	Y40del	TAC	---	12	12	AY.46.4	0.001974
ORF7a	40	Y40Y	taC	taT	12	12	AY.9.2	0.000441
ORF7a	40	Y40X	taC	taA	11	12	B.1	0.000101
ORF7a	40	Y40X	taC	taG	1	12	B.1	0.000009
ORF7a	40	Y40Y	taC	taT	12	12	B.1.1.28	0.003735
ORF7a	40	Y40del	TAC	---	12	12	B.1.324	0.019262
ORF7a	40	Y40C	tAc	tGc	11	11	AY.4	0.000017
ORF7a	40	Y40Y	taC	taT	11	11	AY.47	0.000342
ORF7a	40	Y40del	TAC	---	11	11	AY.47	0.000342
ORF7a	40	Y40Y	taC	taT	11	11	AY.9	0.000744
ORF7a	40	Y40S	tAc	tCc	4	11	B.1	0.000037
ORF7a	40	Y40S	tAC	tCT	4	11	B.1	0.000037
ORF7a	40	Y40S	tAC	tCA	3	11	B.1	0.000027
ORF7a	40	Y40Y	taC	taT	11	11	B.1.1.258	0.035831
ORF7a	40	Y40del	TAC	---	11	11	C.37	0.001277
ORF7a	40	Y40Y	taC	taT	10	10	AE.8	0.00489
ORF7a	40	Y40del	TAC	---	10	10	AY.20	0.000389
ORF7a	40	Y40Y	taC	taT	10	10	AY.46	0.001041
ORF7a	40	Y40L	tAC	tTA	9	10	B.1	0.000082
ORF7a	40	Y40L	tAC	tTG	1	10	B.1	0.000009
ORF7a	40	Y40Y	taC	taT	10	10	B.1.1.168	0.263158
ORF7a	40	Y40del	TAC	---	10	10	B.1.177	0.000132
ORF7a	40	Y40Y	taC	taT	10	10	B.1.400	0.00429
ORF7a	40	Y40F	tAC	tTT	8	10	B.1.617.2	0.00003
ORF7a	40	Y40F	tAc	tTc	2	10	B.1.617.2	0.000008
ORF7a	40	Y40H	Tac	Cac	10	10	P.1.7	0.003193
ORF7a	40	Y40del	TAC	---	9	9	AY.100	0.000414
ORF7a	40	Y40H	Tac	Cac	9	9	AY.111	0.001648
ORF7a	40	Y40del	TAC	---	9	9	AY.23	0.000628
ORF7a	40	Y40H	Tac	Cac	9	9	AY.26	0.000255
ORF7a	40	Y40del	TAC	---	9	9	AY.26	0.000255
ORF7a	40	Y40X	taC	taA	9	9	AY.5	0.000186
ORF7a	40	Y40Y	taC	taT	9	9	AY.75.1	0.001623
ORF7a	40	Y40Y	taC	taT	9	9	B.1.1.25	0.005117
ORF7a	40	Y40del1	Tac	-ac	6	9	B.1.1.7	0.000005
ORF7a	40	Y40del1	tAC	t-N	2	9	B.1.1.7	0.000002
ORF7a	40	Y40del1	TaC	-aN	1	9	B.1.1.7	0.000001
ORF7a	40	Y40Y	taC	taT	9	9	B.1.258	0.000599
ORF7a	40	Y40C	tAc	tGc	7	9	B.1.617.2	0.000026
ORF7a	40	Y40L	tAC	tTG	6	9	B.1.617.2	0.000023
ORF7a	40	Y40L	tAC	tTA	3	9	B.1.617.2	0.000011
ORF7a	40	Y40C	tAC	tGT	2	9	B.1.617.2	0.000008
ORF7a	40	Y40del	TAC	---	9	9	P.1	0.000142
ORF7a	40	Y40Y	taC	taT	9	9	P.1.1	0.002859
ORF7a	40	Y40Y	taC	taT	9	9	P.2	0.00168
ORF7a	40	Y40del2	TAc	--c	8	8	AY.103	0.00005
ORF7a	40	Y40Y	taC	taT	8	8	AY.116	0.002294
ORF7a	40	Y40N	Tac	Aac	8	8	AY.14	0.000704
ORF7a	40	Y40F	tAC	tTT	6	8	AY.25	0.000036
ORF7a	40	Y40F	tAc	tTc	2	8	AY.25	0.000012
ORF7a	40	Y40Y	taC	taT	8	8	AY.35	0.001864
ORF7a	40	Y40H	Tac	Cac	8	8	AY.39	0.000198
ORF7a	40	Y40del	TAC	---	8	8	B.1.2	0.00007
ORF7a	40	Y40Y	taC	taT	8	8	B.1.293	0.1
ORF7a	40	Y40Y	taC	taT	8	8	B.1.433	0.025559
ORF7a	40	Y40Y	taC	taT	7	7	AY.13	0.001127
ORF7a	40	Y40Y	taC	taT	7	7	AY.23.1	0.002922
ORF7a	40	Y40Y	taC	taT	7	7	AY.3.1	0.000597
ORF7a	40	Y40del1	Tac	-ac	7	7	AY.44	0.000043
ORF7a	40	Y40Y	taC	taT	7	7	AY.46.6	0.000505
ORF7a	40	Y40Y	taC	taT	7	7	AY.61	0.000733
ORF7a	40	Y40L	tAC	tTA	5	7	B.1.1.7	0.000004
ORF7a	40	Y40L	TAc	CTc	2	7	B.1.1.7	0.000002
ORF7a	40	Y40Y	taC	taT	7	7	B.1.177.10	0.006146
ORF7a	40	Y40Y	taC	taT	7	7	B.1.36.16	0.009972
ORF7a	40	Y40H	Tac	Cac	7	7	B.1.621	0.00062
ORF7a	40	Y40Y	taC	taT	7	7	C.37	0.000812
ORF7a	40	Y40X	taC	taA	6	6	AY.103	0.000037
ORF7a	40	Y40Y	taC	taT	6	6	AY.120.2.1	0.00299
ORF7a	40	Y40L	tAC	tTA	6	6	AY.25	0.000036
ORF7a	40	Y40X	taC	taA	5	6	AY.25	0.00003
ORF7a	40	Y40X	tAC	tGA	1	6	AY.25	0.000006
ORF7a	40	Y40C	tAc	tGc	6	6	AY.26	0.00017
ORF7a	40	Y40X	taC	taG	5	6	AY.3	0.00005
ORF7a	40	Y40X	taC	taA	1	6	AY.3	0.00001
ORF7a	40	Y40H	Tac	Cac	6	6	AY.3.1	0.000512
ORF7a	40	Y40N	Tac	Aac	6	6	AY.4	0.000009
ORF7a	40	Y40X	taC	taA	6	6	AY.46.4	0.000987
ORF7a	40	Y40Y	taC	taT	6	6	AY.85	0.002563
ORF7a	40	Y40Y	taC	taT	6	6	B.1.1.207	0.007092
ORF7a	40	Y40F	tAc	tTc	5	6	B.1.1.7	0.000004
ORF7a	40	Y40F	tAC	tTT	1	6	B.1.1.7	0.000001
ORF7a	40	Y40del1	Tac	-ac	6	6	B.1.177	0.000079
ORF7a	40	Y40H	Tac	Cac	6	6	B.1.2	0.000053
ORF7a	40	Y40del	TAC	---	6	6	B.1.429	0.000141
ORF7a	40	Y40Y	taC	taT	6	6	B.1.452	0.082192
ORF7a	40	Y40Y	taC	taT	6	6	B.1.466.2	0.002347
ORF7a	40	Y40Y	taC	taT	6	6	B.1.517	0.002562
ORF7a	40	Y40del	TAC	---	6	6	B.1.526	0.000141
ORF7a	40	Y40Y	taC	taT	6	6	B.1.564.1	0.009464
ORF7a	40	Y40Y	taC	taT	6	6	B.1.582	0.002944
ORF7a	40	Y40Y	taC	taT	6	6	B.1.617.1	0.000774
ORF7a	40	Y40del	TAC	---	6	6	B.1.637	0.000438
ORF7a	40	Y40del1	Tac	-ac	6	6	P.1	0.000095
ORF7a	40	Y40Y	taC	taT	5	5	A.2.5	0.002495
ORF7a	40	Y40Q	TaC	CaA	4	5	All	0.000001
ORF7a	40	Y40Q	TaC	CaG	1	5	All	0
ORF7a	40	Y40del1	Tac	-ac	3	5	AY.103	0.000019
ORF7a	40	Y40del1	taC	ta-	2	5	AY.103	0.000012
ORF7a	40	Y40H	Tac	Cac	5	5	AY.109	0.003698
ORF7a	40	Y40Y	taC	taT	5	5	AY.113	0.000712
ORF7a	40	Y40Y	taC	taT	5	5	AY.14	0.00044
ORF7a	40	Y40Y	taC	taT	5	5	AY.32	0.002662
ORF7a	40	Y40Y	taC	taT	5	5	AY.34	0.000485
ORF7a	40	Y40del2	tAC	t--	5	5	AY.4.2	0.000108
ORF7a	40	Y40Y	taC	taT	5	5	AY.40	0.004822
ORF7a	40	Y40del2	tAC	t--	5	5	AY.44	0.00003
ORF7a	40	Y40Y	taC	taT	5	5	AY.54	0.000477
ORF7a	40	Y40Y	taC	taT	5	5	AY.55	0.004587
ORF7a	40	Y40del2	TAc	--c	5	5	AY.9.2	0.000184
ORF7a	40	Y40del	TAC	---	5	5	AY.98.1	0.000242
ORF7a	40	Y40del	TAC	---	5	5	B.1.1	0.000091
ORF7a	40	Y40Y	taC	taT	5	5	B.1.1.161	0.017668
ORF7a	40	Y40Y	taC	taT	5	5	B.1.1.189	0.007564
ORF7a	40	Y40Y	taC	taT	5	5	B.1.1.317	0.002058
ORF7a	40	Y40del	TAC	---	5	5	B.1.1.56	0.089286
ORF7a	40	Y40del2	tAC	t--	5	5	B.1.1.7	0.000004
ORF7a	40	Y40del	TAC	---	5	5	B.1.160	0.000156
ORF7a	40	Y40del	TAC	---	5	5	B.1.177.44	0.002595
ORF7a	40	Y40Y	taC	taT	5	5	B.1.232	0.002687
ORF7a	40	Y40del	TAC	---	5	5	B.1.525	0.000566
ORF7a	40	Y40Y	taC	taT	5	5	B.1.596	0.000436
ORF7a	40	Y40Y	taC	taT	5	5	P.1.14	0.000239
ORF7a	40	Y40Y	taC	taT	5	5	P.5	0.068493
ORF7a	40	Y40H	Tac	Cac	2	4		0.111111
ORF7a	40	Y40H	TaC	CaT	2	4		0.111111
ORF7a	40	Y40H	Tac	Cac	4	4	AY.100	0.000184
ORF7a	40	Y40Y	taC	taT	4	4	AY.111	0.000733
ORF7a	40	Y40del	TAC	---	4	4	AY.121	0.000541
ORF7a	40	Y40Y	taC	taT	4	4	AY.121	0.000541
ORF7a	40	Y40del1	taC	ta-	4	4	AY.25	0.000024
ORF7a	40	Y40S	tAC	tCT	2	4	AY.25	0.000012
ORF7a	40	Y40S	tAC	tCA	1	4	AY.25	0.000006
ORF7a	40	Y40S	tAc	tCc	1	4	AY.25	0.000006
ORF7a	40	Y40F	tAC	tTT	2	4	AY.3	0.00002
ORF7a	40	Y40F	tAc	tTc	2	4	AY.3	0.00002
ORF7a	40	Y40F	tAC	tTT	4	4	AY.3.1	0.000341
ORF7a	40	Y40Q	TaC	CaA	4	4	AY.4	0.000006
ORF7a	40	Y40del1	Tac	-ac	3	4	AY.4	0.000005
ORF7a	40	Y40del1	tAC	t-N	1	4	AY.4	0.000002
ORF7a	40	Y40del	TAC	---	4	4	AY.4.2	0.000087
ORF7a	40	Y40H	Tac	Cac	4	4	AY.4.2	0.000087
ORF7a	40	Y40X	taC	taG	3	4	AY.43	0.000013
ORF7a	40	Y40X	taC	taA	1	4	AY.43	0.000004
ORF7a	40	Y40N	Tac	Aac	4	4	AY.46	0.000416
ORF7a	40	Y40del	TAC	---	4	4	AY.5	0.000083
ORF7a	40	Y40Y	taC	taT	4	4	AY.50	0.003197
ORF7a	40	Y40H	Tac	Cac	4	4	AY.54	0.000381
ORF7a	40	Y40Y	taC	taT	4	4	AY.62	0.001743
ORF7a	40	Y40Y	taC	taT	4	4	AY.7.1	0.000451
ORF7a	40	Y40Y	taC	taT	4	4	AY.99.2	0.000369
ORF7a	40	Y40X	taC	taA	4	4	B.1.1	0.000073
ORF7a	40	Y40H	Tac	Cac	4	4	B.1.1.176	0.001757
ORF7a	40	Y40Y	taC	taT	4	4	B.1.1.214	0.000222
ORF7a	40	Y40Y	taC	taT	4	4	B.1.1.232	0.00726
ORF7a	40	Y40Y	taC	taT	4	4	B.1.1.431	0.064516
ORF7a	40	Y40Y	taC	taT	4	4	B.1.1.50	0.002716
ORF7a	40	Y40N	Tac	Aac	4	4	B.1.1.7	0.000004
ORF7a	40	Y40Y	taC	taT	4	4	B.1.1.70	0.001364
ORF7a	40	Y40H	Tac	Cac	4	4	B.1.128	0.002541
ORF7a	40	Y40H	Tac	Cac	4	4	B.1.160	0.000125
ORF7a	40	Y40F	tAc	tTc	3	4	B.1.160	0.000094
ORF7a	40	Y40F	tAC	tTT	1	4	B.1.160	0.000031
ORF7a	40	Y40F	tAc	tTc	3	4	B.1.177	0.00004
ORF7a	40	Y40F	tAC	tTT	1	4	B.1.177	0.000013
ORF7a	40	Y40Y	taC	taT	4	4	B.1.177.17	0.003284
ORF7a	40	Y40Y	taC	taT	4	4	B.1.258.3	0.0067
ORF7a	40	Y40Y	taC	taT	4	4	B.1.311	0.001098
ORF7a	40	Y40Y	taC	taT	4	4	B.1.369	0.001141
ORF7a	40	Y40Y	taC	taT	4	4	B.1.438.1	0.000429
ORF7a	40	Y40D	Tac	Gac	4	4	B.1.561	0.001588
ORF7a	40	Y40Y	taC	taT	4	4	B.1.600	0.023392
ORF7a	40	Y40Y	taC	taT	4	4	C.13	0.102564
ORF7a	40	Y40H	Tac	Cac	4	4	P.1.10	0.001078
ORF7a	40	Y40Y	taC	taT	4	4	Q.8	0.00066
ORF7a	40	Y40Y	taC	taT	3	3	A.2.5.2	0.004717
ORF7a	40	Y40X	taC	taA	3	3	AY.102	0.00008
ORF7a	40	Y40H	Tac	Cac	3	3	AY.102	0.00008
ORF7a	40	Y40del	TAC	---	3	3	AY.102	0.00008
ORF7a	40	Y40Y	taC	taT	3	3	AY.107	0.001398
ORF7a	40	Y40Y	taC	taT	3	3	AY.108	0.003308
ORF7a	40	Y40del	TAC	---	3	3	AY.118	0.000188
ORF7a	40	Y40del	TAC	---	3	3	AY.120	0.000112
ORF7a	40	Y40H	Tac	Cac	3	3	AY.14	0.000264
ORF7a	40	Y40del1	Tac	-ac	3	3	AY.20	0.000117
ORF7a	40	Y40X	taC	taA	3	3	AY.29	0.000047
ORF7a	40	Y40del1	Tac	-ac	3	3	AY.3	0.00003
ORF7a	40	Y40C	tAc	tGc	3	3	AY.3	0.00003
ORF7a	40	Y40del	TAC	---	3	3	AY.33	0.0002
ORF7a	40	Y40del	TAC	---	3	3	AY.35	0.000699
ORF7a	40	Y40del	TAC	---	3	3	AY.4.5	0.000322
ORF7a	40	Y40del	TAC	---	3	3	AY.42	0.000121
ORF7a	40	Y40S	tAc	tCc	3	3	AY.44	0.000018
ORF7a	40	Y40H	Tac	Cac	3	3	AY.46.6	0.000217
ORF7a	40	Y40Y	taC	taT	3	3	AY.5.3	0.001012
ORF7a	40	Y40del	TAC	---	3	3	AY.54	0.000286
ORF7a	40	Y40Y	taC	taT	3	3	AY.6	0.000123
ORF7a	40	Y40Y	taC	taT	3	3	AY.66	0.003209
ORF7a	40	Y40del	TAC	---	3	3	AY.75	0.000168
ORF7a	40	Y40del2	tAC	t--	3	3	AY.88	0.002653
ORF7a	40	Y40del	TAC	---	3	3	AY.9	0.000203
ORF7a	40	Y40Y	taC	taT	3	3	AY.98	0.000237
ORF7a	40	Y40D	Tac	Gac	3	3	B.1	0.000027
ORF7a	40	Y40del2	tAC	t--	3	3	B.1	0.000027
ORF7a	40	Y40N	Tac	Aac	3	3	B.1.1	0.000054
ORF7a	40	Y40H	Tac	Cac	3	3	B.1.1	0.000054
ORF7a	40	Y40S	tAc	tCc	1	3	B.1.1	0.000018
ORF7a	40	Y40S	tAC	tCA	1	3	B.1.1	0.000018
ORF7a	40	Y40S	tAC	tCT	1	3	B.1.1	0.000018
ORF7a	40	Y40Y	taC	taT	3	3	B.1.1.220	0.005576
ORF7a	40	Y40Y	taC	taT	3	3	B.1.1.222	0.000612
ORF7a	40	Y40del	TAC	---	3	3	B.1.1.25	0.001706
ORF7a	40	Y40Y	taC	taT	3	3	B.1.1.306	0.001315
ORF7a	40	Y40F	tAc	tTc	3	3	B.1.1.311	0.001074
ORF7a	40	Y40H	Tac	Cac	3	3	B.1.1.519	0.000119
ORF7a	40	Y40Y	taC	taT	3	3	B.1.177.56	0.002003
ORF7a	40	Y40del1	Tac	-ac	3	3	B.1.2	0.000026
ORF7a	40	Y40del	TAC	---	3	3	B.1.234	0.000396
ORF7a	40	Y40F	tAc	tTc	2	3	B.1.258	0.000133
ORF7a	40	Y40F	tAC	tTT	1	3	B.1.258	0.000067
ORF7a	40	Y40Y	taC	taT	3	3	B.1.351.2	0.000908
ORF7a	40	Y40Y	taC	taT	3	3	B.1.36	0.000438
ORF7a	40	Y40Y	taC	taT	3	3	B.1.36.1	0.003421
ORF7a	40	Y40Y	taC	taT	3	3	B.1.416	0.003807
ORF7a	40	Y40Y	taC	taT	3	3	B.1.532	0.018634
ORF7a	40	Y40del1	taC	ta-	2	3	B.1.617.2	0.000008
ORF7a	40	Y40del1	Tac	-ac	1	3	B.1.617.2	0.000004
ORF7a	40	Y40Y	taC	taT	3	3	B.1.619.1	0.001924
ORF7a	40	Y40del	TAC	---	3	3	B.1.626	0.017143
ORF7a	40	Y40Y	taC	taT	3	3	B.1.628	0.001057
ORF7a	40	Y40C	tAc	tGc	3	3	P.1.1	0.000953
ORF7a	40	Y40Y	taC	taT	3	3	P.1.12	0.001452
ORF7a	40	Y40del	TAC	---	3	3	Q.8	0.000495
ORF7a	40	Y40Y	taC	taT	2	2		0.111111
ORF7a	40	Y40del	TAC	---	2	2	A	0.000774
ORF7a	40	Y40del	TAC	---	2	2	A.28	0.005291
ORF7a	40	Y40Y	taC	taT	2	2	AD.2	0.000438
ORF7a	40	Y40Y	taC	taT	2	2	AY.1	0.000791
ORF7a	40	Y40F	tAc	tTc	2	2	AY.103	0.000012
ORF7a	40	Y40Y	taC	taT	2	2	AY.105	0.001286
ORF7a	40	Y40del	TAC	---	2	2	AY.110	0.000225
ORF7a	40	Y40H	Tac	Cac	2	2	AY.114	0.000462
ORF7a	40	Y40del	TAC	---	2	2	AY.114	0.000462
ORF7a	40	Y40H	Tac	Cac	2	2	AY.117	0.000169
ORF7a	40	Y40del	TAC	---	2	2	AY.119	0.000071
ORF7a	40	Y40H	Tac	Cac	2	2	AY.119	0.000071
ORF7a	40	Y40X	taC	taA	2	2	AY.120	0.000074
ORF7a	40	Y40del	TAC	---	2	2	AY.120.1	0.000642
ORF7a	40	Y40H	Tac	Cac	2	2	AY.13	0.000322
ORF7a	40	Y40Y	taC	taT	2	2	AY.19	0.002281
ORF7a	40	Y40H	Tac	Cac	2	2	AY.23	0.000139
ORF7a	40	Y40del2	tAC	t--	2	2	AY.25	0.000012
ORF7a	40	Y40F	tAC	tTT	1	2	AY.26	0.000028
ORF7a	40	Y40F	tAc	tTc	1	2	AY.26	0.000028
ORF7a	40	Y40del1	Tac	-ac	1	2	AY.29	0.000016
ORF7a	40	Y40del1	taC	ta-	1	2	AY.29	0.000016
ORF7a	40	Y40del	TAC	---	2	2	AY.29.1	0.000441
ORF7a	40	Y40del	TAC	---	2	2	AY.34	0.000194
ORF7a	40	Y40F	tAc	tTc	2	2	AY.4	0.000003
ORF7a	40	Y40Y	taC	taT	2	2	AY.4.4	0.000818
ORF7a	40	Y40Y	taC	taT	2	2	AY.4.5	0.000215
ORF7a	40	Y40del2	tAC	t--	2	2	AY.43	0.000009
ORF7a	40	Y40del1	Tac	-ac	2	2	AY.43	0.000009
ORF7a	40	Y40F	tAc	tTc	2	2	AY.44	0.000012
ORF7a	40	Y40X	taC	taA	1	2	AY.44	0.000006
ORF7a	40	Y40X	taC	taG	1	2	AY.44	0.000006
ORF7a	40	Y40X	taC	taA	2	2	AY.47	0.000062
ORF7a	40	Y40H	Tac	Cac	2	2	AY.47	0.000062
ORF7a	40	Y40H	Tac	Cac	2	2	AY.49	0.00639
ORF7a	40	Y40Y	taC	taT	2	2	AY.51	0.001818
ORF7a	40	Y40Y	taC	taT	2	2	AY.84	0.000875
ORF7a	40	Y40H	Tac	Cac	2	2	AZ.2	0.001642
ORF7a	40	Y40Y	taC	taT	2	2	B	0.000256
ORF7a	40	Y40L	tAC	tTA	2	2	B.1.1	0.000036
ORF7a	40	Y40F	tAC	tTT	1	2	B.1.1	0.000018
ORF7a	40	Y40F	tAc	tTc	1	2	B.1.1	0.000018
ORF7a	40	Y40Y	taC	taT	2	2	B.1.1.157	0.001826
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.1.210	0.011429
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.1.222	0.000408
ORF7a	40	Y40Y	taC	taT	2	2	B.1.1.280	0.006173
ORF7a	40	Y40Y	taC	taT	2	2	B.1.1.335	0.025974
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.1.372	0.001377
ORF7a	40	Y40X	taC	taA	2	2	B.1.1.385	0.008929
ORF7a	40	Y40Y	taC	taT	2	2	B.1.1.467	0.038462
ORF7a	40	Y40Y	taC	taT	2	2	B.1.1.51	0.003436
ORF7a	40	Y40Y	taC	taT	2	2	B.1.1.61	0.017544
ORF7a	40	Y40Y	taC	taT	2	2	B.1.110	0.00905
ORF7a	40	Y40Y	taC	taT	2	2	B.1.147	0.001512
ORF7a	40	Y40C	tAC	tGT	1	2	B.1.160	0.000031
ORF7a	40	Y40C	tAc	tGc	1	2	B.1.160	0.000031
ORF7a	40	Y40del2	tAC	t--	2	2	B.1.177	0.000026
ORF7a	40	Y40X	taC	taA	2	2	B.1.177	0.000026
ORF7a	40	Y40S	tAc	tCc	1	2	B.1.177	0.000013
ORF7a	40	Y40S	tAC	tCA	1	2	B.1.177	0.000013
ORF7a	40	Y40Y	taC	taT	2	2	B.1.177.21	0.000153
ORF7a	40	Y40Y	taC	taT	2	2	B.1.177.33	0.003289
ORF7a	40	Y40Y	taC	taT	2	2	B.1.177.4	0.000422
ORF7a	40	Y40del	TAC	---	2	2	B.1.177.43	0.002954
ORF7a	40	Y40Y	taC	taT	2	2	B.1.177.58	0.002663
ORF7a	40	Y40Y	taC	taT	2	2	B.1.177.60	0.000437
ORF7a	40	Y40X	taC	taA	2	2	B.1.177.76	0.004988
ORF7a	40	Y40Y	taC	taT	2	2	B.1.177.80	0.003824
ORF7a	40	Y40del	TAC	---	2	2	B.1.177.86	0.000367
ORF7a	40	Y40C	tAc	tGc	2	2	B.1.2	0.000018
ORF7a	40	Y40del2	tAC	t--	1	2	B.1.2	0.000009
ORF7a	40	Y40del2	TAc	--c	1	2	B.1.2	0.000009
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.243	0.000139
ORF7a	40	Y40del	TAC	---	2	2	B.1.258.11	0.000793
ORF7a	40	Y40del	TAC	---	2	2	B.1.351	0.000059
ORF7a	40	Y40del	TAC	---	2	2	B.1.36	0.000292
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.36.10	0.009569
ORF7a	40	Y40Y	taC	taT	2	2	B.1.36.38	0.003284
ORF7a	40	Y40Y	taC	taT	2	2	B.1.375	0.001639
ORF7a	40	Y40Y	taC	taT	2	2	B.1.397	0.009709
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.429	0.000047
ORF7a	40	Y40del1	Tac	-ac	1	2	B.1.436	0.001029
ORF7a	40	Y40del1	TaC	-aN	1	2	B.1.436	0.001029
ORF7a	40	Y40Y	taC	taT	2	2	B.1.474	0.003802
ORF7a	40	Y40Y	taC	taT	2	2	B.1.509	0.001732
ORF7a	40	Y40Y	taC	taT	2	2	B.1.560	0.009259
ORF7a	40	Y40X	taC	taA	2	2	B.1.575	0.000607
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.596	0.000174
ORF7a	40	Y40del	TAC	---	2	2	B.1.596	0.000174
ORF7a	40	Y40H	Tac	Cac	2	2	B.1.617.1	0.000258
ORF7a	40	Y40N	Tac	Aac	2	2	B.1.617.2	0.000008
ORF7a	40	Y40C	tAc	tGc	2	2	B.1.621	0.000177
ORF7a	40	Y40Y	taC	taT	2	2	B.1.621.1	0.001012
ORF7a	40	Y40del	TAC	---	2	2	C.36.3	0.001134
ORF7a	40	Y40X	taC	taA	2	2	P.1	0.000032
ORF7a	40	Y40Y	taC	taT	2	2	P.1.15	0.000465
ORF7a	40	Y40Y	taC	taT	2	2	P.1.16	0.000748
ORF7a	40	Y40del	TAC	---	2	2	R.1	0.00018
ORF7a	40	Y40del1	TaC	Ga-	2	2	R.1	0.00018
ORF7a	40	Y40del	TAC	---	1	1	A.1	0.000282
ORF7a	40	Y40Y	taC	taT	1	1	A.2	0.000662
ORF7a	40	Y40Y	taC	taT	1	1	A.23	0.010526
ORF7a	40	Y40Y	taC	taT	1	1	A.29	0.005319
ORF7a	40	Y40Y	taC	taT	1	1	AD.1	0.004115
ORF7a	40	Y40W	tAC	tGG	1	1	All	0
ORF7a	40	Y40E	TaC	GaA	1	1	All	0
ORF7a	40	Y40K	TaC	AaG	1	1	All	0
ORF7a	40	Y40H	Tac	Cac	1	1	AM.4	0.003571
ORF7a	40	Y40C	tAc	tGc	1	1	AY.10	0.00053
ORF7a	40	Y40D	Tac	Gac	1	1	AY.100	0.000046
ORF7a	40	Y40N	Tac	Aac	1	1	AY.103	0.000006
ORF7a	40	Y40C	tAc	tGc	1	1	AY.103	0.000006
ORF7a	40	Y40S	tAc	tCc	1	1	AY.103	0.000006
ORF7a	40	Y40L	tAC	tTA	1	1	AY.103	0.000006
ORF7a	40	Y40Y	taC	taT	1	1	AY.106	0.000335
ORF7a	40	Y40del	TAC	---	1	1	AY.108	0.001103
ORF7a	40	Y40L	TAc	CTc	1	1	AY.110	0.000113
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.113	0.000142
ORF7a	40	Y40del	TAC	---	1	1	AY.113	0.000142
ORF7a	40	Y40H	Tac	Cac	1	1	AY.116	0.000287
ORF7a	40	Y40C	tAc	tGc	1	1	AY.118	0.000063
ORF7a	40	Y40X	taC	taG	1	1	AY.119	0.000035
ORF7a	40	Y40N	Tac	Aac	1	1	AY.119	0.000035
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.119	0.000035
ORF7a	40	Y40del2	tAC	t--	1	1	AY.119	0.000035
ORF7a	40	Y40del	TAC	---	1	1	AY.12	0.000316
ORF7a	40	Y40C	tAc	tGc	1	1	AY.120	0.000037
ORF7a	40	Y40X	taC	taA	1	1	AY.121	0.000135
ORF7a	40	Y40del	TAC	---	1	1	AY.13	0.000161
ORF7a	40	Y40del	TAC	---	1	1	AY.16	0.00038
ORF7a	40	Y40del	TAC	---	1	1	AY.16.1	0.00047
ORF7a	40	Y40H	Tac	Cac	1	1	AY.20	0.000039
ORF7a	40	Y40Y	taC	taT	1	1	AY.24	0.000431
ORF7a	40	Y40F	tAc	tTc	1	1	AY.24	0.000431
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.24	0.000431
ORF7a	40	Y40N	Tac	Aac	1	1	AY.25	0.000006
ORF7a	40	Y40C	tAC	tGT	1	1	AY.25	0.000006
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.26	0.000028
ORF7a	40	Y40X	taC	taA	1	1	AY.26	0.000028
ORF7a	40	Y40F	tAc	tTc	1	1	AY.27	0.000065
ORF7a	40	Y40H	Tac	Cac	1	1	AY.29	0.000016
ORF7a	40	Y40del2	tAC	t--	1	1	AY.3	0.00001
ORF7a	40	Y40L	TAc	CTc	1	1	AY.3.1	0.000085
ORF7a	40	Y40K	TaC	AaG	1	1	AY.30	0.000396
ORF7a	40	Y40C	tAc	tGc	1	1	AY.30	0.000396
ORF7a	40	Y40Y	taC	taT	1	1	AY.36	0.000148
ORF7a	40	Y40D	Tac	Gac	1	1	AY.37	0.000316
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.39	0.000025
ORF7a	40	Y40X	taC	taA	1	1	AY.39	0.000025
ORF7a	40	Y40C	tAc	tGc	1	1	AY.39	0.000025
ORF7a	40	Y40H	Tac	Cac	1	1	AY.39.1	0.00004
ORF7a	40	Y40F	tAC	tTT	1	1	AY.39.1	0.00004
ORF7a	40	Y40del	TAC	---	1	1	AY.39.1	0.00004
ORF7a	40	Y40D	Tac	Gac	1	1	AY.4	0.000002
ORF7a	40	Y40N	Tac	Aac	1	1	AY.4.2	0.000022
ORF7a	40	Y40Y	taC	taT	1	1	AY.4.2.1	0.000149
ORF7a	40	Y40C	tAc	tGc	1	1	AY.43	0.000004
ORF7a	40	Y40E	TaC	GaA	1	1	AY.44	0.000006
ORF7a	40	Y40N	Tac	Aac	1	1	AY.44	0.000006
ORF7a	40	Y40L	tAC	tTA	1	1	AY.44	0.000006
ORF7a	40	Y40C	tAc	tGc	1	1	AY.45	0.000122
ORF7a	40	Y40del	TAC	---	1	1	AY.45	0.000122
ORF7a	40	Y40H	Tac	Cac	1	1	AY.45	0.000122
ORF7a	40	Y40del	TAC	---	1	1	AY.46	0.000104
ORF7a	40	Y40del1	taC	ta-	1	1	AY.46.4	0.000165
ORF7a	40	Y40Y	taC	taT	1	1	AY.46.4	0.000165
ORF7a	40	Y40H	Tac	Cac	1	1	AY.46.4	0.000165
ORF7a	40	Y40H	Tac	Cac	1	1	AY.46.5	0.000198
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.46.6	0.000072
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.47	0.000031
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.5	0.000021
ORF7a	40	Y40Y	taC	taT	1	1	AY.5.1	0.003759
ORF7a	40	Y40C	tAc	tGc	1	1	AY.5.4	0.000277
ORF7a	40	Y40del	TAC	---	1	1	AY.5.4	0.000277
ORF7a	40	Y40C	tAc	tGc	1	1	AY.53	0.000288
ORF7a	40	Y40Y	taC	taT	1	1	AY.58	0.000907
ORF7a	40	Y40del2	TAc	--c	1	1	AY.58	0.000907
ORF7a	40	Y40del	TAC	---	1	1	AY.6	0.000041
ORF7a	40	Y40del	TAC	---	1	1	AY.61	0.000105
ORF7a	40	Y40H	Tac	Cac	1	1	AY.66	0.00107
ORF7a	40	Y40del	TAC	---	1	1	AY.66	0.00107
ORF7a	40	Y40Y	taC	taT	1	1	AY.67	0.000464
ORF7a	40	Y40Y	taC	taT	1	1	AY.68	0.000274
ORF7a	40	Y40X	taC	taA	1	1	AY.70	0.000209
ORF7a	40	Y40Y	taC	taT	1	1	AY.70	0.000209
ORF7a	40	Y40del	TAC	---	1	1	AY.73	0.000665
ORF7a	40	Y40del	TAC	---	1	1	AY.74	0.000116
ORF7a	40	Y40Y	taC	taT	1	1	AY.76	0.004831
ORF7a	40	Y40del	TAC	---	1	1	AY.76	0.004831
ORF7a	40	Y40H	Tac	Cac	1	1	AY.77	0.001127
ORF7a	40	Y40del	TAC	---	1	1	AY.79	0.001211
ORF7a	40	Y40del1	Tac	-ac	1	1	AY.79	0.001211
ORF7a	40	Y40Y	taC	taT	1	1	AY.79	0.001211
ORF7a	40	Y40del2	tAC	t--	1	1	AY.80	0.001129
ORF7a	40	Y40H	Tac	Cac	1	1	AY.82	0.001357
ORF7a	40	Y40del	TAC	---	1	1	AY.85	0.000427
ORF7a	40	Y40F	tAc	tTc	1	1	AY.85	0.000427
ORF7a	40	Y40H	Tac	Cac	1	1	AY.9	0.000068
ORF7a	40	Y40Y	taC	taT	1	1	AY.9.1	0.000084
ORF7a	40	Y40del	TAC	---	1	1	AY.9.1	0.000084
ORF7a	40	Y40del	TAC	---	1	1	AY.9.2	0.000037
ORF7a	40	Y40H	Tac	Cac	1	1	AY.9.2	0.000037
ORF7a	40	Y40del	TAC	---	1	1	AY.92	0.000287
ORF7a	40	Y40H	Tac	Cac	1	1	AY.93	0.000273
ORF7a	40	Y40del	TAC	---	1	1	AY.94	0.000443
ORF7a	40	Y40del2	tAC	t--	1	1	AY.95	0.000761
ORF7a	40	Y40Y	taC	taT	1	1	AY.95	0.000761
ORF7a	40	Y40Y	taC	taT	1	1	AY.96	0.002075
ORF7a	40	Y40del	TAC	---	1	1	AY.98	0.000079
ORF7a	40	Y40D	Tac	Gac	1	1	AY.98	0.000079
ORF7a	40	Y40H	Tac	Cac	1	1	AY.98.1	0.000048
ORF7a	40	Y40Y	taC	taT	1	1	AY.99	0.001049
ORF7a	40	Y40H	Tac	Cac	1	1	AY.99.2	0.000092
ORF7a	40	Y40del	TAC	---	1	1	AY.99.2	0.000092
ORF7a	40	Y40Y	taC	taT	1	1	AZ.2	0.000821
ORF7a	40	Y40del	TAC	---	1	1	B	0.000128
ORF7a	40	Y40W	tAC	tGG	1	1	B.1	0.000009
ORF7a	40	Y40N	Tac	Aac	1	1	B.1	0.000009
ORF7a	40	Y40del2	tAC	t--	1	1	B.1.1	0.000018
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.152	0.04
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.190	0.05
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.194	0.00495
ORF7a	40	Y40del	TAC	---	1	1	B.1.1.207	0.001182
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.216	0.00089
ORF7a	40	Y40del	TAC	---	1	1	B.1.1.222	0.000204
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.243	0.004082
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.269	0.001353
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.272	0.005208
ORF7a	40	Y40del	TAC	---	1	1	B.1.1.277	0.000759
ORF7a	40	Y40D	Tac	Gac	1	1	B.1.1.284	0.000107
ORF7a	40	Y40N	Tac	Aac	1	1	B.1.1.306	0.000438
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.311	0.000358
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.316	0.000925
ORF7a	40	Y40del2	tAC	t--	1	1	B.1.1.317	0.000412
ORF7a	40	Y40del	TAC	---	1	1	B.1.1.318	0.000302
ORF7a	40	Y40del	TAC	---	1	1	B.1.1.33	0.000421
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.344	0.010753
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.1.348	0.000796
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.371	0.010417
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.375	0.011905
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.397	0.002252
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.409	0.002833
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.412	0.007634
ORF7a	40	Y40S	tAc	tCc	1	1	B.1.1.416	0.000905
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.419	0.007407
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.420	0.001006
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.429	0.004608
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.462	0.008621
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.486	0.001577
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.500	0.02
ORF7a	40	Y40del	TAC	---	1	1	B.1.1.519	0.00004
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.52	0.012195
ORF7a	40	Y40del	TAC	---	1	1	B.1.1.522	0.017241
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.528	0.004808
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.63	0.000386
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.83	0.00271
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.98	0.018519
ORF7a	40	Y40Y	taC	taT	1	1	B.1.1.99	0.02381
ORF7a	40	Y40Y	taC	taT	1	1	B.1.111	0.001175
ORF7a	40	Y40S	tAc	tCc	1	1	B.1.111	0.001175
ORF7a	40	Y40del	TAC	---	1	1	B.1.115	0.021739
ORF7a	40	Y40Y	taC	taT	1	1	B.1.126	0.001276
ORF7a	40	Y40Y	taC	taT	1	1	B.1.139	0.000733
ORF7a	40	Y40L	tAC	tTA	1	1	B.1.160	0.000031
ORF7a	40	Y40Y	taC	taT	1	1	B.1.160.28	0.002924
ORF7a	40	Y40Y	taC	taT	1	1	B.1.160.32	0.004292
ORF7a	40	Y40N	Tac	Aac	1	1	B.1.177	0.000013
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.177	0.000013
ORF7a	40	Y40Y	taC	taT	1	1	B.1.177.12	0.000152
ORF7a	40	Y40Y	taC	taT	1	1	B.1.177.20	0.001517
ORF7a	40	Y40Y	taC	taT	1	1	B.1.177.44	0.000519
ORF7a	40	Y40N	Tac	Aac	1	1	B.1.177.56	0.000668
ORF7a	40	Y40del	TAC	---	1	1	B.1.177.62	0.001192
ORF7a	40	Y40H	TaC	CaT	1	1	B.1.177.63	0.002703
ORF7a	40	Y40Y	taC	taT	1	1	B.1.177.63	0.002703
ORF7a	40	Y40Y	taC	taT	1	1	B.1.177.7	0.000165
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.177.7	0.000165
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.177.7	0.000165
ORF7a	40	Y40C	tAc	tGc	1	1	B.1.177.7	0.000165
ORF7a	40	Y40Y	taC	taT	1	1	B.1.177.73	0.000566
ORF7a	40	Y40del	TAC	---	1	1	B.1.177.80	0.001912
ORF7a	40	Y40del	TAC	---	1	1	B.1.177.81	0.000189
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.177.81	0.000189
ORF7a	40	Y40del	TAC	---	1	1	B.1.177.83	0.001481
ORF7a	40	Y40Y	taC	taT	1	1	B.1.177.84	0.006667
ORF7a	40	Y40Q	TaC	CaG	1	1	B.1.2	0.000009
ORF7a	40	Y40del	TAC	---	1	1	B.1.214.2	0.0006
ORF7a	40	Y40X	taC	taA	1	1	B.1.221	0.000071
ORF7a	40	Y40del	TAC	---	1	1	B.1.221	0.000071
ORF7a	40	Y40N	Tac	Aac	1	1	B.1.221	0.000071
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.221	0.000071
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.221	0.000071
ORF7a	40	Y40Y	taC	taT	1	1	B.1.222	0.001692
ORF7a	40	Y40Y	taC	taT	1	1	B.1.234	0.000132
ORF7a	40	Y40Y	taC	taT	1	1	B.1.239	0.001221
ORF7a	40	Y40del	TAC	---	1	1	B.1.240	0.000216
ORF7a	40	Y40del	TAC	---	1	1	B.1.243	0.00007
ORF7a	40	Y40Y	taC	taT	1	1	B.1.258.10	0.011364
ORF7a	40	Y40del	TAC	---	1	1	B.1.258.17	0.000104
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.258.17	0.000104
ORF7a	40	Y40S	tAc	tCc	1	1	B.1.311	0.000275
ORF7a	40	Y40Y	taC	taT	1	1	B.1.313	0.006579
ORF7a	40	Y40Y	taC	taT	1	1	B.1.320	0.001245
ORF7a	40	Y40Y	taC	taT	1	1	B.1.346	0.001311
ORF7a	40	Y40Y	taC	taT	1	1	B.1.349	0.000715
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.351	0.00003
ORF7a	40	Y40C	tAc	tGc	1	1	B.1.351	0.00003
ORF7a	40	Y40X	taC	taA	1	1	B.1.351	0.00003
ORF7a	40	Y40N	Tac	Aac	1	1	B.1.351	0.00003
ORF7a	40	Y40del	TAC	---	1	1	B.1.351.2	0.000303
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.36	0.000146
ORF7a	40	Y40S	tAc	tCc	1	1	B.1.36	0.000146
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.36.16	0.001425
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.36.22	0.001208
ORF7a	40	Y40Y	taC	taT	1	1	B.1.36.22	0.001208
ORF7a	40	Y40Y	taC	taT	1	1	B.1.36.29	0.000517
ORF7a	40	Y40N	Tac	Aac	1	1	B.1.36.36	0.000602
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.36.8	0.001
ORF7a	40	Y40C	tAc	tGc	1	1	B.1.36.8	0.001
ORF7a	40	Y40Y	taC	taT	1	1	B.1.389	0.001002
ORF7a	40	Y40Y	taC	taT	1	1	B.1.404	0.001302
ORF7a	40	Y40Y	taC	taT	1	1	B.1.408	0.00369
ORF7a	40	Y40C	tAc	tGc	1	1	B.1.409	0.000781
ORF7a	40	Y40Y	taC	taT	1	1	B.1.409	0.000781
ORF7a	40	Y40Y	taC	taT	1	1	B.1.411	0.003704
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.416.1	0.001563
ORF7a	40	Y40S	tAc	tCc	1	1	B.1.417	0.028571
ORF7a	40	Y40Y	taC	taT	1	1	B.1.422	0.000812
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.427	0.00005
ORF7a	40	Y40X	taC	taG	1	1	B.1.427	0.00005
ORF7a	40	Y40C	tAc	tGc	1	1	B.1.427	0.00005
ORF7a	40	Y40del	TAC	---	1	1	B.1.427	0.00005
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.429	0.000024
ORF7a	40	Y40X	taC	taG	1	1	B.1.429	0.000024
ORF7a	40	Y40del	TAC	---	1	1	B.1.438.1	0.000107
ORF7a	40	Y40Y	taC	taT	1	1	B.1.453	0.003236
ORF7a	40	Y40Y	taC	taT	1	1	B.1.456	0.003268
ORF7a	40	Y40del	TAC	---	1	1	B.1.459	0.004082
ORF7a	40	Y40del	TAC	---	1	1	B.1.466.2	0.000391
ORF7a	40	Y40del	TAC	---	1	1	B.1.468	0.005714
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.468	0.005714
ORF7a	40	Y40del	TAC	---	1	1	B.1.470	0.001404
ORF7a	40	Y40Y	taC	taT	1	1	B.1.508	0.025641
ORF7a	40	Y40del2	tAC	t--	1	1	B.1.525	0.000113
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.525	0.000113
ORF7a	40	Y40Y	taC	taT	1	1	B.1.526	0.000024
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.526	0.000024
ORF7a	40	Y40del	TAC	---	1	1	B.1.535	0.028571
ORF7a	40	Y40X	tAC	tGA	1	1	B.1.538	0.008065
ORF7a	40	Y40Y	taC	taT	1	1	B.1.546	0.003704
ORF7a	40	Y40Y	taC	taT	1	1	B.1.551	0.00129
ORF7a	40	Y40Y	taC	taT	1	1	B.1.561	0.000397
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.564	0.000426
ORF7a	40	Y40F	tAc	tTc	1	1	B.1.565	0.00081
ORF7a	40	Y40C	tAc	tGc	1	1	B.1.567	0.003333
ORF7a	40	Y40Y	taC	taT	1	1	B.1.575.2	0.004808
ORF7a	40	Y40F	tAC	tTT	1	1	B.1.576	0.000907
ORF7a	40	Y40L	tAC	tTA	1	1	B.1.576	0.000907
ORF7a	40	Y40X	taC	taA	1	1	B.1.576	0.000907
ORF7a	40	Y40Y	taC	taT	1	1	B.1.577	0.000687
ORF7a	40	Y40del	TAC	---	1	1	B.1.582	0.000491
ORF7a	40	Y40Y	taC	taT	1	1	B.1.595	0.000261
ORF7a	40	Y40C	tAc	tGc	1	1	B.1.596	0.000087
ORF7a	40	Y40Y	taC	taT	1	1	B.1.597	0.00463
ORF7a	40	Y40Y	taC	taT	1	1	B.1.610	0.003546
ORF7a	40	Y40S	tAc	tCc	1	1	B.1.617.2	0.000004
ORF7a	40	Y40D	Tac	Gac	1	1	B.1.617.2	0.000004
ORF7a	40	Y40del	TAC	---	1	1	B.1.617.3	0.002985
ORF7a	40	Y40N	TaC	AaT	1	1	B.1.617.3	0.002985
ORF7a	40	Y40del	TAC	---	1	1	B.1.620	0.000946
ORF7a	40	Y40Y	taC	taT	1	1	B.1.627	0.00202
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.628	0.000352
ORF7a	40	Y40del1	Tac	-ac	1	1	B.1.630	0.005236
ORF7a	40	Y40Y	taC	taT	1	1	B.1.634	0.003425
ORF7a	40	Y40del	TAC	---	1	1	B.1.636	0.006711
ORF7a	40	Y40del	TAC	---	1	1	B.1.638	0.052632
ORF7a	40	Y40H	Tac	Cac	1	1	B.1.88.1	0.004808
ORF7a	40	Y40Y	taC	taT	1	1	B.12	0.00641
ORF7a	40	Y40Y	taC	taT	1	1	B.3	0.000831
ORF7a	40	Y40Y	taC	taT	1	1	B.31	0.003731
ORF7a	40	Y40Y	taC	taT	1	1	B.40	0.000364
ORF7a	40	Y40Y	taC	taT	1	1	B.55	0.00295
ORF7a	40	Y40H	Tac	Cac	1	1	C.1.2	0.004255
ORF7a	40	Y40X	taC	taA	1	1	C.37	0.000116
ORF7a	40	Y40Y	taC	taT	1	1	C.5	0.090909
ORF7a	40	Y40H	Tac	Cac	1	1	D.2	0.000075
ORF7a	40	Y40F	tAc	tTc	1	1	D.2	0.000075
ORF7a	40	Y40Y	taC	taT	1	1	N.4	0.004255
ORF7a	40	Y40Y	taC	taT	1	1	N.5	0.001767
ORF7a	40	Y40C	tAc	tGc	1	1	P.1	0.000016
ORF7a	40	Y40S	tAc	tCc	1	1	P.1.1	0.000318
ORF7a	40	Y40H	Tac	Cac	1	1	P.1.14	0.000048
ORF7a	40	Y40H	Tac	Cac	1	1	P.1.15	0.000232
ORF7a	40	Y40del	TAC	---	1	1	P.1.15	0.000232
ORF7a	40	Y40del	TAC	---	1	1	P.1.16	0.000374
ORF7a	40	Y40C	tAc	tGc	1	1	P.1.16	0.000374
ORF7a	40	Y40Y	taC	taT	1	1	P.1.17	0.000162
ORF7a	40	Y40del1	Tac	-ac	1	1	P.1.4	0.000977
ORF7a	40	Y40del	TAC	---	1	1	P.2	0.000187
ORF7a	40	Y40Y	taC	taT	1	1	P.3	0.001595
ORF7a	40	Y40H	Tac	Cac	1	1	Q.8	0.000165
ORF7a	40	Y40H	Tac	Cac	1	1	R.1	0.00009
ORF7a	40	Y40H	Tac	Cac	1	1	S.1	0.00495
ORF7a	40	Y40Y	taC	taT	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.