CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 20

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
S	20	T20N		nonsyn	aCc	aAc	112479	112270	0.998142	21620-21622
S	20	T20N		nonsyn	aCC	aAT	112479	209	0.00185812	21620-21622
S	20	T20T		syn	acC	acT	32402	30753	0.949108	21620-21622
S	20	T20T		syn	acC	acA	32402	1544	0.0476514	21620-21622
S	20	T20T		syn	acC	acG	32402	105	0.00324054	21620-21622
S	20	T20I		nonsyn	aCc	aTc	10994	10947	0.995725	21620-21622
S	20	T20I		nonsyn	aCC	aTT	10994	44	0.00400218	21620-21622
S	20	T20I		nonsyn	aCC	aTA	10994	3	0.000272876	21620-21622
S	20	T20A		nonsyn	Acc	Gcc	323	322	0.996904	21620-21622
S	20	T20A		nonsyn	AcC	GcT	323	1	0.00309598	21620-21622
S	20	T20P		nonsyn	Acc	Ccc	190	189	0.994737	21620-21622
S	20	T20P		nonsyn	AcC	CcA	190	1	0.00526316	21620-21622
S	20	T20del		del	ACC	---	151	151	1	21620-21622
S	20	T20S		nonsyn	aCc	aGc	135	117	0.866667	21620-21622
S	20	T20S		nonsyn	Acc	Tcc	135	17	0.125926	21620-21622
S	20	T20S		nonsyn	AcC	TcT	135	1	0.00740741	21620-21622
S	20	T20K		nonsyn	aCC	aAA	15	15	1	21620-21622
S	20	T20F		nonsyn	ACc	TTc	6	5	0.833333	21620-21622
S	20	T20F		nonsyn	ACC	TTT	6	1	0.166667	21620-21622
S	20	T20del1		del	aCc	a-c	4	3	0.75	21620-21622
S	20	T20del1		del	ACc	G-c	4	1	0.25	21620-21622
S	20	T20V		nonsyn	ACc	GTc	1	1	1	21620-21622
S	20	T20H		nonsyn	ACc	CAc	1	1	1	21620-21622

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
S	20	T20N	aCc	aAc	112270	112479	All	0.021473
S	20	T20N	aCC	aAT	209	112479	All	0.00004
S	20	T20N	aCc	aAc	61403	61537	P.1	0.967342
S	20	T20N	aCC	aAT	134	61537	P.1	0.002111
S	20	T20T	acC	acT	30753	32402	All	0.005882
S	20	T20T	acC	acA	1544	32402	All	0.000295
S	20	T20T	acC	acG	105	32402	All	0.00002
S	20	T20N	aCc	aAc	20820	20830	P.1.14	0.99522
S	20	T20N	aCC	aAT	10	20830	P.1.14	0.000478
S	20	T20T	acC	acT	15999	15999	AY.75	0.896303
S	20	T20I	aCc	aTc	10947	10994	All	0.002094
S	20	T20I	aCC	aTT	44	10994	All	0.000008
S	20	T20I	aCC	aTA	3	10994	All	0.000001
S	20	T20N	aCc	aAc	6068	6069	P.1.17	0.981559
S	20	T20N	aCC	aAT	1	6069	P.1.17	0.000162
S	20	T20N	aCc	aAc	4205	4211	P.1.15	0.976998
S	20	T20N	aCC	aAT	6	4211	P.1.15	0.001394
S	20	T20T	acC	acT	3886	3888	AY.75.1	0.700685
S	20	T20T	acC	acA	2	3888	AY.75.1	0.000361
S	20	T20N	aCc	aAc	3654	3660	P.1.10	0.98464
S	20	T20N	aCC	aAT	6	3660	P.1.10	0.001617
S	20	T20N	aCc	aAc	3090	3101	P.1.7	0.98659
S	20	T20N	aCC	aAT	11	3101	P.1.7	0.003512
S	20	T20I	aCc	aTc	3033	3045	B.1.1.7	0.002715
S	20	T20I	aCC	aTT	12	3045	B.1.1.7	0.000011
S	20	T20N	aCc	aAc	2945	2948	P.1.1	0.935515
S	20	T20N	aCC	aAT	3	2948	P.1.1	0.000953
S	20	T20N	aCc	aAc	2522	2550	P.1.16	0.943509
S	20	T20N	aCC	aAT	28	2550	P.1.16	0.010475
S	20	T20T	acC	acT	2265	2482	B.1.1.7	0.002028
S	20	T20T	acC	acA	215	2482	B.1.1.7	0.000192
S	20	T20T	acC	acG	2	2482	B.1.1.7	0.000002
S	20	T20I	aCc	aTc	1920	1923	B.1.1.176	0.843585
S	20	T20I	aCC	aTT	3	1923	B.1.1.176	0.001318
S	20	T20N	aCc	aAc	1789	1793	P.1.12	0.865924
S	20	T20N	aCC	aAT	4	1793	P.1.12	0.001936
S	20	T20T	acC	acT	1696	1729	B.1.617.2	0.006386
S	20	T20T	acC	acA	32	1729	B.1.617.2	0.00012
S	20	T20T	acC	acG	1	1729	B.1.617.2	0.000004
S	20	T20N	aCc	aAc	1141	1141	P.1.17.1	0.99825
S	20	T20N	aCc	aAc	1079	1079	P.1.13	0.969452
S	20	T20I	aCc	aTc	1068	1071	B.1.588	0.971793
S	20	T20I	aCC	aTA	3	1071	B.1.588	0.00273
S	20	T20N	aCc	aAc	1017	1022	P.1.4	0.993164
S	20	T20N	aCC	aAT	5	1022	P.1.4	0.004883
S	20	T20N	aCc	aAc	856	856	P.1.2	0.989595
S	20	T20T	acC	acT	759	770	B.1.427	0.038328
S	20	T20T	acC	acA	11	770	B.1.427	0.000555
S	20	T20T	acC	acT	679	731	AY.4	0.001057
S	20	T20T	acC	acA	50	731	AY.4	0.000078
S	20	T20T	acC	acG	2	731	AY.4	0.000003
S	20	T20T	acC	acA	650	650	B.1.524	0.914205
S	20	T20I	aCc	aTc	623	624	AY.103	0.003868
S	20	T20I	aCC	aTT	1	624	AY.103	0.000006
S	20	T20T	acC	acT	538	538	AY.105	0.345981
S	20	T20I	aCc	aTc	520	521	AY.4	0.000809
S	20	T20I	aCC	aTT	1	521	AY.4	0.000002
S	20	T20N	aCc	aAc	512	512	P.1.6	0.996109
S	20	T20T	acC	acT	430	430	AY.58	0.3902
S	20	T20T	acC	acT	421	427	AY.47	0.013095
S	20	T20T	acC	acA	6	427	AY.47	0.000187
S	20	T20T	acC	acT	391	425	AY.103	0.002428
S	20	T20T	acC	acA	34	425	AY.103	0.000211
S	20	T20T	acC	acT	370	406	AY.25	0.002225
S	20	T20T	acC	acA	35	406	AY.25	0.000211
S	20	T20T	acC	acG	1	406	AY.25	0.000006
S	20	T20I	aCc	aTc	375	376	B.1.160	0.011695
S	20	T20I	aCC	aTT	1	376	B.1.160	0.000031
S	20	T20I	aCc	aTc	374	375	B.1.2	0.003293
S	20	T20I	aCC	aTT	1	375	B.1.2	0.000009
S	20	T20A	Acc	Gcc	322	323	All	0.000062
S	20	T20A	AcC	GcT	1	323	All	0
S	20	T20I	aCc	aTc	314	317	B.1.617.2	0.001182
S	20	T20I	aCC	aTT	3	317	B.1.617.2	0.000011
S	20	T20T	acC	acT	191	271	B.1.2	0.001682
S	20	T20T	acC	acA	60	271	B.1.2	0.000528
S	20	T20T	acC	acG	20	271	B.1.2	0.000176
S	20	T20A	Acc	Gcc	220	221	AY.47	0.006843
S	20	T20A	AcC	GcT	1	221	AY.47	0.000031
S	20	T20I	aCc	aTc	221	221	AY.80	0.249436
S	20	T20N	aCc	aAc	208	208	P.1.8	0.995215
S	20	T20I	aCc	aTc	204	204	B.1	0.001869
S	20	T20N	aCc	aAc	204	204	P.1.9	0.980769
S	20	T20I	aCc	aTc	191	191	AY.43	0.000846
S	20	T20P	Acc	Ccc	189	190	All	0.000036
S	20	T20P	AcC	CcA	1	190	All	0
S	20	T20T	acC	acT	141	156	AY.4.2	0.003058
S	20	T20T	acC	acA	13	156	AY.4.2	0.000282
S	20	T20T	acC	acG	2	156	AY.4.2	0.000043
S	20	T20T	acC	acT	149	155	AY.42	0.005994
S	20	T20T	acC	acA	6	155	AY.42	0.000241
S	20	T20del	ACC	---	151	151	All	0.000029
S	20	T20P	Acc	Ccc	146	146	B.1.1.7	0.000131
S	20	T20T	acC	acT	118	144	B.1.1	0.002141
S	20	T20T	acC	acA	24	144	B.1.1	0.000435
S	20	T20T	acC	acG	2	144	B.1.1	0.000036
S	20	T20T	acC	acT	120	143	AY.44	0.00073
S	20	T20T	acC	acA	21	143	AY.44	0.000128
S	20	T20T	acC	acG	2	143	AY.44	0.000012
S	20	T20T	acC	acT	107	139	AY.43	0.000474
S	20	T20T	acC	acA	29	139	AY.43	0.000128
S	20	T20T	acC	acG	3	139	AY.43	0.000013
S	20	T20S	aCc	aGc	117	135	All	0.000022
S	20	T20S	Acc	Tcc	17	135	All	0.000003
S	20	T20S	AcC	TcT	1	135	All	0
S	20	T20T	acC	acT	94	127	B.1	0.000861
S	20	T20T	acC	acA	33	127	B.1	0.000302
S	20	T20I	aCc	aTc	126	127	B.1.1.519	0.005004
S	20	T20I	aCC	aTT	1	127	B.1.1.519	0.00004
S	20	T20I	aCc	aTc	122	122	AY.25	0.000734
S	20	T20N	aCc	aAc	106	106	P.1.10.1	0.861789
S	20	T20I	aCc	aTc	98	98	AP.1	0.147147
S	20	T20N	aCc	aAc	98	98	P.1.11	1
S	20	T20S	aCc	aGc	94	94	C.37	0.01091
S	20	T20I	aCc	aTc	91	91	AY.46	0.009471
S	20	T20T	acC	acT	89	89	AY.69	0.016614
S	20	T20T	acC	acT	89	89	B.1.561	0.035331
S	20	T20I	aCc	aTc	77	85	C.23	0.447674
S	20	T20I	aCC	aTT	8	85	C.23	0.046512
S	20	T20I	aCc	aTc	84	84	AY.44	0.000511
S	20	T20T	acC	acT	80	80	AY.118	0.005012
S	20	T20N	aCc	aAc	78	78	B.1	0.000714
S	20	T20T	acC	acT	70	70	AY.51	0.063636
S	20	T20N	aCc	aAc	64	65	B.1.1.7	0.000057
S	20	T20N	aCC	aAT	1	65	B.1.1.7	0.000001
S	20	T20T	acC	acT	65	65	B.1.258.21	0.503876
S	20	T20I	aCc	aTc	65	65	B.1.619.1	0.041693
S	20	T20T	acC	acT	50	64	B.1.429	0.001176
S	20	T20T	acC	acA	14	64	B.1.429	0.000329
S	20	T20I	aCc	aTc	63	63	C.37	0.007312
S	20	T20T	acC	acT	59	60	AY.34	0.005721
S	20	T20T	acC	acA	1	60	AY.34	0.000097
S	20	T20T	acC	acT	49	59	AY.39	0.001211
S	20	T20T	acC	acA	9	59	AY.39	0.000222
S	20	T20T	acC	acG	1	59	AY.39	0.000025
S	20	T20T	acC	acT	54	54	B.1.1.214	0.002995
S	20	T20T	acC	acT	53	53	AY.54	0.005053
S	20	T20T	acC	acT	50	52	AY.26	0.001416
S	20	T20T	acC	acA	2	52	AY.26	0.000057
S	20	T20T	acC	acT	50	51	B.1.1.519	0.001986
S	20	T20T	acC	acA	1	51	B.1.1.519	0.00004
S	20	T20T	acC	acT	47	51	B.1.177	0.000619
S	20	T20T	acC	acA	4	51	B.1.177	0.000053
S	20	T20N	aCc	aAc	50	50	B.1.1	0.000907
S	20	T20I	aCc	aTc	50	50	B.1.595	0.013048
S	20	T20T	acC	acT	49	49	B.1.177.60	0.010703
S	20	T20I	aCc	aTc	49	49	B.1.596	0.00427
S	20	T20T	acC	acG	42	48	B.1.1.284	0.004511
S	20	T20T	acC	acT	6	48	B.1.1.284	0.000644
S	20	T20T	acC	acT	46	46	B.1.1.128	0.326241
S	20	T20T	acC	acT	44	45	AY.119	0.001554
S	20	T20T	acC	acA	1	45	AY.119	0.000035
S	20	T20T	acC	acT	28	45	AY.3	0.000278
S	20	T20T	acC	acA	15	45	AY.3	0.000149
S	20	T20T	acC	acG	2	45	AY.3	0.00002
S	20	T20T	acC	acT	41	43	AY.33	0.002738
S	20	T20T	acC	acA	2	43	AY.33	0.000134
S	20	T20I	aCc	aTc	43	43	AY.4.2	0.000933
S	20	T20T	acC	acA	33	41	AY.120	0.001227
S	20	T20T	acC	acT	8	41	AY.120	0.000297
S	20	T20I	aCc	aTc	41	41	AY.29	0.000647
S	20	T20T	acC	acT	41	41	AY.99.2	0.003778
S	20	T20I	aCc	aTc	41	41	B.1.177	0.00054
S	20	T20T	acC	acT	40	40	AY.32	0.021299
S	20	T20I	aCc	aTc	40	40	B.1.526	0.00094
S	20	T20T	acC	acT	39	39	B.1.1.28	0.012138
S	20	T20I	aCc	aTc	39	39	B.1.429	0.000918
S	20	T20T	acC	acA	23	39	B.1.637	0.001681
S	20	T20T	acC	acT	16	39	B.1.637	0.001169
S	20	T20I	aCc	aTc	37	37	AY.118	0.002318
S	20	T20T	acC	acT	37	37	Q.3	0.005366
S	20	T20I	aCc	aTc	34	34	AY.102	0.000901
S	20	T20T	acC	acT	34	34	AY.85	0.014524
S	20	T20I	aCc	aTc	34	34	B.1.1	0.000617
S	20	T20T	acC	acT	34	34	B.1.1.369	0.015172
S	20	T20T	acC	acT	33	33	B.1.518	0.388235
S	20	T20I	aCc	aTc	31	31	AY.3.1	0.002643
S	20	T20T	acC	acT	30	30	B.1.369	0.008557
S	20	T20T	acC	acT	22	29	B.1.160	0.000686
S	20	T20T	acC	acA	7	29	B.1.160	0.000218
S	20	T20T	acC	acA	29	29	B.1.177.10	0.025461
S	20	T20T	acC	acA	25	29	B.1.258.17	0.002599
S	20	T20T	acC	acT	4	29	B.1.258.17	0.000416
S	20	T20N	aCc	aAc	29	29	B.1.497	0.009128
S	20	T20N	aCc	aAc	29	29	P.1.3	1
S	20	T20I	aCc	aTc	28	28	AY.71	0.013302
S	20	T20N	aCc	aAc	28	28	B.1.617.2	0.000105
S	20	T20A	Acc	Gcc	26	26	AY.29	0.00041
S	20	T20I	aCc	aTc	26	26	AY.39	0.000642
S	20	T20T	acC	acT	26	26	AY.70	0.005421
S	20	T20T	acC	acT	26	26	B.1.221	0.001847
S	20	T20I	aCc	aTc	26	26	B.1.588.1	1
S	20	T20N	aCc	aAc	25	25	B.1.1.528	0.120192
S	20	T20T	acC	acT	24	24	AD.2	0.005255
S	20	T20I	aCc	aTc	24	24	AY.88	0.02122
S	20	T20T	acC	acT	24	24	B.1.351	0.000713
S	20	T20I	aCc	aTc	24	24	B.1.575	0.007282
S	20	T20T	acC	acT	18	24	B.1.621	0.001593
S	20	T20T	acC	acA	6	24	B.1.621	0.000531
S	20	T20N	aCc	aAc	24	24	P.1.10.2	1
S	20	T20T	acC	acT	22	23	AY.62	0.009586
S	20	T20T	acC	acA	1	23	AY.62	0.000436
S	20	T20T	acC	acT	18	23	AY.9.2	0.000661
S	20	T20T	acC	acA	5	23	AY.9.2	0.000184
S	20	T20T	acC	acT	22	23	B.1.526	0.000517
S	20	T20T	acC	acG	1	23	B.1.526	0.000024
S	20	T20T	acC	acA	12	22	C.37	0.001393
S	20	T20T	acC	acT	10	22	C.37	0.001161
S	20	T20I	aCc	aTc	21	21	AY.26	0.000595
S	20	T20I	aCc	aTc	21	21	AY.3	0.000209
S	20	T20del	ACC	---	21	21	AY.39.1	0.000832
S	20	T20T	acC	acT	21	21	AY.5.4	0.005811
S	20	T20N	aCc	aAc	21	21	B.1.1.28	0.006536
S	20	T20T	acC	acT	21	21	B.1.234	0.002771
S	20	T20N	aCc	aAc	21	21	C.37	0.002437
S	20	T20T	acC	acT	20	20	AY.20	0.000777
S	20	T20I	aCc	aTc	20	20	B.1.1.122	0.909091
S	20	T20I	aCc	aTc	20	20	B.1.1.284	0.002148
S	20	T20T	acC	acT	20	20	B.1.243	0.001392
S	20	T20I	aCc	aTc	20	20	B.1.258	0.001331
S	20	T20I	aCc	aTc	19	19	AY.20	0.000738
S	20	T20T	acC	acT	19	19	B.1.1.218	0.146154
S	20	T20I	aCc	aTc	18	18	AY.47	0.00056
S	20	T20T	acC	acT	18	18	B.1.1.222	0.003672
S	20	T20del	ACC	---	18	18	B.1.1.7	0.000016
S	20	T20T	acC	acT	18	18	B.1.206	0.014682
S	20	T20T	acC	acT	17	18	B.1.240	0.003665
S	20	T20T	acC	acG	1	18	B.1.240	0.000216
S	20	T20I	aCc	aTc	17	17	AY.120	0.000632
S	20	T20T	acC	acT	17	17	AY.98.1	0.000823
S	20	T20I	aCc	aTc	17	17	B.1.1.28	0.005291
S	20	T20I	aCc	aTc	17	17	B.1.258.17	0.001768
S	20	T20T	acC	acT	15	16	AY.39.1	0.000594
S	20	T20T	acC	acA	1	16	AY.39.1	0.00004
S	20	T20K	aCC	aAA	15	15	All	0.000003
S	20	T20I	aCc	aTc	15	15	AY.100	0.00069
S	20	T20T	acC	acT	13	15	AY.23	0.000907
S	20	T20T	acC	acA	2	15	AY.23	0.000139
S	20	T20N	aCc	aAc	15	15	AY.43	0.000066
S	20	T20T	acC	acT	15	15	AY.74	0.001735
S	20	T20T	acC	acT	10	15	B.1.258	0.000665
S	20	T20T	acC	acA	5	15	B.1.258	0.000333
S	20	T20T	acC	acT	14	14	AY.117	0.001183
S	20	T20T	acC	acT	14	14	AY.24	0.006034
S	20	T20I	aCc	aTc	14	14	AY.46.5	0.002778
S	20	T20T	acC	acT	14	14	B.1.1.486	0.022082
S	20	T20A	Acc	Gcc	14	14	B.1.1.7	0.000013
S	20	T20T	acC	acT	14	14	B.1.177.18	0.016241
S	20	T20I	aCc	aTc	14	14	B.1.36	0.002043
S	20	T20T	acC	acT	14	14	B.1.517	0.005978
S	20	T20A	Acc	Gcc	14	14	B.1.617.2	0.000053
S	20	T20T	acC	acA	14	14	B.6.6	0.012444
S	20	T20N	aCc	aAc	14	14	Q.1	0.001769
S	20	T20T	acC	acT	13	13	AY.46.6	0.000939
S	20	T20I	aCc	aTc	13	13	B.1.1.201	0.317073
S	20	T20I	aCc	aTc	13	13	B.1.221	0.000923
S	20	T20I	aCc	aTc	13	13	B.1.509	0.011255
S	20	T20N	aCc	aAc	13	13	P.1.5	1
S	20	T20T	acC	acT	12	13	P.2	0.00224
S	20	T20T	acC	acA	1	13	P.2	0.000187
S	20	T20I	aCc	aTc	12	12	AY.23	0.000837
S	20	T20I	aCc	aTc	12	12	AY.33	0.000801
S	20	T20T	acC	acT	12	12	B.1.497	0.003777
S	20	T20I	aCc	aTc	11	12	C.36.3	0.006239
S	20	T20I	aCC	aTT	1	12	C.36.3	0.000567
S	20	T20I	aCc	aTc	12	12	Q.2	0.007362
S	20	T20T	acC	acT	11	11	AU.3	0.023207
S	20	T20T	acC	acT	11	11	AY.93	0.003004
S	20	T20T	acC	acA	8	11	B.1.1.216	0.007124
S	20	T20T	acC	acT	3	11	B.1.1.216	0.002671
S	20	T20I	aCc	aTc	11	11	B.1.111	0.012926
S	20	T20T	acC	acT	11	11	B.1.177.21	0.000841
S	20	T20T	acC	acT	7	11	B.1.596	0.00061
S	20	T20T	acC	acA	3	11	B.1.596	0.000261
S	20	T20T	acC	acG	1	11	B.1.596	0.000087
S	20	T20T	acC	acT	11	11	B.1.617.1	0.001419
S	20	T20T	acC	acT	6	10	AY.100	0.000276
S	20	T20T	acC	acA	4	10	AY.100	0.000184
S	20	T20T	acC	acG	10	10	AY.41	0.002939
S	20	T20I	aCc	aTc	10	10	AY.5	0.000206
S	20	T20I	aCc	aTc	10	10	B.1.351	0.000297
S	20	T20T	acC	acT	10	10	B.1.582	0.004907
S	20	T20I	aCc	aTc	10	10	Q.8	0.001649
S	20	T20N	aCc	aAc	9	9	AY.103	0.000056
S	20	T20I	aCc	aTc	9	9	AY.42	0.000362
S	20	T20I	aCc	aTc	9	9	AY.6	0.00037
S	20	T20T	acC	acT	8	9	AY.61	0.000838
S	20	T20T	acC	acA	1	9	AY.61	0.000105
S	20	T20I	aCc	aTc	9	9	B.1.1.174	0.030405
S	20	T20T	acC	acT	8	9	B.1.466.2	0.00313
S	20	T20T	acC	acA	1	9	B.1.466.2	0.000391
S	20	T20I	aCc	aTc	9	9	B.1.567	0.03
S	20	T20N	aCc	aAc	9	9	P.2	0.00168
S	20	T20T	acC	acT	9	9	P.5	0.123288
S	20	T20P	Acc	Ccc	9	9	Q.8	0.001484
S	20	T20T	acC	acT	5	9	Q.8	0.000825
S	20	T20T	acC	acA	3	9	Q.8	0.000495
S	20	T20T	acC	acG	1	9	Q.8	0.000165
S	20	T20del	ACC	---	8	8	AY.33	0.000534
S	20	T20N	aCc	aAc	8	8	AY.4	0.000012
S	20	T20T	acC	acT	6	8	AY.45	0.00073
S	20	T20T	acC	acA	2	8	AY.45	0.000243
S	20	T20I	aCc	aTc	8	8	AY.46.6	0.000578
S	20	T20I	aCC	aTT	8	8	AY.75	0.000448
S	20	T20I	aCc	aTc	8	8	B.1.1.214	0.000444
S	20	T20I	aCc	aTc	8	8	B.1.1.33	0.003367
S	20	T20T	acC	acT	8	8	B.1.1.434	0.002788
S	20	T20K	aCC	aAA	8	8	B.1.1.7	0.000007
S	20	T20I	aCc	aTc	8	8	B.1.177.60	0.001747
S	20	T20T	acC	acT	7	8	B.1.214.2	0.004197
S	20	T20T	acC	acA	1	8	B.1.214.2	0.0006
S	20	T20T	acC	acT	7	8	B.1.36	0.001021
S	20	T20T	acC	acA	1	8	B.1.36	0.000146
S	20	T20T	acC	acT	8	8	D.2	0.0006
S	20	T20T	acC	acT	8	8	Q.1	0.001011
S	20	T20T	acC	acA	6	7	AY.121	0.000812
S	20	T20T	acC	acT	1	7	AY.121	0.000135
S	20	T20I	aCc	aTc	7	7	AY.46.4	0.001152
S	20	T20del	ACC	---	7	7	AY.59	0.003708
S	20	T20T	acC	acT	7	7	B	0.000895
S	20	T20del	ACC	---	7	7	B.1.1	0.000127
S	20	T20I	aCc	aTc	6	7	B.1.1.306	0.00263
S	20	T20I	aCC	aTT	1	7	B.1.1.306	0.000438
S	20	T20T	acC	acT	7	7	B.1.1.458	0.291667
S	20	T20T	acC	acG	7	7	B.1.1.464	0.010309
S	20	T20I	aCc	aTc	7	7	B.1.177.21	0.000535
S	20	T20S	Acc	Tcc	7	7	B.1.2	0.000062
S	20	T20I	aCc	aTc	7	7	B.1.525	0.000792
S	20	T20I	aCc	aTc	7	7	B.1.561	0.002779
S	20	T20T	acC	acT	7	7	B.1.93	0.006536
S	20	T20T	acC	acT	6	6	A.2.5	0.002994
S	20	T20F	ACc	TTc	5	6	All	0.000001
S	20	T20F	ACC	TTT	1	6	All	0
S	20	T20I	aCc	aTc	6	6	AS.1	0.057143
S	20	T20del	ACC	---	6	6	AY.103	0.000037
S	20	T20T	acC	acT	6	6	AY.108	0.006615
S	20	T20I	aCc	aTc	6	6	AY.113	0.000854
S	20	T20I	aCc	aTc	6	6	AY.39.1	0.000238
S	20	T20A	Acc	Gcc	6	6	AY.4	0.000009
S	20	T20A	Acc	Gcc	6	6	AY.43	0.000027
S	20	T20I	aCc	aTc	6	6	AY.73	0.003992
S	20	T20I	aCc	aTc	6	6	AY.9.1	0.000502
S	20	T20T	acC	acA	4	6	AY.9.1	0.000335
S	20	T20T	acC	acT	2	6	AY.9.1	0.000167
S	20	T20T	acC	acT	6	6	AY.98	0.000474
S	20	T20P	Acc	Ccc	5	6	B.1.1	0.000091
S	20	T20P	AcC	CcA	1	6	B.1.1	0.000018
S	20	T20I	aCc	aTc	5	6	B.1.1.1	0.001633
S	20	T20I	aCC	aTT	1	6	B.1.1.1	0.000327
S	20	T20T	acC	acA	6	6	B.1.1.253	0.015038
S	20	T20T	acC	acT	6	6	B.1.1.298	0.005172
S	20	T20T	acC	acA	5	6	B.1.1.316	0.004625
S	20	T20T	acC	acT	1	6	B.1.1.316	0.000925
S	20	T20I	aCc	aTc	6	6	B.1.243	0.000418
S	20	T20I	aCc	aTc	6	6	B.1.351.2	0.001815
S	20	T20T	acC	acT	6	6	B.1.397	0.029126
S	20	T20I	aCc	aTc	6	6	B.1.427	0.000303
S	20	T20del	ACC	---	6	6	B.1.525	0.000679
S	20	T20T	acC	acT	6	6	B.1.567	0.02
S	20	T20T	acC	acT	5	6	B.1.595	0.001305
S	20	T20T	acC	acG	1	6	B.1.595	0.000261
S	20	T20del	ACC	---	6	6	B.1.617.2	0.000023
S	20	T20T	acC	acA	4	5	AY.27	0.000259
S	20	T20T	acC	acT	1	5	AY.27	0.000065
S	20	T20N	aCc	aAc	5	5	AY.29	0.000079
S	20	T20del	ACC	---	5	5	AY.4	0.000008
S	20	T20del	ACC	---	5	5	AY.43	0.000022
S	20	T20del	ACC	---	5	5	AY.44	0.00003
S	20	T20N	aCc	aAc	5	5	AY.44	0.00003
S	20	T20I	aCc	aTc	5	5	AY.45	0.000608
S	20	T20I	aCc	aTc	5	5	AY.54	0.000477
S	20	T20T	acC	acT	3	5	AY.6	0.000123
S	20	T20T	acC	acA	2	5	AY.6	0.000082
S	20	T20I	aCc	aTc	5	5	AY.83	0.008621
S	20	T20T	acC	acT	5	5	B.1.1.1	0.001633
S	20	T20T	acC	acT	5	5	B.1.1.228	0.015244
S	20	T20T	acC	acT	5	5	B.1.1.231	0.01548
S	20	T20T	acC	acT	5	5	B.1.1.317	0.002058
S	20	T20I	aCc	aTc	5	5	B.1.1.37	0.000964
S	20	T20T	acC	acT	3	5	B.1.1.70	0.001023
S	20	T20T	acC	acA	2	5	B.1.1.70	0.000682
S	20	T20I	aCc	aTc	5	5	B.1.177.4	0.001055
S	20	T20T	acC	acT	5	5	B.1.177.56	0.003338
S	20	T20T	acC	acT	4	5	B.1.177.75	0.004162
S	20	T20T	acC	acA	1	5	B.1.177.75	0.001041
S	20	T20S	aCc	aGc	5	5	B.1.177.81	0.000947
S	20	T20T	acC	acT	5	5	B.1.192	0.046296
S	20	T20I	aCc	aTc	5	5	B.1.234	0.00066
S	20	T20I	aCc	aTc	5	5	B.1.240	0.001078
S	20	T20T	acC	acT	5	5	B.1.367	0.003962
S	20	T20T	acC	acT	5	5	B.1.575	0.001517
S	20	T20N	aCc	aAc	5	5	B.1.596	0.000436
S	20	T20T	acC	acT	5	5	B.1.600	0.02924
S	20	T20I	aCc	aTc	5	5	Q.1	0.000632
S	20	T20I	aCc	aTc	5	5	R.1	0.00045
S	20	T20T	acC	acT	3	4	A.23.1	0.002113
S	20	T20T	acC	acA	1	4	A.23.1	0.000704
S	20	T20del1	aCc	a-c	3	4	All	0.000001
S	20	T20del1	ACc	G-c	1	4	All	0
S	20	T20T	acC	acA	3	4	AY.102	0.00008
S	20	T20T	acC	acT	1	4	AY.102	0.000027
S	20	T20A	Acc	Gcc	4	4	AY.103	0.000025
S	20	T20del	ACC	---	4	4	AY.120	0.000149
S	20	T20N	aCc	aAc	4	4	AY.20	0.000155
S	20	T20del	ACC	---	4	4	AY.39	0.000099
S	20	T20T	acC	acT	4	4	AY.67	0.001857
S	20	T20I	aCc	aTc	4	4	AY.7.1	0.000451
S	20	T20T	acC	acT	4	4	AY.73	0.002661
S	20	T20del	ACC	---	4	4	AY.75	0.000224
S	20	T20S	aCc	aGc	4	4	AY.85	0.001709
S	20	T20I	aCc	aTc	4	4	AY.98	0.000316
S	20	T20N	aCc	aAc	4	4	B.1.1.161	0.014134
S	20	T20T	acC	acT	4	4	B.1.1.170	0.004988
S	20	T20I	aCc	aTc	4	4	B.1.1.216	0.003562
S	20	T20I	aCc	aTc	4	4	B.1.1.220	0.007435
S	20	T20T	acC	acT	3	4	B.1.1.33	0.001263
S	20	T20T	acC	acA	1	4	B.1.1.33	0.000421
S	20	T20T	acC	acT	3	4	B.1.177.7	0.000495
S	20	T20T	acC	acA	1	4	B.1.177.7	0.000165
S	20	T20T	acC	acT	4	4	B.1.177.81	0.000757
S	20	T20T	acC	acT	4	4	B.1.177.87	0.002911
S	20	T20P	Acc	Ccc	4	4	B.1.2	0.000035
S	20	T20T	acC	acA	3	4	B.1.351.2	0.000908
S	20	T20T	acC	acT	1	4	B.1.351.2	0.000303
S	20	T20T	acC	acA	4	4	B.1.36.1	0.004561
S	20	T20T	acC	acT	4	4	B.1.36.17	0.001976
S	20	T20T	acC	acT	4	4	B.1.36.29	0.002069
S	20	T20I	aCc	aTc	4	4	B.1.369	0.001141
S	20	T20I	aCc	aTc	4	4	B.1.396	0.002823
S	20	T20F	ACc	TTc	4	4	B.1.427	0.000202
S	20	T20I	aCc	aTc	4	4	B.1.448	0.010499
S	20	T20T	acC	acT	4	4	B.1.543	0.04
S	20	T20T	acC	acT	4	4	B.1.551	0.005161
S	20	T20T	acC	acT	4	4	B.1.564	0.001704
S	20	T20I	aCc	aTc	4	4	B.1.621	0.000354
S	20	T20N	aCc	aAc	4	4	B.1.621	0.000354
S	20	T20N	aCc	aAc	4	4	B.1.636	0.026846
S	20	T20T	acC	acT	4	4	L.3	0.014184
S	20	T20S	aCc	aGc	4	4	P.1	0.000063
S	20	T20I	aCc	aTc	4	4	P.2	0.000747
S	20	T20I	aCc	aTc	4	4	Q.4	0.001819
S	20	T20T	acC	acT	4	4	Q.7	0.004444
S	20	T20I	aCc	aTc	4	4	W.2	0.019324
S	20	T20T	acC	acT	3	3	A.2	0.001985
S	20	T20A	Acc	Gcc	3	3	AY.100	0.000138
S	20	T20I	aCc	aTc	3	3	AY.111	0.000549
S	20	T20I	aCc	aTc	3	3	AY.29.1	0.000662
S	20	T20A	Acc	Gcc	3	3	AY.3	0.00003
S	20	T20del	ACC	---	3	3	AY.3	0.00003
S	20	T20T	acC	acA	3	3	AY.3.1	0.000256
S	20	T20T	acC	acA	3	3	AY.36	0.000445
S	20	T20N	aCc	aAc	3	3	AY.39	0.000074
S	20	T20T	acC	acT	3	3	AY.4.1	0.002212
S	20	T20T	acC	acT	3	3	AY.4.5	0.000322
S	20	T20P	Acc	Ccc	3	3	AY.43	0.000013
S	20	T20P	Acc	Ccc	3	3	AY.47	0.000093
S	20	T20T	acC	acA	2	3	AY.5	0.000041
S	20	T20T	acC	acG	1	3	AY.5	0.000021
S	20	T20I	aCc	aTc	3	3	AY.7	0.000588
S	20	T20del	ACC	---	3	3	AY.75.1	0.000541
S	20	T20I	aCc	aTc	3	3	AY.9	0.000203
S	20	T20T	acC	acT	2	3	AY.9	0.000135
S	20	T20T	acC	acG	1	3	AY.9	0.000068
S	20	T20A	Acc	Gcc	3	3	B.1	0.000027
S	20	T20A	Acc	Gcc	3	3	B.1.1	0.000054
S	20	T20I	aCc	aTc	3	3	B.1.1.222	0.000612
S	20	T20T	acC	acA	2	3	B.1.1.277	0.001517
S	20	T20T	acC	acT	1	3	B.1.1.277	0.000759
S	20	T20N	aCc	aAc	3	3	B.1.1.348	0.002389
S	20	T20T	acC	acT	3	3	B.1.1.348	0.002389
S	20	T20T	acC	acT	3	3	B.1.1.409	0.008499
S	20	T20T	acC	acT	3	3	B.1.1.416	0.002715
S	20	T20N	aCc	aAc	3	3	B.1.1.519	0.000119
S	20	T20S	AcC	TcT	1	3	B.1.1.7	0.000001
S	20	T20S	aCc	aGc	1	3	B.1.1.7	0.000001
S	20	T20S	Acc	Tcc	1	3	B.1.1.7	0.000001
S	20	T20T	acC	acT	3	3	B.1.110.3	0.002155
S	20	T20T	acC	acT	2	3	B.1.160.16	0.001859
S	20	T20T	acC	acA	1	3	B.1.160.16	0.000929
S	20	T20P	Acc	Ccc	3	3	B.1.177	0.00004
S	20	T20T	acC	acT	3	3	B.1.177.83	0.004444
S	20	T20I	aCc	aTc	3	3	B.1.195	0.015075
S	20	T20I	aCc	aTc	3	3	B.1.214.2	0.001799
S	20	T20I	aCc	aTc	3	3	B.1.241	0.002435
S	20	T20I	aCc	aTc	3	3	B.1.258.3	0.005025
S	20	T20N	aCc	aAc	3	3	B.1.351	0.000089
S	20	T20I	aCc	aTc	3	3	B.1.36.31	0.005254
S	20	T20T	acC	acT	3	3	B.1.525	0.000339
S	20	T20I	aCc	aTc	3	3	B.1.582	0.001472
S	20	T20N	aCc	aAc	3	3	B.1.600	0.017544
S	20	T20I	aCc	aTc	3	3	B.1.609	0.001438
S	20	T20K	aCC	aAA	3	3	B.1.617.2	0.000011
S	20	T20I	aCc	aTc	3	3	B.1.637	0.000219
S	20	T20I	aCc	aTc	3	3	D.2	0.000225
S	20	T20del	ACC	---	3	3	P.1	0.000047
S	20	T20K	aCC	aAA	3	3	P.1	0.000047
S	20	T20P	Acc	Ccc	3	3	P.5	0.041096
S	20	T20N	aCc	aAc	2	2	A.2.5	0.000998
S	20	T20I	aCc	aTc	2	2	AY.10	0.00106
S	20	T20I	aCc	aTc	2	2	AY.101	0.000981
S	20	T20N	aCc	aAc	2	2	AY.102	0.000053
S	20	T20T	acC	acA	1	2	AY.106	0.000335
S	20	T20T	acC	acT	1	2	AY.106	0.000335
S	20	T20T	acC	acT	1	2	AY.109	0.00074
S	20	T20T	acC	acA	1	2	AY.109	0.00074
S	20	T20T	acC	acT	2	2	AY.111	0.000366
S	20	T20I	aCc	aTc	2	2	AY.114	0.000462
S	20	T20T	acC	acA	2	2	AY.116	0.000574
S	20	T20I	aCc	aTc	2	2	AY.116.1	0.000623
S	20	T20I	aCc	aTc	2	2	AY.119	0.000071
S	20	T20T	acC	acT	2	2	AY.120.1	0.000642
S	20	T20I	aCc	aTc	2	2	AY.121	0.000271
S	20	T20P	Acc	Ccc	2	2	AY.20	0.000078
S	20	T20N	aCc	aAc	2	2	AY.23	0.000139
S	20	T20del	ACC	---	2	2	AY.25	0.000012
S	20	T20I	aCc	aTc	2	2	AY.27	0.000129
S	20	T20T	acC	acT	2	2	AY.30	0.000791
S	20	T20I	aCc	aTc	2	2	AY.35	0.000466
S	20	T20T	acC	acT	2	2	AY.35	0.000466
S	20	T20T	acC	acT	2	2	AY.39.2	0.003082
S	20	T20I	aCc	aTc	2	2	AY.40	0.001929
S	20	T20S	Acc	Tcc	1	2	AY.44	0.000006
S	20	T20S	aCc	aGc	1	2	AY.44	0.000006
S	20	T20N	aCc	aAc	2	2	AY.45	0.000243
S	20	T20T	acC	acA	1	2	AY.46	0.000104
S	20	T20T	acC	acT	1	2	AY.46	0.000104
S	20	T20T	acC	acT	2	2	AY.46.2	0.001271
S	20	T20T	acC	acT	2	2	AY.46.5	0.000397
S	20	T20T	acC	acA	2	2	AY.60	0.001876
S	20	T20I	aCc	aTc	2	2	AY.61	0.00021
S	20	T20N	aCc	aAc	2	2	AY.67	0.000929
S	20	T20I	aCc	aTc	2	2	AY.69	0.000373
S	20	T20I	aCC	aTT	1	2	AY.75.1	0.00018
S	20	T20I	aCc	aTc	1	2	AY.75.1	0.00018
S	20	T20I	aCc	aTc	2	2	AY.84	0.000875
S	20	T20I	aCc	aTc	2	2	AY.9.2	0.000073
S	20	T20N	aCc	aAc	2	2	AY.9.2	0.000073
S	20	T20T	acC	acT	2	2	AY.91	0.001461
S	20	T20I	aCc	aTc	2	2	AY.95	0.001522
S	20	T20I	aCc	aTc	2	2	AY.98.1	0.000097
S	20	T20N	aCc	aAc	2	2	AY.99.2	0.000184
S	20	T20P	Acc	Ccc	2	2	B.1	0.000018
S	20	T20del	ACC	---	2	2	B.1	0.000018
S	20	T20S	aCc	aGc	1	2	B.1.1	0.000018
S	20	T20S	Acc	Tcc	1	2	B.1.1	0.000018
S	20	T20I	aCc	aTc	2	2	B.1.1.161	0.007067
S	20	T20I	aCc	aTc	2	2	B.1.1.207	0.002364
S	20	T20T	acC	acT	2	2	B.1.1.273	0.013514
S	20	T20P	Acc	Ccc	2	2	B.1.1.28	0.000622
S	20	T20T	acC	acT	2	2	B.1.1.318	0.000604
S	20	T20I	aCc	aTc	2	2	B.1.1.326	0.003521
S	20	T20N	aCc	aAc	2	2	B.1.1.332	0.0625
S	20	T20I	aCc	aTc	2	2	B.1.1.389	0.012121
S	20	T20I	aCc	aTc	2	2	B.1.1.39	0.001019
S	20	T20T	acC	acT	2	2	B.1.1.39	0.001019
S	20	T20I	aCc	aTc	2	2	B.1.1.466	0.017391
S	20	T20T	acC	acT	2	2	B.1.1.63	0.000772
S	20	T20del1	aCc	a-c	2	2	B.1.1.7	0.000002
S	20	T20I	aCc	aTc	2	2	B.1.1.70	0.000682
S	20	T20I	aCc	aTc	2	2	B.1.103	0.038462
S	20	T20T	acC	acT	2	2	B.1.118	0.013423
S	20	T20T	acC	acT	2	2	B.1.126	0.002551
S	20	T20T	acC	acA	1	2	B.1.157	0.002985
S	20	T20T	acC	acT	1	2	B.1.157	0.002985
S	20	T20A	Acc	Gcc	2	2	B.1.160	0.000062
S	20	T20T	acC	acT	2	2	B.1.160.8	0.002577
S	20	T20T	acC	acT	2	2	B.1.177.15	0.001262
S	20	T20I	aCc	aTc	2	2	B.1.177.2	0.009091
S	20	T20T	acC	acG	1	2	B.1.177.33	0.001645
S	20	T20T	acC	acT	1	2	B.1.177.33	0.001645
S	20	T20I	aCc	aTc	2	2	B.1.177.35	0.001382
S	20	T20T	acC	acT	2	2	B.1.177.57	0.000562
S	20	T20I	aCc	aTc	2	2	B.1.177.58	0.002663
S	20	T20I	aCc	aTc	2	2	B.1.177.7	0.00033
S	20	T20N	aCc	aAc	2	2	B.1.177.73	0.001133
S	20	T20I	aCc	aTc	2	2	B.1.177.75	0.002081
S	20	T20I	aCc	aTc	2	2	B.1.177.82	0.000955
S	20	T20T	acC	acT	2	2	B.1.177.86	0.000367
S	20	T20I	aCc	aTc	2	2	B.1.210	0.004264
S	20	T20T	acC	acT	2	2	B.1.22	0.002635
S	20	T20I	aCc	aTc	2	2	B.1.221.4	0.008333
S	20	T20T	acC	acT	2	2	B.1.232	0.001075
S	20	T20I	aCc	aTc	2	2	B.1.258.4	0.006897
S	20	T20T	acC	acT	2	2	B.1.313	0.013158
S	20	T20I	aCc	aTc	2	2	B.1.36.10	0.009569
S	20	T20T	acC	acT	2	2	B.1.36.18	0.00084
S	20	T20N	aCc	aAc	2	2	B.1.36.27	0.001527
S	20	T20N	aCc	aAc	2	2	B.1.369	0.00057
S	20	T20T	acC	acA	1	2	B.1.391	0.001127
S	20	T20T	acC	acT	1	2	B.1.391	0.001127
S	20	T20T	acC	acT	2	2	B.1.396	0.001411
S	20	T20del	ACC	---	2	2	B.1.429	0.000047
S	20	T20T	acC	acT	2	2	B.1.466.1	0.014388
S	20	T20T	acC	acT	2	2	B.1.468	0.011429
S	20	T20T	acC	acT	2	2	B.1.470	0.002809
S	20	T20N	aCc	aAc	2	2	B.1.517	0.000854
S	20	T20N	aCc	aAc	2	2	B.1.526	0.000047
S	20	T20T	acC	acT	2	2	B.1.549	0.014388
S	20	T20I	aCc	aTc	2	2	B.1.551	0.002581
S	20	T20T	acC	acT	2	2	B.1.565	0.001621
S	20	T20T	acC	acT	2	2	B.1.576	0.001813
S	20	T20I	aCc	aTc	2	2	B.1.621.1	0.001012
S	20	T20T	acC	acT	2	2	B.1.623	0.001073
S	20	T20T	acC	acT	2	2	B.40	0.000729
S	20	T20N	aCc	aAc	2	2	C.37.1	0.005236
S	20	T20T	acC	acT	2	2	P.1	0.000032
S	20	T20I	aCc	aTc	2	2	P.1.1	0.000635
S	20	T20T	acC	acT	2	2	Q.4	0.00091
S	20	T20T	acC	acT	2	2	Y.1	0.025641
S	20	T20P	Acc	Ccc	1	1	A.2	0.000662
S	20	T20del	ACC	---	1	1	A.2.4	0.003367
S	20	T20I	aCc	aTc	1	1	A.23.1	0.000704
S	20	T20T	acC	acT	1	1	A.27	0.001656
S	20	T20I	aCc	aTc	1	1	A.4	0.012821
S	20	T20I	aCc	aTc	1	1	AE.8	0.000489
S	20	T20V	ACc	GTc	1	1	All	0
S	20	T20H	ACc	CAc	1	1	All	0
S	20	T20T	acC	acT	1	1	AU.1	0.001266
S	20	T20T	acC	acT	1	1	AY.10	0.00053
S	20	T20N	aCc	aAc	1	1	AY.100	0.000046
S	20	T20del	ACC	---	1	1	AY.100	0.000046
S	20	T20del	ACC	---	1	1	AY.101	0.00049
S	20	T20S	aCc	aGc	1	1	AY.103	0.000006
S	20	T20I	aCc	aTc	1	1	AY.104	0.001984
S	20	T20T	acC	acA	1	1	AY.113	0.000142
S	20	T20T	acC	acT	1	1	AY.114	0.000231
S	20	T20del	ACC	---	1	1	AY.116.1	0.000311
S	20	T20A	Acc	Gcc	1	1	AY.117	0.000085
S	20	T20S	aCc	aGc	1	1	AY.120.1	0.000321
S	20	T20T	acC	acT	1	1	AY.120.2	0.001285
S	20	T20I	aCc	aTc	1	1	AY.120.2.1	0.000498
S	20	T20T	acC	acA	1	1	AY.120.2.1	0.000498
S	20	T20T	acC	acT	1	1	AY.13	0.000161
S	20	T20I	aCc	aTc	1	1	AY.14	0.000088
S	20	T20I	aCc	aTc	1	1	AY.16	0.00038
S	20	T20T	acC	acT	1	1	AY.16	0.00038
S	20	T20T	acC	acT	1	1	AY.19	0.00114
S	20	T20T	acC	acT	1	1	AY.23.1	0.000417
S	20	T20N	aCc	aAc	1	1	AY.25	0.000006
S	20	T20S	aCc	aGc	1	1	AY.26	0.000028
S	20	T20N	aCc	aAc	1	1	AY.26	0.000028
S	20	T20del	ACC	---	1	1	AY.29	0.000016
S	20	T20T	acC	acT	1	1	AY.29	0.000016
S	20	T20N	aCc	aAc	1	1	AY.3	0.00001
S	20	T20I	aCc	aTc	1	1	AY.32	0.000532
S	20	T20del	ACC	---	1	1	AY.32	0.000532
S	20	T20I	aCc	aTc	1	1	AY.34	0.000097
S	20	T20N	aCc	aAc	1	1	AY.34.1	0.00051
S	20	T20I	aCc	aTc	1	1	AY.36	0.000148
S	20	T20T	acC	acA	1	1	AY.39.1.1	0.000725
S	20	T20I	aCc	aTc	1	1	AY.39.2	0.001541
S	20	T20P	Acc	Ccc	1	1	AY.4	0.000002
S	20	T20A	Acc	Gcc	1	1	AY.4.2	0.000022
S	20	T20T	acC	acT	1	1	AY.4.2.1	0.000149
S	20	T20I	aCc	aTc	1	1	AY.4.4	0.000409
S	20	T20del	ACC	---	1	1	AY.42	0.00004
S	20	T20N	aCc	aAc	1	1	AY.42	0.00004
S	20	T20A	Acc	Gcc	1	1	AY.44	0.000006
S	20	T20del	ACC	---	1	1	AY.46	0.000104
S	20	T20T	acC	acT	1	1	AY.46.1	0.001027
S	20	T20I	aCc	aTc	1	1	AY.46.1	0.001027
S	20	T20T	acC	acT	1	1	AY.46.4	0.000165
S	20	T20S	Acc	Tcc	1	1	AY.5	0.000021
S	20	T20N	aCc	aAc	1	1	AY.5.3	0.000337
S	20	T20I	aCc	aTc	1	1	AY.5.3	0.000337
S	20	T20T	acC	acA	1	1	AY.5.3	0.000337
S	20	T20I	aCC	aTT	1	1	AY.51	0.000909
S	20	T20T	acC	acT	1	1	AY.52	0.000814
S	20	T20T	acC	acA	1	1	AY.53	0.000288
S	20	T20del	ACC	---	1	1	AY.54	0.000095
S	20	T20I	aCc	aTc	1	1	AY.56	0.001605
S	20	T20I	aCc	aTc	1	1	AY.57	0.000656
S	20	T20del	ACC	---	1	1	AY.6	0.000041
S	20	T20A	Acc	Gcc	1	1	AY.60	0.000938
S	20	T20T	acC	acT	1	1	AY.65	0.000533
S	20	T20T	acC	acA	1	1	AY.66	0.00107
S	20	T20del	ACC	---	1	1	AY.68	0.000274
S	20	T20T	acC	acT	1	1	AY.68	0.000274
S	20	T20N	aCc	aAc	1	1	AY.68	0.000274
S	20	T20T	acC	acT	1	1	AY.7.1	0.000113
S	20	T20I	aCc	aTc	1	1	AY.70	0.000209
S	20	T20I	aCc	aTc	1	1	AY.72	0.001361
S	20	T20I	aCc	aTc	1	1	AY.74	0.000116
S	20	T20A	Acc	Gcc	1	1	AY.75.1	0.00018
S	20	T20S	Acc	Tcc	1	1	AY.78	0.001541
S	20	T20I	aCc	aTc	1	1	AY.79	0.001211
S	20	T20I	aCc	aTc	1	1	AY.82	0.001357
S	20	T20T	acC	acA	1	1	AY.84	0.000437
S	20	T20I	aCc	aTc	1	1	AY.86	0.00083
S	20	T20I	aCc	aTc	1	1	AY.87	0.000833
S	20	T20T	acC	acA	1	1	AY.88	0.000884
S	20	T20del	ACC	---	1	1	AY.9.2	0.000037
S	20	T20I	aCc	aTc	1	1	AY.91	0.00073
S	20	T20T	acC	acT	1	1	AY.92	0.000287
S	20	T20I	aCc	aTc	1	1	AY.92	0.000287
S	20	T20A	Acc	Gcc	1	1	AY.95	0.000761
S	20	T20T	acC	acT	1	1	AY.96	0.002075
S	20	T20I	aCc	aTc	1	1	AY.97	0.001701
S	20	T20N	aCc	aAc	1	1	AY.98	0.000079
S	20	T20A	Acc	Gcc	1	1	AY.98	0.000079
S	20	T20del	ACC	---	1	1	AY.98	0.000079
S	20	T20A	Acc	Gcc	1	1	AY.98.1	0.000048
S	20	T20N	aCc	aAc	1	1	AY.98.1	0.000048
S	20	T20I	aCc	aTc	1	1	AY.99.2	0.000092
S	20	T20A	Acc	Gcc	1	1	B	0.000128
S	20	T20I	aCc	aTc	1	1	B	0.000128
S	20	T20N	aCc	aAc	1	1	B	0.000128
S	20	T20V	ACc	GTc	1	1	B	0.000128
S	20	T20S	Acc	Tcc	1	1	B	0.000128
S	20	T20S	Acc	Tcc	1	1	B.1	0.000009
S	20	T20I	aCc	aTc	1	1	B.1.1.10	0.001115
S	20	T20P	Acc	Ccc	1	1	B.1.1.117	0.009709
S	20	T20N	aCc	aAc	1	1	B.1.1.117	0.009709
S	20	T20K	aCC	aAA	1	1	B.1.1.141	0.002012
S	20	T20T	acC	acT	1	1	B.1.1.141	0.002012
S	20	T20T	acC	acT	1	1	B.1.1.15	0.013514
S	20	T20I	aCc	aTc	1	1	B.1.1.153	0.001095
S	20	T20T	acC	acA	1	1	B.1.1.157	0.000913
S	20	T20T	acC	acA	1	1	B.1.1.161	0.003534
S	20	T20I	aCc	aTc	1	1	B.1.1.172	0.018182
S	20	T20T	acC	acT	1	1	B.1.1.174	0.003378
S	20	T20I	aCc	aTc	1	1	B.1.1.177	0.019231
S	20	T20T	acC	acA	1	1	B.1.1.189	0.001513
S	20	T20T	acC	acT	1	1	B.1.1.197	0.037037
S	20	T20I	aCc	aTc	1	1	B.1.1.198	0.001468
S	20	T20T	acC	acT	1	1	B.1.1.204	0.00304
S	20	T20N	aCc	aAc	1	1	B.1.1.220	0.001859
S	20	T20I	aCc	aTc	1	1	B.1.1.228	0.003049
S	20	T20I	aCc	aTc	1	1	B.1.1.232	0.001815
S	20	T20T	acC	acT	1	1	B.1.1.234	0.012048
S	20	T20N	aCc	aAc	1	1	B.1.1.236	0.006897
S	20	T20T	acC	acT	1	1	B.1.1.241	0.00207
S	20	T20T	acC	acT	1	1	B.1.1.25	0.000569
S	20	T20T	acC	acT	1	1	B.1.1.263	0.001558
S	20	T20I	aCc	aTc	1	1	B.1.1.268	0.014925
S	20	T20I	aCc	aTc	1	1	B.1.1.277	0.000759
S	20	T20A	Acc	Gcc	1	1	B.1.1.284	0.000107
S	20	T20I	aCc	aTc	1	1	B.1.1.289	0.002083
S	20	T20I	aCc	aTc	1	1	B.1.1.291	0.000742
S	20	T20T	acC	acT	1	1	B.1.1.294	0.001266
S	20	T20I	aCc	aTc	1	1	B.1.1.301	0.001179
S	20	T20I	aCc	aTc	1	1	B.1.1.304	0.002809
S	20	T20T	acC	acA	1	1	B.1.1.306	0.000438
S	20	T20del	ACC	---	1	1	B.1.1.306	0.000438
S	20	T20I	aCc	aTc	1	1	B.1.1.311	0.000358
S	20	T20del	ACC	---	1	1	B.1.1.315	0.008475
S	20	T20T	acC	acT	1	1	B.1.1.315	0.008475
S	20	T20I	aCc	aTc	1	1	B.1.1.317	0.000412
S	20	T20T	acC	acT	1	1	B.1.1.323	0.014085
S	20	T20N	aCc	aAc	1	1	B.1.1.33	0.000421
S	20	T20I	aCc	aTc	1	1	B.1.1.347	0.018182
S	20	T20T	acC	acT	1	1	B.1.1.349	0.010309
S	20	T20T	acC	acT	1	1	B.1.1.37	0.000193
S	20	T20T	acC	acT	1	1	B.1.1.371	0.010417
S	20	T20T	acC	acT	1	1	B.1.1.376	0.005952
S	20	T20T	acC	acT	1	1	B.1.1.379	0.03125
S	20	T20I	aCc	aTc	1	1	B.1.1.386	0.066667
S	20	T20T	acC	acT	1	1	B.1.1.388	0.045455
S	20	T20T	acC	acT	1	1	B.1.1.389	0.006061
S	20	T20N	aCc	aAc	1	1	B.1.1.39	0.00051
S	20	T20I	aCc	aTc	1	1	B.1.1.396	0.045455
S	20	T20T	acC	acT	1	1	B.1.1.397	0.002252
S	20	T20I	aCc	aTc	1	1	B.1.1.398	0.003226
S	20	T20del	ACC	---	1	1	B.1.1.401	0.066667
S	20	T20I	aCc	aTc	1	1	B.1.1.402	0.011111
S	20	T20F	ACC	TTT	1	1	B.1.1.411	0.014706
S	20	T20I	aCc	aTc	1	1	B.1.1.411	0.014706
S	20	T20T	acC	acT	1	1	B.1.1.413	0.006897
S	20	T20T	acC	acT	1	1	B.1.1.420	0.001006
S	20	T20T	acC	acT	1	1	B.1.1.433	0.001425
S	20	T20T	acC	acT	1	1	B.1.1.44	0.00241
S	20	T20T	acC	acT	1	1	B.1.1.448	0.002033
S	20	T20del	ACC	---	1	1	B.1.1.46	0.004367
S	20	T20T	acC	acT	1	1	B.1.1.49	0.017544
S	20	T20T	acC	acT	1	1	B.1.1.51	0.001718
S	20	T20T	acC	acA	1	1	B.1.1.518	0.006329
S	20	T20T	acC	acA	1	1	B.1.1.59	0.006494
S	20	T20T	acC	acT	1	1	B.1.1.61	0.008772
S	20	T20F	ACc	TTc	1	1	B.1.1.7	0.000001
S	20	T20T	acC	acA	1	1	B.1.1.8	0.003584
S	20	T20S	Acc	Tcc	1	1	B.1.110.3	0.000718
S	20	T20T	acC	acT	1	1	B.1.111	0.001175
S	20	T20T	acC	acT	1	1	B.1.12	0.008
S	20	T20I	aCc	aTc	1	1	B.1.127	0.002198
S	20	T20T	acC	acT	1	1	B.1.139	0.000733
S	20	T20I	aCc	aTc	1	1	B.1.160.28	0.002924
S	20	T20T	acC	acT	1	1	B.1.160.28	0.002924
S	20	T20T	acC	acT	1	1	B.1.162	0.005025
S	20	T20A	Acc	Gcc	1	1	B.1.177	0.000013
S	20	T20N	aCc	aAc	1	1	B.1.177	0.000013
S	20	T20I	aCc	aTc	1	1	B.1.177.12	0.000152
S	20	T20I	aCc	aTc	1	1	B.1.177.16	0.000664
S	20	T20I	aCc	aTc	1	1	B.1.177.18	0.00116
S	20	T20N	aCc	aAc	1	1	B.1.177.31	0.011494
S	20	T20T	acC	acA	1	1	B.1.177.39	0.015385
S	20	T20I	aCc	aTc	1	1	B.1.177.41	0.0025
S	20	T20T	acC	acT	1	1	B.1.177.43	0.001477
S	20	T20T	acC	acT	1	1	B.1.177.45	0.000381
S	20	T20S	aCc	aGc	1	1	B.1.177.50	0.004695
S	20	T20T	acC	acT	1	1	B.1.177.53	0.002392
S	20	T20T	acC	acT	1	1	B.1.177.54	0.000606
S	20	T20A	Acc	Gcc	1	1	B.1.177.54	0.000606
S	20	T20del	ACC	---	1	1	B.1.177.6	0.000977
S	20	T20del	ACC	---	1	1	B.1.177.68	0.015152
S	20	T20T	acC	acT	1	1	B.1.177.69	0.001484
S	20	T20N	aCc	aAc	1	1	B.1.177.7	0.000165
S	20	T20I	aCc	aTc	1	1	B.1.177.73	0.000566
S	20	T20I	aCc	aTc	1	1	B.1.177.80	0.001912
S	20	T20I	aCc	aTc	1	1	B.1.177.81	0.000189
S	20	T20del	ACC	---	1	1	B.1.177.83	0.001481
S	20	T20N	aCc	aAc	1	1	B.1.177.86	0.000183
S	20	T20I	aCc	aTc	1	1	B.1.178	0.02381
S	20	T20N	aCc	aAc	1	1	B.1.2	0.000009
S	20	T20del	ACC	---	1	1	B.1.2	0.000009
S	20	T20N	aCc	aAc	1	1	B.1.214	0.003663
S	20	T20del	ACC	---	1	1	B.1.221	0.000071
S	20	T20S	Acc	Tcc	1	1	B.1.221	0.000071
S	20	T20I	aCc	aTc	1	1	B.1.223	0.002778
S	20	T20T	acC	acT	1	1	B.1.235	0.002519
S	20	T20I	aCc	aTc	1	1	B.1.239	0.001221
S	20	T20T	acC	acT	1	1	B.1.241	0.000812
S	20	T20T	acC	acT	1	1	B.1.258.11	0.000396
S	20	T20T	acC	acT	1	1	B.1.260	0.003344
S	20	T20del1	aCc	a-c	1	1	B.1.289	0.00266
S	20	T20I	aCc	aTc	1	1	B.1.293	0.0125
S	20	T20T	acC	acT	1	1	B.1.305	0.002151
S	20	T20N	aCc	aAc	1	1	B.1.311	0.000275
S	20	T20I	aCc	aTc	1	1	B.1.311	0.000275
S	20	T20T	acC	acA	1	1	B.1.311	0.000275
S	20	T20I	aCc	aTc	1	1	B.1.320	0.001245
S	20	T20N	aCc	aAc	1	1	B.1.349	0.000715
S	20	T20T	acC	acT	1	1	B.1.350	0.002933
S	20	T20del	ACC	---	1	1	B.1.351	0.00003
S	20	T20S	aCc	aGc	1	1	B.1.351	0.00003
S	20	T20A	Acc	Gcc	1	1	B.1.351	0.00003
S	20	T20del1	ACc	G-c	1	1	B.1.351	0.00003
S	20	T20I	aCc	aTc	1	1	B.1.351.3	0.000876
S	20	T20T	acC	acA	1	1	B.1.351.3	0.000876
S	20	T20del	ACC	---	1	1	B.1.36	0.000146
S	20	T20T	acC	acA	1	1	B.1.36.16	0.001425
S	20	T20I	aCc	aTc	1	1	B.1.36.18	0.00042
S	20	T20I	aCc	aTc	1	1	B.1.36.2	0.010753
S	20	T20T	acC	acT	1	1	B.1.36.22	0.001208
S	20	T20I	aCc	aTc	1	1	B.1.36.27	0.000763
S	20	T20I	aCc	aTc	1	1	B.1.36.29	0.000517
S	20	T20N	aCc	aAc	1	1	B.1.36.29	0.000517
S	20	T20T	acC	acA	1	1	B.1.36.38	0.001642
S	20	T20T	acC	acT	1	1	B.1.36.39	0.002217
S	20	T20I	aCc	aTc	1	1	B.1.36.8	0.001
S	20	T20T	acC	acA	1	1	B.1.362	0.001541
S	20	T20I	aCc	aTc	1	1	B.1.366	0.004878
S	20	T20N	aCc	aAc	1	1	B.1.375	0.00082
S	20	T20I	aCc	aTc	1	1	B.1.377	0.004566
S	20	T20N	aCc	aAc	1	1	B.1.399	0.001934
S	20	T20I	aCc	aTc	1	1	B.1.404	0.001302
S	20	T20A	Acc	Gcc	1	1	B.1.409	0.000781
S	20	T20T	acC	acT	1	1	B.1.409	0.000781
S	20	T20N	aCc	aAc	1	1	B.1.415	0.014286
S	20	T20T	acC	acA	1	1	B.1.416.1	0.001563
S	20	T20I	aCc	aTc	1	1	B.1.422	0.000812
S	20	T20T	acC	acT	1	1	B.1.425	0.002994
S	20	T20T	acC	acT	1	1	B.1.426	0.001009
S	20	T20del	ACC	---	1	1	B.1.427	0.00005
S	20	T20S	aCc	aGc	1	1	B.1.429	0.000024
S	20	T20P	Acc	Ccc	1	1	B.1.429	0.000024
S	20	T20N	aCc	aAc	1	1	B.1.429	0.000024
S	20	T20A	Acc	Gcc	1	1	B.1.433	0.003195
S	20	T20T	acC	acT	1	1	B.1.438.1	0.000107
S	20	T20I	aCc	aTc	1	1	B.1.470	0.001404
S	20	T20del	ACC	---	1	1	B.1.497	0.000315
S	20	T20I	aCc	aTc	1	1	B.1.507	0.011236
S	20	T20N	aCc	aAc	1	1	B.1.525	0.000113
S	20	T20del	ACC	---	1	1	B.1.526	0.000024
S	20	T20N	aCc	aAc	1	1	B.1.533	0.009615
S	20	T20I	aCc	aTc	1	1	B.1.541	0.004425
S	20	T20I	aCc	aTc	1	1	B.1.544	0.006024
S	20	T20T	acC	acT	1	1	B.1.546	0.003704
S	20	T20T	acC	acT	1	1	B.1.560	0.00463
S	20	T20T	acC	acT	1	1	B.1.568	0.001111
S	20	T20N	aCc	aAc	1	1	B.1.577	0.000687
S	20	T20T	acC	acT	1	1	B.1.577	0.000687
S	20	T20I	aCc	aTc	1	1	B.1.577	0.000687
S	20	T20T	acC	acT	1	1	B.1.597	0.00463
S	20	T20N	aCc	aAc	1	1	B.1.609	0.000479
S	20	T20T	acC	acT	1	1	B.1.612	0.002653
S	20	T20I	aCc	aTc	1	1	B.1.617.1	0.000129
S	20	T20S	Acc	Tcc	1	1	B.1.617.2	0.000004
S	20	T20T	acC	acT	1	1	B.1.619.1	0.000641
S	20	T20del	ACC	---	1	1	B.1.620	0.000946
S	20	T20N	aCc	aAc	1	1	B.1.620	0.000946
S	20	T20A	Acc	Gcc	1	1	B.1.623	0.000536
S	20	T20N	aCc	aAc	1	1	B.1.623	0.000536
S	20	T20I	aCc	aTc	1	1	B.1.623	0.000536
S	20	T20T	acC	acT	1	1	B.1.625	0.002353
S	20	T20I	aCc	aTc	1	1	B.1.625	0.002353
S	20	T20I	aCc	aTc	1	1	B.1.628	0.000352
S	20	T20I	aCc	aTc	1	1	B.1.630	0.005236
S	20	T20I	aCc	aTc	1	1	B.1.631	0.003367
S	20	T20T	acC	acT	1	1	B.1.631	0.003367
S	20	T20T	acC	acT	1	1	B.1.78	0.008547
S	20	T20T	acC	acT	1	1	B.1.8	0.001972
S	20	T20T	acC	acT	1	1	B.1.9.4	0.006135
S	20	T20N	aCc	aAc	1	1	B.11	0.005128
S	20	T20T	acC	acT	1	1	B.23	0.002924
S	20	T20I	aCc	aTc	1	1	B.23	0.002924
S	20	T20N	aCc	aAc	1	1	B.3	0.000831
S	20	T20T	acC	acT	1	1	B.3	0.000831
S	20	T20I	aCc	aTc	1	1	B.3.1	0.001658
S	20	T20I	aCc	aTc	1	1	B.34	0.013699
S	20	T20T	acC	acT	1	1	B.39	0.002331
S	20	T20A	Acc	Gcc	1	1	B.4	0.002208
S	20	T20I	aCc	aTc	1	1	B.4.1	0.018868
S	20	T20A	Acc	Gcc	1	1	B.6.6	0.000889
S	20	T20del	ACC	---	1	1	B.61	0.005747
S	20	T20T	acC	acT	1	1	C.1	0.002392
S	20	T20I	aCc	aTc	1	1	C.1.2	0.004255
S	20	T20N	aCc	aAc	1	1	C.16	0.00106
S	20	T20N	aCc	aAc	1	1	C.35	0.000774
S	20	T20I	aCc	aTc	1	1	C.35	0.000774
S	20	T20T	acC	acT	1	1	C.36	0.000911
S	20	T20del	ACC	---	1	1	C.36.3	0.000567
S	20	T20T	acC	acT	1	1	C.36.3	0.000567
S	20	T20P	Acc	Ccc	1	1	C.4	0.01
S	20	T20P	Acc	Ccc	1	1	D.2	0.000075
S	20	T20T	acC	acT	1	1	N.10	0.029412
S	20	T20H	ACc	CAc	1	1	P.1	0.000016
S	20	T20I	aCc	aTc	1	1	P.1	0.000016
S	20	T20S	aCc	aGc	1	1	P.1.17	0.000162
S	20	T20T	acC	acA	1	1	P.3	0.001595
S	20	T20N	aCc	aAc	1	1	P.7	0.004367
S	20	T20P	Acc	Ccc	1	1	Q.1	0.000126
S	20	T20N	aCc	aAc	1	1	Q.3	0.000145
S	20	T20N	aCc	aAc	1	1	Q.4	0.000455
S	20	T20T	acC	acT	1	1	R.1	0.00009
S	20	T20T	acC	acT	1	1	U.2	0.008772

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.