CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 26

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	26	P26S		nonsyn	Cct	Tct	124887	124884	0.999976	21638-21640
S	26	P26S		nonsyn	CcT	TcC	124887	3	0.0000240217	21638-21640
S	26	P26L		nonsyn	cCt	cTt	3957	3951	0.998484	21638-21640
S	26	P26L		nonsyn	cCT	cTG	3957	4	0.00101087	21638-21640
S	26	P26L		nonsyn	CCT	TTG	3957	2	0.000505433	21638-21640
S	26	P26H		nonsyn	cCt	cAt	531	531	1	21638-21640
S	26	P26P		syn	ccT	ccC	372	310	0.833333	21638-21640
S	26	P26P		syn	ccT	ccA	372	34	0.0913979	21638-21640
S	26	P26P		syn	ccT	ccG	372	28	0.0752688	21638-21640
S	26	P26R		nonsyn	cCt	cGt	175	175	1	21638-21640
S	26	P26F		nonsyn	CCt	TTt	163	163	1	21638-21640
S	26	P26del		del	CCT	---	117	117	1	21638-21640
S	26	P26T		nonsyn	Cct	Act	74	74	1	21638-21640
S	26	P26Y		nonsyn	CCt	TAt	9	9	1	21638-21640
S	26	P26A		nonsyn	Cct	Gct	8	7	0.875	21638-21640
S	26	P26A		nonsyn	CcT	GcG	8	1	0.125	21638-21640
S	26	P26del1		del	ccT	cc-	7	7	1	21638-21640
S	26	P26Q		nonsyn	cCT	cAG	2	2	1	21638-21640
S	26	P26X		nonsyn	CCT	TAG	2	2	1	21638-21640
S	26	P26del2		del	cCT	c--	2	2	1	21638-21640
S	26	P26C		nonsyn	CCt	TGt	1	1	1	21638-21640
S	26	P26G		nonsyn	CCT	GGA	1	1	1	21638-21640

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	26	P26S	Cct	Tct	124884	124887	All	0.023886
S	26	P26S	CcT	TcC	3	124887	All	0.000001
S	26	P26S	Cct	Tct	61937	61940	P.1	0.975755
S	26	P26S	CcT	TcC	3	61940	P.1	0.000047
S	26	P26S	Cct	Tct	20838	20838	P.1.14	0.99608
S	26	P26S	Cct	Tct	6080	6080	P.1.17	0.9835
S	26	P26S	Cct	Tct	4197	4197	P.1.15	0.975139
S	26	P26S	Cct	Tct	4096	4096	B.1.429	0.096374
S	26	P26L	cCt	cTt	3951	3957	All	0.000756
S	26	P26L	cCT	cTG	4	3957	All	0.000001
S	26	P26L	CCT	TTG	2	3957	All	0
S	26	P26S	Cct	Tct	3660	3660	P.1.10	0.986257
S	26	P26S	Cct	Tct	3055	3055	P.1.7	0.975415
S	26	P26S	Cct	Tct	2957	2957	P.1.1	0.939327
S	26	P26S	Cct	Tct	2542	2542	P.1.16	0.950991
S	26	P26S	Cct	Tct	1802	1802	P.1.12	0.872217
S	26	P26S	Cct	Tct	1273	1273	B.1.1.7	0.00114
S	26	P26S	Cct	Tct	1141	1141	P.1.17.1	0.99825
S	26	P26S	Cct	Tct	1080	1080	P.1.13	0.97035
S	26	P26S	Cct	Tct	1029	1029	AY.4	0.001602
S	26	P26S	Cct	Tct	1023	1023	P.1.4	0.999023
S	26	P26S	Cct	Tct	1021	1021	B.1.620	0.965941
S	26	P26S	Cct	Tct	994	994	AY.4.3	0.8367
S	26	P26S	Cct	Tct	858	858	P.1.2	0.991908
S	26	P26L	cCt	cTt	636	637	AY.103	0.003949
S	26	P26L	cCT	cTG	1	637	AY.103	0.000006
S	26	P26H	cCt	cAt	531	531	All	0.000102
S	26	P26S	Cct	Tct	512	512	P.1.6	0.996109
S	26	P26L	cCt	cTt	444	444	B.1.1.7	0.000397
S	26	P26S	Cct	Tct	423	423	B.1.36.36	0.254666
S	26	P26P	ccT	ccC	310	372	All	0.000059
S	26	P26P	ccT	ccA	34	372	All	0.000007
S	26	P26P	ccT	ccG	28	372	All	0.000005
S	26	P26S	Cct	Tct	370	370	B.1.177.57	0.103962
S	26	P26S	Cct	Tct	332	332	B.1.2	0.002923
S	26	P26L	cCt	cTt	319	319	AY.4	0.000496
S	26	P26L	cCt	cTt	276	276	B.1.1.372	0.190083
S	26	P26S	Cct	Tct	268	268	B.1.617.2	0.001009
S	26	P26L	cCt	cTt	215	215	B.1.258.17	0.022354
S	26	P26S	Cct	Tct	212	212	B.1	0.001942
S	26	P26S	Cct	Tct	208	208	P.1.8	0.995215
S	26	P26S	Cct	Tct	204	204	P.1.9	0.980769
S	26	P26R	cCt	cGt	175	175	All	0.000033
S	26	P26F	CCt	TTt	163	163	All	0.000031
S	26	P26H	cCt	cAt	159	159	B.1.1.7	0.000142
S	26	P26L	cCt	cTt	158	158	B.1.351	0.004697
S	26	P26L	cCt	cTt	156	157	B.1.617.2	0.000587
S	26	P26L	cCT	cTG	1	157	B.1.617.2	0.000004
S	26	P26S	Cct	Tct	140	140	AY.103	0.000869
S	26	P26L	cCt	cTt	136	136	B.1.544	0.819277
S	26	P26S	Cct	Tct	134	134	B.1.160	0.004179
S	26	P26del	CCT	---	117	117	All	0.000022
S	26	P26S	Cct	Tct	116	116	B.1.1.420	0.1167
S	26	P26H	cCt	cAt	114	114	B.1.2	0.001004
S	26	P26R	cCt	cGt	110	110	B.1.1.7	0.000098
S	26	P26S	Cct	Tct	106	106	P.1.10.1	0.861789
S	26	P26F	CCt	TTt	103	103	P.1	0.001623
S	26	P26L	cCt	cTt	101	101	B.1.2	0.000889
S	26	P26S	Cct	Tct	99	99	B.1.1	0.001796
S	26	P26S	Cct	Tct	99	99	B.1.427	0.004999
S	26	P26S	Cct	Tct	98	98	P.1.11	1
S	26	P26S	Cct	Tct	94	94	AY.44	0.000572
S	26	P26S	Cct	Tct	94	94	B.1.526	0.002209
S	26	P26S	Cct	Tct	91	91	AY.9.1	0.007619
S	26	P26S	Cct	Tct	89	89	B.1.369	0.025385
S	26	P26L	cCt	cTt	84	84	B.1.1	0.001524
S	26	P26L	cCt	cTt	82	82	AY.43	0.000363
S	26	P26S	Cct	Tct	79	79	AY.100	0.003635
S	26	P26L	cCt	cTt	75	75	B.1.429	0.001765
S	26	P26T	Cct	Act	74	74	All	0.000014
S	26	P26L	cCt	cTt	67	67	B.1.265	0.085133
S	26	P26S	Cct	Tct	66	66	B.1.177	0.000869
S	26	P26L	cCt	cTt	63	63	AY.33	0.004207
S	26	P26L	cCt	cTt	62	62	AY.23	0.004324
S	26	P26S	Cct	Tct	61	61	AY.43	0.00027
S	26	P26L	cCt	cTt	60	60	AY.3	0.000597
S	26	P26L	cCt	cTt	59	59	AY.44	0.000359
S	26	P26L	cCt	cTt	59	59	B.1	0.00054
S	26	P26P	ccT	ccC	52	52	AZ.2	0.042693
S	26	P26L	cCt	cTt	52	52	B.1.177	0.000685
S	26	P26S	Cct	Tct	50	50	AY.25	0.000301
S	26	P26S	Cct	Tct	49	49	AY.3	0.000487
S	26	P26S	Cct	Tct	47	47	B.1.1.519	0.001866
S	26	P26H	cCt	cAt	47	47	B.1.596	0.004096
S	26	P26S	Cct	Tct	45	45	AY.120	0.001673
S	26	P26P	ccT	ccC	31	45	B.1.1.7	0.000028
S	26	P26P	ccT	ccA	13	45	B.1.1.7	0.000012
S	26	P26P	ccT	ccG	1	45	B.1.1.7	0.000001
S	26	P26F	CCt	TTt	43	43	P.1.7	0.013729
S	26	P26L	cCt	cTt	41	41	B.1.637	0.002996
S	26	P26H	cCt	cAt	40	40	B.1.177.42	0.035778
S	26	P26L	cCt	cTt	39	39	AY.5	0.000805
S	26	P26L	cCt	cTt	38	38	AY.25	0.000229
S	26	P26L	cCt	cTt	38	38	B.1.241	0.030844
S	26	P26P	ccT	ccC	37	37	AY.4	0.000058
S	26	P26S	Cct	Tct	34	34	AY.14	0.002992
S	26	P26S	Cct	Tct	34	34	AY.46.3	0.031746
S	26	P26P	ccT	ccC	33	33	AY.4.2.1	0.004917
S	26	P26S	Cct	Tct	30	30	AY.29.1	0.006615
S	26	P26H	cCt	cAt	29	29	B.1.1.50	0.019688
S	26	P26S	Cct	Tct	29	29	P.1.3	1
S	26	P26S	Cct	Tct	28	28	AY.118	0.001754
S	26	P26P	ccT	ccC	27	28	B.1.2	0.000238
S	26	P26P	ccT	ccG	1	28	B.1.2	0.000009
S	26	P26S	Cct	Tct	28	28	B.1.36.29	0.014485
S	26	P26L	cCt	cTt	28	28	B.1.577	0.019244
S	26	P26L	cCt	cTt	26	26	AY.119	0.000918
S	26	P26L	cCt	cTt	26	26	AY.46.4	0.004277
S	26	P26S	Cct	Tct	26	26	B.1.351	0.000773
S	26	P26L	cCt	cTt	25	25	AY.20	0.000972
S	26	P26P	ccT	ccC	25	25	AY.5	0.000516
S	26	P26S	Cct	Tct	25	25	B.1.1.70	0.008527
S	26	P26S	Cct	Tct	25	25	B.1.551	0.032258
S	26	P26S	Cct	Tct	25	25	B.1.637	0.001827
S	26	P26S	Cct	Tct	25	25	C.37	0.002902
S	26	P26S	Cct	Tct	24	24	P.1.10.2	1
S	26	P26L	cCt	cTt	24	24	P.2	0.004479
S	26	P26S	Cct	Tct	23	23	B.1.1.528	0.110577
S	26	P26del	CCT	---	23	23	B.1.1.7	0.000021
S	26	P26S	Cct	Tct	23	23	B.1.221	0.001634
S	26	P26S	Cct	Tct	23	23	B.1.234	0.003035
S	26	P26L	cCt	cTt	22	22	P.1	0.000347
S	26	P26H	cCt	cAt	21	21	AY.26	0.000595
S	26	P26S	Cct	Tct	20	20	AY.39	0.000494
S	26	P26P	ccT	ccC	16	20	B.1.1	0.00029
S	26	P26P	ccT	ccG	3	20	B.1.1	0.000054
S	26	P26P	ccT	ccA	1	20	B.1.1	0.000018
S	26	P26L	cCt	cTt	19	19	AY.14	0.001672
S	26	P26L	cCt	cTt	19	19	AY.7.2	0.010626
S	26	P26H	cCt	cAt	18	18	AY.111	0.003297
S	26	P26L	cCt	cTt	18	18	AY.121	0.002436
S	26	P26S	Cct	Tct	17	17	AY.45	0.002069
S	26	P26S	Cct	Tct	17	17	AY.95	0.012938
S	26	P26L	cCt	cTt	17	17	B.1.160	0.00053
S	26	P26S	Cct	Tct	17	17	B.1.160.8	0.021907
S	26	P26S	Cct	Tct	17	17	B.1.258	0.001131
S	26	P26S	Cct	Tct	17	17	B.1.596	0.001481
S	26	P26S	Cct	Tct	15	15	AY.26	0.000425
S	26	P26S	Cct	Tct	15	15	B.1.1.28	0.004669
S	26	P26S	Cct	Tct	15	15	B.1.243	0.001044
S	26	P26S	Cct	Tct	15	15	B.1.351.2	0.004539
S	26	P26H	cCt	cAt	15	15	B.1.617.2	0.000056
S	26	P26L	cCt	cTt	15	15	Q.3	0.002175
S	26	P26R	cCt	cGt	14	14	AY.25	0.000084
S	26	P26L	cCt	cTt	14	14	AY.39	0.000346
S	26	P26S	Cct	Tct	13	13	AY.119	0.000459
S	26	P26L	cCt	cTt	13	13	B.1.221	0.000923
S	26	P26L	cCt	cTt	13	13	B.1.258	0.000865
S	26	P26S	Cct	Tct	13	13	B.1.621	0.001151
S	26	P26S	Cct	Tct	13	13	P.1.5	1
S	26	P26L	cCt	cTt	12	12	AY.106	0.004019
S	26	P26L	cCt	cTt	12	12	AY.118	0.000752
S	26	P26L	cCt	cTt	12	12	AY.120	0.000446
S	26	P26L	cCt	cTt	12	12	AY.26	0.00034
S	26	P26S	Cct	Tct	12	12	AY.29	0.000189
S	26	P26T	Cct	Act	12	12	B.1	0.00011
S	26	P26P	ccT	ccA	7	12	B.1	0.000064
S	26	P26P	ccT	ccC	4	12	B.1	0.000037
S	26	P26P	ccT	ccG	1	12	B.1	0.000009
S	26	P26S	Cct	Tct	12	12	B.1.177.44	0.006227
S	26	P26P	ccT	ccG	12	12	B.1.630	0.062827
S	26	P26S	Cct	Tct	11	11	A.2.5	0.005489
S	26	P26S	Cct	Tct	11	11	AY.46.6	0.000794
S	26	P26S	Cct	Tct	11	11	AY.5	0.000227
S	26	P26H	cCt	cAt	11	11	B.1	0.000101
S	26	P26R	cCt	cGt	11	11	B.1.351	0.000327
S	26	P26S	Cct	Tct	10	10	AY.102	0.000265
S	26	P26del	CCT	---	10	10	AY.33	0.000668
S	26	P26S	Cct	Tct	10	10	AY.69	0.001867
S	26	P26L	cCt	cTt	10	10	B.1.177.75	0.010406
S	26	P26L	cCt	cTt	10	10	B.1.243	0.000696
S	26	P26L	cCt	cTt	10	10	B.1.526	0.000235
S	26	P26S	Cct	Tct	10	10	P.2	0.001866
S	26	P26Y	CCt	TAt	9	9	All	0.000002
S	26	P26L	cCt	cTt	9	9	AY.100	0.000414
S	26	P26L	cCt	cTt	9	9	AY.102	0.000239
S	26	P26R	cCt	cGt	9	9	AY.114	0.00208
S	26	P26del	CCT	---	9	9	AY.4	0.000014
S	26	P26S	Cct	Tct	9	9	AY.4.2	0.000195
S	26	P26T	Cct	Act	9	9	AY.98.1	0.000436
S	26	P26P	ccT	ccC	9	9	B.1.1.318	0.002716
S	26	P26R	cCt	cGt	9	9	B.1.229	0.087379
S	26	P26S	Cct	Tct	9	9	B.1.240	0.00194
S	26	P26A	Cct	Gct	7	8	All	0.000001
S	26	P26A	CcT	GcG	1	8	All	0
S	26	P26S	Cct	Tct	8	8	AY.110	0.000902
S	26	P26L	cCt	cTt	8	8	AY.117	0.000676
S	26	P26S	Cct	Tct	8	8	AY.117	0.000676
S	26	P26H	cCt	cAt	8	8	AY.4	0.000012
S	26	P26T	Cct	Act	8	8	AY.4	0.000012
S	26	P26S	Cct	Tct	8	8	AY.9.2	0.000294
S	26	P26S	Cct	Tct	8	8	AY.99.2	0.000737
S	26	P26S	Cct	Tct	8	8	B.1.1.214	0.000444
S	26	P26L	cCt	cTt	8	8	B.1.1.519	0.000318
S	26	P26P	ccT	ccC	7	8	B.1.1.519	0.000278
S	26	P26P	ccT	ccA	1	8	B.1.1.519	0.00004
S	26	P26P	ccT	ccC	7	8	B.1.177	0.000092
S	26	P26P	ccT	ccA	1	8	B.1.177	0.000013
S	26	P26S	Cct	Tct	8	8	B.1.438.1	0.000858
S	26	P26S	Cct	Tct	8	8	B.1.525	0.000905
S	26	P26L	cCt	cTt	8	8	B.1.596	0.000697
S	26	P26del1	ccT	cc-	7	7	All	0.000001
S	26	P26del	CCT	---	7	7	AY.103	0.000043
S	26	P26S	Cct	Tct	7	7	AY.23	0.000488
S	26	P26H	cCt	cAt	7	7	AY.23	0.000488
S	26	P26S	Cct	Tct	7	7	AY.4.5	0.000752
S	26	P26S	Cct	Tct	7	7	AY.46	0.000729
S	26	P26L	cCt	cTt	7	7	AY.61	0.000733
S	26	P26S	Cct	Tct	7	7	AY.9	0.000473
S	26	P26S	Cct	Tct	7	7	AY.98	0.000553
S	26	P26del	CCT	---	7	7	B.1.177	0.000092
S	26	P26Y	CCt	TAt	7	7	B.1.2	0.000062
S	26	P26S	Cct	Tct	7	7	B.1.589	0.05303
S	26	P26F	CCt	TTt	7	7	B.1.620	0.006623
S	26	P26L	cCt	cTt	7	7	B.40	0.00255
S	26	P26L	CCT	TTG	2	6		0.111111
S	26	P26L	cCt	cTt	2	6		0.111111
S	26	P26L	cCT	cTG	2	6		0.111111
S	26	P26H	cCt	cAt	6	6	AY.102	0.000159
S	26	P26S	Cct	Tct	6	6	AY.121	0.000812
S	26	P26T	Cct	Act	6	6	AY.3	0.00006
S	26	P26R	cCt	cGt	6	6	AY.43	0.000027
S	26	P26P	ccT	ccC	5	6	AY.44	0.00003
S	26	P26P	ccT	ccA	1	6	AY.44	0.000006
S	26	P26L	cCt	cTt	6	6	AY.47	0.000187
S	26	P26S	Cct	Tct	6	6	AY.59	0.003178
S	26	P26del	CCT	---	6	6	B.1.1	0.000109
S	26	P26S	Cct	Tct	6	6	B.1.1.416	0.00543
S	26	P26S	Cct	Tct	6	6	B.1.177.21	0.000459
S	26	P26S	Cct	Tct	6	6	B.1.177.60	0.001311
S	26	P26S	Cct	Tct	6	6	B.1.346	0.007864
S	26	P26S	Cct	Tct	6	6	B.1.36	0.000875
S	26	P26L	cCt	cTt	6	6	B.1.427	0.000303
S	26	P26L	cCt	cTt	6	6	B.1.524	0.008439
S	26	P26P	ccT	ccC	5	6	B.1.617.2	0.000019
S	26	P26P	ccT	ccA	1	6	B.1.617.2	0.000004
S	26	P26L	cCt	cTt	6	6	C.37	0.000696
S	26	P26S	Cct	Tct	5	5	AY.107	0.00233
S	26	P26S	Cct	Tct	5	5	AY.20	0.000194
S	26	P26L	cCt	cTt	5	5	AY.24	0.002155
S	26	P26S	Cct	Tct	5	5	AY.33	0.000334
S	26	P26S	Cct	Tct	5	5	AY.34	0.000485
S	26	P26L	cCt	cTt	5	5	AY.34.1	0.00255
S	26	P26S	Cct	Tct	5	5	AY.46.4	0.000823
S	26	P26H	cCt	cAt	5	5	AY.5	0.000103
S	26	P26S	Cct	Tct	5	5	AY.54	0.000477
S	26	P26S	Cct	Tct	5	5	AY.6	0.000206
S	26	P26S	Cct	Tct	5	5	AY.75.1	0.000902
S	26	P26L	cCt	cTt	5	5	AY.98	0.000395
S	26	P26S	Cct	Tct	5	5	B.1.1.48	0.014368
S	26	P26T	Cct	Act	5	5	B.1.1.7	0.000004
S	26	P26S	Cct	Tct	5	5	B.1.139	0.003666
S	26	P26S	Cct	Tct	5	5	B.1.349	0.003574
S	26	P26L	cCt	cTt	5	5	B.1.399	0.009671
S	26	P26L	cCt	cTt	5	5	B.1.466.2	0.001956
S	26	P26S	Cct	Tct	5	5	B.1.609	0.002397
S	26	P26S	Cct	Tct	5	5	R.1	0.00045
S	26	P26L	cCt	cTt	4	4	A.21	0.01108
S	26	P26S	Cct	Tct	4	4	AY.114	0.000924
S	26	P26del	CCT	---	4	4	AY.120	0.000149
S	26	P26T	Cct	Act	4	4	AY.14	0.000352
S	26	P26P	ccT	ccC	4	4	AY.25	0.000024
S	26	P26P	ccT	ccC	4	4	AY.26	0.000113
S	26	P26L	cCt	cTt	4	4	AY.29	0.000063
S	26	P26L	cCt	cTt	4	4	AY.39.1	0.000158
S	26	P26L	cCt	cTt	4	4	AY.4.2	0.000087
S	26	P26T	Cct	Act	4	4	AY.45	0.000487
S	26	P26S	Cct	Tct	4	4	AY.47	0.000124
S	26	P26S	Cct	Tct	4	4	AY.53	0.00115
S	26	P26L	cCt	cTt	4	4	AY.71	0.0019
S	26	P26S	Cct	Tct	4	4	AY.75	0.000224
S	26	P26S	Cct	Tct	4	4	AY.98.1	0.000194
S	26	P26S	Cct	Tct	4	4	B.1.1.161	0.014134
S	26	P26S	Cct	Tct	4	4	B.1.1.222	0.000816
S	26	P26S	Cct	Tct	4	4	B.1.1.317	0.001647
S	26	P26L	cCt	cTt	4	4	B.1.159	0.04878
S	26	P26S	Cct	Tct	4	4	B.1.160.16	0.003717
S	26	P26L	cCt	cTt	4	4	B.1.177.4	0.000844
S	26	P26P	ccT	ccC	4	4	B.1.177.60	0.000874
S	26	P26L	cCt	cTt	4	4	B.1.177.80	0.007648
S	26	P26S	Cct	Tct	4	4	B.1.22	0.00527
S	26	P26S	Cct	Tct	4	4	B.1.36.9	0.012862
S	26	P26L	cCt	cTt	4	4	B.1.525	0.000453
S	26	P26S	Cct	Tct	4	4	B.1.577	0.002749
S	26	P26del	CCT	---	4	4	B.1.617.2	0.000015
S	26	P26P	ccT	ccC	4	4	B.1.621	0.000354
S	26	P26L	cCt	cTt	4	4	B.1.621	0.000354
S	26	P26S	Cct	Tct	4	4	B.1.623	0.002146
S	26	P26S	Cct	Tct	4	4	B.1.636	0.026846
S	26	P26P	ccT	ccG	3	4	P.2	0.00056
S	26	P26P	ccT	ccC	1	4	P.2	0.000187
S	26	P26L	cCt	cTt	4	4	Q.1	0.000505
S	26	P26L	cCt	cTt	4	4	R.1	0.00036
S	26	P26L	cCt	cTt	3	3	A.2.5	0.001497
S	26	P26S	Cct	Tct	3	3	A.23.1	0.002113
S	26	P26S	Cct	Tct	3	3	AT.1	0.015385
S	26	P26H	cCt	cAt	3	3	AY.100	0.000138
S	26	P26P	ccT	ccG	2	3	AY.103	0.000012
S	26	P26P	ccT	ccC	1	3	AY.103	0.000006
S	26	P26L	cCt	cTt	3	3	AY.27	0.000194
S	26	P26L	cCt	cTt	3	3	AY.35	0.000699
S	26	P26S	Cct	Tct	3	3	AY.35	0.000699
S	26	P26S	Cct	Tct	3	3	AY.42	0.000121
S	26	P26P	ccT	ccC	2	3	AY.43	0.000009
S	26	P26P	ccT	ccG	1	3	AY.43	0.000004
S	26	P26L	cCt	cTt	3	3	AY.45	0.000365
S	26	P26L	cCt	cTt	3	3	AY.46	0.000312
S	26	P26L	cCt	cTt	3	3	AY.52	0.002443
S	26	P26S	Cct	Tct	3	3	AY.61	0.000314
S	26	P26R	cCt	cGt	3	3	AY.64	0.001786
S	26	P26S	Cct	Tct	3	3	AY.65	0.001599
S	26	P26L	cCt	cTt	3	3	AY.68	0.000821
S	26	P26S	Cct	Tct	3	3	AY.92	0.000862
S	26	P26S	Cct	Tct	3	3	B	0.000383
S	26	P26del	CCT	---	3	3	B.1	0.000027
S	26	P26S	Cct	Tct	3	3	B.1.1.258	0.009772
S	26	P26S	Cct	Tct	3	3	B.1.1.294	0.003797
S	26	P26S	Cct	Tct	3	3	B.1.1.297	0.006711
S	26	P26L	cCt	cTt	3	3	B.1.1.306	0.001315
S	26	P26S	Cct	Tct	3	3	B.1.1.316	0.002775
S	26	P26S	Cct	Tct	3	3	B.1.1.33	0.001263
S	26	P26S	Cct	Tct	3	3	B.1.1.348	0.002389
S	26	P26S	Cct	Tct	3	3	B.1.1.349	0.030928
S	26	P26S	Cct	Tct	3	3	B.1.1.408	0.083333
S	26	P26S	Cct	Tct	3	3	B.1.1.464	0.004418
S	26	P26S	Cct	Tct	3	3	B.1.177.73	0.001699
S	26	P26L	cCt	cTt	3	3	B.1.177.81	0.000568
S	26	P26S	Cct	Tct	3	3	B.1.239	0.003663
S	26	P26T	Cct	Act	3	3	B.1.242	0.056604
S	26	P26S	Cct	Tct	3	3	B.1.258.17	0.000312
S	26	P26L	cCt	cTt	3	3	B.1.36	0.000438
S	26	P26L	cCt	cTt	3	3	B.1.369	0.000856
S	26	P26S	Cct	Tct	3	3	B.1.396	0.002117
S	26	P26F	CCt	TTt	3	3	B.1.429	0.000071
S	26	P26S	Cct	Tct	3	3	B.1.429.1	0.036145
S	26	P26S	Cct	Tct	3	3	B.1.465	0.011407
S	26	P26S	Cct	Tct	3	3	B.1.466.2	0.001174
S	26	P26P	ccT	ccC	3	3	B.1.526	0.000071
S	26	P26S	Cct	Tct	3	3	B.1.576	0.00272
S	26	P26H	cCt	cAt	3	3	B.1.609	0.001438
S	26	P26S	Cct	Tct	3	3	B.1.93	0.002801
S	26	P26S	Cct	Tct	3	3	B.40	0.001093
S	26	P26S	Cct	Tct	3	3	C.1.2	0.012766
S	26	P26S	Cct	Tct	3	3	D.2	0.000225
S	26	P26L	cCt	cTt	3	3	N.6	0.021277
S	26	P26del	CCT	---	3	3	P.1	0.000047
S	26	P26S	Cct	Tct	3	3	Q.8	0.000495
S	26	P26X	CCT	TAG	2	2		0.111111
S	26	P26Y	CCt	TAt	2	2		0.111111
S	26	P26H	cCt	cAt	2	2		0.111111
S	26	P26Q	cCT	cAG	2	2		0.111111
S	26	P26F	CCt	TTt	2	2		0.111111
S	26	P26del2	cCT	c--	2	2	All	0
S	26	P26X	CCT	TAG	2	2	All	0
S	26	P26Q	cCT	cAG	2	2	All	0
S	26	P26P	ccT	ccC	2	2	AY.100	0.000092
S	26	P26H	cCt	cAt	2	2	AY.103	0.000012
S	26	P26L	cCt	cTt	2	2	AY.110	0.000225
S	26	P26P	ccT	ccC	2	2	AY.118	0.000125
S	26	P26L	cCt	cTt	2	2	AY.22	0.004184
S	26	P26P	ccT	ccC	2	2	AY.23	0.000139
S	26	P26del	CCT	---	2	2	AY.25	0.000012
S	26	P26P	ccT	ccC	2	2	AY.3	0.00002
S	26	P26P	ccT	ccC	2	2	AY.3.1	0.000171
S	26	P26L	cCt	cTt	2	2	AY.36	0.000296
S	26	P26S	Cct	Tct	2	2	AY.38	0.000999
S	26	P26R	cCt	cGt	2	2	AY.4	0.000003
S	26	P26T	Cct	Act	2	2	AY.4.2	0.000043
S	26	P26L	cCt	cTt	2	2	AY.4.4	0.000818
S	26	P26L	cCt	cTt	2	2	AY.4.5	0.000215
S	26	P26L	cCt	cTt	2	2	AY.40	0.001929
S	26	P26H	cCt	cAt	2	2	AY.43	0.000009
S	26	P26del	CCT	---	2	2	AY.43	0.000009
S	26	P26T	Cct	Act	2	2	AY.44	0.000012
S	26	P26H	cCt	cAt	2	2	AY.46	0.000208
S	26	P26S	Cct	Tct	2	2	AY.46.2	0.001271
S	26	P26P	ccT	ccC	2	2	AY.46.4	0.000329
S	26	P26S	Cct	Tct	2	2	AY.46.5	0.000397
S	26	P26H	cCt	cAt	2	2	AY.47	0.000062
S	26	P26L	cCt	cTt	2	2	AY.5.3	0.000675
S	26	P26L	cCt	cTt	2	2	AY.5.4	0.000553
S	26	P26L	cCt	cTt	2	2	AY.54	0.000191
S	26	P26L	cCt	cTt	2	2	AY.55	0.001835
S	26	P26S	Cct	Tct	2	2	AY.58	0.001815
S	26	P26S	Cct	Tct	2	2	AY.62	0.000871
S	26	P26L	cCt	cTt	2	2	AY.7.1	0.000225
S	26	P26L	cCt	cTt	2	2	AY.70	0.000417
S	26	P26S	Cct	Tct	2	2	AY.71	0.00095
S	26	P26L	cCt	cTt	2	2	AY.75.1	0.000361
S	26	P26S	Cct	Tct	2	2	AY.84	0.000875
S	26	P26S	Cct	Tct	2	2	AY.89	0.009804
S	26	P26L	cCt	cTt	2	2	AY.9.1	0.000167
S	26	P26L	cCt	cTt	2	2	AY.93	0.000546
S	26	P26L	cCt	cTt	2	2	AY.99.2	0.000184
S	26	P26S	Cct	Tct	2	2	B.1.1.171	0.007353
S	26	P26L	cCt	cTt	2	2	B.1.1.214	0.000111
S	26	P26H	cCt	cAt	2	2	B.1.1.219	0.01
S	26	P26S	Cct	Tct	2	2	B.1.1.220	0.003717
S	26	P26L	cCt	cTt	2	2	B.1.1.25	0.001137
S	26	P26S	Cct	Tct	2	2	B.1.1.261	0.017241
S	26	P26S	Cct	Tct	2	2	B.1.1.318	0.000604
S	26	P26S	Cct	Tct	2	2	B.1.1.332	0.0625
S	26	P26S	Cct	Tct	2	2	B.1.1.354	0.008772
S	26	P26L	cCt	cTt	2	2	B.1.1.39	0.001019
S	26	P26S	Cct	Tct	2	2	B.1.1.526	0.007092
S	26	P26del1	ccT	cc-	2	2	B.1.1.7	0.000002
S	26	P26del1	ccT	cc-	2	2	B.1.177	0.000026
S	26	P26H	cCt	cAt	2	2	B.1.177	0.000026
S	26	P26S	Cct	Tct	2	2	B.1.177.32	0.002699
S	26	P26P	ccT	ccA	2	2	B.1.177.81	0.000379
S	26	P26del	CCT	---	2	2	B.1.177.86	0.000367
S	26	P26S	Cct	Tct	2	2	B.1.177.87	0.001456
S	26	P26P	ccT	ccC	2	2	B.1.234	0.000264
S	26	P26L	cCt	cTt	2	2	B.1.240	0.000431
S	26	P26H	cCt	cAt	2	2	B.1.241	0.001623
S	26	P26T	Cct	Act	2	2	B.1.320	0.002491
S	26	P26L	cCt	cTt	2	2	B.1.348	0.036364
S	26	P26L	cCt	cTt	2	2	B.1.36.29	0.001035
S	26	P26L	cCt	cTt	2	2	B.1.400	0.000858
S	26	P26L	cCt	cTt	2	2	B.1.471	0.005464
S	26	P26del	CCT	---	2	2	B.1.525	0.000226
S	26	P26L	cCt	cTt	2	2	B.1.565	0.001621
S	26	P26L	cCt	cTt	2	2	B.1.575	0.000607
S	26	P26S	Cct	Tct	2	2	B.1.595	0.000522
S	26	P26S	Cct	Tct	2	2	B.1.612	0.005305
S	26	P26S	Cct	Tct	2	2	B.1.618	0.008065
S	26	P26S	Cct	Tct	2	2	B.1.628	0.000705
S	26	P26L	cCt	cTt	2	2	C.1	0.004785
S	26	P26L	cCt	cTt	2	2	C.14	0.008658
S	26	P26S	Cct	Tct	2	2	C.35	0.001548
S	26	P26S	Cct	Tct	2	2	C.36	0.001821
S	26	P26S	Cct	Tct	2	2	C.37.1	0.005236
S	26	P26A	Cct	Gct	2	2	P.1	0.000032
S	26	P26S	Cct	Tct	2	2	Q.1	0.000253
S	26	P26L	cCt	cTt	2	2	Q.8	0.00033
S	26	P26L	cCt	cTt	1	1	A.2	0.000662
S	26	P26S	Cct	Tct	1	1	A.2	0.000662
S	26	P26del	CCT	---	1	1	A.2.4	0.003367
S	26	P26L	cCt	cTt	1	1	A.23.1	0.000704
S	26	P26S	Cct	Tct	1	1	A.27	0.001656
S	26	P26S	Cct	Tct	1	1	A.28	0.002646
S	26	P26L	cCt	cTt	1	1	AA.1	0.007246
S	26	P26S	Cct	Tct	1	1	AD.2	0.000219
S	26	P26S	Cct	Tct	1	1	AE.8	0.000489
S	26	P26S	Cct	Tct	1	1	AH.3	0.003802
S	26	P26C	CCt	TGt	1	1	All	0
S	26	P26G	CCT	GGA	1	1	All	0
S	26	P26P	ccT	ccC	1	1	AU.3	0.00211
S	26	P26del	CCT	---	1	1	AY.100	0.000046
S	26	P26del	CCT	---	1	1	AY.101	0.00049
S	26	P26P	ccT	ccG	1	1	AY.102	0.000027
S	26	P26A	Cct	Gct	1	1	AY.103	0.000006
S	26	P26R	cCt	cGt	1	1	AY.106	0.000335
S	26	P26P	ccT	ccC	1	1	AY.111	0.000183
S	26	P26S	Cct	Tct	1	1	AY.113	0.000142
S	26	P26H	cCt	cAt	1	1	AY.116	0.000287
S	26	P26S	Cct	Tct	1	1	AY.116	0.000287
S	26	P26L	cCt	cTt	1	1	AY.116	0.000287
S	26	P26H	cCt	cAt	1	1	AY.117	0.000085
S	26	P26P	ccT	ccC	1	1	AY.119	0.000035
S	26	P26T	Cct	Act	1	1	AY.119	0.000035
S	26	P26L	cCt	cTt	1	1	AY.12	0.000316
S	26	P26L	cCt	cTt	1	1	AY.120.2.1	0.000498
S	26	P26L	cCt	cTt	1	1	AY.13	0.000161
S	26	P26L	cCt	cTt	1	1	AY.16	0.00038
S	26	P26S	Cct	Tct	1	1	AY.16.1	0.00047
S	26	P26T	Cct	Act	1	1	AY.19	0.00114
S	26	P26P	ccT	ccC	1	1	AY.20	0.000039
S	26	P26H	cCt	cAt	1	1	AY.20	0.000039
S	26	P26L	cCt	cTt	1	1	AY.23.1	0.000417
S	26	P26S	Cct	Tct	1	1	AY.24	0.000431
S	26	P26H	cCt	cAt	1	1	AY.25	0.000006
S	26	P26T	Cct	Act	1	1	AY.25	0.000006
S	26	P26del	CCT	---	1	1	AY.26	0.000028
S	26	P26S	Cct	Tct	1	1	AY.27	0.000065
S	26	P26R	cCt	cGt	1	1	AY.29.1	0.000221
S	26	P26del	CCT	---	1	1	AY.3	0.00001
S	26	P26H	cCt	cAt	1	1	AY.3	0.00001
S	26	P26S	Cct	Tct	1	1	AY.3.1	0.000085
S	26	P26L	cCt	cTt	1	1	AY.30	0.000396
S	26	P26del	CCT	---	1	1	AY.32	0.000532
S	26	P26H	cCt	cAt	1	1	AY.33	0.000067
S	26	P26A	Cct	Gct	1	1	AY.34.1	0.00051
S	26	P26T	Cct	Act	1	1	AY.34.1	0.00051
S	26	P26S	Cct	Tct	1	1	AY.36	0.000148
S	26	P26del	CCT	---	1	1	AY.39	0.000025
S	26	P26S	Cct	Tct	1	1	AY.39.1	0.00004
S	26	P26S	Cct	Tct	1	1	AY.39.2	0.001541
S	26	P26P	ccT	ccA	1	1	AY.4.2	0.000022
S	26	P26H	cCt	cAt	1	1	AY.4.2	0.000022
S	26	P26L	cCt	cTt	1	1	AY.4.2.1	0.000149
S	26	P26S	Cct	Tct	1	1	AY.4.4	0.000409
S	26	P26del	CCT	---	1	1	AY.4.5	0.000107
S	26	P26P	ccT	ccA	1	1	AY.4.5	0.000107
S	26	P26L	cCt	cTt	1	1	AY.41	0.000294
S	26	P26P	ccT	ccG	1	1	AY.42	0.00004
S	26	P26H	cCt	cAt	1	1	AY.42	0.00004
S	26	P26del	CCT	---	1	1	AY.42	0.00004
S	26	P26L	cCt	cTt	1	1	AY.42	0.00004
S	26	P26T	Cct	Act	1	1	AY.43	0.000004
S	26	P26H	cCt	cAt	1	1	AY.44	0.000006
S	26	P26del2	cCT	c--	1	1	AY.44	0.000006
S	26	P26H	cCt	cAt	1	1	AY.45	0.000122
S	26	P26L	cCt	cTt	1	1	AY.46.5	0.000198
S	26	P26L	cCt	cTt	1	1	AY.46.6	0.000072
S	26	P26H	cCt	cAt	1	1	AY.46.6	0.000072
S	26	P26del	CCT	---	1	1	AY.47	0.000031
S	26	P26P	ccT	ccC	1	1	AY.47	0.000031
S	26	P26S	Cct	Tct	1	1	AY.5.3	0.000337
S	26	P26S	Cct	Tct	1	1	AY.5.4	0.000277
S	26	P26R	cCt	cGt	1	1	AY.55	0.000917
S	26	P26L	cCt	cTt	1	1	AY.57	0.000656
S	26	P26L	cCt	cTt	1	1	AY.6	0.000041
S	26	P26H	cCt	cAt	1	1	AY.61	0.000105
S	26	P26T	Cct	Act	1	1	AY.61	0.000105
S	26	P26L	cCt	cTt	1	1	AY.63	0.000387
S	26	P26S	Cct	Tct	1	1	AY.67	0.000464
S	26	P26L	cCt	cTt	1	1	AY.67	0.000464
S	26	P26S	Cct	Tct	1	1	AY.68	0.000274
S	26	P26del	CCT	---	1	1	AY.68	0.000274
S	26	P26L	cCt	cTt	1	1	AY.69	0.000187
S	26	P26S	Cct	Tct	1	1	AY.7.1	0.000113
S	26	P26H	cCt	cAt	1	1	AY.7.1	0.000113
S	26	P26P	ccT	ccA	1	1	AY.71	0.000475
S	26	P26S	Cct	Tct	1	1	AY.74	0.000116
S	26	P26L	cCt	cTt	1	1	AY.75	0.000056
S	26	P26del	CCT	---	1	1	AY.75.1	0.00018
S	26	P26H	cCt	cAt	1	1	AY.75.1	0.00018
S	26	P26L	cCt	cTt	1	1	AY.79	0.001211
S	26	P26H	cCt	cAt	1	1	AY.79	0.001211
S	26	P26L	cCt	cTt	1	1	AY.80	0.001129
S	26	P26L	cCt	cTt	1	1	AY.84	0.000437
S	26	P26R	cCt	cGt	1	1	AY.85	0.000427
S	26	P26H	cCt	cAt	1	1	AY.87	0.000833
S	26	P26L	cCt	cTt	1	1	AY.9	0.000068
S	26	P26P	ccT	ccG	1	1	AY.9.2	0.000037
S	26	P26T	Cct	Act	1	1	AY.9.2	0.000037
S	26	P26del	CCT	---	1	1	AY.9.2	0.000037
S	26	P26L	cCt	cTt	1	1	AY.9.2	0.000037
S	26	P26L	cCt	cTt	1	1	AY.92	0.000287
S	26	P26S	Cct	Tct	1	1	AY.93	0.000273
S	26	P26L	cCt	cTt	1	1	AY.94	0.000443
S	26	P26H	cCt	cAt	1	1	AY.96	0.002075
S	26	P26del	CCT	---	1	1	AY.98	0.000079
S	26	P26del1	ccT	cc-	1	1	AY.98	0.000079
S	26	P26L	cCt	cTt	1	1	AY.98.1	0.000048
S	26	P26H	cCt	cAt	1	1	AY.98.1	0.000048
S	26	P26L	cCt	cTt	1	1	AY.99	0.001049
S	26	P26A	CcT	GcG	1	1	B	0.000128
S	26	P26T	Cct	Act	1	1	B	0.000128
S	26	P26T	Cct	Act	1	1	B.1.1	0.000018
S	26	P26S	Cct	Tct	1	1	B.1.1.1	0.000327
S	26	P26S	Cct	Tct	1	1	B.1.1.117	0.009709
S	26	P26S	Cct	Tct	1	1	B.1.1.147	0.090909
S	26	P26S	Cct	Tct	1	1	B.1.1.157	0.000913
S	26	P26H	cCt	cAt	1	1	B.1.1.164	0.005155
S	26	P26L	cCt	cTt	1	1	B.1.1.176	0.000439
S	26	P26S	Cct	Tct	1	1	B.1.1.189	0.001513
S	26	P26S	Cct	Tct	1	1	B.1.1.200	0.007463
S	26	P26S	Cct	Tct	1	1	B.1.1.207	0.001182
S	26	P26L	cCt	cTt	1	1	B.1.1.222	0.000204
S	26	P26S	Cct	Tct	1	1	B.1.1.236	0.006897
S	26	P26L	cCt	cTt	1	1	B.1.1.241	0.00207
S	26	P26S	Cct	Tct	1	1	B.1.1.25	0.000569
S	26	P26S	Cct	Tct	1	1	B.1.1.265	0.003155
S	26	P26L	cCt	cTt	1	1	B.1.1.28	0.000311
S	26	P26L	cCt	cTt	1	1	B.1.1.284	0.000107
S	26	P26L	cCt	cTt	1	1	B.1.1.302	0.002075
S	26	P26del	CCT	---	1	1	B.1.1.306	0.000438
S	26	P26S	Cct	Tct	1	1	B.1.1.312	0.001912
S	26	P26L	cCt	cTt	1	1	B.1.1.312	0.001912
S	26	P26del	CCT	---	1	1	B.1.1.315	0.008475
S	26	P26P	ccT	ccA	1	1	B.1.1.317	0.000412
S	26	P26L	cCt	cTt	1	1	B.1.1.318	0.000302
S	26	P26L	cCt	cTt	1	1	B.1.1.325	0.025641
S	26	P26L	cCt	cTt	1	1	B.1.1.328	0.016949
S	26	P26L	cCt	cTt	1	1	B.1.1.33	0.000421
S	26	P26L	cCt	cTt	1	1	B.1.1.348	0.000796
S	26	P26S	Cct	Tct	1	1	B.1.1.359	0.027778
S	26	P26R	cCt	cGt	1	1	B.1.1.362	0.005618
S	26	P26S	Cct	Tct	1	1	B.1.1.37	0.000193
S	26	P26L	cCt	cTt	1	1	B.1.1.377	0.001381
S	26	P26S	Cct	Tct	1	1	B.1.1.39	0.00051
S	26	P26S	Cct	Tct	1	1	B.1.1.397	0.002252
S	26	P26del	CCT	---	1	1	B.1.1.401	0.066667
S	26	P26S	Cct	Tct	1	1	B.1.1.411	0.014706
S	26	P26P	ccT	ccC	1	1	B.1.1.412	0.007634
S	26	P26P	ccT	ccC	1	1	B.1.1.418	0.022727
S	26	P26T	Cct	Act	1	1	B.1.1.420	0.001006
S	26	P26S	Cct	Tct	1	1	B.1.1.430	0.041667
S	26	P26L	cCt	cTt	1	1	B.1.1.431	0.016129
S	26	P26L	cCt	cTt	1	1	B.1.1.432	0.001266
S	26	P26S	Cct	Tct	1	1	B.1.1.432	0.001266
S	26	P26del	CCT	---	1	1	B.1.1.46	0.004367
S	26	P26L	cCt	cTt	1	1	B.1.1.50	0.000679
S	26	P26L	cCt	cTt	1	1	B.1.1.523	0.001563
S	26	P26P	ccT	ccA	1	1	B.1.1.523	0.001563
S	26	P26L	cCt	cTt	1	1	B.1.1.59	0.006494
S	26	P26A	Cct	Gct	1	1	B.1.1.7	0.000001
S	26	P26G	CCT	GGA	1	1	B.1.1.7	0.000001
S	26	P26C	CCt	TGt	1	1	B.1.1.7	0.000001
S	26	P26del2	cCT	c--	1	1	B.1.1.7	0.000001
S	26	P26S	Cct	Tct	1	1	B.1.1.71	0.006061
S	26	P26S	Cct	Tct	1	1	B.1.1.8	0.003584
S	26	P26S	Cct	Tct	1	1	B.1.111	0.001175
S	26	P26L	cCt	cTt	1	1	B.1.118	0.006711
S	26	P26A	Cct	Gct	1	1	B.1.120	0.007692
S	26	P26S	Cct	Tct	1	1	B.1.120	0.007692
S	26	P26S	Cct	Tct	1	1	B.1.126	0.001276
S	26	P26L	cCt	cTt	1	1	B.1.146	0.004237
S	26	P26H	cCt	cAt	1	1	B.1.147	0.000756
S	26	P26R	cCt	cGt	1	1	B.1.160	0.000031
S	26	P26P	ccT	ccC	1	1	B.1.160.16	0.000929
S	26	P26L	cCt	cTt	1	1	B.1.160.16	0.000929
S	26	P26S	Cct	Tct	1	1	B.1.160.30	0.002976
S	26	P26S	Cct	Tct	1	1	B.1.160.9	0.007194
S	26	P26T	Cct	Act	1	1	B.1.177	0.000013
S	26	P26L	cCt	cTt	1	1	B.1.177.15	0.000631
S	26	P26del	CCT	---	1	1	B.1.177.17	0.000821
S	26	P26S	Cct	Tct	1	1	B.1.177.19	0.001431
S	26	P26L	cCt	cTt	1	1	B.1.177.21	0.000076
S	26	P26S	Cct	Tct	1	1	B.1.177.30	0.002513
S	26	P26S	Cct	Tct	1	1	B.1.177.33	0.001645
S	26	P26S	Cct	Tct	1	1	B.1.177.35	0.000691
S	26	P26S	Cct	Tct	1	1	B.1.177.48	0.003125
S	26	P26S	Cct	Tct	1	1	B.1.177.5	0.001242
S	26	P26L	cCt	cTt	1	1	B.1.177.51	0.004566
S	26	P26S	Cct	Tct	1	1	B.1.177.54	0.000606
S	26	P26S	Cct	Tct	1	1	B.1.177.56	0.000668
S	26	P26S	Cct	Tct	1	1	B.1.177.59	0.016129
S	26	P26T	Cct	Act	1	1	B.1.177.60	0.000218
S	26	P26del	CCT	---	1	1	B.1.177.60	0.000218
S	26	P26S	Cct	Tct	1	1	B.1.177.63	0.002703
S	26	P26del	CCT	---	1	1	B.1.177.68	0.015152
S	26	P26del	CCT	---	1	1	B.1.177.7	0.000165
S	26	P26S	Cct	Tct	1	1	B.1.177.7	0.000165
S	26	P26S	Cct	Tct	1	1	B.1.177.75	0.001041
S	26	P26del	CCT	---	1	1	B.1.177.83	0.001481
S	26	P26S	Cct	Tct	1	1	B.1.177.83	0.001481
S	26	P26S	Cct	Tct	1	1	B.1.177.86	0.000183
S	26	P26S	Cct	Tct	1	1	B.1.179	0.003759
S	26	P26del1	ccT	cc-	1	1	B.1.2	0.000009
S	26	P26R	cCt	cGt	1	1	B.1.2	0.000009
S	26	P26del	CCT	---	1	1	B.1.2	0.000009
S	26	P26L	cCt	cTt	1	1	B.1.210	0.002132
S	26	P26S	Cct	Tct	1	1	B.1.214	0.003663
S	26	P26L	cCt	cTt	1	1	B.1.214.2	0.0006
S	26	P26del	CCT	---	1	1	B.1.221	0.000071
S	26	P26H	cCt	cAt	1	1	B.1.221	0.000071
S	26	P26H	cCt	cAt	1	1	B.1.223	0.002778
S	26	P26L	cCt	cTt	1	1	B.1.234	0.000132
S	26	P26L	cCt	cTt	1	1	B.1.236	0.002053
S	26	P26T	Cct	Act	1	1	B.1.236	0.002053
S	26	P26L	cCt	cTt	1	1	B.1.239	0.001221
S	26	P26P	ccT	ccC	1	1	B.1.243	0.00007
S	26	P26R	cCt	cGt	1	1	B.1.258	0.000067
S	26	P26del	CCT	---	1	1	B.1.258	0.000067
S	26	P26T	Cct	Act	1	1	B.1.258	0.000067
S	26	P26S	Cct	Tct	1	1	B.1.258.14	0.00098
S	26	P26P	ccT	ccC	1	1	B.1.258.4	0.003448
S	26	P26H	cCt	cAt	1	1	B.1.305	0.002151
S	26	P26S	Cct	Tct	1	1	B.1.311	0.000275
S	26	P26S	Cct	Tct	1	1	B.1.324	0.001605
S	26	P26H	cCt	cAt	1	1	B.1.351	0.00003
S	26	P26H	cCt	cAt	1	1	B.1.356	0.001727
S	26	P26del	CCT	---	1	1	B.1.36	0.000146
S	26	P26P	ccT	ccC	1	1	B.1.36	0.000146
S	26	P26S	Cct	Tct	1	1	B.1.36.1	0.00114
S	26	P26L	cCt	cTt	1	1	B.1.36.17	0.000494
S	26	P26S	Cct	Tct	1	1	B.1.36.17	0.000494
S	26	P26del	CCT	---	1	1	B.1.36.17	0.000494
S	26	P26S	Cct	Tct	1	1	B.1.36.18	0.00042
S	26	P26L	cCt	cTt	1	1	B.1.36.27	0.000763
S	26	P26S	Cct	Tct	1	1	B.1.362	0.001541
S	26	P26S	Cct	Tct	1	1	B.1.382	0.008929
S	26	P26del	CCT	---	1	1	B.1.396	0.000706
S	26	P26H	cCt	cAt	1	1	B.1.398	0.002976
S	26	P26S	Cct	Tct	1	1	B.1.399	0.001934
S	26	P26S	Cct	Tct	1	1	B.1.400	0.000429
S	26	P26P	ccT	ccA	1	1	B.1.404	0.001302
S	26	P26L	cCt	cTt	1	1	B.1.404	0.001302
S	26	P26S	Cct	Tct	1	1	B.1.415	0.014286
S	26	P26S	Cct	Tct	1	1	B.1.416	0.001269
S	26	P26L	cCt	cTt	1	1	B.1.416	0.001269
S	26	P26L	cCt	cTt	1	1	B.1.426	0.001009
S	26	P26H	cCt	cAt	1	1	B.1.429	0.000024
S	26	P26del	CCT	---	1	1	B.1.429	0.000024
S	26	P26L	cCt	cTt	1	1	B.1.433	0.003195
S	26	P26L	cCt	cTt	1	1	B.1.438.1	0.000107
S	26	P26L	cCt	cTt	1	1	B.1.468	0.005714
S	26	P26S	Cct	Tct	1	1	B.1.470	0.001404
S	26	P26P	ccT	ccC	1	1	B.1.497	0.000315
S	26	P26L	cCt	cTt	1	1	B.1.517	0.000427
S	26	P26S	Cct	Tct	1	1	B.1.517	0.000427
S	26	P26L	cCt	cTt	1	1	B.1.521	0.004975
S	26	P26S	Cct	Tct	1	1	B.1.533	0.009615
S	26	P26S	Cct	Tct	1	1	B.1.538	0.008065
S	26	P26S	Cct	Tct	1	1	B.1.541	0.004425
S	26	P26F	CCt	TTt	1	1	B.1.544	0.006024
S	26	P26S	Cct	Tct	1	1	B.1.561	0.000397
S	26	P26S	Cct	Tct	1	1	B.1.564	0.000426
S	26	P26L	cCt	cTt	1	1	B.1.564	0.000426
S	26	P26S	Cct	Tct	1	1	B.1.564.1	0.001577
S	26	P26S	Cct	Tct	1	1	B.1.568	0.001111
S	26	P26S	Cct	Tct	1	1	B.1.573	0.006098
S	26	P26S	Cct	Tct	1	1	B.1.574	0.002151
S	26	P26S	Cct	Tct	1	1	B.1.575	0.000303
S	26	P26P	ccT	ccC	1	1	B.1.576	0.000907
S	26	P26S	Cct	Tct	1	1	B.1.590	0.004545
S	26	P26L	cCt	cTt	1	1	B.1.590	0.004545
S	26	P26L	cCt	cTt	1	1	B.1.591	0.010638
S	26	P26P	ccT	ccG	1	1	B.1.596	0.000087
S	26	P26del1	ccT	cc-	1	1	B.1.596	0.000087
S	26	P26L	cCt	cTt	1	1	B.1.605	0.005952
S	26	P26del	CCT	---	1	1	B.1.605	0.005952
S	26	P26L	cCt	cTt	1	1	B.1.617.1	0.000129
S	26	P26R	cCt	cGt	1	1	B.1.617.2	0.000004
S	26	P26T	Cct	Act	1	1	B.1.617.2	0.000004
S	26	P26L	cCt	cTt	1	1	B.1.619	0.000871
S	26	P26del	CCT	---	1	1	B.1.620	0.000946
S	26	P26T	Cct	Act	1	1	B.1.621	0.000089
S	26	P26L	cCt	cTt	1	1	B.1.623	0.000536
S	26	P26L	cCt	cTt	1	1	B.1.630	0.005236
S	26	P26L	cCt	cTt	1	1	B.1.631	0.003367
S	26	P26S	Cct	Tct	1	1	B.1.632	0.006711
S	26	P26L	cCt	cTt	1	1	B.1.9.5	0.005682
S	26	P26L	cCt	cTt	1	1	B.1.93	0.000934
S	26	P26S	Cct	Tct	1	1	B.3	0.000831
S	26	P26S	Cct	Tct	1	1	B.39	0.002331
S	26	P26A	Cct	Gct	1	1	B.40	0.000364
S	26	P26P	ccT	ccA	1	1	B.40	0.000364
S	26	P26S	Cct	Tct	1	1	B.6	0.00091
S	26	P26S	Cct	Tct	1	1	B.6.6	0.000889
S	26	P26S	Cct	Tct	1	1	C.1	0.002392
S	26	P26S	Cct	Tct	1	1	C.16	0.00106
S	26	P26S	Cct	Tct	1	1	C.36.1	0.004149
S	26	P26S	Cct	Tct	1	1	C.36.2	0.034483
S	26	P26L	cCt	cTt	1	1	C.36.3	0.000567
S	26	P26S	Cct	Tct	1	1	C.36.3	0.000567
S	26	P26H	cCt	cAt	1	1	C.37	0.000116
S	26	P26P	ccT	ccC	1	1	C.37	0.000116
S	26	P26L	cCt	cTt	1	1	C.38	0.008065
S	26	P26L	cCt	cTt	1	1	D.2	0.000075
S	26	P26F	CCt	TTt	1	1	D.2	0.000075
S	26	P26P	ccT	ccC	1	1	D.2	0.000075
S	26	P26L	cCt	cTt	1	1	L.3	0.003546
S	26	P26T	Cct	Act	1	1	P.1	0.000016
S	26	P26F	CCt	TTt	1	1	P.1.10	0.000269
S	26	P26F	CCt	TTt	1	1	P.1.14	0.000048
S	26	P26F	CCt	TTt	1	1	P.1.16	0.000374
S	26	P26L	cCt	cTt	1	1	P.1.7	0.000319
S	26	P26H	cCt	cAt	1	1	P.2	0.000187
S	26	P26R	cCt	cGt	1	1	P.2	0.000187
S	26	P26S	Cct	Tct	1	1	P.7	0.004367
S	26	P26del	CCT	---	1	1	Q.1	0.000126
S	26	P26S	Cct	Tct	1	1	Q.3	0.000145
S	26	P26S	Cct	Tct	1	1	Q.4	0.000455
S	26	P26R	cCt	cGt	1	1	Q.8	0.000165
S	26	P26S	Cct	Tct	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.