CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1238

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	1238	T1238T		syn	acC	acT	15737	7974	0.506704	25274-25276
S	1238	T1238T		syn	acC	acA	15737	7715	0.490246	25274-25276
S	1238	T1238T		syn	acC	acG	15737	48	0.00305014	25274-25276
S	1238	T1238I		nonsyn	aCc	aTc	991	989	0.997982	25274-25276
S	1238	T1238I		nonsyn	aCC	aTT	991	2	0.00201816	25274-25276
S	1238	T1238del		del	ACC	---	130	130	1	25274-25276
S	1238	T1238N		nonsyn	aCc	aAc	125	125	1	25274-25276
S	1238	T1238A		nonsyn	Acc	Gcc	45	40	0.888889	25274-25276
S	1238	T1238A		nonsyn	AcC	GcA	45	2	0.0444444	25274-25276
S	1238	T1238A		nonsyn	AcC	GcT	45	2	0.0444444	25274-25276
S	1238	T1238A		nonsyn	AcC	GcG	45	1	0.0222222	25274-25276
S	1238	T1238S		nonsyn	aCc	aGc	22	16	0.727273	25274-25276
S	1238	T1238S		nonsyn	Acc	Tcc	22	5	0.227273	25274-25276
S	1238	T1238S		nonsyn	AcC	TcT	22	1	0.0454545	25274-25276
S	1238	T1238P		nonsyn	Acc	Ccc	4	4	1	25274-25276
S	1238	T1238V		nonsyn	ACc	GTc	4	2	0.5	25274-25276
S	1238	T1238V		nonsyn	ACC	GTG	4	1	0.25	25274-25276
S	1238	T1238V		nonsyn	ACC	GTT	4	1	0.25	25274-25276
S	1238	T1238del2		del	ACc	--c	3	3	1	25274-25276
S	1238	T1238H		nonsyn	ACc	CAc	2	2	1	25274-25276
S	1238	T1238M		nonsyn	aCC	aTG	1	1	1	25274-25276
S	1238	T1238Y		nonsyn	ACc	TAc	1	1	1	25274-25276
S	1238	T1238D		nonsyn	ACc	GAc	1	1	1	25274-25276
S	1238	T1238K		nonsyn	aCC	aAA	1	1	1	25274-25276

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	1238	T1238T	acC	acT	7974	15737	All	0.001525
S	1238	T1238T	acC	acA	7715	15737	All	0.001476
S	1238	T1238T	acC	acG	48	15737	All	0.000009
S	1238	T1238T	acC	acA	3272	3272	B.1.1.318	0.987326
S	1238	T1238T	acC	acT	2678	2763	B.1.1.7	0.002397
S	1238	T1238T	acC	acA	84	2763	B.1.1.7	0.000075
S	1238	T1238T	acC	acG	1	2763	B.1.1.7	0.000001
S	1238	T1238T	acC	acT	1343	1400	AY.4	0.00209
S	1238	T1238T	acC	acA	57	1400	AY.4	0.000089
S	1238	T1238T	acC	acA	1210	1210	AZ.2	0.993432
S	1238	T1238T	acC	acA	1152	1152	AZ.1	0.999133
S	1238	T1238I	aCc	aTc	989	991	All	0.000189
S	1238	T1238I	aCC	aTT	2	991	All	0
S	1238	T1238T	acC	acA	656	656	AZ.3	0.99696
S	1238	T1238I	aCc	aTc	424	424	B.1.1.7	0.00038
S	1238	T1238T	acC	acT	396	396	R.1	0.035644
S	1238	T1238T	acC	acT	331	332	B.1.617.1	0.042688
S	1238	T1238T	acC	acA	1	332	B.1.617.1	0.000129
S	1238	T1238T	acC	acT	288	295	AY.119	0.010169
S	1238	T1238T	acC	acA	7	295	AY.119	0.000247
S	1238	T1238T	acC	acA	294	294	AZ.4	0.986577
S	1238	T1238T	acC	acA	285	285	AZ.5	1
S	1238	T1238T	acC	acT	199	222	AY.103	0.001236
S	1238	T1238T	acC	acA	23	222	AY.103	0.000143
S	1238	T1238T	acC	acT	201	201	B.1.1.214	0.011147
S	1238	T1238T	acC	acT	154	185	B.1.617.2	0.00058
S	1238	T1238T	acC	acA	29	185	B.1.617.2	0.000109
S	1238	T1238T	acC	acG	2	185	B.1.617.2	0.000008
S	1238	T1238T	acC	acT	154	171	B.1.2	0.001356
S	1238	T1238T	acC	acA	17	171	B.1.2	0.00015
S	1238	T1238T	acC	acT	88	161	AY.3	0.000875
S	1238	T1238T	acC	acA	72	161	AY.3	0.000716
S	1238	T1238T	acC	acG	1	161	AY.3	0.00001
S	1238	T1238del	ACC	---	130	130	All	0.000025
S	1238	T1238N	aCc	aAc	125	125	All	0.000024
S	1238	T1238T	acC	acA	123	123	AZ.2.1	1
S	1238	T1238T	acC	acA	118	118	AZ.6	0.991597
S	1238	T1238I	aCc	aTc	111	111	AY.4	0.000173
S	1238	T1238T	acC	acT	72	95	AY.25	0.000433
S	1238	T1238T	acC	acA	17	95	AY.25	0.000102
S	1238	T1238T	acC	acG	6	95	AY.25	0.000036
S	1238	T1238T	acC	acT	92	95	P.1	0.001449
S	1238	T1238T	acC	acA	3	95	P.1	0.000047
S	1238	T1238T	acC	acT	76	94	B.1	0.000696
S	1238	T1238T	acC	acA	16	94	B.1	0.000147
S	1238	T1238T	acC	acG	2	94	B.1	0.000018
S	1238	T1238T	acC	acT	90	93	B.1.429	0.002118
S	1238	T1238T	acC	acA	3	93	B.1.429	0.000071
S	1238	T1238T	acC	acT	88	88	AY.18	0.888889
S	1238	T1238T	acC	acT	72	85	B.1.1	0.001306
S	1238	T1238T	acC	acA	13	85	B.1.1	0.000236
S	1238	T1238T	acC	acT	63	75	AY.43	0.000279
S	1238	T1238T	acC	acA	8	75	AY.43	0.000035
S	1238	T1238T	acC	acG	4	75	AY.43	0.000018
S	1238	T1238T	acC	acT	66	71	AY.44	0.000402
S	1238	T1238T	acC	acA	5	71	AY.44	0.00003
S	1238	T1238T	acC	acT	61	61	B.1.627	0.123232
S	1238	T1238T	acC	acT	58	59	AY.74	0.006708
S	1238	T1238T	acC	acA	1	59	AY.74	0.000116
S	1238	T1238T	acC	acT	37	59	B.1.177	0.000487
S	1238	T1238T	acC	acA	22	59	B.1.177	0.00029
S	1238	T1238T	acC	acT	59	59	B.1.177.86	0.010824
S	1238	T1238T	acC	acA	48	53	AY.47	0.001493
S	1238	T1238T	acC	acT	5	53	AY.47	0.000156
S	1238	T1238I	aCc	aTc	52	52	B.1.1.289	0.108333
S	1238	T1238del	ACC	---	52	52	B.1.1.7	0.000047
S	1238	T1238T	acC	acT	47	47	B.1.160.21	0.959184
S	1238	T1238T	acC	acT	46	46	B.1.311	0.01263
S	1238	T1238A	Acc	Gcc	40	45	All	0.000008
S	1238	T1238A	AcC	GcT	2	45	All	0
S	1238	T1238A	AcC	GcA	2	45	All	0
S	1238	T1238A	AcC	GcG	1	45	All	0
S	1238	T1238T	acC	acT	41	41	AY.98.1	0.001986
S	1238	T1238T	acC	acA	26	39	B.1.427	0.001313
S	1238	T1238T	acC	acT	13	39	B.1.427	0.000656
S	1238	T1238T	acC	acT	36	36	B.1.609	0.017258
S	1238	T1238T	acC	acT	33	35	AY.75	0.001849
S	1238	T1238T	acC	acA	2	35	AY.75	0.000112
S	1238	T1238T	acC	acT	35	35	B.1.1.519	0.00139
S	1238	T1238T	acC	acT	34	35	B.1.526	0.000799
S	1238	T1238T	acC	acG	1	35	B.1.526	0.000024
S	1238	T1238T	acC	acT	35	35	C.36.3	0.019853
S	1238	T1238T	acC	acT	33	33	B.1.619.1	0.021167
S	1238	T1238T	acC	acA	33	33	K.1	0.785714
S	1238	T1238T	acC	acG	23	32	AY.14	0.002024
S	1238	T1238T	acC	acT	9	32	AY.14	0.000792
S	1238	T1238T	acC	acT	27	27	B.1.160	0.000842
S	1238	T1238T	acC	acT	26	26	B.1.177.32	0.035088
S	1238	T1238I	aCc	aTc	26	26	B.1.617.2	0.000098
S	1238	T1238I	aCc	aTc	25	25	B.1.561	0.009925
S	1238	T1238I	aCc	aTc	24	24	B.1	0.00022
S	1238	T1238T	acC	acT	24	24	B.1.139	0.017595
S	1238	T1238T	acC	acT	24	24	Q.3	0.003481
S	1238	T1238T	acC	acT	22	23	AY.42	0.000885
S	1238	T1238T	acC	acA	1	23	AY.42	0.00004
S	1238	T1238T	acC	acT	19	23	B.1.36	0.002772
S	1238	T1238T	acC	acA	4	23	B.1.36	0.000584
S	1238	T1238S	aCc	aGc	16	22	All	0.000003
S	1238	T1238S	Acc	Tcc	5	22	All	0.000001
S	1238	T1238S	AcC	TcT	1	22	All	0
S	1238	T1238T	acC	acA	21	22	AY.27	0.001359
S	1238	T1238T	acC	acT	1	22	AY.27	0.000065
S	1238	T1238T	acC	acT	21	21	AY.120.1	0.006742
S	1238	T1238T	acC	acT	21	21	B.1.177.81	0.003976
S	1238	T1238N	aCc	aAc	20	20	AY.4	0.000031
S	1238	T1238I	aCc	aTc	20	20	AY.43	0.000089
S	1238	T1238I	aCc	aTc	20	20	AY.44	0.000122
S	1238	T1238I	aCc	aTc	20	20	B.1.36.36	0.012041
S	1238	T1238T	acC	acT	19	19	AY.20	0.000738
S	1238	T1238T	acC	acT	16	19	B.1.351	0.000476
S	1238	T1238T	acC	acA	3	19	B.1.351	0.000089
S	1238	T1238T	acC	acT	11	18	AY.4.2	0.000239
S	1238	T1238T	acC	acA	7	18	AY.4.2	0.000152
S	1238	T1238T	acC	acT	17	17	AY.117	0.001437
S	1238	T1238T	acC	acT	16	17	AY.39	0.000395
S	1238	T1238T	acC	acA	1	17	AY.39	0.000025
S	1238	T1238T	acC	acA	17	17	AY.39.1	0.000673
S	1238	T1238T	acC	acT	16	17	AY.5	0.00033
S	1238	T1238T	acC	acA	1	17	AY.5	0.000021
S	1238	T1238T	acC	acT	17	17	AY.6	0.000699
S	1238	T1238I	aCc	aTc	16	16	AY.25	0.000096
S	1238	T1238del	ACC	---	16	16	AY.4.5	0.00172
S	1238	T1238T	acC	acT	16	16	AY.70	0.003336
S	1238	T1238T	acC	acT	16	16	AY.85	0.006835
S	1238	T1238N	aCc	aAc	16	16	B.1.1.7	0.000014
S	1238	T1238T	acC	acT	16	16	B.1.596	0.001394
S	1238	T1238T	acC	acT	16	16	C.37	0.001857
S	1238	T1238T	acC	acT	15	15	B.1.1.434	0.005228
S	1238	T1238I	aCc	aTc	15	15	B.1.2	0.000132
S	1238	T1238T	acC	acT	11	15	B.1.243	0.000765
S	1238	T1238T	acC	acA	3	15	B.1.243	0.000209
S	1238	T1238T	acC	acG	1	15	B.1.243	0.00007
S	1238	T1238T	acC	acT	15	15	B.1.517	0.006405
S	1238	T1238T	acC	acT	15	15	P.1.15	0.003485
S	1238	T1238T	acC	acT	12	14	AY.102	0.000318
S	1238	T1238T	acC	acG	1	14	AY.102	0.000027
S	1238	T1238T	acC	acA	1	14	AY.102	0.000027
S	1238	T1238I	aCc	aTc	14	14	B.1.177	0.000184
S	1238	T1238T	acC	acT	14	14	P.1.14	0.000669
S	1238	T1238T	acC	acT	12	13	AY.100	0.000552
S	1238	T1238T	acC	acA	1	13	AY.100	0.000046
S	1238	T1238T	acC	acT	13	13	AY.16	0.004935
S	1238	T1238T	acC	acT	13	13	AY.4.2.1	0.001937
S	1238	T1238A	Acc	Gcc	13	13	B.1.617.2	0.000049
S	1238	T1238T	acC	acT	11	12	AY.118	0.000689
S	1238	T1238T	acC	acA	1	12	AY.118	0.000063
S	1238	T1238T	acC	acT	10	12	AY.29	0.000158
S	1238	T1238T	acC	acG	2	12	AY.29	0.000032
S	1238	T1238T	acC	acT	12	12	AY.9	0.000811
S	1238	T1238S	aCc	aGc	12	12	B.1.1.7	0.000011
S	1238	T1238del	ACC	---	12	12	B.1.177	0.000158
S	1238	T1238I	aCc	aTc	12	12	B.1.243	0.000835
S	1238	T1238T	acC	acT	11	12	B.1.466.2	0.004304
S	1238	T1238T	acC	acA	1	12	B.1.466.2	0.000391
S	1238	T1238T	acC	acT	11	12	B.1.470	0.015449
S	1238	T1238T	acC	acA	1	12	B.1.470	0.001404
S	1238	T1238I	aCc	aTc	12	12	B.1.526	0.000282
S	1238	T1238I	aCc	aTc	11	11	AY.21	0.020873
S	1238	T1238T	acC	acT	9	11	AY.99.2	0.000829
S	1238	T1238T	acC	acA	2	11	AY.99.2	0.000184
S	1238	T1238T	acC	acA	7	10	B.1.1.222	0.001428
S	1238	T1238T	acC	acT	3	10	B.1.1.222	0.000612
S	1238	T1238T	acC	acT	10	10	B.1.1.512	0.285714
S	1238	T1238T	acC	acT	9	10	B.1.599	0.032847
S	1238	T1238T	acC	acA	1	10	B.1.599	0.00365
S	1238	T1238T	acC	acT	9	10	B.1.621	0.000797
S	1238	T1238T	acC	acA	1	10	B.1.621	0.000089
S	1238	T1238I	aCc	aTc	9	9	AY.103	0.000056
S	1238	T1238N	aCc	aAc	9	9	AY.43	0.00004
S	1238	T1238T	acC	acT	7	9	AY.98	0.000553
S	1238	T1238T	acC	acA	2	9	AY.98	0.000158
S	1238	T1238T	acC	acT	9	9	B.1.575	0.002731
S	1238	T1238N	aCc	aAc	9	9	B.1.617.2	0.000034
S	1238	T1238T	acC	acT	8	8	AY.5.4	0.002214
S	1238	T1238T	acC	acT	8	8	B.1.438.1	0.000858
S	1238	T1238T	acC	acT	7	8	B.1.623	0.003755
S	1238	T1238T	acC	acA	1	8	B.1.623	0.000536
S	1238	T1238T	acC	acT	8	8	Q.1	0.001011
S	1238	T1238T	acC	acT	7	7	B.1.36.29	0.003621
S	1238	T1238T	acC	acT	7	7	B.1.577	0.004811
S	1238	T1238N	aCc	aAc	6	6	AY.103	0.000037
S	1238	T1238T	acC	acT	6	6	AY.33	0.000401
S	1238	T1238T	acC	acT	6	6	AY.34	0.000582
S	1238	T1238I	aCc	aTc	6	6	AY.4.1	0.004425
S	1238	T1238N	aCc	aAc	6	6	AY.44	0.000037
S	1238	T1238T	acC	acT	6	6	AY.5.3	0.002024
S	1238	T1238I	aCc	aTc	6	6	AY.84	0.002625
S	1238	T1238T	acC	acT	6	6	B.1.1.28	0.001867
S	1238	T1238T	acC	acT	6	6	B.1.240	0.001293
S	1238	T1238I	aCc	aTc	6	6	B.1.258	0.000399
S	1238	T1238T	acC	acT	6	6	B.1.258	0.000399
S	1238	T1238T	acC	acT	6	6	B.1.403	0.019608
S	1238	T1238T	acC	acT	5	6	B.1.637	0.000365
S	1238	T1238T	acC	acA	1	6	B.1.637	0.000073
S	1238	T1238I	aCc	aTc	6	6	P.1	0.000095
S	1238	T1238I	aCc	aTc	6	6	Q.8	0.000989
S	1238	T1238I	aCc	aTc	5	5	AY.100	0.00023
S	1238	T1238I	aCc	aTc	5	5	AY.102	0.000133
S	1238	T1238T	acC	acT	5	5	AY.120	0.000186
S	1238	T1238T	acC	acT	3	5	AY.3.1	0.000256
S	1238	T1238T	acC	acA	2	5	AY.3.1	0.000171
S	1238	T1238I	aCc	aTc	5	5	AY.34.1	0.00255
S	1238	T1238del	ACC	---	5	5	AY.4	0.000008
S	1238	T1238I	aCc	aTc	5	5	AY.4.5	0.000537
S	1238	T1238T	acC	acA	5	5	AY.45	0.000608
S	1238	T1238T	acC	acT	3	5	AY.9.2	0.00011
S	1238	T1238T	acC	acA	2	5	AY.9.2	0.000073
S	1238	T1238A	Acc	Gcc	4	5	B.1	0.000037
S	1238	T1238A	AcC	GcT	1	5	B.1	0.000009
S	1238	T1238T	acC	acT	5	5	B.1.1.39	0.002548
S	1238	T1238T	acC	acT	5	5	B.1.1.50	0.003394
S	1238	T1238A	Acc	Gcc	5	5	B.1.177	0.000066
S	1238	T1238T	acC	acT	5	5	B.1.177.18	0.0058
S	1238	T1238T	acC	acT	3	5	B.1.525	0.000339
S	1238	T1238T	acC	acA	2	5	B.1.525	0.000226
S	1238	T1238T	acC	acA	5	5	B.1.576	0.004533
S	1238	T1238P	Acc	Ccc	4	4	All	0.000001
S	1238	T1238V	ACc	GTc	2	4	All	0
S	1238	T1238V	ACC	GTT	1	4	All	0
S	1238	T1238V	ACC	GTG	1	4	All	0
S	1238	T1238N	aCc	aAc	4	4	AY.3	0.00004
S	1238	T1238I	aCc	aTc	3	4	AY.39	0.000074
S	1238	T1238I	aCC	aTT	1	4	AY.39	0.000025
S	1238	T1238N	aCc	aAc	4	4	AY.39.1	0.000158
S	1238	T1238I	aCc	aTc	4	4	AY.42	0.000161
S	1238	T1238N	aCc	aAc	4	4	AY.5	0.000083
S	1238	T1238T	acC	acT	4	4	AY.51	0.003636
S	1238	T1238T	acC	acT	4	4	AY.88	0.003537
S	1238	T1238T	acC	acT	3	4	B	0.000383
S	1238	T1238T	acC	acA	1	4	B	0.000128
S	1238	T1238T	acC	acT	4	4	B.1.1.303	0.01105
S	1238	T1238T	acC	acT	4	4	B.1.177.43	0.005908
S	1238	T1238T	acC	acT	4	4	B.1.177.60	0.000874
S	1238	T1238I	aCc	aTc	4	4	B.1.177.7	0.000659
S	1238	T1238I	aCc	aTc	4	4	B.1.351	0.000119
S	1238	T1238I	aCc	aTc	4	4	B.1.429	0.000094
S	1238	T1238T	acC	acT	4	4	B.1.595	0.001044
S	1238	T1238T	acC	acT	4	4	B.1.78	0.034188
S	1238	T1238T	acC	acT	4	4	D.2	0.0003
S	1238	T1238T	acC	acT	4	4	P.1.10	0.001078
S	1238	T1238V	ACc	GTc	1	3		0.055556
S	1238	T1238V	ACC	GTG	1	3		0.055556
S	1238	T1238V	ACC	GTT	1	3		0.055556
S	1238	T1238A	Acc	Gcc	1	3		0.055556
S	1238	T1238A	AcC	GcT	1	3		0.055556
S	1238	T1238A	AcC	GcG	1	3		0.055556
S	1238	T1238I	aCc	aTc	3	3	A.2.5.2	0.004717
S	1238	T1238T	acC	acT	2	3	AD.2	0.000438
S	1238	T1238T	acC	acA	1	3	AD.2	0.000219
S	1238	T1238del2	ACc	--c	3	3	All	0.000001
S	1238	T1238T	acC	acA	3	3	AT.1	0.015385
S	1238	T1238A	Acc	Gcc	3	3	AY.100	0.000138
S	1238	T1238I	aCc	aTc	3	3	AY.120	0.000112
S	1238	T1238del	ACC	---	3	3	AY.120	0.000112
S	1238	T1238T	acC	acA	2	3	AY.23	0.000139
S	1238	T1238T	acC	acT	1	3	AY.23	0.00007
S	1238	T1238I	aCc	aTc	3	3	AY.26	0.000085
S	1238	T1238T	acC	acT	3	3	AY.26	0.000085
S	1238	T1238I	aCc	aTc	3	3	AY.3	0.00003
S	1238	T1238T	acC	acT	3	3	AY.4.1	0.002212
S	1238	T1238T	acC	acT	2	3	AY.61	0.00021
S	1238	T1238T	acC	acG	1	3	AY.61	0.000105
S	1238	T1238T	acC	acT	3	3	AY.86	0.00249
S	1238	T1238T	acC	acT	3	3	AY.9.1	0.000251
S	1238	T1238T	acC	acT	3	3	AY.97	0.005102
S	1238	T1238I	aCc	aTc	3	3	AY.98.1	0.000145
S	1238	T1238I	aCc	aTc	3	3	B.1.1	0.000054
S	1238	T1238T	acC	acT	3	3	B.1.1.1	0.00098
S	1238	T1238I	aCc	aTc	3	3	B.1.1.180	0.032258
S	1238	T1238T	acC	acT	3	3	B.1.1.220	0.005576
S	1238	T1238T	acC	acT	3	3	B.1.1.280	0.009259
S	1238	T1238T	acC	acT	3	3	B.1.1.33	0.001263
S	1238	T1238A	Acc	Gcc	2	3	B.1.1.7	0.000002
S	1238	T1238A	AcC	GcA	1	3	B.1.1.7	0.000001
S	1238	T1238T	acC	acT	3	3	B.1.1.70	0.001023
S	1238	T1238N	aCc	aAc	3	3	B.1.2	0.000026
S	1238	T1238T	acC	acT	3	3	B.1.416	0.003807
S	1238	T1238N	aCc	aAc	3	3	B.1.429	0.000071
S	1238	T1238T	acC	acA	2	3	B.1.551	0.002581
S	1238	T1238T	acC	acT	1	3	B.1.551	0.00129
S	1238	T1238I	aCc	aTc	3	3	B.1.609	0.001438
S	1238	T1238del	ACC	---	3	3	B.1.617.2	0.000011
S	1238	T1238T	acC	acT	3	3	B.30	0.044118
S	1238	T1238T	acC	acT	3	3	C.1	0.007177
S	1238	T1238I	aCc	aTc	3	3	D.2	0.000225
S	1238	T1238T	acC	acT	3	3	Q.8	0.000495
S	1238	T1238N	aCc	aAc	2	2		0.111111
S	1238	T1238T	acC	acT	1	2		0.055556
S	1238	T1238I	aCC	aTT	1	2		0.055556
S	1238	T1238T	acC	acG	1	2		0.055556
S	1238	T1238I	aCc	aTc	1	2		0.055556
S	1238	T1238T	acC	acT	2	2	AJ.1	0.090909
S	1238	T1238H	ACc	CAc	2	2	All	0
S	1238	T1238N	aCc	aAc	2	2	AY.100	0.000092
S	1238	T1238T	acC	acT	2	2	AY.111	0.000366
S	1238	T1238T	acC	acT	2	2	AY.12	0.000632
S	1238	T1238del	ACC	---	2	2	AY.25	0.000012
S	1238	T1238N	aCc	aAc	2	2	AY.25	0.000012
S	1238	T1238N	aCc	aAc	2	2	AY.26	0.000057
S	1238	T1238A	Acc	Gcc	2	2	AY.3	0.00002
S	1238	T1238T	acC	acT	1	2	AY.30	0.000396
S	1238	T1238T	acC	acA	1	2	AY.30	0.000396
S	1238	T1238T	acC	acT	2	2	AY.32	0.001065
S	1238	T1238A	Acc	Gcc	2	2	AY.33	0.000134
S	1238	T1238N	aCc	aAc	2	2	AY.39	0.000049
S	1238	T1238I	aCc	aTc	2	2	AY.39.1	0.000079
S	1238	T1238I	aCc	aTc	2	2	AY.4.2	0.000043
S	1238	T1238I	aCc	aTc	2	2	AY.45	0.000243
S	1238	T1238T	acC	acT	1	2	AY.46	0.000104
S	1238	T1238T	acC	acA	1	2	AY.46	0.000104
S	1238	T1238T	acC	acT	2	2	AY.46.6	0.000144
S	1238	T1238I	aCc	aTc	2	2	AY.46.6	0.000144
S	1238	T1238I	aCc	aTc	2	2	AY.5	0.000041
S	1238	T1238N	aCc	aAc	2	2	AY.54	0.000191
S	1238	T1238T	acC	acG	1	2	AY.55	0.000917
S	1238	T1238T	acC	acT	1	2	AY.55	0.000917
S	1238	T1238T	acC	acT	2	2	AY.56	0.00321
S	1238	T1238T	acC	acT	2	2	AY.58	0.001815
S	1238	T1238I	aCc	aTc	2	2	AY.61	0.00021
S	1238	T1238T	acC	acT	2	2	AY.64	0.00119
S	1238	T1238T	acC	acA	2	2	AY.75.1	0.000361
S	1238	T1238T	acC	acT	2	2	AY.77	0.002255
S	1238	T1238T	acC	acT	2	2	AY.92	0.000575
S	1238	T1238I	aCc	aTc	2	2	AY.99.2	0.000184
S	1238	T1238N	aCc	aAc	2	2	B.1	0.000018
S	1238	T1238del	ACC	---	2	2	B.1	0.000018
S	1238	T1238N	aCc	aAc	2	2	B.1.1	0.000036
S	1238	T1238del	ACC	---	2	2	B.1.1	0.000036
S	1238	T1238T	acC	acT	2	2	B.1.1.174	0.006757
S	1238	T1238T	acC	acT	2	2	B.1.1.326	0.003521
S	1238	T1238I	aCc	aTc	2	2	B.1.1.333	0.002153
S	1238	T1238T	acC	acT	2	2	B.1.1.37	0.000386
S	1238	T1238del	ACC	---	2	2	B.1.1.37	0.000386
S	1238	T1238T	acC	acA	1	2	B.1.1.389	0.006061
S	1238	T1238T	acC	acT	1	2	B.1.1.389	0.006061
S	1238	T1238I	aCc	aTc	2	2	B.1.1.519	0.000079
S	1238	T1238T	acC	acT	2	2	B.1.1.63	0.000772
S	1238	T1238del2	ACc	--c	2	2	B.1.1.7	0.000002
S	1238	T1238T	acC	acT	2	2	B.1.111	0.00235
S	1238	T1238I	aCc	aTc	2	2	B.1.160	0.000062
S	1238	T1238del	ACC	---	2	2	B.1.160	0.000062
S	1238	T1238T	acC	acT	2	2	B.1.161	0.034483
S	1238	T1238T	acC	acT	2	2	B.1.177.17	0.001642
S	1238	T1238del	ACC	---	2	2	B.1.177.4	0.000422
S	1238	T1238T	acC	acT	2	2	B.1.177.7	0.00033
S	1238	T1238I	aCc	aTc	2	2	B.1.177.86	0.000367
S	1238	T1238T	acC	acT	2	2	B.1.214	0.007326
S	1238	T1238T	acC	acA	1	2	B.1.221	0.000071
S	1238	T1238T	acC	acT	1	2	B.1.221	0.000071
S	1238	T1238T	acC	acT	2	2	B.1.234	0.000264
S	1238	T1238I	aCc	aTc	2	2	B.1.311	0.000549
S	1238	T1238S	aCc	aGc	2	2	B.1.351	0.000059
S	1238	T1238T	acC	acT	2	2	B.1.36.18	0.00084
S	1238	T1238T	acC	acT	2	2	B.1.367	0.001585
S	1238	T1238I	aCc	aTc	2	2	B.1.438.1	0.000215
S	1238	T1238I	aCc	aTc	2	2	B.1.466.2	0.000782
S	1238	T1238N	aCc	aAc	2	2	B.1.526	0.000047
S	1238	T1238T	acC	acT	1	2	B.1.565	0.00081
S	1238	T1238T	acC	acG	1	2	B.1.565	0.00081
S	1238	T1238T	acC	acT	2	2	B.1.589	0.015152
S	1238	T1238I	aCc	aTc	2	2	B.1.596	0.000174
S	1238	T1238I	aCc	aTc	2	2	B.1.617.1	0.000258
S	1238	T1238T	acC	acT	2	2	B.6	0.00182
S	1238	T1238T	acC	acT	1	2	C.36	0.000911
S	1238	T1238T	acC	acA	1	2	C.36	0.000911
S	1238	T1238N	aCc	aAc	2	2	D.2	0.00015
S	1238	T1238T	acC	acT	2	2	N.3	0.011628
S	1238	T1238N	aCc	aAc	2	2	N.4	0.008511
S	1238	T1238T	acC	acT	2	2	P.1.12	0.000968
S	1238	T1238del	ACC	---	2	2	P.1.15	0.000465
S	1238	T1238T	acC	acT	2	2	P.1.2	0.002312
S	1238	T1238T	acC	acA	1	2	P.2	0.000187
S	1238	T1238T	acC	acT	1	2	P.2	0.000187
S	1238	T1238S	aCc	aGc	2	2	P.7	0.008734
S	1238	T1238I	aCc	aTc	2	2	Q.1	0.000253
S	1238	T1238M	aCC	aTG	1	1		0.055556
S	1238	T1238T	acC	acT	1	1	A.23.1	0.000704
S	1238	T1238T	acC	acT	1	1	A.5	0.001923
S	1238	T1238T	acC	acT	1	1	AE.8	0.000489
S	1238	T1238D	ACc	GAc	1	1	All	0
S	1238	T1238K	aCC	aAA	1	1	All	0
S	1238	T1238Y	ACc	TAc	1	1	All	0
S	1238	T1238M	aCC	aTG	1	1	All	0
S	1238	T1238T	acC	acT	1	1	AU.2	0.002421
S	1238	T1238T	acC	acT	1	1	AY.106	0.000335
S	1238	T1238T	acC	acT	1	1	AY.11	0.001339
S	1238	T1238N	aCc	aAc	1	1	AY.110	0.000113
S	1238	T1238I	aCc	aTc	1	1	AY.111	0.000183
S	1238	T1238del2	ACc	--c	1	1	AY.111	0.000183
S	1238	T1238T	acC	acT	1	1	AY.113	0.000142
S	1238	T1238T	acC	acT	1	1	AY.115	0.005208
S	1238	T1238T	acC	acT	1	1	AY.116	0.000287
S	1238	T1238I	aCc	aTc	1	1	AY.119	0.000035
S	1238	T1238I	aCc	aTc	1	1	AY.12	0.000316
S	1238	T1238H	ACc	CAc	1	1	AY.120	0.000037
S	1238	T1238I	aCc	aTc	1	1	AY.121	0.000135
S	1238	T1238T	acC	acT	1	1	AY.121	0.000135
S	1238	T1238T	acC	acT	1	1	AY.13	0.000161
S	1238	T1238N	aCc	aAc	1	1	AY.14	0.000088
S	1238	T1238I	aCc	aTc	1	1	AY.14	0.000088
S	1238	T1238T	acC	acT	1	1	AY.2	0.000356
S	1238	T1238T	acC	acT	1	1	AY.21	0.001898
S	1238	T1238del	ACC	---	1	1	AY.23	0.00007
S	1238	T1238I	aCc	aTc	1	1	AY.23	0.00007
S	1238	T1238del	ACC	---	1	1	AY.24	0.000431
S	1238	T1238A	Acc	Gcc	1	1	AY.25	0.000006
S	1238	T1238T	acC	acT	1	1	AY.28	0.00189
S	1238	T1238I	aCc	aTc	1	1	AY.29	0.000016
S	1238	T1238T	acC	acT	1	1	AY.29.1	0.000221
S	1238	T1238I	aCc	aTc	1	1	AY.29.1	0.000221
S	1238	T1238I	aCc	aTc	1	1	AY.3.1	0.000085
S	1238	T1238I	aCc	aTc	1	1	AY.33	0.000067
S	1238	T1238I	aCc	aTc	1	1	AY.34	0.000097
S	1238	T1238T	acC	acT	1	1	AY.36	0.000148
S	1238	T1238T	acC	acT	1	1	AY.4.5	0.000107
S	1238	T1238N	aCc	aAc	1	1	AY.42	0.00004
S	1238	T1238H	ACc	CAc	1	1	AY.43	0.000004
S	1238	T1238A	Acc	Gcc	1	1	AY.43	0.000004
S	1238	T1238del	ACC	---	1	1	AY.43	0.000004
S	1238	T1238I	aCc	aTc	1	1	AY.46	0.000104
S	1238	T1238T	acC	acT	1	1	AY.46.1	0.001027
S	1238	T1238T	acC	acT	1	1	AY.46.2	0.000635
S	1238	T1238N	aCc	aAc	1	1	AY.46.5	0.000198
S	1238	T1238I	aCc	aTc	1	1	AY.47	0.000031
S	1238	T1238T	acC	acT	1	1	AY.48	0.000465
S	1238	T1238T	acC	acT	1	1	AY.49	0.003195
S	1238	T1238del	ACC	---	1	1	AY.5	0.000021
S	1238	T1238N	aCc	aAc	1	1	AY.50	0.000799
S	1238	T1238T	acC	acT	1	1	AY.53	0.000288
S	1238	T1238T	acC	acT	1	1	AY.54	0.000095
S	1238	T1238I	aCc	aTc	1	1	AY.6	0.000041
S	1238	T1238del	ACC	---	1	1	AY.6	0.000041
S	1238	T1238N	aCc	aAc	1	1	AY.62	0.000436
S	1238	T1238T	acC	acT	1	1	AY.65	0.000533
S	1238	T1238T	acC	acT	1	1	AY.67	0.000464
S	1238	T1238del	ACC	---	1	1	AY.68	0.000274
S	1238	T1238T	acC	acT	1	1	AY.7	0.000196
S	1238	T1238I	aCc	aTc	1	1	AY.7.2	0.000559
S	1238	T1238T	acC	acT	1	1	AY.71	0.000475
S	1238	T1238I	aCc	aTc	1	1	AY.71	0.000475
S	1238	T1238T	acC	acA	1	1	AY.76	0.004831
S	1238	T1238I	aCc	aTc	1	1	AY.78	0.001541
S	1238	T1238T	acC	acT	1	1	AY.79	0.001211
S	1238	T1238del	ACC	---	1	1	AY.81	0.001992
S	1238	T1238A	Acc	Gcc	1	1	AY.82	0.001357
S	1238	T1238I	aCc	aTc	1	1	AY.83	0.001724
S	1238	T1238I	aCc	aTc	1	1	AY.85	0.000427
S	1238	T1238I	aCc	aTc	1	1	AY.9.2	0.000037
S	1238	T1238T	acC	acT	1	1	AY.91	0.00073
S	1238	T1238T	acC	acT	1	1	AY.93	0.000273
S	1238	T1238I	aCc	aTc	1	1	AY.98	0.000079
S	1238	T1238N	aCc	aAc	1	1	AY.98.1	0.000048
S	1238	T1238I	aCc	aTc	1	1	B	0.000128
S	1238	T1238D	ACc	GAc	1	1	B.1	0.000009
S	1238	T1238V	ACc	GTc	1	1	B.1	0.000009
S	1238	T1238I	aCc	aTc	1	1	B.1.1.10	0.001115
S	1238	T1238T	acC	acA	1	1	B.1.1.121	0.002427
S	1238	T1238T	acC	acT	1	1	B.1.1.153	0.001095
S	1238	T1238T	acC	acT	1	1	B.1.1.163	0.007634
S	1238	T1238I	aCc	aTc	1	1	B.1.1.198	0.001468
S	1238	T1238I	aCc	aTc	1	1	B.1.1.214	0.000055
S	1238	T1238T	acC	acT	1	1	B.1.1.216	0.00089
S	1238	T1238T	acC	acT	1	1	B.1.1.231	0.003096
S	1238	T1238T	acC	acT	1	1	B.1.1.240	0.004695
S	1238	T1238T	acC	acT	1	1	B.1.1.241	0.00207
S	1238	T1238T	acC	acT	1	1	B.1.1.243	0.004082
S	1238	T1238A	Acc	Gcc	1	1	B.1.1.28	0.000311
S	1238	T1238I	aCc	aTc	1	1	B.1.1.28	0.000311
S	1238	T1238T	acC	acT	1	1	B.1.1.284	0.000107
S	1238	T1238T	acC	acT	1	1	B.1.1.301	0.001179
S	1238	T1238I	aCc	aTc	1	1	B.1.1.306	0.000438
S	1238	T1238N	aCc	aAc	1	1	B.1.1.306	0.000438
S	1238	T1238T	acC	acT	1	1	B.1.1.312	0.001912
S	1238	T1238I	aCc	aTc	1	1	B.1.1.315	0.008475
S	1238	T1238I	aCc	aTc	1	1	B.1.1.33	0.000421
S	1238	T1238A	Acc	Gcc	1	1	B.1.1.344	0.010753
S	1238	T1238T	acC	acT	1	1	B.1.1.368	0.003086
S	1238	T1238T	acC	acT	1	1	B.1.1.370	0.012658
S	1238	T1238T	acC	acT	1	1	B.1.1.397	0.002252
S	1238	T1238del	ACC	---	1	1	B.1.1.434	0.000349
S	1238	T1238T	acC	acT	1	1	B.1.1.486	0.001577
S	1238	T1238T	acC	acT	1	1	B.1.1.52	0.012195
S	1238	T1238T	acC	acT	1	1	B.1.1.98	0.018519
S	1238	T1238T	acC	acT	1	1	B.1.110	0.004525
S	1238	T1238T	acC	acT	1	1	B.1.120	0.007692
S	1238	T1238T	acC	acT	1	1	B.1.128	0.000635
S	1238	T1238T	acC	acT	1	1	B.1.158	0.02381
S	1238	T1238T	acC	acT	1	1	B.1.160.20	0.008929
S	1238	T1238del	ACC	---	1	1	B.1.160.23	0.004831
S	1238	T1238P	Acc	Ccc	1	1	B.1.160.24	0.004425
S	1238	T1238del	ACC	---	1	1	B.1.177.10	0.000878
S	1238	T1238del	ACC	---	1	1	B.1.177.17	0.000821
S	1238	T1238del	ACC	---	1	1	B.1.177.18	0.00116
S	1238	T1238del	ACC	---	1	1	B.1.177.19	0.001431
S	1238	T1238T	acC	acT	1	1	B.1.177.24	0.001295
S	1238	T1238T	acC	acT	1	1	B.1.177.4	0.000211
S	1238	T1238T	acC	acT	1	1	B.1.177.52	0.001757
S	1238	T1238T	acC	acT	1	1	B.1.177.54	0.000606
S	1238	T1238del	ACC	---	1	1	B.1.177.54	0.000606
S	1238	T1238I	aCc	aTc	1	1	B.1.177.55	0.002331
S	1238	T1238T	acC	acA	1	1	B.1.177.58	0.001332
S	1238	T1238I	aCc	aTc	1	1	B.1.177.58	0.001332
S	1238	T1238T	acC	acT	1	1	B.1.177.61	0.043478
S	1238	T1238del	ACC	---	1	1	B.1.177.76	0.002494
S	1238	T1238I	aCc	aTc	1	1	B.1.177.85	0.005435
S	1238	T1238A	Acc	Gcc	1	1	B.1.2	0.000009
S	1238	T1238P	Acc	Ccc	1	1	B.1.2	0.000009
S	1238	T1238del	ACC	---	1	1	B.1.218	0.005155
S	1238	T1238del	ACC	---	1	1	B.1.221.1	0.002907
S	1238	T1238del	ACC	---	1	1	B.1.23	0.006061
S	1238	T1238T	acC	acT	1	1	B.1.232	0.000537
S	1238	T1238I	aCc	aTc	1	1	B.1.236	0.002053
S	1238	T1238T	acC	acT	1	1	B.1.236	0.002053
S	1238	T1238T	acC	acT	1	1	B.1.237	0.004975
S	1238	T1238T	acC	acT	1	1	B.1.239	0.001221
S	1238	T1238T	acC	acT	1	1	B.1.241	0.000812
S	1238	T1238T	acC	acT	1	1	B.1.251	0.021739
S	1238	T1238N	aCc	aAc	1	1	B.1.258	0.000067
S	1238	T1238T	acC	acT	1	1	B.1.258.11	0.000396
S	1238	T1238N	aCc	aAc	1	1	B.1.258.11	0.000396
S	1238	T1238T	acC	acT	1	1	B.1.258.17	0.000104
S	1238	T1238N	aCc	aAc	1	1	B.1.258.17	0.000104
S	1238	T1238T	acC	acT	1	1	B.1.265	0.001271
S	1238	T1238T	acC	acT	1	1	B.1.281	0.021739
S	1238	T1238T	acC	acA	1	1	B.1.320	0.001245
S	1238	T1238I	aCc	aTc	1	1	B.1.324	0.001605
S	1238	T1238T	acC	acT	1	1	B.1.332	0.003497
S	1238	T1238T	acC	acT	1	1	B.1.341	0.022727
S	1238	T1238T	acC	acT	1	1	B.1.349	0.000715
S	1238	T1238A	AcC	GcA	1	1	B.1.351	0.00003
S	1238	T1238T	acC	acA	1	1	B.1.351.2	0.000303
S	1238	T1238P	Acc	Ccc	1	1	B.1.36	0.000146
S	1238	T1238del	ACC	---	1	1	B.1.36.17	0.000494
S	1238	T1238del	ACC	---	1	1	B.1.36.18	0.00042
S	1238	T1238I	aCc	aTc	1	1	B.1.36.39	0.002217
S	1238	T1238T	acC	acT	1	1	B.1.369	0.000285
S	1238	T1238A	Acc	Gcc	1	1	B.1.375	0.00082
S	1238	T1238del	ACC	---	1	1	B.1.389	0.001002
S	1238	T1238del	ACC	---	1	1	B.1.409	0.000781
S	1238	T1238S	Acc	Tcc	1	1	B.1.411	0.003704
S	1238	T1238I	aCc	aTc	1	1	B.1.427	0.00005
S	1238	T1238S	Acc	Tcc	1	1	B.1.429	0.000024
S	1238	T1238I	aCc	aTc	1	1	B.1.436	0.001029
S	1238	T1238S	Acc	Tcc	1	1	B.1.462	0.007246
S	1238	T1238K	aCC	aAA	1	1	B.1.462	0.007246
S	1238	T1238T	acC	acT	1	1	B.1.499	0.00105
S	1238	T1238T	acC	acT	1	1	B.1.503	0.002488
S	1238	T1238T	acC	acA	1	1	B.1.521	0.004975
S	1238	T1238I	aCc	aTc	1	1	B.1.525	0.000113
S	1238	T1238T	acC	acT	1	1	B.1.540	0.009709
S	1238	T1238I	aCc	aTc	1	1	B.1.580	0.004065
S	1238	T1238I	aCc	aTc	1	1	B.1.595	0.000261
S	1238	T1238N	aCc	aAc	1	1	B.1.596	0.000087
S	1238	T1238A	Acc	Gcc	1	1	B.1.611	0.04
S	1238	T1238I	aCc	aTc	1	1	B.1.612	0.002653
S	1238	T1238N	aCc	aAc	1	1	B.1.617.1	0.000129
S	1238	T1238S	AcC	TcT	1	1	B.1.617.2	0.000004
S	1238	T1238I	aCc	aTc	1	1	B.1.621	0.000089
S	1238	T1238N	aCc	aAc	1	1	B.1.621	0.000089
S	1238	T1238I	aCc	aTc	1	1	B.1.628	0.000352
S	1238	T1238T	acC	acT	1	1	B.31	0.003731
S	1238	T1238N	aCc	aAc	1	1	B.55	0.00295
S	1238	T1238S	Acc	Tcc	1	1	B.55	0.00295
S	1238	T1238Y	ACc	TAc	1	1	B.55	0.00295
S	1238	T1238T	acC	acT	1	1	B.61	0.005747
S	1238	T1238del	ACC	---	1	1	C.17	0.055556
S	1238	T1238N	aCc	aAc	1	1	C.37	0.000116
S	1238	T1238P	Acc	Ccc	1	1	D.2	0.000075
S	1238	T1238N	aCc	aAc	1	1	P.1	0.000016
S	1238	T1238S	Acc	Tcc	1	1	P.1	0.000016
S	1238	T1238del	ACC	---	1	1	P.1	0.000016
S	1238	T1238T	acC	acA	1	1	P.1.16	0.000374
S	1238	T1238I	aCc	aTc	1	1	P.1.17	0.000162
S	1238	T1238T	acC	acT	1	1	P.1.7	0.000319
S	1238	T1238N	aCc	aAc	1	1	P.1.7	0.000319
S	1238	T1238I	aCc	aTc	1	1	P.1.7	0.000319
S	1238	T1238I	aCc	aTc	1	1	P.2	0.000187
S	1238	T1238I	aCc	aTc	1	1	Q.2	0.000613
S	1238	T1238T	acC	acT	1	1	Q.7	0.001111
S	1238	T1238N	aCc	aAc	1	1	R.1	0.00009
S	1238	T1238del	ACC	---	1	1	U.3	0.003861
S	1238	T1238T	acC	acT	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.