CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 369

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
ORF1ab/nsp2	369	S369S	S549S	syn	tcC	tcT	29792	29513	0.990635	1910-1912
ORF1ab/nsp2	369	S369S	S549S	syn	tcC	tcA	29792	259	0.00869361	1910-1912
ORF1ab/nsp2	369	S369S	S549S	syn	tcC	tcG	29792	19	0.000637755	1910-1912
ORF1ab/nsp2	369	S369S	S549S	syn	TCC	AGT	29792	1	0.0000335661	1910-1912
ORF1ab/nsp2	369	S369F	S549F	nonsyn	tCc	tTc	2753	2741	0.995641	1910-1912
ORF1ab/nsp2	369	S369F	S549F	nonsyn	tCC	tTT	2753	12	0.00435888	1910-1912
ORF1ab/nsp2	369	S369T	S549T	nonsyn	Tcc	Acc	1252	1251	0.999201	1910-1912
ORF1ab/nsp2	369	S369T	S549T	nonsyn	TcC	AcT	1252	1	0.000798722	1910-1912
ORF1ab/nsp2	369	S369A	S549A	nonsyn	Tcc	Gcc	57	57	1	1910-1912
ORF1ab/nsp2	369	S369del	S549del	del	TCC	---	48	48	1	1910-1912
ORF1ab/nsp2	369	S369Y	S549Y	nonsyn	tCc	tAc	32	32	1	1910-1912
ORF1ab/nsp2	369	S369del1	S549del1	del	tCc	t-c	11	7	0.636364	1910-1912
ORF1ab/nsp2	369	S369del1	S549del1	del	Tcc	-cc	11	3	0.272727	1910-1912
ORF1ab/nsp2	369	S369del1	S549del1	del	tcC	tc-	11	1	0.0909091	1910-1912
ORF1ab/nsp2	369	S369C	S549C	nonsyn	tCc	tGc	10	10	1	1910-1912
ORF1ab/nsp2	369	S369P	S549P	nonsyn	Tcc	Ccc	7	7	1	1910-1912
ORF1ab/nsp2	369	S369L	S549L	nonsyn	TCc	CTc	4	4	1	1910-1912
ORF1ab/nsp2	369	S369del2	S549del2	del	tCC	t--	3	2	0.666667	1910-1912
ORF1ab/nsp2	369	S369del2	S549del2	del	TCc	--c	3	1	0.333333	1910-1912
ORF1ab/nsp2	369	S369V	S549V	nonsyn	TCc	GTc	1	1	1	1910-1912

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
ORF1ab/nsp2	369	S369S	tcC	tcT	29513	29792	All	0.005645
ORF1ab/nsp2	369	S369S	tcC	tcA	259	29792	All	0.00005
ORF1ab/nsp2	369	S369S	tcC	tcG	19	29792	All	0.000004
ORF1ab/nsp2	369	S369S	TCC	AGT	1	29792	All	0
ORF1ab/nsp2	369	S369S	tcC	tcT	3530	3530	B.1.429	0.083057
ORF1ab/nsp2	369	S369S	tcC	tcT	3057	3099	B.1.1.7	0.002737
ORF1ab/nsp2	369	S369S	tcC	tcA	31	3099	B.1.1.7	0.000028
ORF1ab/nsp2	369	S369S	tcC	tcG	11	3099	B.1.1.7	0.00001
ORF1ab/nsp2	369	S369S	tcC	tcT	2996	2996	P.1.7	0.956577
ORF1ab/nsp2	369	S369F	tCc	tTc	2741	2753	All	0.000524
ORF1ab/nsp2	369	S369F	tCC	tTT	12	2753	All	0.000002
ORF1ab/nsp2	369	S369S	tcC	tcT	2143	2143	AY.44	0.013044
ORF1ab/nsp2	369	S369S	tcC	tcT	1797	1805	AY.4	0.002797
ORF1ab/nsp2	369	S369S	tcC	tcA	8	1805	AY.4	0.000012
ORF1ab/nsp2	369	S369S	tcC	tcT	1369	1400	B.1.617.2	0.005155
ORF1ab/nsp2	369	S369S	tcC	tcA	31	1400	B.1.617.2	0.000117
ORF1ab/nsp2	369	S369T	Tcc	Acc	1251	1252	All	0.000239
ORF1ab/nsp2	369	S369T	TcC	AcT	1	1252	All	0
ORF1ab/nsp2	369	S369T	Tcc	Acc	1152	1152	AY.4	0.001793
ORF1ab/nsp2	369	S369S	tcC	tcT	1092	1092	P.1.13	0.981132
ORF1ab/nsp2	369	S369S	tcC	tcT	900	900	B.1.1.153	0.985761
ORF1ab/nsp2	369	S369S	tcC	tcT	896	896	AY.5	0.018502
ORF1ab/nsp2	369	S369S	tcC	tcT	846	846	P.1.2	0.978035
ORF1ab/nsp2	369	S369S	tcC	tcT	638	638	B.1.2	0.005618
ORF1ab/nsp2	369	S369S	tcC	tcT	488	569	AY.43	0.002162
ORF1ab/nsp2	369	S369S	tcC	tcA	80	569	AY.43	0.000354
ORF1ab/nsp2	369	S369S	tcC	tcG	1	569	AY.43	0.000004
ORF1ab/nsp2	369	S369S	tcC	tcT	558	563	B.1	0.005111
ORF1ab/nsp2	369	S369S	tcC	tcA	5	563	B.1	0.000046
ORF1ab/nsp2	369	S369S	tcC	tcT	560	560	AY.40	0.540019
ORF1ab/nsp2	369	S369F	tCc	tTc	520	520	AY.44	0.003165
ORF1ab/nsp2	369	S369S	tcC	tcT	487	499	AY.25	0.002929
ORF1ab/nsp2	369	S369S	tcC	tcA	12	499	AY.25	0.000072
ORF1ab/nsp2	369	S369S	tcC	tcT	491	491	B.1.1.51	0.843643
ORF1ab/nsp2	369	S369S	tcC	tcT	477	477	B.1.627	0.963636
ORF1ab/nsp2	369	S369F	tCc	tTc	454	454	AY.119	0.01603
ORF1ab/nsp2	369	S369F	tCc	tTc	411	411	B.1.617.2	0.001548
ORF1ab/nsp2	369	S369S	tcC	tcT	343	345	P.1	0.005404
ORF1ab/nsp2	369	S369S	tcC	tcA	2	345	P.1	0.000032
ORF1ab/nsp2	369	S369S	tcC	tcT	323	325	AY.3	0.003213
ORF1ab/nsp2	369	S369S	tcC	tcG	2	325	AY.3	0.00002
ORF1ab/nsp2	369	S369S	tcC	tcT	319	322	B.1.1	0.005787
ORF1ab/nsp2	369	S369S	tcC	tcA	3	322	B.1.1	0.000054
ORF1ab/nsp2	369	S369S	tcC	tcT	270	274	AY.103	0.001676
ORF1ab/nsp2	369	S369S	tcC	tcG	2	274	AY.103	0.000012
ORF1ab/nsp2	369	S369S	tcC	tcA	2	274	AY.103	0.000012
ORF1ab/nsp2	369	S369S	tcC	tcT	273	274	AY.47	0.008492
ORF1ab/nsp2	369	S369S	tcC	tcA	1	274	AY.47	0.000031
ORF1ab/nsp2	369	S369S	tcC	tcT	264	264	B.1.243	0.01837
ORF1ab/nsp2	369	S369F	tCc	tTc	244	244	B.1.1.7	0.000218
ORF1ab/nsp2	369	S369S	tcC	tcT	217	217	B.1.177	0.002857
ORF1ab/nsp2	369	S369F	tCc	tTc	188	188	AY.4	0.000293
ORF1ab/nsp2	369	S369S	tcC	tcT	166	169	AY.23	0.011578
ORF1ab/nsp2	369	S369S	tcC	tcA	3	169	AY.23	0.000209
ORF1ab/nsp2	369	S369S	tcC	tcT	144	144	B.1.1.519	0.005718
ORF1ab/nsp2	369	S369S	tcC	tcT	126	126	AY.46.6	0.009098
ORF1ab/nsp2	369	S369S	tcC	tcT	125	125	B.1.427	0.006312
ORF1ab/nsp2	369	S369S	tcC	tcT	122	122	B.1.177.21	0.009329
ORF1ab/nsp2	369	S369S	tcC	tcT	120	120	B.1.160	0.003743
ORF1ab/nsp2	369	S369S	tcC	tcT	113	113	AY.100	0.005199
ORF1ab/nsp2	369	S369S	tcC	tcT	105	106	AY.26	0.002973
ORF1ab/nsp2	369	S369S	tcC	tcA	1	106	AY.26	0.000028
ORF1ab/nsp2	369	S369S	tcC	tcT	97	97	B.1.221	0.00689
ORF1ab/nsp2	369	S369S	tcC	tcT	90	90	B.1.1.47	0.481283
ORF1ab/nsp2	369	S369S	tcC	tcT	84	84	AY.102	0.002227
ORF1ab/nsp2	369	S369S	tcC	tcT	76	76	B.1.1.318	0.022933
ORF1ab/nsp2	369	S369S	tcC	tcT	65	72	AY.39	0.001606
ORF1ab/nsp2	369	S369S	tcC	tcA	7	72	AY.39	0.000173
ORF1ab/nsp2	369	S369F	tCc	tTc	71	71	AY.103	0.000441
ORF1ab/nsp2	369	S369S	tcC	tcT	71	71	B.1.1.317	0.02923
ORF1ab/nsp2	369	S369S	tcC	tcT	70	70	AY.119	0.002472
ORF1ab/nsp2	369	S369S	tcC	tcT	68	68	AY.116	0.019501
ORF1ab/nsp2	369	S369S	tcC	tcT	68	68	AY.120	0.002528
ORF1ab/nsp2	369	S369S	tcC	tcT	65	65	B.1.177.7	0.010715
ORF1ab/nsp2	369	S369S	tcC	tcT	63	64	B.1.351	0.001873
ORF1ab/nsp2	369	S369S	tcC	tcA	1	64	B.1.351	0.00003
ORF1ab/nsp2	369	S369F	tCc	tTc	63	63	AY.43	0.000279
ORF1ab/nsp2	369	S369S	tcC	tcT	56	61	AY.29	0.000883
ORF1ab/nsp2	369	S369S	tcC	tcA	5	61	AY.29	0.000079
ORF1ab/nsp2	369	S369S	tcC	tcT	56	60	AY.118	0.003508
ORF1ab/nsp2	369	S369S	tcC	tcA	4	60	AY.118	0.000251
ORF1ab/nsp2	369	S369S	tcC	tcT	60	60	B.1.234	0.007917
ORF1ab/nsp2	369	S369S	tcC	tcT	58	60	B.1.526	0.001363
ORF1ab/nsp2	369	S369S	tcC	tcG	1	60	B.1.526	0.000024
ORF1ab/nsp2	369	S369S	tcC	tcA	1	60	B.1.526	0.000024
ORF1ab/nsp2	369	S369A	Tcc	Gcc	57	57	All	0.000011
ORF1ab/nsp2	369	S369S	tcC	tcT	56	57	B	0.007157
ORF1ab/nsp2	369	S369S	TCC	AGT	1	57	B	0.000128
ORF1ab/nsp2	369	S369S	tcC	tcT	57	57	B.1.1.1	0.018621
ORF1ab/nsp2	369	S369S	tcC	tcT	56	56	B.1.177.57	0.015735
ORF1ab/nsp2	369	S369S	tcC	tcT	54	54	B.1.325	0.372414
ORF1ab/nsp2	369	S369S	tcC	tcT	53	53	C.37	0.006151
ORF1ab/nsp2	369	S369S	tcC	tcT	49	49	AY.14	0.004313
ORF1ab/nsp2	369	S369del	TCC	---	48	48	All	0.000009
ORF1ab/nsp2	369	S369S	tcC	tcT	47	47	B.1.1.311	0.016834
ORF1ab/nsp2	369	S369F	tCc	tTc	46	47	B.1.2	0.000405
ORF1ab/nsp2	369	S369F	tCC	tTT	1	47	B.1.2	0.000009
ORF1ab/nsp2	369	S369S	tcC	tcT	47	47	B.1.637	0.003434
ORF1ab/nsp2	369	S369S	tcC	tcT	46	46	AY.4.2	0.000998
ORF1ab/nsp2	369	S369S	tcC	tcT	46	46	AY.99.2	0.004239
ORF1ab/nsp2	369	S369S	tcC	tcT	41	43	AY.6	0.001686
ORF1ab/nsp2	369	S369S	tcC	tcA	2	43	AY.6	0.000082
ORF1ab/nsp2	369	S369S	tcC	tcT	39	42	AY.20	0.001516
ORF1ab/nsp2	369	S369S	tcC	tcA	3	42	AY.20	0.000117
ORF1ab/nsp2	369	S369S	tcC	tcT	42	42	B.1.1.368	0.12963
ORF1ab/nsp2	369	S369S	tcC	tcT	41	41	B.1.258	0.002728
ORF1ab/nsp2	369	S369S	tcC	tcT	40	40	AY.24	0.017241
ORF1ab/nsp2	369	S369S	tcC	tcT	40	40	AY.93	0.010923
ORF1ab/nsp2	369	S369S	tcC	tcT	39	39	AY.42	0.001569
ORF1ab/nsp2	369	S369F	tCc	tTc	39	39	B.1	0.000357
ORF1ab/nsp2	369	S369S	tcC	tcT	38	39	B.1.621	0.003364
ORF1ab/nsp2	369	S369S	tcC	tcA	1	39	B.1.621	0.000089
ORF1ab/nsp2	369	S369S	tcC	tcT	36	38	AY.61	0.003772
ORF1ab/nsp2	369	S369S	tcC	tcA	2	38	AY.61	0.00021
ORF1ab/nsp2	369	S369S	tcC	tcT	38	38	P.1.1	0.012071
ORF1ab/nsp2	369	S369F	tCc	tTc	36	36	AY.3	0.000358
ORF1ab/nsp2	369	S369S	tcC	tcT	36	36	AY.85	0.015378
ORF1ab/nsp2	369	S369S	tcC	tcT	36	36	B.1.1.28	0.011204
ORF1ab/nsp2	369	S369S	tcC	tcT	36	36	B.1.36	0.005252
ORF1ab/nsp2	369	S369S	tcC	tcA	30	35	B.1.177.81	0.00568
ORF1ab/nsp2	369	S369S	tcC	tcT	5	35	B.1.177.81	0.000947
ORF1ab/nsp2	369	S369S	tcC	tcT	35	35	P.1.14	0.001673
ORF1ab/nsp2	369	S369S	tcC	tcT	34	34	AY.4.5	0.003655
ORF1ab/nsp2	369	S369S	tcC	tcT	33	33	P.1.17	0.005338
ORF1ab/nsp2	369	S369Y	tCc	tAc	32	32	All	0.000006
ORF1ab/nsp2	369	S369S	tcC	tcT	32	32	B.1.177.86	0.00587
ORF1ab/nsp2	369	S369F	tCc	tTc	32	32	B.1.243	0.002227
ORF1ab/nsp2	369	S369S	tcC	tcT	30	30	AY.121	0.00406
ORF1ab/nsp2	369	S369S	tcC	tcT	30	30	AY.9.2	0.001102
ORF1ab/nsp2	369	S369S	tcC	tcT	29	29	B.1.1.222	0.005916
ORF1ab/nsp2	369	S369S	tcC	tcT	29	29	P.2	0.005412
ORF1ab/nsp2	369	S369S	tcC	tcT	28	28	AY.45	0.003407
ORF1ab/nsp2	369	S369S	tcC	tcT	28	28	AY.75	0.001569
ORF1ab/nsp2	369	S369S	tcC	tcT	28	28	B.1.591	0.297872
ORF1ab/nsp2	369	S369F	tCc	tTc	28	28	P.1	0.000441
ORF1ab/nsp2	369	S369S	tcC	tcT	27	27	AY.33	0.001803
ORF1ab/nsp2	369	S369S	tcC	tcT	27	27	B.1.36.29	0.013968
ORF1ab/nsp2	369	S369S	tcC	tcT	26	26	AD.2	0.005693
ORF1ab/nsp2	369	S369S	tcC	tcT	26	26	B.1.232	0.013971
ORF1ab/nsp2	369	S369F	tCc	tTc	25	25	AY.102	0.000663
ORF1ab/nsp2	369	S369S	tcC	tcT	25	25	B.1.258.14	0.02451
ORF1ab/nsp2	369	S369F	tCc	tTc	25	25	R.1	0.00225
ORF1ab/nsp2	369	S369F	tCc	tTc	24	24	AY.25	0.000144
ORF1ab/nsp2	369	S369S	tcC	tcT	23	23	AY.50	0.018385
ORF1ab/nsp2	369	S369S	tcC	tcT	23	23	B.1.1.214	0.001276
ORF1ab/nsp2	369	S369S	tcC	tcT	23	23	B.1.588	0.020928
ORF1ab/nsp2	369	S369S	tcC	tcT	22	22	A.28	0.058201
ORF1ab/nsp2	369	S369S	tcC	tcT	22	22	AY.117	0.001859
ORF1ab/nsp2	369	S369T	Tcc	Acc	22	22	B.1.177	0.00029
ORF1ab/nsp2	369	S369S	tcC	tcT	21	21	AY.98	0.001659
ORF1ab/nsp2	369	S369S	tcC	tcT	21	21	B.1.1.209	0.1875
ORF1ab/nsp2	369	S369S	tcC	tcT	21	21	B.1.1.50	0.014257
ORF1ab/nsp2	369	S369S	tcC	tcT	21	21	B.1.438.1	0.002252
ORF1ab/nsp2	369	S369S	tcC	tcT	21	21	B.1.8	0.04142
ORF1ab/nsp2	369	S369S	tcC	tcT	20	20	AY.36	0.002964
ORF1ab/nsp2	369	S369A	Tcc	Gcc	20	20	B.1.1.369	0.008925
ORF1ab/nsp2	369	S369S	tcC	tcT	20	20	B.1.1.487	0.111732
ORF1ab/nsp2	369	S369S	tcC	tcT	19	20	B.1.596	0.001656
ORF1ab/nsp2	369	S369S	tcC	tcA	1	20	B.1.596	0.000087
ORF1ab/nsp2	369	S369S	tcC	tcT	19	19	AY.27	0.00123
ORF1ab/nsp2	369	S369S	tcC	tcT	19	19	B.1.1.448	0.038618
ORF1ab/nsp2	369	S369F	tCc	tTc	19	19	B.1.177	0.00025
ORF1ab/nsp2	369	S369S	tcC	tcT	19	19	B.1.324	0.030498
ORF1ab/nsp2	369	S369S	tcC	tcT	18	18	AY.39.1	0.000713
ORF1ab/nsp2	369	S369S	tcC	tcT	18	18	B.1.1.37	0.003472
ORF1ab/nsp2	369	S369S	tcC	tcT	18	18	B.1.177.60	0.003932
ORF1ab/nsp2	369	S369S	tcC	tcT	16	17	AY.46	0.001665
ORF1ab/nsp2	369	S369S	tcC	tcA	1	17	AY.46	0.000104
ORF1ab/nsp2	369	S369S	tcC	tcT	17	17	AY.9	0.001149
ORF1ab/nsp2	369	S369F	tCc	tTc	16	17	B.1.1	0.00029
ORF1ab/nsp2	369	S369F	tCC	tTT	1	17	B.1.1	0.000018
ORF1ab/nsp2	369	S369S	tcC	tcT	17	17	B.1.177.16	0.011296
ORF1ab/nsp2	369	S369S	tcC	tcT	17	17	B.1.577	0.011684
ORF1ab/nsp2	369	S369S	tcC	tcT	17	17	B.1.582	0.008342
ORF1ab/nsp2	369	S369S	tcC	tcT	17	17	C.1.2	0.07234
ORF1ab/nsp2	369	S369S	tcC	tcT	17	17	R.1	0.00153
ORF1ab/nsp2	369	S369F	tCc	tTc	16	16	A.2.5.2	0.025157
ORF1ab/nsp2	369	S369S	tcC	tcT	16	16	AY.66	0.017112
ORF1ab/nsp2	369	S369F	tCc	tTc	8	16	B.1.429	0.000188
ORF1ab/nsp2	369	S369F	tCC	tTT	8	16	B.1.429	0.000188
ORF1ab/nsp2	369	S369S	tcC	tcT	16	16	B.1.466.2	0.00626
ORF1ab/nsp2	369	S369S	tcC	tcT	16	16	B.1.617.1	0.002063
ORF1ab/nsp2	369	S369S	tcC	tcT	16	16	P.1.16	0.005986
ORF1ab/nsp2	369	S369F	tCc	tTc	15	15	AY.42	0.000603
ORF1ab/nsp2	369	S369S	tcC	tcT	15	15	AY.48	0.006977
ORF1ab/nsp2	369	S369F	tCc	tTc	15	15	AY.75	0.00084
ORF1ab/nsp2	369	S369S	tcC	tcT	15	15	B.1.1.25	0.008528
ORF1ab/nsp2	369	S369S	tcC	tcT	13	15	D.2	0.000976
ORF1ab/nsp2	369	S369S	tcC	tcA	2	15	D.2	0.00015
ORF1ab/nsp2	369	S369S	tcC	tcT	14	14	C.27	0.259259
ORF1ab/nsp2	369	S369S	tcC	tcT	14	14	Q.8	0.002309
ORF1ab/nsp2	369	S369S	tcC	tcT	13	13	AY.35	0.00303
ORF1ab/nsp2	369	S369F	tCc	tTc	13	13	AY.5	0.000268
ORF1ab/nsp2	369	S369F	tCc	tTc	13	13	B.1.1.397	0.029279
ORF1ab/nsp2	369	S369S	tcC	tcT	13	13	C.1	0.0311
ORF1ab/nsp2	369	S369S	tcC	tcT	12	12	AY.5.4	0.00332
ORF1ab/nsp2	369	S369S	tcC	tcT	12	12	B.1.1.244	0.184615
ORF1ab/nsp2	369	S369S	tcC	tcT	12	12	B.1.1.258	0.039088
ORF1ab/nsp2	369	S369S	tcC	tcT	12	12	B.1.162	0.060302
ORF1ab/nsp2	369	S369F	tCc	tTc	12	12	B.1.234	0.001583
ORF1ab/nsp2	369	S369S	tcC	tcT	12	12	B.1.480	0.029851
ORF1ab/nsp2	369	S369F	tCc	tTc	12	12	B.3	0.009967
ORF1ab/nsp2	369	S369F	tCc	tTc	12	12	Q.3	0.00174
ORF1ab/nsp2	369	S369S	tcC	tcT	11	11	A	0.004257
ORF1ab/nsp2	369	S369S	tcC	tcT	11	11	A.2.5	0.005489
ORF1ab/nsp2	369	S369del1	tCc	t-c	7	11	All	0.000001
ORF1ab/nsp2	369	S369del1	Tcc	-cc	3	11	All	0.000001
ORF1ab/nsp2	369	S369del1	tcC	tc-	1	11	All	0
ORF1ab/nsp2	369	S369S	tcC	tcT	11	11	AY.110	0.00124
ORF1ab/nsp2	369	S369S	tcC	tcT	11	11	AY.5.3	0.003711
ORF1ab/nsp2	369	S369S	tcC	tcT	11	11	AY.98.1	0.000533
ORF1ab/nsp2	369	S369del	TCC	---	11	11	B.1.1.7	0.00001
ORF1ab/nsp2	369	S369S	tcC	tcT	11	11	B.1.236	0.022587
ORF1ab/nsp2	369	S369T	Tcc	Acc	11	11	B.1.243	0.000765
ORF1ab/nsp2	369	S369S	tcC	tcT	11	11	B.1.623	0.005901
ORF1ab/nsp2	369	S369C	tCc	tGc	10	10	All	0.000002
ORF1ab/nsp2	369	S369S	tcC	tcT	9	10	AY.4.2.1	0.001341
ORF1ab/nsp2	369	S369S	tcC	tcA	1	10	AY.4.2.1	0.000149
ORF1ab/nsp2	369	S369F	tCc	tTc	10	10	AY.47	0.000311
ORF1ab/nsp2	369	S369S	tcC	tcT	10	10	AY.68	0.002737
ORF1ab/nsp2	369	S369S	tcC	tcT	10	10	AY.74	0.001156
ORF1ab/nsp2	369	S369F	tCc	tTc	10	10	AY.9	0.000676
ORF1ab/nsp2	369	S369F	tCc	tTc	10	10	B.1.1.519	0.000397
ORF1ab/nsp2	369	S369S	tcC	tcT	10	10	B.1.258.17	0.00104
ORF1ab/nsp2	369	S369S	tcC	tcT	10	10	B.1.469	0.036101
ORF1ab/nsp2	369	S369S	tcC	tcT	10	10	B.6.6	0.008889
ORF1ab/nsp2	369	S369S	tcC	tcT	8	9	AY.111	0.001465
ORF1ab/nsp2	369	S369S	tcC	tcA	1	9	AY.111	0.000183
ORF1ab/nsp2	369	S369F	tCc	tTc	9	9	AY.26	0.000255
ORF1ab/nsp2	369	S369F	tCc	tTc	9	9	AY.39	0.000222
ORF1ab/nsp2	369	S369S	tcC	tcT	9	9	B.1.1.326	0.015845
ORF1ab/nsp2	369	S369S	tcC	tcT	9	9	B.1.177.52	0.015817
ORF1ab/nsp2	369	S369F	tCc	tTc	9	9	B.1.324	0.014446
ORF1ab/nsp2	369	S369F	tCc	tTc	9	9	B.1.402	0.088235
ORF1ab/nsp2	369	S369S	tcC	tcT	9	9	P.1.15	0.002091
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	AY.106	0.002679
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	AY.12	0.002528
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	AY.34.1	0.00408
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	B.1.1.125	0.081633
ORF1ab/nsp2	369	S369F	tCc	tTc	8	8	B.1.1.50	0.005431
ORF1ab/nsp2	369	S369T	Tcc	Acc	8	8	B.1.1.7	0.000007
ORF1ab/nsp2	369	S369C	tCc	tGc	8	8	B.1.1.7	0.000007
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	B.1.311	0.002197
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	B.1.367	0.006339
ORF1ab/nsp2	369	S369F	tCc	tTc	8	8	B.1.400	0.003432
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	B.1.576	0.007253
ORF1ab/nsp2	369	S369F	tCc	tTc	8	8	B.1.595	0.002088
ORF1ab/nsp2	369	S369S	tcC	tcT	8	8	B.1.634	0.027397
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	A.1	0.001973
ORF1ab/nsp2	369	S369P	Tcc	Ccc	7	7	All	0.000001
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	AY.114	0.001618
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	AY.30	0.00277
ORF1ab/nsp2	369	S369A	Tcc	Gcc	7	7	AY.4	0.000011
ORF1ab/nsp2	369	S369F	tCc	tTc	7	7	AY.46.6	0.000505
ORF1ab/nsp2	369	S369S	tcC	tcT	6	7	AY.9.1	0.000502
ORF1ab/nsp2	369	S369S	tcC	tcA	1	7	AY.9.1	0.000084
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	B.1.1.294	0.008861
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	B.1.1.389	0.042424
ORF1ab/nsp2	369	S369S	tcC	tcT	4	7	B.1.36.8	0.004
ORF1ab/nsp2	369	S369S	tcC	tcA	3	7	B.1.36.8	0.003
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	B.1.400	0.003003
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	B.1.470	0.009831
ORF1ab/nsp2	369	S369S	tcC	tcT	7	7	B.1.595	0.001827
ORF1ab/nsp2	369	S369Y	tCc	tAc	7	7	B.1.617.2	0.000026
ORF1ab/nsp2	369	S369F	tCc	tTc	7	7	B.3.1	0.011609
ORF1ab/nsp2	369	S369F	tCc	tTc	6	6	AY.104	0.011905
ORF1ab/nsp2	369	S369F	tCc	tTc	6	6	AY.16	0.002278
ORF1ab/nsp2	369	S369F	tCc	tTc	6	6	AY.29	0.000095
ORF1ab/nsp2	369	S369F	tCc	tTc	6	6	AY.33	0.000401
ORF1ab/nsp2	369	S369Y	tCc	tAc	6	6	AY.4	0.000009
ORF1ab/nsp2	369	S369T	Tcc	Acc	6	6	AY.43	0.000027
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	AY.52	0.004886
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	AY.69	0.00112
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	AY.75.1	0.001082
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	AY.8	0.003636
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	B.1.1.280	0.018519
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	B.1.240	0.001293
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	B.1.416	0.007614
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	B.1.525	0.000679
ORF1ab/nsp2	369	S369A	Tcc	Gcc	6	6	B.1.617.2	0.000023
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	C.36	0.005464
ORF1ab/nsp2	369	S369S	tcC	tcT	6	6	P.3	0.009569
ORF1ab/nsp2	369	S369S	tcC	tcT	5	6	Q.3	0.000725
ORF1ab/nsp2	369	S369S	tcC	tcG	1	6	Q.3	0.000145
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.1	0.001979
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	AY.100	0.00023
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	AY.120.2	0.006427
ORF1ab/nsp2	369	S369T	Tcc	Acc	5	5	AY.3	0.00005
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.3.1	0.000426
ORF1ab/nsp2	369	S369Y	tCc	tAc	5	5	AY.44	0.00003
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	AY.46.2	0.003177
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.54	0.000477
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.77	0.005637
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.78	0.007704
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.84	0.002187
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.90	0.003422
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.92	0.001436
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	AY.99	0.005247
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.1.159	0.023364
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.1.170	0.006234
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	B.1.1.291	0.003712
ORF1ab/nsp2	369	S369T	Tcc	Acc	5	5	B.1.1.33	0.002104
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.1.33	0.002104
ORF1ab/nsp2	369	S369A	Tcc	Gcc	5	5	B.1.1.7	0.000004
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	B.1.160	0.000156
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.177.58	0.006658
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	B.1.258.17	0.00052
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.389	0.00501
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.404	0.00651
ORF1ab/nsp2	369	S369F	tCc	tTc	4	5	B.1.427	0.000202
ORF1ab/nsp2	369	S369F	tCC	tTT	1	5	B.1.427	0.00005
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.429.1	0.060241
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	B.1.497	0.001574
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.564.1	0.007886
ORF1ab/nsp2	369	S369F	tCc	tTc	5	5	B.1.596	0.000436
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	B.1.605	0.029762
ORF1ab/nsp2	369	S369T	Tcc	Acc	5	5	B.40	0.001821
ORF1ab/nsp2	369	S369S	tcC	tcT	5	5	Q.1	0.000632
ORF1ab/nsp2	369	S369L	TCc	CTc	4	4	All	0.000001
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	AY.113	0.00057
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	AY.118	0.000251
ORF1ab/nsp2	369	S369S	tcC	tcT	2	4	AY.120.1	0.000642
ORF1ab/nsp2	369	S369S	tcC	tcA	2	4	AY.120.1	0.000642
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	AY.120.2	0.005141
ORF1ab/nsp2	369	S369S	tcC	tcT	3	4	AY.16.1	0.00141
ORF1ab/nsp2	369	S369S	tcC	tcA	1	4	AY.16.1	0.00047
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	AY.32	0.00213
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	AY.45	0.000487
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	AY.53	0.00115
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	AY.7	0.000784
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	AY.75.1	0.000721
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.1.121	0.009709
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.1.207	0.004728
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.1.265	0.012618
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.1.306	0.001754
ORF1ab/nsp2	369	S369del	TCC	---	4	4	B.1.1.33	0.001684
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.1.434	0.001394
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.1.516	0.266667
ORF1ab/nsp2	369	S369Y	tCc	tAc	4	4	B.1.1.7	0.000004
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.1.74	0.017241
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.158	0.095238
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	B.1.177.15	0.002524
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.177.45	0.001525
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.177.5	0.004969
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.177.82	0.001909
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	B.1.177.86	0.000734
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	B.1.258	0.000266
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.265	0.005083
ORF1ab/nsp2	369	S369T	Tcc	Acc	4	4	B.1.351	0.000119
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	B.1.351	0.000119
ORF1ab/nsp2	369	S369S	tcC	tcT	3	4	B.1.351.3	0.002629
ORF1ab/nsp2	369	S369S	tcC	tcA	1	4	B.1.351.3	0.000876
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.36.18	0.001681
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.396	0.002823
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	B.1.526	0.000094
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.537	0.08
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	B.1.561	0.001588
ORF1ab/nsp2	369	S369T	Tcc	Acc	4	4	B.1.617.2	0.000015
ORF1ab/nsp2	369	S369F	tCc	tTc	4	4	D.2	0.0003
ORF1ab/nsp2	369	S369S	tcC	tcT	4	4	N.6	0.028369
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	AB.1	0.02459
ORF1ab/nsp2	369	S369del2	tCC	t--	2	3	All	0
ORF1ab/nsp2	369	S369del2	TCc	--c	1	3	All	0
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	AY.101	0.001471
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	AY.34	0.000291
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	AY.34	0.000291
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	AY.4.5	0.000322
ORF1ab/nsp2	369	S369T	Tcc	Acc	3	3	AY.4.5	0.000322
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	AY.41	0.000882
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	AY.46.2	0.001906
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	AY.5.1	0.011278
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	AY.51	0.002727
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	AY.62	0.001307
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	AY.88	0.002653
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	AY.9.2	0.00011
ORF1ab/nsp2	369	S369del	TCC	---	3	3	B.1	0.000027
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.141	0.006036
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.219	0.015
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.220	0.005576
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.1.25	0.001706
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.284	0.000322
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.316	0.002775
ORF1ab/nsp2	369	S369del	TCC	---	3	3	B.1.1.348	0.002389
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.354	0.013158
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.1.37	0.000579
ORF1ab/nsp2	369	S369T	Tcc	Acc	3	3	B.1.1.39	0.001529
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.433	0.004274
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.1.464	0.004418
ORF1ab/nsp2	369	S369L	TCc	CTc	3	3	B.1.1.7	0.000003
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.111	0.003525
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.126	0.003827
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.139	0.002199
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.147	0.002268
ORF1ab/nsp2	369	S369del	TCC	---	3	3	B.1.177	0.00004
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.177.69	0.004451
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.177.81	0.000568
ORF1ab/nsp2	369	S369T	Tcc	Acc	3	3	B.1.2	0.000026
ORF1ab/nsp2	369	S369del1	tCc	t-c	3	3	B.1.2	0.000026
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.214.2	0.001799
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.240	0.000647
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.258.11	0.001189
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.361	0.003866
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.369	0.000856
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.399	0.005803
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.525	0.000339
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.1.549	0.021583
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.565	0.002431
ORF1ab/nsp2	369	S369F	tCc	tTc	3	3	B.1.637	0.000219
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	B.4	0.006623
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	C.11	0.031915
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	C.35	0.002322
ORF1ab/nsp2	369	S369S	tcC	tcT	3	3	P.1.12	0.001452
ORF1ab/nsp2	369	S369del	TCC	---	3	3	P.2	0.00056
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	A.2.5	0.000998
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	A.2.5.3	0.020619
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AE.8	0.000978
ORF1ab/nsp2	369	S369A	Tcc	Gcc	2	2	AY.103	0.000012
ORF1ab/nsp2	369	S369S	tcC	tcA	2	2	AY.108	0.002205
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AY.117	0.000169
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.16	0.000759
ORF1ab/nsp2	369	S369A	Tcc	Gcc	2	2	AY.25	0.000012
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AY.27	0.000129
ORF1ab/nsp2	369	S369A	Tcc	Gcc	2	2	AY.29	0.000032
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AY.37	0.000632
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AY.39.1	0.000079
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.39.2	0.003082
ORF1ab/nsp2	369	S369del	TCC	---	2	2	AY.4	0.000003
ORF1ab/nsp2	369	S369A	Tcc	Gcc	2	2	AY.4.2.1	0.000298
ORF1ab/nsp2	369	S369del	TCC	---	2	2	AY.4.5	0.000215
ORF1ab/nsp2	369	S369S	tcC	tcA	2	2	AY.41	0.000588
ORF1ab/nsp2	369	S369T	Tcc	Acc	2	2	AY.42	0.00008
ORF1ab/nsp2	369	S369A	Tcc	Gcc	2	2	AY.44	0.000012
ORF1ab/nsp2	369	S369T	TcC	AcT	1	2	AY.44	0.000006
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	2	AY.44	0.000006
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.46.3	0.001867
ORF1ab/nsp2	369	S369T	Tcc	Acc	2	2	AY.47	0.000062
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.65	0.001066
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AY.7	0.000392
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.70	0.000417
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AY.71	0.00095
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.72	0.002721
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.79	0.002421
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.81	0.003984
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.82	0.002714
ORF1ab/nsp2	369	S369T	Tcc	Acc	2	2	AY.89	0.009804
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AY.9.2.1	0.003953
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	AY.99.2	0.000184
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	AZ.3	0.00304
ORF1ab/nsp2	369	S369Y	tCc	tAc	2	2	B.1	0.000018
ORF1ab/nsp2	369	S369del1	tCc	t-c	1	2	B.1	0.000009
ORF1ab/nsp2	369	S369del1	Tcc	-cc	1	2	B.1	0.000009
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.161	0.007067
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.176	0.000879
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.1.214	0.000111
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.216	0.001781
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.1.219	0.01
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.1.222	0.000408
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.1.284	0.000215
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.307	0.005063
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.312	0.003824
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.1.348	0.001592
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.374	0.004751
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.39	0.001019
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.397	0.004505
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.420	0.002012
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.467	0.038462
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.525	0.010929
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.528	0.009615
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.53	0.027397
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.63	0.000772
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.70	0.000682
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.1.89	0.012121
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.110.3	0.001437
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.126	0.002551
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.160.14	0.004237
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.177.44	0.001038
ORF1ab/nsp2	369	S369S	tcC	tcA	2	2	B.1.177.50	0.00939
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.177.54	0.001213
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.177.64	0.181818
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.177.65	0.001331
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.177.69	0.002967
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.177.73	0.001133
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.182	0.014493
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.189	0.008584
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.221	0.000142
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.258.11	0.000793
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.258.14	0.001961
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.258.7	0.003824
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.265	0.002541
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.311	0.000549
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.336	0.004878
ORF1ab/nsp2	369	S369S	tcC	tcA	1	2	B.1.351.2	0.000303
ORF1ab/nsp2	369	S369S	tcC	tcT	1	2	B.1.351.2	0.000303
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.36	0.000292
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.36.16	0.002849
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.36.18	0.00084
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.36.31	0.003503
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.375	0.001639
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.420	0.020833
ORF1ab/nsp2	369	S369del	TCC	---	2	2	B.1.424	0.016129
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.428	0.002041
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.436	0.002058
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.466.2	0.000782
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.473	0.038462
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.497	0.00063
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.507	0.022472
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.524	0.002813
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.538	0.016129
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.567	0.006667
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.575	0.000607
ORF1ab/nsp2	369	S369P	Tcc	Ccc	2	2	B.1.596	0.000174
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.597	0.009259
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.609	0.000959
ORF1ab/nsp2	369	S369del2	tCC	t--	2	2	B.1.617.2	0.000008
ORF1ab/nsp2	369	S369S	tcC	tcT	1	2	B.1.620	0.000946
ORF1ab/nsp2	369	S369S	tcC	tcA	1	2	B.1.620	0.000946
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	B.1.621	0.000177
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.621.1	0.001012
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.1.631	0.006734
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.3	0.001661
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.3.1	0.003317
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.40	0.000729
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	B.6	0.00182
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	C.16	0.002121
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	N.3	0.011628
ORF1ab/nsp2	369	S369S	tcC	tcT	2	2	N.5	0.003534
ORF1ab/nsp2	369	S369del	TCC	---	2	2	N.6	0.014184
ORF1ab/nsp2	369	S369F	tCc	tTc	2	2	P.1.15	0.000465
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	A	0.000387
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	A	0.000387
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	A	0.000387
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	A.1	0.000282
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	A.2.5.1	0.004808
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	A.2.5.2	0.001572
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	A.23.1	0.000704
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	A.5	0.001923
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AE.8	0.000489
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AH.3	0.003802
ORF1ab/nsp2	369	S369V	TCc	GTc	1	1	All	0
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.10	0.00053
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	AY.102	0.000027
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	AY.102	0.000027
ORF1ab/nsp2	369	S369C	tCc	tGc	1	1	AY.103	0.000006
ORF1ab/nsp2	369	S369del1	tCc	t-c	1	1	AY.103	0.000006
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.104	0.001984
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.105	0.000643
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.106	0.000335
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	AY.107	0.000466
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.109	0.00074
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.109	0.00074
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.111	0.000183
ORF1ab/nsp2	369	S369del	TCC	---	1	1	AY.111	0.000183
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.115	0.005208
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.12	0.000316
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.120	0.000037
ORF1ab/nsp2	369	S369del1	tCc	t-c	1	1	AY.120.1	0.000321
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.121	0.000135
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.13	0.000161
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	AY.17	0.008197
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.23	0.00007
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.23.1	0.000417
ORF1ab/nsp2	369	S369del	TCC	---	1	1	AY.25	0.000006
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.28	0.00189
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	AY.29	0.000016
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.35	0.000233
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.36	0.000148
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.38	0.000499
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	AY.39	0.000025
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.4.1	0.000737
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.4.2	0.000022
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.4.3	0.000842
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.4.4	0.000409
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.4.4	0.000409
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.40	0.000964
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	AY.43	0.000004
ORF1ab/nsp2	369	S369del	TCC	---	1	1	AY.43	0.000004
ORF1ab/nsp2	369	S369P	Tcc	Ccc	1	1	AY.44	0.000006
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.46	0.000104
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.46.3	0.000934
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.46.4	0.000165
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.46.4	0.000165
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.46.5	0.000198
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.46.5	0.000198
ORF1ab/nsp2	369	S369del1	tCc	t-c	1	1	AY.47	0.000031
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.5.2	0.002463
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.5.3	0.000337
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.5.4	0.000277
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.53	0.000288
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.55	0.000917
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.56	0.001605
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.56	0.001605
ORF1ab/nsp2	369	S369S	tcC	tcA	1	1	AY.58	0.000907
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	AY.59	0.00053
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	AY.6	0.000041
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.60	0.000938
ORF1ab/nsp2	369	S369del	TCC	---	1	1	AY.66	0.00107
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.67	0.000464
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.68	0.000274
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.69	0.000187
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.7.1	0.000113
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.71	0.000475
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.73	0.000665
ORF1ab/nsp2	369	S369del1	Tcc	-cc	1	1	AY.79	0.001211
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.84	0.000437
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	AY.9.2	0.000037
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.92	0.000287
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AY.95	0.000761
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.98	0.000079
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.98.1	0.000048
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	AY.99	0.001049
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	AY.99	0.001049
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AZ.1	0.000867
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	AZ.2	0.000821
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	B	0.000128
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B	0.000128
ORF1ab/nsp2	369	S369C	tCc	tGc	1	1	B.1	0.000009
ORF1ab/nsp2	369	S369P	Tcc	Ccc	1	1	B.1	0.000009
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.1	0.000327
ORF1ab/nsp2	369	S369S	tcC	tcA	1	1	B.1.1.10	0.001115
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.101	0.01
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.128	0.007092
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.135	0.004695
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.138	0.006061
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.144	0.028571
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.15	0.013514
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.157	0.000913
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.166	0.033333
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.176	0.000439
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.189	0.001513
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.192	0.002309
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.198	0.001468
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.200	0.007463
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.201	0.02439
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.216	0.00089
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.231	0.003096
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.232	0.001815
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.234	0.012048
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.28	0.000311
ORF1ab/nsp2	369	S369del	TCC	---	1	1	B.1.1.284	0.000107
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.289	0.002083
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.291	0.000742
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.302	0.002075
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.306	0.000438
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	B.1.1.306	0.000438
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.309	0.005848
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.317	0.000412
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.322	0.008772
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.323	0.014085
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.347	0.018182
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.348	0.000796
ORF1ab/nsp2	369	S369P	Tcc	Ccc	1	1	B.1.1.348	0.000796
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	B.1.1.351	0.002793
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.351	0.002793
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.363	0.005988
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.368	0.003086
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.369	0.000446
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	B.1.1.37	0.000193
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.370	0.012658
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.385	0.004464
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.402	0.011111
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.416	0.000905
ORF1ab/nsp2	369	S369del	TCC	---	1	1	B.1.1.416	0.000905
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.432	0.001266
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.437	0.010417
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.44	0.00241
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.442	0.018519
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.518	0.006329
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.1.523	0.001563
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.525	0.005464
ORF1ab/nsp2	369	S369P	Tcc	Ccc	1	1	B.1.1.7	0.000001
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.1.74	0.00431
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.110	0.004525
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.111	0.001175
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.112	0.005181
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.128	0.000635
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.128	0.000635
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.143	0.021277
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.149	0.003425
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.157	0.002985
ORF1ab/nsp2	369	S369V	TCc	GTc	1	1	B.1.160	0.000031
ORF1ab/nsp2	369	S369L	TCc	CTc	1	1	B.1.160	0.000031
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.160.26	0.002421
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.160.33	0.004425
ORF1ab/nsp2	369	S369del1	tcC	tc-	1	1	B.1.160.7	0.002079
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.160.8	0.001289
ORF1ab/nsp2	369	S369P	Tcc	Ccc	1	1	B.1.177	0.000013
ORF1ab/nsp2	369	S369del2	TCc	--c	1	1	B.1.177	0.000013
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.10	0.000878
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.12	0.000152
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.15	0.000631
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.20	0.001517
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.21	0.000076
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.26	0.006993
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.30	0.002513
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.31	0.011494
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.32	0.00135
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.33	0.001645
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.4	0.000211
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.43	0.001477
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.46	0.000918
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.5	0.001242
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.54	0.000606
ORF1ab/nsp2	369	S369del	TCC	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.58	0.001332
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.59	0.016129
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.65	0.000665
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.73	0.000566
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.74	0.015152
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.177.8	0.000752
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.177.82	0.000477
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	B.1.2	0.000009
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	B.1.2	0.000009
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.203	0.0625
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.206	0.000816
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.210	0.002132
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.214	0.003663
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.221.4	0.004167
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.223	0.002778
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	B.1.234	0.000132
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.237	0.004975
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.243.2	0.014493
ORF1ab/nsp2	369	S369S	tcC	tcG	1	1	B.1.258.16	0.001637
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.258.4	0.003448
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.298	0.002114
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.302	0.013333
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.305	0.002151
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	B.1.311	0.000275
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.329	0.000608
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.337	0.005587
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.338	0.008621
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.340	0.004292
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.346	0.001311
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.349	0.000715
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.350	0.002933
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	B.1.351.2	0.000303
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.351.2	0.000303
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.356	0.001727
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.36.1	0.00114
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.36.10	0.004785
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	B.1.36.17	0.000494
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.36.17	0.000494
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.36.20	0.016949
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.36.22	0.001208
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.36.22	0.001208
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.36.24	0.006173
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.36.25	0.002208
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.36.38	0.001642
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.371	0.001122
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.391	0.001127
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.398	0.002976
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.406	0.006061
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.409	0.000781
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.411	0.003704
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.421	0.007463
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.428	0.00102
ORF1ab/nsp2	369	S369del	TCC	---	1	1	B.1.429	0.000024
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.436	0.001029
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.438.1	0.000107
ORF1ab/nsp2	369	S369del	TCC	---	1	1	B.1.439	0.005917
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.441	0.009615
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.460	0.017857
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.462	0.007246
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	B.1.469	0.00361
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.471	0.002732
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.474	0.001901
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.475	0.142857
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.495	0.009091
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	B.1.509	0.000866
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.510	0.026316
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.517	0.000427
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.517	0.000427
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.530	0.007143
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.556	0.007519
ORF1ab/nsp2	369	S369del	TCC	---	1	1	B.1.561	0.000397
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.564	0.000426
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.565	0.00081
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.574	0.002151
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.575	0.000303
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.582	0.000491
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	B.1.596	0.000087
ORF1ab/nsp2	369	S369F	tCC	tTT	1	1	B.1.617.1	0.000129
ORF1ab/nsp2	369	S369del1	Tcc	-cc	1	1	B.1.617.2	0.000004
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.617.3	0.002985
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.618	0.004032
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.619	0.000871
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	B.1.619.1	0.000641
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.1.630	0.005236
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	B.1.637	0.000073
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	B.55	0.00295
ORF1ab/nsp2	369	S369del	TCC	---	1	1	B.57	0.015152
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	C.23	0.005814
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	C.35	0.000774
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	C.36.3	0.000567
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	C.37	0.000116
ORF1ab/nsp2	369	S369Y	tCc	tAc	1	1	C.37	0.000116
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	C.37.1	0.002618
ORF1ab/nsp2	369	S369T	Tcc	Acc	1	1	P.1	0.000016
ORF1ab/nsp2	369	S369A	Tcc	Gcc	1	1	P.1	0.000016
ORF1ab/nsp2	369	S369del	TCC	---	1	1	P.1	0.000016
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	P.1.17	0.000162
ORF1ab/nsp2	369	S369S	tcC	tcT	1	1	P.1.6	0.001946
ORF1ab/nsp2	369	S369F	tCc	tTc	1	1	P.2	0.000187
ORF1ab/nsp2	369	S369del	TCC	---	1	1	Q.1	0.000126

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.