CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp9 : CodonNum = 16

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/nsp9	16	A16A	A4156A	syn	gcC	gcT	3002	2636	0.878081	12731-12733
ORF1ab/nsp9	16	A16A	A4156A	syn	gcC	gcA	3002	366	0.121919	12731-12733
ORF1ab/nsp9	16	A16T	A4156T	nonsyn	Gcc	Acc	124	124	1	12731-12733
ORF1ab/nsp9	16	A16del	A4156del	del	GCC	---	35	35	1	12731-12733
ORF1ab/nsp9	16	A16S	A4156S	nonsyn	Gcc	Tcc	25	24	0.96	12731-12733
ORF1ab/nsp9	16	A16S	A4156S	nonsyn	GcC	TcA	25	1	0.04	12731-12733
ORF1ab/nsp9	16	A16V	A4156V	nonsyn	gCc	gTc	24	24	1	12731-12733
ORF1ab/nsp9	16	A16G	A4156G	nonsyn	gCc	gGc	6	5	0.833333	12731-12733
ORF1ab/nsp9	16	A16G	A4156G	nonsyn	gCC	gGG	6	1	0.166667	12731-12733
ORF1ab/nsp9	16	A16C	A4156C	nonsyn	GCc	TGc	4	4	1	12731-12733
ORF1ab/nsp9	16	A16P	A4156P	nonsyn	Gcc	Ccc	3	3	1	12731-12733
ORF1ab/nsp9	16	A16del1	A4156del1	del	gCc	g-c	2	1	0.5	12731-12733
ORF1ab/nsp9	16	A16del1	A4156del1	del	gcC	gc-	2	1	0.5	12731-12733
ORF1ab/nsp9	16	A16D	A4156D	nonsyn	gCc	gAc	1	1	1	12731-12733
ORF1ab/nsp9	16	A16E	A4156E	nonsyn	gCC	gAA	1	1	1	12731-12733
ORF1ab/nsp9	16	A16del2	A4156del2	del	GCc	--c	1	1	1	12731-12733

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/nsp9	16	A16A	gcC	gcT	2636	3002	All	0.000504
ORF1ab/nsp9	16	A16A	gcC	gcA	366	3002	All	0.00007
ORF1ab/nsp9	16	A16A	gcC	gcT	693	693	B.1.177	0.009125
ORF1ab/nsp9	16	A16A	gcC	gcA	244	244	B.1.1.243	0.995918
ORF1ab/nsp9	16	A16A	gcC	gcT	228	232	AY.4	0.000355
ORF1ab/nsp9	16	A16A	gcC	gcA	4	232	AY.4	0.000006
ORF1ab/nsp9	16	A16A	gcC	gcT	184	198	B.1.1.7	0.000165
ORF1ab/nsp9	16	A16A	gcC	gcA	14	198	B.1.1.7	0.000013
ORF1ab/nsp9	16	A16A	gcC	gcT	157	158	AY.103	0.000975
ORF1ab/nsp9	16	A16A	gcC	gcA	1	158	AY.103	0.000006
ORF1ab/nsp9	16	A16A	gcC	gcT	143	143	B.1.427	0.007221
ORF1ab/nsp9	16	A16T	Gcc	Acc	124	124	All	0.000024
ORF1ab/nsp9	16	A16A	gcC	gcT	92	98	B.1.617.2	0.000346
ORF1ab/nsp9	16	A16A	gcC	gcA	6	98	B.1.617.2	0.000023
ORF1ab/nsp9	16	A16A	gcC	gcT	93	93	P.1	0.001465
ORF1ab/nsp9	16	A16A	gcC	gcT	92	92	B.1.240	0.019832
ORF1ab/nsp9	16	A16A	gcC	gcT	75	76	AY.44	0.000457
ORF1ab/nsp9	16	A16A	gcC	gcA	1	76	AY.44	0.000006
ORF1ab/nsp9	16	A16A	gcC	gcT	56	56	B.1.429	0.001318
ORF1ab/nsp9	16	A16A	gcC	gcT	46	49	AY.43	0.000204
ORF1ab/nsp9	16	A16A	gcC	gcA	3	49	AY.43	0.000013
ORF1ab/nsp9	16	A16A	gcC	gcA	30	47	B.1.1	0.000544
ORF1ab/nsp9	16	A16A	gcC	gcT	17	47	B.1.1	0.000308
ORF1ab/nsp9	16	A16A	gcC	gcT	39	39	B.1.1.519	0.001549
ORF1ab/nsp9	16	A16A	gcC	gcT	37	37	AY.42	0.001489
ORF1ab/nsp9	16	A16A	gcC	gcT	36	37	B.1.2	0.000317
ORF1ab/nsp9	16	A16A	gcC	gcA	1	37	B.1.2	0.000009
ORF1ab/nsp9	16	A16A	gcC	gcT	36	36	B.1.1.214	0.001996
ORF1ab/nsp9	16	A16del	GCC	---	35	35	All	0.000007
ORF1ab/nsp9	16	A16A	gcC	gcT	35	35	Q.1	0.004421
ORF1ab/nsp9	16	A16A	gcC	gcT	24	30	B.1	0.00022
ORF1ab/nsp9	16	A16A	gcC	gcA	6	30	B.1	0.000055
ORF1ab/nsp9	16	A16A	gcC	gcT	28	28	AY.102	0.000742
ORF1ab/nsp9	16	A16T	Gcc	Acc	28	28	AY.4	0.000044
ORF1ab/nsp9	16	A16S	Gcc	Tcc	24	25	All	0.000005
ORF1ab/nsp9	16	A16S	GcC	TcA	1	25	All	0
ORF1ab/nsp9	16	A16A	gcC	gcT	24	25	AY.47	0.000747
ORF1ab/nsp9	16	A16A	gcC	gcA	1	25	AY.47	0.000031
ORF1ab/nsp9	16	A16V	gCc	gTc	24	24	All	0.000005
ORF1ab/nsp9	16	A16A	gcC	gcT	21	24	AY.3	0.000209
ORF1ab/nsp9	16	A16A	gcC	gcA	3	24	AY.3	0.00003
ORF1ab/nsp9	16	A16A	gcC	gcT	21	23	AY.5	0.000434
ORF1ab/nsp9	16	A16A	gcC	gcA	2	23	AY.5	0.000041
ORF1ab/nsp9	16	A16A	gcC	gcT	23	23	AY.85	0.009825
ORF1ab/nsp9	16	A16A	gcC	gcT	23	23	B.1.258	0.001531
ORF1ab/nsp9	16	A16A	gcC	gcT	17	22	AY.25	0.000102
ORF1ab/nsp9	16	A16A	gcC	gcA	5	22	AY.25	0.00003
ORF1ab/nsp9	16	A16T	Gcc	Acc	22	22	AY.3	0.000219
ORF1ab/nsp9	16	A16A	gcC	gcT	16	17	B.1.160	0.000499
ORF1ab/nsp9	16	A16A	gcC	gcA	1	17	B.1.160	0.000031
ORF1ab/nsp9	16	A16A	gcC	gcT	9	16	AY.100	0.000414
ORF1ab/nsp9	16	A16A	gcC	gcA	7	16	AY.100	0.000322
ORF1ab/nsp9	16	A16T	Gcc	Acc	15	15	B.1.574	0.032258
ORF1ab/nsp9	16	A16A	gcC	gcT	14	14	AY.29	0.000221
ORF1ab/nsp9	16	A16A	gcC	gcT	13	13	AY.36	0.001927
ORF1ab/nsp9	16	A16A	gcC	gcT	12	12	AY.14	0.001056
ORF1ab/nsp9	16	A16A	gcC	gcT	12	12	B.1.221	0.000852
ORF1ab/nsp9	16	A16T	Gcc	Acc	11	11	B.1.1.7	0.00001
ORF1ab/nsp9	16	A16A	gcC	gcT	11	11	B.1.426	0.0111
ORF1ab/nsp9	16	A16A	gcC	gcT	10	10	AE.8	0.00489
ORF1ab/nsp9	16	A16V	gCc	gTc	10	10	AY.42	0.000402
ORF1ab/nsp9	16	A16A	gcC	gcT	10	10	B.1.602	0.065359
ORF1ab/nsp9	16	A16del	GCC	---	9	9	AY.25	0.000054
ORF1ab/nsp9	16	A16A	gcC	gcT	6	9	AY.26	0.00017
ORF1ab/nsp9	16	A16A	gcC	gcA	3	9	AY.26	0.000085
ORF1ab/nsp9	16	A16A	gcC	gcT	9	9	AY.39	0.000222
ORF1ab/nsp9	16	A16T	Gcc	Acc	9	9	AY.4.5	0.000967
ORF1ab/nsp9	16	A16A	gcC	gcT	9	9	B.1.311	0.002471
ORF1ab/nsp9	16	A16A	gcC	gcT	8	8	AY.54	0.000763
ORF1ab/nsp9	16	A16A	gcC	gcT	8	8	B.1.1.366	0.126984
ORF1ab/nsp9	16	A16A	gcC	gcT	8	8	P.1.14	0.000382
ORF1ab/nsp9	16	A16T	Gcc	Acc	7	7	A.2.3	0.033175
ORF1ab/nsp9	16	A16A	gcC	gcT	5	7	AY.20	0.000194
ORF1ab/nsp9	16	A16A	gcC	gcA	2	7	AY.20	0.000078
ORF1ab/nsp9	16	A16A	gcC	gcT	7	7	B.1.351	0.000208
ORF1ab/nsp9	16	A16G	gCc	gGc	5	6	All	0.000001
ORF1ab/nsp9	16	A16G	gCC	gGG	1	6	All	0
ORF1ab/nsp9	16	A16A	gcC	gcT	6	6	AY.119	0.000212
ORF1ab/nsp9	16	A16A	gcC	gcT	5	6	AY.9.2	0.000184
ORF1ab/nsp9	16	A16A	gcC	gcA	1	6	AY.9.2	0.000037
ORF1ab/nsp9	16	A16A	gcC	gcT	6	6	B.1.1.284	0.000644
ORF1ab/nsp9	16	A16del	GCC	---	6	6	B.1.1.7	0.000005
ORF1ab/nsp9	16	A16A	gcC	gcT	6	6	B.1.160.30	0.017857
ORF1ab/nsp9	16	A16A	gcC	gcT	4	6	C.37	0.000464
ORF1ab/nsp9	16	A16A	gcC	gcA	2	6	C.37	0.000232
ORF1ab/nsp9	16	A16A	gcC	gcT	5	5	AY.33	0.000334
ORF1ab/nsp9	16	A16S	Gcc	Tcc	5	5	AY.43	0.000022
ORF1ab/nsp9	16	A16A	gcC	gcT	5	5	AY.75.1	0.000902
ORF1ab/nsp9	16	A16A	gcC	gcA	3	5	B	0.000383
ORF1ab/nsp9	16	A16A	gcC	gcT	2	5	B	0.000256
ORF1ab/nsp9	16	A16A	gcC	gcT	5	5	B.1.1.122	0.227273
ORF1ab/nsp9	16	A16A	gcC	gcT	5	5	B.1.1.28	0.001556
ORF1ab/nsp9	16	A16A	gcC	gcT	5	5	B.1.177.67	0.038168
ORF1ab/nsp9	16	A16A	gcC	gcT	5	5	B.1.369	0.001426
ORF1ab/nsp9	16	A16A	gcC	gcA	5	5	B.1.416.1	0.007812
ORF1ab/nsp9	16	A16A	gcC	gcT	5	5	B.1.561	0.001985
ORF1ab/nsp9	16	A16S	Gcc	Tcc	5	5	B.1.617.2	0.000019
ORF1ab/nsp9	16	A16C	GCc	TGc	4	4	All	0.000001
ORF1ab/nsp9	16	A16A	gcC	gcT	4	4	AY.120	0.000149
ORF1ab/nsp9	16	A16S	Gcc	Tcc	3	4	AY.4	0.000005
ORF1ab/nsp9	16	A16S	GcC	TcA	1	4	AY.4	0.000002
ORF1ab/nsp9	16	A16A	gcC	gcT	4	4	AY.6	0.000165
ORF1ab/nsp9	16	A16A	gcC	gcT	3	4	B.1.243	0.000209
ORF1ab/nsp9	16	A16A	gcC	gcA	1	4	B.1.243	0.00007
ORF1ab/nsp9	16	A16T	Gcc	Acc	4	4	B.1.36	0.000584
ORF1ab/nsp9	16	A16A	gcC	gcT	4	4	B.1.621	0.000354
ORF1ab/nsp9	16	A16A	gcC	gcT	4	4	D.2	0.0003
ORF1ab/nsp9	16	A16A	gcC	gcT	4	4	P.1.12	0.001936
ORF1ab/nsp9	16	A16A	gcC	gcT	4	4	P.1.15	0.000929
ORF1ab/nsp9	16	A16G	gCc	gGc	3	3		0.166667
ORF1ab/nsp9	16	A16P	Gcc	Ccc	3	3	All	0.000001
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	AT.1	0.015385
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	AY.1	0.001187
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	AY.29.1	0.000662
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	AY.40	0.002893
ORF1ab/nsp9	16	A16T	Gcc	Acc	3	3	AY.41	0.000882
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	AY.45	0.000365
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	AY.46.6	0.000217
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	AY.70	0.000626
ORF1ab/nsp9	16	A16V	gCc	gTc	3	3	B.1	0.000027
ORF1ab/nsp9	16	A16S	Gcc	Tcc	3	3	B.1.1	0.000054
ORF1ab/nsp9	16	A16A	gcC	gcT	2	3	B.1.1.70	0.000682
ORF1ab/nsp9	16	A16A	gcC	gcA	1	3	B.1.1.70	0.000341
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	B.1.177.77	0.002179
ORF1ab/nsp9	16	A16A	gcC	gcT	3	3	B.1.596	0.000261
ORF1ab/nsp9	16	A16T	Gcc	Acc	3	3	B.1.617.2	0.000011
ORF1ab/nsp9	16	A16A	gcC	gcA	3	3	B.1.78	0.025641
ORF1ab/nsp9	16	A16A	gcC	gcA	2	3	R.1	0.00018
ORF1ab/nsp9	16	A16A	gcC	gcT	1	3	R.1	0.00009
ORF1ab/nsp9	16	A16S	Gcc	Tcc	2	2		0.111111
ORF1ab/nsp9	16	A16C	GCc	TGc	2	2		0.111111
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	A.2.5	0.000998
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	A.27	0.003311
ORF1ab/nsp9	16	A16del1	gcC	gc-	1	2	All	0
ORF1ab/nsp9	16	A16del1	gCc	g-c	1	2	All	0
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.19	0.002281
ORF1ab/nsp9	16	A16T	Gcc	Acc	2	2	AY.25	0.000012
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.3.1	0.000171
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.34	0.000194
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.39.1	0.000079
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.4.2.1	0.000298
ORF1ab/nsp9	16	A16T	Gcc	Acc	2	2	AY.43	0.000009
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.61	0.00021
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.79	0.002421
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.9	0.000135
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.98	0.000158
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	AY.98.1	0.000097
ORF1ab/nsp9	16	A16V	gCc	gTc	2	2	AY.99.2	0.000184
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.1.269	0.002706
ORF1ab/nsp9	16	A16A	gcC	gcA	2	2	B.1.1.370	0.025316
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.177.40	0.010309
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.177.57	0.000562
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.177.60	0.000437
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.177.73	0.001133
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.241	0.001623
ORF1ab/nsp9	16	A16A	gcC	gcA	2	2	B.1.36	0.000292
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.36.29	0.001035
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.441	0.019231
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.620	0.001892
ORF1ab/nsp9	16	A16A	gcC	gcT	2	2	B.1.93	0.001867
ORF1ab/nsp9	16	A16del2	GCc	--c	1	1	All	0
ORF1ab/nsp9	16	A16D	gCc	gAc	1	1	All	0
ORF1ab/nsp9	16	A16E	gCC	gAA	1	1	All	0
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	AY.100	0.000046
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.111	0.000183
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.113	0.000142
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.116.1	0.000311
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.117	0.000085
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	AY.119	0.000035
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.13	0.000161
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.2	0.000356
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.23	0.00007
ORF1ab/nsp9	16	A16del1	gcC	gc-	1	1	AY.25	0.000006
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	AY.26	0.000028
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.27	0.000065
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	AY.32	0.000532
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.35	0.000233
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	AY.39	0.000025
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.39.1.1	0.000725
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	AY.4	0.000002
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.4	0.000002
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.4.2	0.000022
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.4.4	0.000409
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.41	0.000294
ORF1ab/nsp9	16	A16S	Gcc	Tcc	1	1	AY.42	0.00004
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.43	0.000004
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.46	0.000104
ORF1ab/nsp9	16	A16P	Gcc	Ccc	1	1	AY.46	0.000104
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.46.1	0.001027
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.46.3	0.000934
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.46.4	0.000165
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	AY.46.4	0.000165
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.46.6	0.000072
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.5.2	0.002463
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.5.4	0.000277
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.53	0.000288
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	AY.56	0.001605
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	AY.6	0.000041
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	AY.65	0.000533
ORF1ab/nsp9	16	A16del2	GCc	--c	1	1	AY.67	0.000464
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.67	0.000464
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.68	0.000274
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.7	0.000196
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.7.1	0.000113
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.75	0.000056
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	AY.75	0.000056
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	AY.75.1	0.00018
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	AY.88	0.000884
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.89	0.004902
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.9.1	0.000084
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.9.2	0.000037
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.91	0.00073
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.99	0.001049
ORF1ab/nsp9	16	A16del	GCC	---	1	1	AY.99	0.001049
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	AY.99.2	0.000092
ORF1ab/nsp9	16	A16del	GCC	---	1	1	B	0.000128
ORF1ab/nsp9	16	A16S	Gcc	Tcc	1	1	B.1	0.000009
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1	0.000009
ORF1ab/nsp9	16	A16P	Gcc	Ccc	1	1	B.1	0.000009
ORF1ab/nsp9	16	A16G	gCc	gGc	1	1	B.1	0.000009
ORF1ab/nsp9	16	A16C	GCc	TGc	1	1	B.1	0.000009
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.1	0.000018
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	B.1.1	0.000018
ORF1ab/nsp9	16	A16del	GCC	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.1.176	0.000439
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	B.1.1.192	0.002309
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	B.1.1.280	0.003086
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	B.1.1.309	0.005848
ORF1ab/nsp9	16	A16del	GCC	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.1.351	0.002793
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.1.356	0.008547
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.1.376	0.005952
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.1.39	0.00051
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.1.409	0.002833
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.1.434	0.000349
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	B.1.1.486	0.001577
ORF1ab/nsp9	16	A16S	Gcc	Tcc	1	1	B.1.1.519	0.00004
ORF1ab/nsp9	16	A16P	Gcc	Ccc	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	16	A16S	Gcc	Tcc	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.105	0.009615
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.111	0.001175
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.126	0.001276
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.160.15	0.00495
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.177.21	0.000076
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.177.5	0.001242
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.177.53	0.002392
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.177.69	0.001484
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.177.85	0.005435
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.2	0.000009
ORF1ab/nsp9	16	A16S	Gcc	Tcc	1	1	B.1.221	0.000071
ORF1ab/nsp9	16	A16C	GCc	TGc	1	1	B.1.221	0.000071
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.221	0.000071
ORF1ab/nsp9	16	A16G	gCc	gGc	1	1	B.1.221	0.000071
ORF1ab/nsp9	16	A16S	Gcc	Tcc	1	1	B.1.234	0.000132
ORF1ab/nsp9	16	A16del	GCC	---	1	1	B.1.258	0.000067
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.265	0.001271
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	B.1.301	0.005917
ORF1ab/nsp9	16	A16E	gCC	gAA	1	1	B.1.301	0.005917
ORF1ab/nsp9	16	A16D	gCc	gAc	1	1	B.1.301	0.005917
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.332	0.003497
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	B.1.338	0.008621
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.351.3	0.000876
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	B.1.36.10	0.004785
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.36.17	0.000494
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.36.17	0.000494
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.36.26	0.002857
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.367	0.000792
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.382	0.008929
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.438.1	0.000107
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.466.2	0.000391
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.469	0.00361
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.516	0.001957
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.521	0.004975
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.526	0.000024
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.538	0.008065
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.558	0.004566
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.564	0.000426
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.565	0.00081
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.575	0.000303
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.575	0.000303
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.576	0.000907
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.577	0.000687
ORF1ab/nsp9	16	A16del	GCC	---	1	1	B.1.595	0.000261
ORF1ab/nsp9	16	A16T	Gcc	Acc	1	1	B.1.609	0.000479
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.609	0.000479
ORF1ab/nsp9	16	A16del1	gCc	g-c	1	1	B.1.617.1	0.000129
ORF1ab/nsp9	16	A16del	GCC	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp9	16	A16G	gCC	gGG	1	1	B.1.617.2	0.000004
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.619	0.000871
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.623	0.000536
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	B.1.9.5	0.005682
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	B.6	0.00091
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	B.6.6	0.000889
ORF1ab/nsp9	16	A16del	GCC	---	1	1	C.36	0.000911
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	C.36.3.1	0.002717
ORF1ab/nsp9	16	A16V	gCc	gTc	1	1	D.2	0.000075
ORF1ab/nsp9	16	A16del	GCC	---	1	1	N.4	0.004255
ORF1ab/nsp9	16	A16del	GCC	---	1	1	P.1	0.000016
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	P.1.16	0.000374
ORF1ab/nsp9	16	A16A	gcC	gcT	1	1	P.1.8	0.004785
ORF1ab/nsp9	16	A16del	GCC	---	1	1	Q.2	0.000613
ORF1ab/nsp9	16	A16A	gcC	gcA	1	1	Q.8	0.000165

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.