CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 321

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	321	Q321Q		syn	caA	caG	4898	4898	1	22523-22525
S	321	Q321L		nonsyn	cAa	cTa	442	439	0.993213	22523-22525
S	321	Q321L		nonsyn	CAa	TTa	442	2	0.00452489	22523-22525
S	321	Q321L		nonsyn	cAA	cTT	442	1	0.00226244	22523-22525
S	321	Q321E		nonsyn	Caa	Gaa	311	311	1	22523-22525
S	321	Q321K		nonsyn	Caa	Aaa	109	109	1	22523-22525
S	321	Q321P		nonsyn	cAa	cCa	76	75	0.986842	22523-22525
S	321	Q321P		nonsyn	cAA	cCT	76	1	0.0131579	22523-22525
S	321	Q321R		nonsyn	cAa	cGa	66	66	1	22523-22525
S	321	Q321X		nonsyn	Caa	Taa	48	48	1	22523-22525
S	321	Q321H		nonsyn	caA	caC	44	34	0.772727	22523-22525
S	321	Q321H		nonsyn	caA	caT	44	10	0.227273	22523-22525
S	321	Q321del		del	CAA	---	31	31	1	22523-22525
S	321	Q321T		nonsyn	CAa	ACa	5	4	0.8	22523-22525
S	321	Q321del1		del	Caa	-aa	5	3	0.6	22523-22525
S	321	Q321T		nonsyn	CAA	ACT	5	1	0.2	22523-22525
S	321	Q321del1		del	cAa	c-a	5	1	0.2	22523-22525
S	321	Q321del1		del	CaA	-aN	5	1	0.2	22523-22525
S	321	Q321N		nonsyn	CaA	AaT	3	2	0.666667	22523-22525
S	321	Q321S		nonsyn	CAa	TCa	3	2	0.666667	22523-22525
S	321	Q321N		nonsyn	CaA	AaC	3	1	0.333333	22523-22525
S	321	Q321S		nonsyn	CAA	TCC	3	1	0.333333	22523-22525
S	321	Q321I		nonsyn	CAA	ATT	2	1	0.5	22523-22525
S	321	Q321I		nonsyn	CAa	ATa	2	1	0.5	22523-22525
S	321	Q321G		nonsyn	CAa	GGa	1	1	1	22523-22525
S	321	Q321F		nonsyn	CAA	TTC	1	1	1	22523-22525
S	321	Q321Y		nonsyn	CaA	TaC	1	1	1	22523-22525

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	321	Q321Q	caA	caG	4898	4898	All	0.000937
S	321	Q321Q	caA	caG	1637	1637	A.2.5	0.816866
S	321	Q321Q	caA	caG	668	668	B.1.1.7	0.000598
S	321	Q321Q	caA	caG	587	587	A.2.5.2	0.922956
S	321	Q321L	cAa	cTa	439	442	All	0.000084
S	321	Q321L	CAa	TTa	2	442	All	0
S	321	Q321L	cAA	cTT	1	442	All	0
S	321	Q321Q	caA	caG	351	351	AY.29	0.005537
S	321	Q321E	Caa	Gaa	311	311	All	0.000059
S	321	Q321Q	caA	caG	188	188	A.2.5.1	0.903846
S	321	Q321Q	caA	caG	150	150	P.1.16	0.056117
S	321	Q321L	cAa	cTa	143	143	AY.43	0.000634
S	321	Q321K	Caa	Aaa	109	109	All	0.000021
S	321	Q321Q	caA	caG	109	109	B.1.617.2	0.00041
S	321	Q321Q	caA	caG	107	107	AY.4	0.000167
S	321	Q321Q	caA	caG	85	85	B.1.177	0.001119
S	321	Q321L	cAa	cTa	78	78	AY.4	0.000121
S	321	Q321P	cAa	cCa	75	76	All	0.000014
S	321	Q321P	cAA	cCT	1	76	All	0
S	321	Q321Q	caA	caG	69	69	AY.43	0.000306
S	321	Q321Q	caA	caG	69	69	B.1.575	0.020934
S	321	Q321R	cAa	cGa	66	66	All	0.000013
S	321	Q321Q	caA	caG	65	65	B.1.435	0.738636
S	321	Q321Q	caA	caG	62	62	AY.3	0.000617
S	321	Q321Q	caA	caG	58	58	A.2.5.3	0.597938
S	321	Q321Q	caA	caG	58	58	AY.44	0.000353
S	321	Q321L	cAa	cTa	56	56	AY.103	0.000348
S	321	Q321K	Caa	Aaa	51	51	B.1.1.7	0.000046
S	321	Q321X	Caa	Taa	48	48	All	0.000009
S	321	Q321H	caA	caC	34	44	All	0.000007
S	321	Q321H	caA	caT	10	44	All	0.000002
S	321	Q321P	cAa	cCa	43	43	B.1.351	0.001278
S	321	Q321E	Caa	Gaa	36	36	B.1.1.7	0.000032
S	321	Q321R	cAa	cGa	35	35	B.1.1.7	0.000031
S	321	Q321Q	caA	caG	35	35	B.1.2	0.000308
S	321	Q321del	CAA	---	31	31	All	0.000006
S	321	Q321E	Caa	Gaa	31	31	B.1.2	0.000273
S	321	Q321Q	caA	caG	30	30	AY.39	0.000741
S	321	Q321Q	caA	caG	26	26	B.1	0.000238
S	321	Q321Q	caA	caG	25	25	AY.20	0.000972
S	321	Q321Q	caA	caG	24	24	AY.103	0.000149
S	321	Q321Q	caA	caG	24	24	B.1.1.219	0.12
S	321	Q321E	Caa	Gaa	23	23	B.1	0.000211
S	321	Q321Q	caA	caG	22	22	AY.46.2	0.013977
S	321	Q321E	Caa	Gaa	21	21	B.1.427	0.00106
S	321	Q321Q	caA	caG	21	21	P.1	0.000331
S	321	Q321Q	caA	caG	20	20	B.1.351	0.000595
S	321	Q321Q	caA	caG	19	19	AY.25	0.000114
S	321	Q321E	Caa	Gaa	19	19	B.1.429	0.000447
S	321	Q321L	cAa	cTa	18	18	B.1.1.7	0.000016
S	321	Q321Q	caA	caG	18	18	B.1.160	0.000561
S	321	Q321Q	caA	caG	16	16	AY.4.2.1	0.002384
S	321	Q321Q	caA	caG	16	16	AY.42	0.000644
S	321	Q321L	cAa	cTa	16	16	B.1.2	0.000141
S	321	Q321L	cAa	cTa	15	15	AY.44	0.000091
S	321	Q321Q	caA	caG	14	14	B.1.621	0.001239
S	321	Q321del	CAA	---	13	13	B.1.1.7	0.000012
S	321	Q321H	caA	caC	11	12	B.1.1.7	0.00001
S	321	Q321H	caA	caT	1	12	B.1.1.7	0.000001
S	321	Q321E	Caa	Gaa	12	12	B.1.177.44	0.006227
S	321	Q321Q	caA	caG	12	12	B.1.36.29	0.006208
S	321	Q321Q	caA	caG	12	12	B.1.526	0.000282
S	321	Q321L	cAa	cTa	12	12	B.1.617.2	0.000045
S	321	Q321Q	caA	caG	11	11	AY.102	0.000292
S	321	Q321L	cAa	cTa	11	11	AY.3	0.000109
S	321	Q321Q	caA	caG	11	11	AY.47	0.000342
S	321	Q321Q	caA	caG	11	11	AY.9.2	0.000404
S	321	Q321Q	caA	caG	11	11	B.1.214.2	0.006595
S	321	Q321E	Caa	Gaa	10	10	AY.43	0.000044
S	321	Q321H	caA	caC	10	10	B.1	0.000092
S	321	Q321Q	caA	caG	10	10	B.1.1	0.000181
S	321	Q321E	Caa	Gaa	10	10	B.1.160	0.000312
S	321	Q321Q	caA	caG	10	10	B.1.429	0.000235
S	321	Q321E	Caa	Gaa	10	10	D.2	0.00075
S	321	Q321L	cAa	cTa	9	9	AY.42	0.000362
S	321	Q321E	Caa	Gaa	9	9	B.1.1	0.000163
S	321	Q321L	cAa	cTa	9	9	B.1.1	0.000163
S	321	Q321P	cAa	cCa	9	9	B.1.1.7	0.000008
S	321	Q321X	Caa	Taa	9	9	D.2	0.000675
S	321	Q321E	Caa	Gaa	8	8	B.1.243	0.000557
S	321	Q321L	cAa	cTa	8	8	B.1.380	0.05298
S	321	Q321Q	caA	caG	8	8	C.37	0.000929
S	321	Q321Q	caA	caG	7	7	AY.4.4	0.002864
S	321	Q321Q	caA	caG	7	7	B.1.1.25	0.00398
S	321	Q321E	Caa	Gaa	7	7	B.1.177	0.000092
S	321	Q321E	Caa	Gaa	7	7	B.1.416.1	0.010937
S	321	Q321Q	caA	caG	6	6	AY.118	0.000376
S	321	Q321K	Caa	Aaa	6	6	AY.43	0.000027
S	321	Q321Q	caA	caG	6	6	AY.6	0.000247
S	321	Q321Q	caA	caG	6	6	B.1.1.214	0.000333
S	321	Q321Q	caA	caG	6	6	B.1.1.519	0.000238
S	321	Q321X	Caa	Taa	6	6	B.1.1.7	0.000005
S	321	Q321Q	caA	caG	6	6	B.1.1.70	0.002046
S	321	Q321Q	caA	caG	6	6	B.1.177.81	0.001136
S	321	Q321Q	caA	caG	6	6	B.1.617.1	0.000774
S	321	Q321Q	caA	caG	6	6	Q.1	0.000758
S	321	Q321T	CAa	ACa	4	5	All	0.000001
S	321	Q321del1	Caa	-aa	3	5	All	0.000001
S	321	Q321del1	CaA	-aN	1	5	All	0
S	321	Q321del1	cAa	c-a	1	5	All	0
S	321	Q321T	CAA	ACT	1	5	All	0
S	321	Q321Q	caA	caG	5	5	AY.23	0.000349
S	321	Q321Q	caA	caG	5	5	AY.24	0.002155
S	321	Q321E	Caa	Gaa	5	5	AY.3	0.00005
S	321	Q321Q	caA	caG	5	5	AY.75.1	0.000902
S	321	Q321K	Caa	Aaa	5	5	B.1	0.000046
S	321	Q321K	Caa	Aaa	5	5	B.1.2	0.000044
S	321	Q321E	Caa	Gaa	5	5	B.1.240	0.001078
S	321	Q321K	Caa	Aaa	5	5	B.1.258.17	0.00052
S	321	Q321E	Caa	Gaa	5	5	B.1.596	0.000436
S	321	Q321L	cAa	cTa	5	5	P.1.7	0.001596
S	321	Q321Q	caA	caG	4	4	A.2.4	0.013468
S	321	Q321Q	caA	caG	4	4	AY.19	0.004561
S	321	Q321R	cAa	cGa	4	4	AY.39.1	0.000158
S	321	Q321E	Caa	Gaa	4	4	AY.4	0.000006
S	321	Q321Q	caA	caG	4	4	AY.4.5	0.00043
S	321	Q321X	Caa	Taa	4	4	AY.43	0.000018
S	321	Q321H	caA	caC	4	4	AY.44	0.000024
S	321	Q321K	Caa	Aaa	4	4	B.1.1	0.000073
S	321	Q321E	Caa	Gaa	4	4	B.1.1.222	0.000816
S	321	Q321Q	caA	caG	4	4	B.1.177.9	0.005326
S	321	Q321X	Caa	Taa	4	4	B.1.2	0.000035
S	321	Q321E	Caa	Gaa	4	4	B.1.234	0.000528
S	321	Q321L	cAa	cTa	4	4	B.1.258	0.000266
S	321	Q321E	Caa	Gaa	4	4	B.1.311	0.001098
S	321	Q321L	cAa	cTa	4	4	B.1.413	0.017021
S	321	Q321Q	caA	caG	4	4	B.1.516	0.007828
S	321	Q321K	Caa	Aaa	4	4	D.2	0.0003
S	321	Q321L	cAa	cTa	4	4	P.1	0.000063
S	321	Q321Q	caA	caG	4	4	P.1.14	0.000191
S	321	Q321Q	caA	caG	4	4	Q.8	0.00066
S	321	Q321K	Caa	Aaa	3	3		0.166667
S	321	Q321H	caA	caC	2	3		0.111111
S	321	Q321L	cAa	cTa	2	3		0.111111
S	321	Q321T	CAa	ACa	2	3		0.111111
S	321	Q321P	cAa	cCa	2	3		0.111111
S	321	Q321L	cAA	cTT	1	3		0.055556
S	321	Q321P	cAA	cCT	1	3		0.055556
S	321	Q321T	CAA	ACT	1	3		0.055556
S	321	Q321H	caA	caT	1	3		0.055556
S	321	Q321N	CaA	AaT	2	3	All	0
S	321	Q321S	CAa	TCa	2	3	All	0
S	321	Q321N	CaA	AaC	1	3	All	0
S	321	Q321S	CAA	TCC	1	3	All	0
S	321	Q321Q	caA	caG	3	3	AY.1	0.001187
S	321	Q321Q	caA	caG	3	3	AY.100	0.000138
S	321	Q321K	Caa	Aaa	3	3	AY.103	0.000019
S	321	Q321K	Caa	Aaa	3	3	AY.110	0.000338
S	321	Q321L	cAa	cTa	3	3	AY.27	0.000194
S	321	Q321X	Caa	Taa	3	3	AY.3	0.00003
S	321	Q321Q	caA	caG	3	3	AY.33	0.0002
S	321	Q321K	Caa	Aaa	3	3	AY.4	0.000005
S	321	Q321R	cAa	cGa	3	3	AY.4	0.000005
S	321	Q321P	cAa	cCa	3	3	AY.4	0.000005
S	321	Q321Q	caA	caG	3	3	AY.4.2	0.000065
S	321	Q321R	cAa	cGa	3	3	AY.74	0.000347
S	321	Q321R	cAa	cGa	3	3	AY.75	0.000168
S	321	Q321L	cAa	cTa	3	3	AY.9.2	0.00011
S	321	Q321Q	caA	caG	3	3	AZ.2	0.002463
S	321	Q321del	CAA	---	3	3	B.1	0.000027
S	321	Q321P	cAa	cCa	3	3	B.1	0.000027
S	321	Q321E	Caa	Gaa	3	3	B.1.1.144	0.085714
S	321	Q321E	Caa	Gaa	3	3	B.1.160.16	0.002788
S	321	Q321L	cAa	cTa	3	3	B.1.177	0.00004
S	321	Q321E	Caa	Gaa	3	3	B.1.177.23	0.009709
S	321	Q321R	cAa	cGa	3	3	B.1.258	0.0002
S	321	Q321X	Caa	Taa	3	3	B.1.429	0.000071
S	321	Q321Q	caA	caG	3	3	B.1.470	0.004213
S	321	Q321E	Caa	Gaa	3	3	B.1.503	0.007463
S	321	Q321Q	caA	caG	3	3	B.1.609	0.001438
S	321	Q321R	cAa	cGa	3	3	B.1.617.2	0.000011
S	321	Q321K	Caa	Aaa	3	3	B.1.617.2	0.000011
S	321	Q321Q	caA	caG	3	3	B.1.620	0.002838
S	321	Q321Q	caA	caG	3	3	C.23	0.017442
S	321	Q321H	caA	caT	3	3	P.1	0.000047
S	321	Q321I	CAA	ATT	1	2		0.055556
S	321	Q321I	CAa	ATa	1	2		0.055556
S	321	Q321I	CAa	ATa	1	2	All	0
S	321	Q321I	CAA	ATT	1	2	All	0
S	321	Q321K	Caa	Aaa	2	2	AY.102	0.000053
S	321	Q321E	Caa	Gaa	2	2	AY.102	0.000053
S	321	Q321E	Caa	Gaa	2	2	AY.110	0.000225
S	321	Q321L	cAa	cTa	2	2	AY.118	0.000125
S	321	Q321L	cAa	cTa	2	2	AY.119	0.000071
S	321	Q321L	cAa	cTa	2	2	AY.20	0.000078
S	321	Q321L	cAa	cTa	2	2	AY.22	0.004184
S	321	Q321L	cAa	cTa	2	2	AY.25	0.000012
S	321	Q321P	cAa	cCa	2	2	AY.3	0.00002
S	321	Q321K	Caa	Aaa	2	2	AY.3	0.00002
S	321	Q321Q	caA	caG	2	2	AY.3.1	0.000171
S	321	Q321L	cAa	cTa	2	2	AY.4.4	0.000818
S	321	Q321E	Caa	Gaa	2	2	AY.42	0.00008
S	321	Q321del	CAA	---	2	2	AY.43	0.000009
S	321	Q321P	cAa	cCa	2	2	AY.45	0.000243
S	321	Q321Q	caA	caG	2	2	AY.46	0.000208
S	321	Q321Q	caA	caG	2	2	AY.5.2	0.004926
S	321	Q321Q	caA	caG	2	2	AY.5.3	0.000675
S	321	Q321Q	caA	caG	2	2	AY.7.1	0.000225
S	321	Q321Q	caA	caG	2	2	AY.73	0.001331
S	321	Q321Q	caA	caG	2	2	AY.8	0.001212
S	321	Q321Q	caA	caG	2	2	AY.9	0.000135
S	321	Q321Q	caA	caG	2	2	AY.98.1	0.000097
S	321	Q321E	Caa	Gaa	2	2	AY.98.1	0.000097
S	321	Q321L	cAa	cTa	2	2	AY.98.1	0.000097
S	321	Q321Q	caA	caG	2	2	B	0.000256
S	321	Q321X	Caa	Taa	2	2	B.1	0.000018
S	321	Q321E	Caa	Gaa	2	2	B.1.1.1	0.000653
S	321	Q321E	Caa	Gaa	2	2	B.1.1.174	0.006757
S	321	Q321Q	caA	caG	2	2	B.1.1.236	0.013793
S	321	Q321Q	caA	caG	2	2	B.1.1.28	0.000622
S	321	Q321E	Caa	Gaa	2	2	B.1.1.464	0.002946
S	321	Q321N	CaA	AaC	1	2	B.1.1.7	0.000001
S	321	Q321N	CaA	AaT	1	2	B.1.1.7	0.000001
S	321	Q321E	Caa	Gaa	2	2	B.1.110	0.00905
S	321	Q321Q	caA	caG	2	2	B.1.157	0.00597
S	321	Q321X	Caa	Taa	2	2	B.1.177	0.000026
S	321	Q321Q	caA	caG	2	2	B.1.177.20	0.003035
S	321	Q321Q	caA	caG	2	2	B.1.177.86	0.000367
S	321	Q321E	Caa	Gaa	2	2	B.1.221	0.000142
S	321	Q321P	cAa	cCa	2	2	B.1.221	0.000142
S	321	Q321Q	caA	caG	2	2	B.1.232	0.001075
S	321	Q321E	Caa	Gaa	2	2	B.1.351	0.000059
S	321	Q321del	CAA	---	2	2	B.1.351.2	0.000605
S	321	Q321Q	caA	caG	2	2	B.1.36	0.000292
S	321	Q321Q	caA	caG	2	2	B.1.36.36	0.001204
S	321	Q321E	Caa	Gaa	2	2	B.1.399	0.003868
S	321	Q321Q	caA	caG	2	2	B.1.426	0.002018
S	321	Q321K	Caa	Aaa	2	2	B.1.427	0.000101
S	321	Q321X	Caa	Taa	2	2	B.1.427	0.000101
S	321	Q321Q	caA	caG	2	2	B.1.438.1	0.000215
S	321	Q321E	Caa	Gaa	2	2	B.1.453	0.006472
S	321	Q321del	CAA	---	2	2	B.1.525	0.000226
S	321	Q321H	caA	caC	2	2	B.1.576	0.001813
S	321	Q321S	CAA	TCC	1	2	B.1.580	0.004065
S	321	Q321S	CAa	TCa	1	2	B.1.580	0.004065
S	321	Q321L	cAa	cTa	2	2	B.1.623	0.001073
S	321	Q321Q	caA	caG	2	2	C.1	0.004785
S	321	Q321H	caA	caT	2	2	C.36.3	0.001134
S	321	Q321Q	caA	caG	2	2	P.6	0.006289
S	321	Q321L	cAa	cTa	2	2	Q.3	0.00029
S	321	Q321N	CaA	AaT	1	1		0.055556
S	321	Q321X	Caa	Taa	1	1	A.1	0.000282
S	321	Q321Q	caA	caG	1	1	A.2	0.000662
S	321	Q321H	caA	caT	1	1	A.2.5	0.000499
S	321	Q321L	cAa	cTa	1	1	A.29	0.005319
S	321	Q321P	cAa	cCa	1	1	A.3	0.002096
S	321	Q321Y	CaA	TaC	1	1	All	0
S	321	Q321F	CAA	TTC	1	1	All	0
S	321	Q321G	CAa	GGa	1	1	All	0
S	321	Q321P	cAa	cCa	1	1	AY.100	0.000046
S	321	Q321R	cAa	cGa	1	1	AY.102	0.000027
S	321	Q321E	Caa	Gaa	1	1	AY.103	0.000006
S	321	Q321R	cAa	cGa	1	1	AY.103	0.000006
S	321	Q321Q	caA	caG	1	1	AY.105	0.000643
S	321	Q321del1	Caa	-aa	1	1	AY.108	0.001103
S	321	Q321Q	caA	caG	1	1	AY.11	0.001339
S	321	Q321X	Caa	Taa	1	1	AY.110	0.000113
S	321	Q321Q	caA	caG	1	1	AY.110	0.000113
S	321	Q321L	cAa	cTa	1	1	AY.111	0.000183
S	321	Q321Q	caA	caG	1	1	AY.111	0.000183
S	321	Q321Q	caA	caG	1	1	AY.113	0.000142
S	321	Q321E	Caa	Gaa	1	1	AY.119	0.000035
S	321	Q321R	cAa	cGa	1	1	AY.119	0.000035
S	321	Q321L	cAa	cTa	1	1	AY.120	0.000037
S	321	Q321H	caA	caT	1	1	AY.120.2.1	0.000498
S	321	Q321E	Caa	Gaa	1	1	AY.121	0.000135
S	321	Q321Q	caA	caG	1	1	AY.2	0.000356
S	321	Q321H	caA	caT	1	1	AY.20	0.000039
S	321	Q321L	cAa	cTa	1	1	AY.23	0.00007
S	321	Q321R	cAa	cGa	1	1	AY.25	0.000006
S	321	Q321del	CAA	---	1	1	AY.26	0.000028
S	321	Q321L	cAa	cTa	1	1	AY.29	0.000016
S	321	Q321Q	caA	caG	1	1	AY.29.1	0.000221
S	321	Q321R	cAa	cGa	1	1	AY.33	0.000067
S	321	Q321Q	caA	caG	1	1	AY.34	0.000097
S	321	Q321Q	caA	caG	1	1	AY.36	0.000148
S	321	Q321P	cAa	cCa	1	1	AY.39	0.000025
S	321	Q321G	CAa	GGa	1	1	AY.4	0.000002
S	321	Q321H	caA	caC	1	1	AY.4	0.000002
S	321	Q321X	Caa	Taa	1	1	AY.4	0.000002
S	321	Q321R	cAa	cGa	1	1	AY.4.2	0.000022
S	321	Q321L	cAa	cTa	1	1	AY.4.2	0.000022
S	321	Q321E	Caa	Gaa	1	1	AY.4.2.1	0.000149
S	321	Q321R	cAa	cGa	1	1	AY.43	0.000004
S	321	Q321del1	CaA	-aN	1	1	AY.43	0.000004
S	321	Q321del	CAA	---	1	1	AY.44	0.000006
S	321	Q321L	cAa	cTa	1	1	AY.45	0.000122
S	321	Q321L	cAa	cTa	1	1	AY.46.4	0.000165
S	321	Q321Q	caA	caG	1	1	AY.46.6	0.000072
S	321	Q321L	cAa	cTa	1	1	AY.47	0.000031
S	321	Q321P	cAa	cCa	1	1	AY.47	0.000031
S	321	Q321Q	caA	caG	1	1	AY.5	0.000021
S	321	Q321Q	caA	caG	1	1	AY.5.4	0.000277
S	321	Q321Q	caA	caG	1	1	AY.57	0.000656
S	321	Q321E	Caa	Gaa	1	1	AY.59	0.00053
S	321	Q321E	Caa	Gaa	1	1	AY.67	0.000464
S	321	Q321L	cAa	cTa	1	1	AY.69	0.000187
S	321	Q321Q	caA	caG	1	1	AY.7.2	0.000559
S	321	Q321E	Caa	Gaa	1	1	AY.70	0.000209
S	321	Q321Q	caA	caG	1	1	AY.70	0.000209
S	321	Q321Q	caA	caG	1	1	AY.83	0.001724
S	321	Q321del1	Caa	-aa	1	1	AY.84	0.000437
S	321	Q321E	Caa	Gaa	1	1	AY.91	0.00073
S	321	Q321Q	caA	caG	1	1	AY.92	0.000287
S	321	Q321L	cAa	cTa	1	1	AY.95	0.000761
S	321	Q321E	Caa	Gaa	1	1	B	0.000128
S	321	Q321R	cAa	cGa	1	1	B	0.000128
S	321	Q321R	cAa	cGa	1	1	B.1	0.000009
S	321	Q321P	cAa	cCa	1	1	B.1.1	0.000018
S	321	Q321X	Caa	Taa	1	1	B.1.1	0.000018
S	321	Q321T	CAa	ACa	1	1	B.1.1	0.000018
S	321	Q321K	Caa	Aaa	1	1	B.1.1.1	0.000327
S	321	Q321E	Caa	Gaa	1	1	B.1.1.153	0.001095
S	321	Q321Q	caA	caG	1	1	B.1.1.216	0.00089
S	321	Q321E	Caa	Gaa	1	1	B.1.1.219	0.005
S	321	Q321L	CAa	TTa	1	1	B.1.1.222	0.000204
S	321	Q321E	Caa	Gaa	1	1	B.1.1.242	0.043478
S	321	Q321Q	caA	caG	1	1	B.1.1.265	0.003155
S	321	Q321Q	caA	caG	1	1	B.1.1.284	0.000107
S	321	Q321E	Caa	Gaa	1	1	B.1.1.291	0.000742
S	321	Q321del	CAA	---	1	1	B.1.1.301	0.001179
S	321	Q321Q	caA	caG	1	1	B.1.1.302	0.002075
S	321	Q321E	Caa	Gaa	1	1	B.1.1.306	0.000438
S	321	Q321E	Caa	Gaa	1	1	B.1.1.316	0.000925
S	321	Q321Q	caA	caG	1	1	B.1.1.348	0.000796
S	321	Q321E	Caa	Gaa	1	1	B.1.1.376	0.005952
S	321	Q321E	Caa	Gaa	1	1	B.1.1.403	0.025641
S	321	Q321E	Caa	Gaa	1	1	B.1.1.416	0.000905
S	321	Q321E	Caa	Gaa	1	1	B.1.1.450	0.034483
S	321	Q321del	CAA	---	1	1	B.1.1.46	0.004367
S	321	Q321E	Caa	Gaa	1	1	B.1.1.512	0.028571
S	321	Q321K	Caa	Aaa	1	1	B.1.1.514	0.038462
S	321	Q321X	Caa	Taa	1	1	B.1.1.519	0.00004
S	321	Q321P	cAa	cCa	1	1	B.1.1.62	0.027027
S	321	Q321Q	caA	caG	1	1	B.1.1.63	0.000386
S	321	Q321Q	caA	caG	1	1	B.1.128	0.000635
S	321	Q321E	Caa	Gaa	1	1	B.1.139	0.000733
S	321	Q321X	Caa	Taa	1	1	B.1.160	0.000031
S	321	Q321E	Caa	Gaa	1	1	B.1.160.10	0.008065
S	321	Q321E	Caa	Gaa	1	1	B.1.160.11	0.005714
S	321	Q321Q	caA	caG	1	1	B.1.160.22	0.006757
S	321	Q321E	Caa	Gaa	1	1	B.1.160.26	0.002421
S	321	Q321H	caA	caC	1	1	B.1.177	0.000013
S	321	Q321del	CAA	---	1	1	B.1.177	0.000013
S	321	Q321Q	caA	caG	1	1	B.1.177.12	0.000152
S	321	Q321Q	caA	caG	1	1	B.1.177.15	0.000631
S	321	Q321H	caA	caC	1	1	B.1.177.32	0.00135
S	321	Q321E	Caa	Gaa	1	1	B.1.177.51	0.004566
S	321	Q321Q	caA	caG	1	1	B.1.177.54	0.000606
S	321	Q321L	cAa	cTa	1	1	B.1.177.60	0.000218
S	321	Q321Q	caA	caG	1	1	B.1.199	0.004132
S	321	Q321Q	caA	caG	1	1	B.1.208	0.04
S	321	Q321Q	caA	caG	1	1	B.1.213	0.014925
S	321	Q321Q	caA	caG	1	1	B.1.214	0.003663
S	321	Q321T	CAa	ACa	1	1	B.1.221	0.000071
S	321	Q321K	Caa	Aaa	1	1	B.1.221	0.000071
S	321	Q321R	cAa	cGa	1	1	B.1.222	0.001692
S	321	Q321E	Caa	Gaa	1	1	B.1.23	0.006061
S	321	Q321E	Caa	Gaa	1	1	B.1.232	0.000537
S	321	Q321K	Caa	Aaa	1	1	B.1.232	0.000537
S	321	Q321X	Caa	Taa	1	1	B.1.234	0.000132
S	321	Q321Q	caA	caG	1	1	B.1.234	0.000132
S	321	Q321X	Caa	Taa	1	1	B.1.243	0.00007
S	321	Q321Q	caA	caG	1	1	B.1.243	0.00007
S	321	Q321del	CAA	---	1	1	B.1.258	0.000067
S	321	Q321E	Caa	Gaa	1	1	B.1.305	0.002151
S	321	Q321K	Caa	Aaa	1	1	B.1.351	0.00003
S	321	Q321X	Caa	Taa	1	1	B.1.351	0.00003
S	321	Q321P	cAa	cCa	1	1	B.1.351.5	0.0006
S	321	Q321L	cAa	cTa	1	1	B.1.351.5	0.0006
S	321	Q321Q	caA	caG	1	1	B.1.36.18	0.00042
S	321	Q321del1	cAa	c-a	1	1	B.1.36.29	0.000517
S	321	Q321L	cAa	cTa	1	1	B.1.36.39	0.002217
S	321	Q321E	Caa	Gaa	1	1	B.1.361	0.001289
S	321	Q321E	Caa	Gaa	1	1	B.1.367	0.000792
S	321	Q321E	Caa	Gaa	1	1	B.1.423	0.010204
S	321	Q321K	Caa	Aaa	1	1	B.1.429	0.000024
S	321	Q321R	cAa	cGa	1	1	B.1.429	0.000024
S	321	Q321Q	caA	caG	1	1	B.1.497	0.000315
S	321	Q321E	Caa	Gaa	1	1	B.1.525	0.000113
S	321	Q321Q	caA	caG	1	1	B.1.541	0.004425
S	321	Q321Q	caA	caG	1	1	B.1.544	0.006024
S	321	Q321E	Caa	Gaa	1	1	B.1.551	0.00129
S	321	Q321E	Caa	Gaa	1	1	B.1.561	0.000397
S	321	Q321Q	caA	caG	1	1	B.1.561	0.000397
S	321	Q321E	Caa	Gaa	1	1	B.1.564	0.000426
S	321	Q321E	Caa	Gaa	1	1	B.1.565	0.00081
S	321	Q321E	Caa	Gaa	1	1	B.1.577	0.000687
S	321	Q321X	Caa	Taa	1	1	B.1.580	0.004065
S	321	Q321L	CAa	TTa	1	1	B.1.580	0.004065
S	321	Q321Y	CaA	TaC	1	1	B.1.580	0.004065
S	321	Q321F	CAA	TTC	1	1	B.1.580	0.004065
S	321	Q321Q	caA	caG	1	1	B.1.581	0.009434
S	321	Q321L	cAa	cTa	1	1	B.1.582	0.000491
S	321	Q321E	Caa	Gaa	1	1	B.1.588	0.00091
S	321	Q321X	Caa	Taa	1	1	B.1.595	0.000261
S	321	Q321E	Caa	Gaa	1	1	B.1.595	0.000261
S	321	Q321K	Caa	Aaa	1	1	B.1.596	0.000087
S	321	Q321E	Caa	Gaa	1	1	B.1.609	0.000479
S	321	Q321L	cAa	cTa	1	1	B.1.610	0.003546
S	321	Q321H	caA	caC	1	1	B.1.617.1	0.000129
S	321	Q321P	cAa	cCa	1	1	B.1.617.2	0.000004
S	321	Q321E	Caa	Gaa	1	1	B.1.617.2	0.000004
S	321	Q321del1	Caa	-aa	1	1	B.1.617.2	0.000004
S	321	Q321S	CAa	TCa	1	1	B.1.617.2	0.000004
S	321	Q321del	CAA	---	1	1	B.1.617.2	0.000004
S	321	Q321Q	caA	caG	1	1	B.1.617.3	0.002985
S	321	Q321del	CAA	---	1	1	B.1.620	0.000946
S	321	Q321X	Caa	Taa	1	1	B.1.621	0.000089
S	321	Q321L	cAa	cTa	1	1	B.1.621	0.000089
S	321	Q321Q	caA	caG	1	1	B.1.621.1	0.000506
S	321	Q321del	CAA	---	1	1	B.1.630	0.005236
S	321	Q321Q	caA	caG	1	1	B.1.637	0.000073
S	321	Q321K	Caa	Aaa	1	1	B.40	0.000364
S	321	Q321Q	caA	caG	1	1	B.52	0.010101
S	321	Q321X	Caa	Taa	1	1	B.6.6	0.000889
S	321	Q321P	cAa	cCa	1	1	C.1.2	0.004255
S	321	Q321Q	caA	caG	1	1	C.36	0.000911
S	321	Q321R	cAa	cGa	1	1	C.36.3	0.000567
S	321	Q321Q	caA	caG	1	1	D.2	0.000075
S	321	Q321Q	caA	caG	1	1	N.5	0.001767
S	321	Q321Q	caA	caG	1	1	P.1.12	0.000484
S	321	Q321Q	caA	caG	1	1	P.1.13	0.000898
S	321	Q321Q	caA	caG	1	1	P.1.15	0.000232
S	321	Q321Q	caA	caG	1	1	P.1.17	0.000162
S	321	Q321Q	caA	caG	1	1	P.2	0.000187
S	321	Q321H	caA	caC	1	1	Q.1	0.000126
S	321	Q321L	cAa	cTa	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.