CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 412

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
N	412	S412S		syn	agC	agT	120872	120872	1	29507-29509
N	412	S412R		nonsyn	Agc	Cgc	15019	14934	0.99434	29507-29509
N	412	S412R		nonsyn	agC	agA	15019	60	0.00399494	29507-29509
N	412	S412R		nonsyn	agC	agG	15019	21	0.00139823	29507-29509
N	412	S412R		nonsyn	AgC	CgT	15019	4	0.000266329	29507-29509
N	412	S412I		nonsyn	aGc	aTc	1118	1107	0.990161	29507-29509
N	412	S412I		nonsyn	aGC	aTT	1118	11	0.009839	29507-29509
N	412	S412N		nonsyn	aGc	aAc	769	767	0.997399	29507-29509
N	412	S412N		nonsyn	aGC	aAT	769	2	0.00260078	29507-29509
N	412	S412G		nonsyn	Agc	Ggc	123	113	0.918699	29507-29509
N	412	S412G		nonsyn	AgC	GgT	123	8	0.0650406	29507-29509
N	412	S412G		nonsyn	AgC	GgG	123	1	0.00813008	29507-29509
N	412	S412G		nonsyn	AgC	GgA	123	1	0.00813008	29507-29509
N	412	S412del		del	AGC	---	26	26	1	29507-29509
N	412	S412C		nonsyn	Agc	Tgc	17	17	1	29507-29509
N	412	S412L		nonsyn	AGc	CTc	13	13	1	29507-29509
N	412	S412T		nonsyn	aGc	aCc	13	13	1	29507-29509
N	412	S412W		nonsyn	AgC	TgG	10	10	1	29507-29509
N	412	S412V		nonsyn	AGc	GTc	7	7	1	29507-29509
N	412	S412K		nonsyn	aGC	aAA	5	3	0.6	29507-29509
N	412	S412K		nonsyn	aGC	aAG	5	2	0.4	29507-29509
N	412	S412D		nonsyn	AGc	GAc	4	2	0.5	29507-29509
N	412	S412D		nonsyn	AGC	GAT	4	2	0.5	29507-29509
N	412	S412del1		del	Agc	-gc	4	2	0.5	29507-29509
N	412	S412del1		del	aGc	a-c	4	1	0.25	29507-29509
N	412	S412del1		del	agC	ag-	4	1	0.25	29507-29509
N	412	S412E		nonsyn	AGC	GAG	1	1	1	29507-29509
N	412	S412del2		del	aGC	a--	1	1	1	29507-29509

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
N	412	S412S	agC	agT	120872	120872	All	0.023118
N	412	S412S	agC	agT	97802	97802	AY.3	0.972777
N	412	S412R	Agc	Cgc	14934	15019	All	0.002856
N	412	S412R	agC	agA	60	15019	All	0.000011
N	412	S412R	agC	agG	21	15019	All	0.000004
N	412	S412R	AgC	CgT	4	15019	All	0.000001
N	412	S412R	Agc	Cgc	14708	14712	AY.27	0.951912
N	412	S412R	AgC	CgT	4	14712	AY.27	0.000259
N	412	S412S	agC	agT	11464	11464	AY.3.1	0.977406
N	412	S412S	agC	agT	1557	1557	B.1.617.2	0.005863
N	412	S412S	agC	agT	1332	1332	B.1.1.7	0.001192
N	412	S412I	aGc	aTc	1107	1118	All	0.000212
N	412	S412I	aGC	aTT	11	1118	All	0.000002
N	412	S412N	aGc	aAc	767	769	All	0.000147
N	412	S412N	aGC	aAT	2	769	All	0
N	412	S412S	agC	agT	677	677	AY.11	0.906292
N	412	S412S	agC	agT	645	645	AY.25	0.00388
N	412	S412S	agC	agT	627	627	AY.4.2	0.013599
N	412	S412S	agC	agT	598	598	AY.117	0.050541
N	412	S412S	agC	agT	504	504	AY.47	0.015677
N	412	S412S	agC	agT	477	477	Q.3	0.069181
N	412	S412S	agC	agT	433	433	AY.92	0.12439
N	412	S412S	agC	agT	301	301	AY.103	0.001869
N	412	S412S	agC	agT	295	295	AY.44	0.001796
N	412	S412S	agC	agT	259	259	B.1.2	0.002281
N	412	S412I	aGc	aTc	249	249	B.1.177	0.003279
N	412	S412S	agC	agT	226	226	AY.4	0.000352
N	412	S412S	agC	agT	209	209	AY.105	0.134405
N	412	S412S	agC	agT	203	203	AY.84	0.088801
N	412	S412N	aGc	aAc	178	178	B.1.630	0.931937
N	412	S412S	agC	agT	169	169	AY.119	0.005967
N	412	S412S	agC	agT	166	166	AY.5.3	0.056005
N	412	S412S	agC	agT	150	150	AY.43	0.000665
N	412	S412S	agC	agT	141	141	AY.46.6	0.010181
N	412	S412S	agC	agT	140	140	AY.102	0.003712
N	412	S412I	aGc	aTc	134	134	B.1.1.7	0.00012
N	412	S412G	Agc	Ggc	113	123	All	0.000022
N	412	S412G	AgC	GgT	8	123	All	0.000002
N	412	S412G	AgC	GgG	1	123	All	0
N	412	S412G	AgC	GgA	1	123	All	0
N	412	S412S	agC	agT	114	114	AY.42	0.004586
N	412	S412I	aGc	aTc	94	94	AY.44	0.000572
N	412	S412S	agC	agT	91	91	AY.39	0.002249
N	412	S412S	agC	agT	91	91	AY.5	0.001879
N	412	S412S	agC	agT	89	89	AY.116	0.025523
N	412	S412I	aGc	aTc	89	89	AZ.4	0.298658
N	412	S412S	agC	agT	82	82	AY.110	0.00924
N	412	S412S	agC	agT	76	76	B.1	0.000696
N	412	S412N	aGc	aAc	76	76	B.1.1.7	0.000068
N	412	S412S	agC	agT	72	72	AY.26	0.002038
N	412	S412N	aGc	aAc	72	72	B.1.177	0.000948
N	412	S412R	Agc	Cgc	67	67	AY.37	0.021176
N	412	S412I	aGc	aTc	65	65	AY.102	0.001723
N	412	S412N	aGc	aAc	60	60	B.1.258	0.003993
N	412	S412S	agC	agT	57	57	AY.45	0.006936
N	412	S412S	agC	agT	56	56	AY.98.1	0.002712
N	412	S412S	agC	agT	54	54	B.1.36.16	0.076923
N	412	S412S	agC	agT	54	54	B.1.427	0.002727
N	412	S412S	agC	agT	53	53	AY.46	0.005516
N	412	S412I	aGc	aTc	52	52	B.1.617.2	0.000196
N	412	S412R	Agc	Cgc	49	51	B.1.617.2	0.000185
N	412	S412R	agC	agA	2	51	B.1.617.2	0.000008
N	412	S412I	aGc	aTc	50	50	AY.4	0.000078
N	412	S412S	agC	agT	49	49	AY.118	0.00307
N	412	S412I	aGc	aTc	48	49	AY.25	0.000289
N	412	S412I	aGC	aTT	1	49	AY.25	0.000006
N	412	S412S	agC	agT	49	49	AY.33	0.003272
N	412	S412S	agC	agT	47	47	AY.113	0.006692
N	412	S412S	agC	agT	46	46	AY.106	0.015405
N	412	S412N	aGc	aAc	42	42	AY.47	0.001306
N	412	S412S	agC	agT	41	41	P.1	0.000646
N	412	S412S	agC	agT	40	40	AY.23	0.00279
N	412	S412I	aGc	aTc	38	38	AY.34	0.003685
N	412	S412S	agC	agT	38	38	AY.73	0.025283
N	412	S412N	aGc	aAc	36	36	AY.39	0.00089
N	412	S412S	agC	agT	36	36	AY.79	0.043584
N	412	S412N	aGc	aAc	35	35	AY.4	0.000054
N	412	S412S	agC	agT	34	34	B.1.177.73	0.019253
N	412	S412S	agC	agT	33	33	AY.62	0.014379
N	412	S412S	agC	agT	33	33	AY.95	0.025114
N	412	S412S	agC	agT	32	32	AY.82	0.043419
N	412	S412S	agC	agT	31	31	AY.99	0.032529
N	412	S412S	agC	agT	30	30	AY.55	0.027523
N	412	S412S	agC	agT	30	30	C.37	0.003482
N	412	S412S	agC	agT	29	29	AY.100	0.001334
N	412	S412R	agC	agA	24	29	B.1.1.7	0.000021
N	412	S412R	agC	agG	4	29	B.1.1.7	0.000004
N	412	S412R	Agc	Cgc	1	29	B.1.1.7	0.000001
N	412	S412S	agC	agT	27	27	B.1.177	0.000356
N	412	S412I	aGc	aTc	27	27	B.1.369	0.007701
N	412	S412del	AGC	---	26	26	All	0.000005
N	412	S412I	aGc	aTc	24	24	AY.116	0.006883
N	412	S412S	agC	agT	24	24	B	0.003067
N	412	S412S	agC	agT	23	23	AY.46.1	0.023614
N	412	S412S	agC	agT	23	23	AY.98	0.001817
N	412	S412S	agC	agT	23	23	B.1.1	0.000417
N	412	S412S	agC	agT	23	23	B.1.1.486	0.036278
N	412	S412N	aGc	aAc	23	23	B.1.160	0.000717
N	412	S412N	aGc	aAc	23	23	P.1	0.000362
N	412	S412S	agC	agT	22	22	AY.54	0.002098
N	412	S412G	Agc	Ggc	22	22	B.1.36.38	0.036125
N	412	S412N	aGc	aAc	22	22	B.1.77	1
N	412	S412S	agC	agT	21	21	AY.114	0.004853
N	412	S412S	agC	agT	20	20	AY.85	0.008543
N	412	S412N	aGc	aAc	20	20	B.1.588	0.018198
N	412	S412I	aGc	aTc	19	19	AY.85	0.008116
N	412	S412S	agC	agT	19	19	AY.93	0.005188
N	412	S412S	agC	agT	19	19	AY.96	0.039419
N	412	S412S	agC	agT	19	19	B.1.405	0.234568
N	412	S412S	agC	agT	19	19	B.1.526	0.000447
N	412	S412G	Agc	Ggc	18	18	AY.44	0.00011
N	412	S412S	agC	agT	18	18	AY.91	0.013148
N	412	S412S	agC	agT	18	18	B.1.177.84	0.12
N	412	S412S	agC	agT	18	18	B.1.466.2	0.007042
N	412	S412C	Agc	Tgc	17	17	All	0.000003
N	412	S412S	agC	agT	17	17	B.1.1.464	0.025037
N	412	S412S	agC	agT	17	17	B.1.243	0.001183
N	412	S412R	Agc	Cgc	16	16	AY.16	0.006074
N	412	S412S	agC	agT	16	16	AY.20	0.000622
N	412	S412S	agC	agT	16	16	AY.34	0.001551
N	412	S412S	agC	agT	16	16	AY.88	0.014147
N	412	S412N	aGc	aAc	15	15	AY.33	0.001002
N	412	S412S	agC	agT	15	15	AY.90	0.010267
N	412	S412N	aGc	aAc	15	15	B.1.2	0.000132
N	412	S412N	aGc	aAc	15	15	B.1.617.2	0.000056
N	412	S412S	agC	agT	14	14	AY.120	0.000521
N	412	S412I	aGc	aTc	14	14	AY.43	0.000062
N	412	S412R	Agc	Cgc	13	14	AY.43	0.000058
N	412	S412R	agC	agA	1	14	AY.43	0.000004
N	412	S412S	agC	agT	14	14	B.1.1.519	0.000556
N	412	S412L	AGc	CTc	13	13	All	0.000002
N	412	S412T	aGc	aCc	13	13	All	0.000002
N	412	S412L	AGc	CTc	13	13	AY.27	0.000841
N	412	S412S	agC	agT	13	13	AY.37	0.004109
N	412	S412S	agC	agT	12	12	AY.13	0.001932
N	412	S412I	aGc	aTc	10	12	AY.20	0.000389
N	412	S412I	aGC	aTT	2	12	AY.20	0.000078
N	412	S412N	aGc	aAc	12	12	AY.25	0.000072
N	412	S412S	agC	agT	12	12	AY.34.1	0.006119
N	412	S412S	agC	agT	12	12	AY.59	0.006356
N	412	S412R	Agc	Cgc	12	12	AY.74	0.001388
N	412	S412S	agC	agT	12	12	AY.75	0.000672
N	412	S412I	aGc	aTc	12	12	B.1.2	0.000106
N	412	S412S	agC	agT	12	12	Q.1	0.001516
N	412	S412S	agC	agT	11	11	AY.39.1	0.000436
N	412	S412G	Agc	Ggc	11	11	AY.4	0.000017
N	412	S412R	Agc	Cgc	11	11	AY.75.1	0.001983
N	412	S412R	agC	agA	8	11	B.1	0.000073
N	412	S412R	Agc	Cgc	3	11	B.1	0.000027
N	412	S412S	agC	agT	11	11	B.1.177.35	0.007602
N	412	S412W	AgC	TgG	10	10	All	0.000002
N	412	S412N	aGc	aAc	10	10	AY.103	0.000062
N	412	S412R	Agc	Cgc	10	10	AY.47	0.000311
N	412	S412G	Agc	Ggc	10	10	AY.69	0.001867
N	412	S412S	agC	agT	10	10	AY.99.2	0.000922
N	412	S412S	agC	agT	10	10	B.1.351	0.000297
N	412	S412W	AgC	TgG	10	10	P.1	0.000158
N	412	S412S	agC	agT	9	9	AY.29	0.000142
N	412	S412S	agC	agT	9	9	AY.32	0.004792
N	412	S412S	agC	agT	9	9	AY.58	0.008167
N	412	S412S	agC	agT	9	9	AY.7	0.001764
N	412	S412S	agC	agT	9	9	AY.71	0.004276
N	412	S412N	aGc	aAc	9	9	AY.75	0.000504
N	412	S412N	aGc	aAc	9	9	B.1	0.000082
N	412	S412I	aGc	aTc	9	9	B.1.351	0.000268
N	412	S412S	agC	agT	9	9	B.1.497	0.002833
N	412	S412R	agC	agG	8	8	AY.120.1	0.002568
N	412	S412R	Agc	Cgc	8	8	AY.20	0.000311
N	412	S412S	agC	agT	8	8	AY.38	0.003994
N	412	S412S	agC	agT	8	8	AY.41	0.002352
N	412	S412S	agC	agT	8	8	AY.63	0.003095
N	412	S412S	agC	agT	8	8	AY.69	0.001493
N	412	S412I	aGc	aTc	8	8	B.1	0.000073
N	412	S412G	Agc	Ggc	8	8	B.1.1.7	0.000007
N	412	S412S	agC	agT	8	8	B.1.160	0.00025
N	412	S412G	Agc	Ggc	7	8	B.1.617.2	0.000026
N	412	S412G	AgC	GgA	1	8	B.1.617.2	0.000004
N	412	S412V	AGc	GTc	7	7	All	0.000001
N	412	S412S	agC	agT	7	7	AY.108	0.007718
N	412	S412R	Agc	Cgc	4	7	AY.25	0.000024
N	412	S412R	agC	agA	3	7	AY.25	0.000018
N	412	S412I	aGC	aTT	7	7	AY.3	0.00007
N	412	S412V	AGc	GTc	7	7	AY.44	0.000043
N	412	S412S	agC	agT	7	7	AY.46.2	0.004447
N	412	S412S	agC	agT	7	7	AY.46.4	0.001152
N	412	S412S	agC	agT	7	7	AY.9.2	0.000257
N	412	S412G	Agc	Ggc	7	7	B.1.1.525	0.038251
N	412	S412N	aGc	aAc	7	7	B.1.311	0.001922
N	412	S412S	agC	agT	7	7	B.1.429	0.000165
N	412	S412S	agC	agT	7	7	B.1.596	0.00061
N	412	S412S	agC	agT	7	7	B.6.6	0.006222
N	412	S412I	aGc	aTc	7	7	C.37	0.000812
N	412	S412I	aGc	aTc	6	6	AY.109	0.004438
N	412	S412R	Agc	Cgc	6	6	AY.26	0.00017
N	412	S412I	aGc	aTc	6	6	AY.4.2.1	0.000894
N	412	S412S	agC	agT	6	6	AY.61	0.000629
N	412	S412S	agC	agT	6	6	AY.74	0.000694
N	412	S412I	aGc	aTc	6	6	B.1.1.176	0.002636
N	412	S412S	agC	agT	6	6	B.1.1.222	0.001224
N	412	S412I	aGc	aTc	6	6	B.1.526	0.000141
N	412	S412K	aGC	aAA	3	5	All	0.000001
N	412	S412K	aGC	aAG	2	5	All	0
N	412	S412S	agC	agT	5	5	AY.111	0.000916
N	412	S412I	aGc	aTc	5	5	AY.39	0.000124
N	412	S412R	agC	agG	5	5	AY.4	0.000008
N	412	S412I	aGc	aTc	5	5	AY.46.6	0.000361
N	412	S412R	Agc	Cgc	5	5	AY.62	0.002179
N	412	S412S	agC	agT	5	5	AY.68	0.001369
N	412	S412I	aGc	aTc	5	5	AY.98	0.000395
N	412	S412N	aGc	aAc	5	5	AY.99.2	0.000461
N	412	S412S	agC	agT	5	5	B.1.1.317	0.002058
N	412	S412S	agC	agT	5	5	B.1.1.63	0.001929
N	412	S412S	agC	agT	5	5	B.1.221	0.000355
N	412	S412N	aGc	aAc	5	5	B.1.234	0.00066
N	412	S412S	agC	agT	5	5	B.1.258	0.000333
N	412	S412S	agC	agT	5	5	D.2	0.000375
N	412	S412D	AGc	GAc	2	4	All	0
N	412	S412del1	Agc	-gc	2	4	All	0
N	412	S412D	AGC	GAT	2	4	All	0
N	412	S412del1	agC	ag-	1	4	All	0
N	412	S412del1	aGc	a-c	1	4	All	0
N	412	S412R	agC	agA	4	4	AY.103	0.000025
N	412	S412I	aGc	aTc	4	4	AY.103	0.000025
N	412	S412S	agC	agT	4	4	AY.109	0.002959
N	412	S412I	aGc	aTc	4	4	AY.119	0.000141
N	412	S412G	AgC	GgT	4	4	AY.3.1	0.000341
N	412	S412C	Agc	Tgc	4	4	AY.4	0.000006
N	412	S412N	aGc	aAc	4	4	AY.4.2	0.000087
N	412	S412S	agC	agT	4	4	AY.4.2.1	0.000596
N	412	S412S	agC	agT	4	4	AY.4.3	0.003367
N	412	S412S	agC	agT	4	4	AY.53	0.00115
N	412	S412S	agC	agT	4	4	AY.6	0.000165
N	412	S412N	aGc	aAc	4	4	AY.74	0.000463
N	412	S412S	agC	agT	4	4	AY.75.1	0.000721
N	412	S412I	aGc	aTc	4	4	AY.81	0.007968
N	412	S412R	Agc	Cgc	4	4	AY.9	0.00027
N	412	S412I	aGc	aTc	4	4	B.1.1	0.000073
N	412	S412N	aGc	aAc	3	4	B.1.1	0.000054
N	412	S412N	aGC	aAT	1	4	B.1.1	0.000018
N	412	S412I	aGc	aTc	4	4	B.1.1.174	0.013514
N	412	S412S	agC	agT	4	4	B.1.1.214	0.000222
N	412	S412S	agC	agT	4	4	B.1.1.312	0.007648
N	412	S412S	agC	agT	4	4	B.1.1.33	0.001684
N	412	S412S	agC	agT	4	4	B.1.111	0.0047
N	412	S412S	agC	agT	4	4	B.1.177.42	0.003578
N	412	S412R	agC	agA	3	4	B.1.2	0.000026
N	412	S412R	Agc	Cgc	1	4	B.1.2	0.000009
N	412	S412I	aGc	aTc	4	4	B.1.221	0.000284
N	412	S412S	agC	agT	4	4	C.36.3	0.002269
N	412	S412I	aGc	aTc	4	4	P.1	0.000063
N	412	S412N	aGc	aAc	4	4	P.1.17	0.000647
N	412	S412S	agC	agT	4	4	P.1.2	0.004624
N	412	S412S	agC	agT	4	4	P.2	0.000747
N	412	S412S	agC	agT	3	3	AY.10	0.00159
N	412	S412I	aGc	aTc	3	3	AY.117	0.000254
N	412	S412S	agC	agT	3	3	AY.121	0.000406
N	412	S412G	Agc	Ggc	3	3	AY.20	0.000117
N	412	S412C	Agc	Tgc	3	3	AY.25	0.000018
N	412	S412I	aGc	aTc	3	3	AY.26	0.000085
N	412	S412C	Agc	Tgc	3	3	AY.29	0.000047
N	412	S412G	Agc	Ggc	2	3	AY.33	0.000134
N	412	S412G	AgC	GgT	1	3	AY.33	0.000067
N	412	S412S	agC	agT	3	3	AY.4.5	0.000322
N	412	S412S	agC	agT	3	3	AY.5.4	0.00083
N	412	S412S	agC	agT	3	3	AY.57	0.001969
N	412	S412S	agC	agT	3	3	AY.64	0.001786
N	412	S412R	Agc	Cgc	3	3	AY.75	0.000168
N	412	S412R	agC	agA	3	3	AY.94	0.001328
N	412	S412G	Agc	Ggc	2	3	B.1.1	0.000036
N	412	S412G	AgC	GgT	1	3	B.1.1	0.000018
N	412	S412S	agC	agT	3	3	B.1.1.1	0.00098
N	412	S412S	agC	agT	3	3	B.1.1.28	0.000934
N	412	S412S	agC	agT	3	3	B.1.1.37	0.000579
N	412	S412S	agC	agT	3	3	B.1.139	0.002199
N	412	S412T	aGc	aCc	3	3	B.1.2	0.000026
N	412	S412I	aGc	aTc	3	3	B.1.243	0.000209
N	412	S412N	aGc	aAc	3	3	B.1.243	0.000209
N	412	S412S	agC	agT	3	3	B.1.369	0.000856
N	412	S412I	aGc	aTc	3	3	B.1.427	0.000151
N	412	S412N	aGc	aAc	3	3	B.1.427	0.000151
N	412	S412S	agC	agT	3	3	B.1.517	0.001281
N	412	S412S	agC	agT	3	3	B.1.525	0.000339
N	412	S412T	aGc	aCc	3	3	B.1.617.2	0.000011
N	412	S412S	agC	agT	3	3	B.1.621	0.000266
N	412	S412I	aGc	aTc	3	3	B.1.621.1	0.001517
N	412	S412I	aGc	aTc	3	3	P.1.14	0.000143
N	412	S412S	agC	agT	3	3	Q.8	0.000495
N	412	S412G	AgC	GgG	1	2		0.055556
N	412	S412G	Agc	Ggc	1	2		0.055556
N	412	S412R	agC	agA	2	2	A.1	0.000564
N	412	S412S	agC	agT	2	2	A.2.5	0.000998
N	412	S412S	agC	agT	2	2	A.23.1	0.001408
N	412	S412I	aGc	aTc	2	2	AH.3	0.007605
N	412	S412I	aGc	aTc	2	2	AY.110	0.000225
N	412	S412N	aGc	aAc	2	2	AY.119	0.000071
N	412	S412N	aGc	aAc	2	2	AY.121	0.000271
N	412	S412I	aGc	aTc	2	2	AY.121	0.000271
N	412	S412del	AGC	---	2	2	AY.25	0.000012
N	412	S412N	aGc	aAc	2	2	AY.29	0.000032
N	412	S412S	agC	agT	2	2	AY.29.1	0.000441
N	412	S412G	AgC	GgT	2	2	AY.3	0.00002
N	412	S412R	Agc	Cgc	2	2	AY.39.1	0.000079
N	412	S412N	aGc	aAc	2	2	AY.39.1	0.000079
N	412	S412I	aGc	aTc	2	2	AY.45	0.000243
N	412	S412I	aGc	aTc	2	2	AY.47	0.000062
N	412	S412S	agC	agT	2	2	AY.48	0.00093
N	412	S412I	aGc	aTc	2	2	AY.64	0.00119
N	412	S412R	Agc	Cgc	2	2	AY.67	0.000929
N	412	S412S	agC	agT	2	2	AY.67	0.000929
N	412	S412S	agC	agT	2	2	AY.7.1	0.000225
N	412	S412S	agC	agT	2	2	AY.7.2	0.001119
N	412	S412I	aGc	aTc	2	2	AY.79	0.002421
N	412	S412S	agC	agT	2	2	AY.9	0.000135
N	412	S412S	agC	agT	2	2	AY.9.1	0.000167
N	412	S412I	aGc	aTc	2	2	AY.9.2	0.000073
N	412	S412I	aGc	aTc	2	2	AY.99.2	0.000184
N	412	S412G	Agc	Ggc	2	2	B.1	0.000018
N	412	S412del	AGC	---	2	2	B.1	0.000018
N	412	S412del	AGC	---	2	2	B.1.1	0.000036
N	412	S412D	AGC	GAT	1	2	B.1.1	0.000018
N	412	S412D	AGc	GAc	1	2	B.1.1	0.000018
N	412	S412R	agC	agA	1	2	B.1.1.1	0.000327
N	412	S412R	agC	agG	1	2	B.1.1.1	0.000327
N	412	S412S	agC	agT	2	2	B.1.1.10	0.00223
N	412	S412I	aGc	aTc	2	2	B.1.1.216	0.001781
N	412	S412I	aGc	aTc	2	2	B.1.1.231	0.006192
N	412	S412S	agC	agT	2	2	B.1.1.301	0.002358
N	412	S412N	aGc	aAc	2	2	B.1.1.317	0.000823
N	412	S412S	agC	agT	2	2	B.1.1.329	0.007692
N	412	S412S	agC	agT	2	2	B.1.1.398	0.006452
N	412	S412I	aGc	aTc	2	2	B.1.1.420	0.002012
N	412	S412S	agC	agT	2	2	B.1.1.420	0.002012
N	412	S412C	Agc	Tgc	2	2	B.1.1.7	0.000002
N	412	S412del1	Agc	-gc	1	2	B.1.1.7	0.000001
N	412	S412del1	aGc	a-c	1	2	B.1.1.7	0.000001
N	412	S412I	aGc	aTc	2	2	B.1.201	0.011364
N	412	S412S	agC	agT	2	2	B.1.234	0.000264
N	412	S412N	aGc	aAc	2	2	B.1.289	0.005319
N	412	S412R	Agc	Cgc	2	2	B.1.351	0.000059
N	412	S412S	agC	agT	2	2	B.1.36	0.000292
N	412	S412S	agC	agT	2	2	B.1.36.29	0.001035
N	412	S412K	aGC	aAA	2	2	B.1.429	0.000047
N	412	S412N	aGc	aAc	2	2	B.1.438.1	0.000215
N	412	S412S	agC	agT	2	2	B.1.438.1	0.000215
N	412	S412S	agC	agT	2	2	B.1.453	0.006472
N	412	S412S	agC	agT	2	2	B.1.474	0.003802
N	412	S412S	agC	agT	2	2	B.1.560	0.009259
N	412	S412S	agC	agT	2	2	B.1.575.1	0.004878
N	412	S412S	agC	agT	2	2	B.1.576	0.001813
N	412	S412I	aGc	aTc	2	2	B.1.577	0.001375
N	412	S412S	agC	agT	2	2	B.1.588	0.00182
N	412	S412N	aGc	aAc	2	2	B.1.595	0.000522
N	412	S412N	aGc	aAc	2	2	B.1.596	0.000174
N	412	S412R	agC	agA	2	2	B.1.596	0.000174
N	412	S412I	aGc	aTc	2	2	B.1.596	0.000174
N	412	S412S	agC	agT	2	2	B.1.604	0.034483
N	412	S412del	AGC	---	2	2	B.1.617.2	0.000008
N	412	S412I	aGc	aTc	2	2	B.1.617.3	0.00597
N	412	S412S	agC	agT	2	2	B.1.619	0.001742
N	412	S412S	agC	agT	2	2	B.1.628	0.000705
N	412	S412S	agC	agT	2	2	C.36	0.001821
N	412	S412I	aGc	aTc	2	2	N.4	0.008511
N	412	S412del	AGC	---	2	2	P.1	0.000032
N	412	S412N	aGc	aAc	1	1		0.055556
N	412	S412R	agC	agG	1	1		0.055556
N	412	S412D	AGc	GAc	1	1		0.055556
N	412	S412K	aGC	aAG	1	1		0.055556
N	412	S412E	AGC	GAG	1	1		0.055556
N	412	S412S	agC	agT	1	1	A.19	0.009434
N	412	S412R	agC	agA	1	1	A.2.5	0.000499
N	412	S412S	agC	agT	1	1	AD.2	0.000219
N	412	S412del2	aGC	a--	1	1	All	0
N	412	S412E	AGC	GAG	1	1	All	0
N	412	S412N	aGc	aAc	1	1	AW.1	0.003049
N	412	S412S	agC	agT	1	1	AY.1	0.000396
N	412	S412S	agC	agT	1	1	AY.101	0.00049
N	412	S412G	Agc	Ggc	1	1	AY.102	0.000027
N	412	S412C	Agc	Tgc	1	1	AY.103	0.000006
N	412	S412G	Agc	Ggc	1	1	AY.103	0.000006
N	412	S412S	agC	agT	1	1	AY.107	0.000466
N	412	S412I	aGc	aTc	1	1	AY.111	0.000183
N	412	S412R	Agc	Cgc	1	1	AY.113	0.000142
N	412	S412del	AGC	---	1	1	AY.114	0.000231
N	412	S412I	aGc	aTc	1	1	AY.114	0.000231
N	412	S412I	aGc	aTc	1	1	AY.118	0.000063
N	412	S412N	aGc	aAc	1	1	AY.120	0.000037
N	412	S412I	aGc	aTc	1	1	AY.120	0.000037
N	412	S412S	agC	agT	1	1	AY.120.1	0.000321
N	412	S412S	agC	agT	1	1	AY.120.2.1	0.000498
N	412	S412N	aGc	aAc	1	1	AY.13	0.000161
N	412	S412S	agC	agT	1	1	AY.14	0.000088
N	412	S412I	aGc	aTc	1	1	AY.16	0.00038
N	412	S412S	agC	agT	1	1	AY.16	0.00038
N	412	S412N	aGc	aAc	1	1	AY.23	0.00007
N	412	S412S	agC	agT	1	1	AY.24	0.000431
N	412	S412G	Agc	Ggc	1	1	AY.25	0.000006
N	412	S412N	aGc	aAc	1	1	AY.26	0.000028
N	412	S412del	AGC	---	1	1	AY.26	0.000028
N	412	S412I	aGc	aTc	1	1	AY.29	0.000016
N	412	S412T	aGc	aCc	1	1	AY.29	0.000016
N	412	S412N	aGC	aAT	1	1	AY.3	0.00001
N	412	S412I	aGc	aTc	1	1	AY.33	0.000067
N	412	S412del1	agC	ag-	1	1	AY.33	0.000067
N	412	S412T	aGc	aCc	1	1	AY.33	0.000067
N	412	S412N	aGc	aAc	1	1	AY.34.1	0.00051
N	412	S412S	agC	agT	1	1	AY.35	0.000233
N	412	S412R	Agc	Cgc	1	1	AY.36	0.000148
N	412	S412I	aGc	aTc	1	1	AY.37	0.000316
N	412	S412G	Agc	Ggc	1	1	AY.39	0.000025
N	412	S412R	Agc	Cgc	1	1	AY.39	0.000025
N	412	S412T	aGc	aCc	1	1	AY.39	0.000025
N	412	S412del	AGC	---	1	1	AY.4	0.000002
N	412	S412G	Agc	Ggc	1	1	AY.4.2	0.000022
N	412	S412I	aGc	aTc	1	1	AY.4.4	0.000409
N	412	S412G	Agc	Ggc	1	1	AY.4.5	0.000107
N	412	S412I	aGc	aTc	1	1	AY.40	0.000964
N	412	S412I	aGc	aTc	1	1	AY.42	0.00004
N	412	S412G	Agc	Ggc	1	1	AY.43	0.000004
N	412	S412N	aGc	aAc	1	1	AY.43	0.000004
N	412	S412C	Agc	Tgc	1	1	AY.43	0.000004
N	412	S412T	aGc	aCc	1	1	AY.43	0.000004
N	412	S412del	AGC	---	1	1	AY.43	0.000004
N	412	S412R	agC	agA	1	1	AY.44	0.000006
N	412	S412G	Agc	Ggc	1	1	AY.45	0.000122
N	412	S412S	agC	agT	1	1	AY.46.3	0.000934
N	412	S412del	AGC	---	1	1	AY.47	0.000031
N	412	S412I	aGc	aTc	1	1	AY.48	0.000465
N	412	S412I	aGc	aTc	1	1	AY.5	0.000021
N	412	S412N	aGc	aAc	1	1	AY.5.3	0.000337
N	412	S412I	aGc	aTc	1	1	AY.50	0.000799
N	412	S412S	agC	agT	1	1	AY.52	0.000814
N	412	S412I	aGc	aTc	1	1	AY.55	0.000917
N	412	S412I	aGc	aTc	1	1	AY.56	0.001605
N	412	S412I	aGc	aTc	1	1	AY.6	0.000041
N	412	S412N	aGc	aAc	1	1	AY.6	0.000041
N	412	S412R	Agc	Cgc	1	1	AY.61	0.000105
N	412	S412del	AGC	---	1	1	AY.62	0.000436
N	412	S412S	agC	agT	1	1	AY.65	0.000533
N	412	S412N	aGc	aAc	1	1	AY.69	0.000187
N	412	S412N	aGc	aAc	1	1	AY.7.1	0.000113
N	412	S412S	agC	agT	1	1	AY.70	0.000209
N	412	S412I	aGc	aTc	1	1	AY.71	0.000475
N	412	S412N	aGc	aAc	1	1	AY.8	0.000606
N	412	S412I	aGc	aTc	1	1	AY.84	0.000437
N	412	S412I	aGc	aTc	1	1	AY.86	0.00083
N	412	S412S	agC	agT	1	1	AY.87	0.000833
N	412	S412S	agC	agT	1	1	AY.89	0.004902
N	412	S412I	aGc	aTc	1	1	AY.9	0.000068
N	412	S412I	aGc	aTc	1	1	AY.90	0.000684
N	412	S412I	aGc	aTc	1	1	AY.98.1	0.000048
N	412	S412S	agC	agT	1	1	AZ.3	0.00152
N	412	S412R	agC	agA	1	1	B	0.000128
N	412	S412I	aGc	aTc	1	1	B	0.000128
N	412	S412T	aGc	aCc	1	1	B.1	0.000009
N	412	S412T	aGc	aCc	1	1	B.1.1	0.000018
N	412	S412N	aGc	aAc	1	1	B.1.1.1	0.000327
N	412	S412I	aGc	aTc	1	1	B.1.1.1	0.000327
N	412	S412C	Agc	Tgc	1	1	B.1.1.132	0.014925
N	412	S412S	agC	agT	1	1	B.1.1.153	0.001095
N	412	S412N	aGc	aAc	1	1	B.1.1.153	0.001095
N	412	S412S	agC	agT	1	1	B.1.1.174	0.003378
N	412	S412I	aGc	aTc	1	1	B.1.1.214	0.000055
N	412	S412I	aGc	aTc	1	1	B.1.1.232	0.001815
N	412	S412S	agC	agT	1	1	B.1.1.25	0.000569
N	412	S412I	aGc	aTc	1	1	B.1.1.25	0.000569
N	412	S412S	agC	agT	1	1	B.1.1.258	0.003257
N	412	S412N	aGc	aAc	1	1	B.1.1.27	0.00565
N	412	S412S	agC	agT	1	1	B.1.1.273	0.006757
N	412	S412N	aGc	aAc	1	1	B.1.1.274	0.005051
N	412	S412G	Agc	Ggc	1	1	B.1.1.291	0.000742
N	412	S412S	agC	agT	1	1	B.1.1.306	0.000438
N	412	S412G	Agc	Ggc	1	1	B.1.1.318	0.000302
N	412	S412S	agC	agT	1	1	B.1.1.351	0.002793
N	412	S412S	agC	agT	1	1	B.1.1.354	0.004386
N	412	S412S	agC	agT	1	1	B.1.1.368	0.003086
N	412	S412S	agC	agT	1	1	B.1.1.369	0.000446
N	412	S412del	AGC	---	1	1	B.1.1.37	0.000193
N	412	S412S	agC	agT	1	1	B.1.1.409	0.002833
N	412	S412S	agC	agT	1	1	B.1.1.434	0.000349
N	412	S412S	agC	agT	1	1	B.1.1.51	0.001718
N	412	S412I	aGc	aTc	1	1	B.1.1.519	0.00004
N	412	S412N	aGc	aAc	1	1	B.1.1.519	0.00004
N	412	S412N	aGc	aAc	1	1	B.1.1.63	0.000386
N	412	S412del	AGC	---	1	1	B.1.1.7	0.000001
N	412	S412N	aGc	aAc	1	1	B.1.1.70	0.000341
N	412	S412I	aGc	aTc	1	1	B.1.128	0.000635
N	412	S412S	agC	agT	1	1	B.1.157	0.002985
N	412	S412S	agC	agT	1	1	B.1.160.16	0.000929
N	412	S412S	agC	agT	1	1	B.1.160.29	0.004219
N	412	S412del	AGC	---	1	1	B.1.162	0.005025
N	412	S412R	agC	agG	1	1	B.1.177	0.000013
N	412	S412N	aGc	aAc	1	1	B.1.177.21	0.000076
N	412	S412del1	Agc	-gc	1	1	B.1.177.21	0.000076
N	412	S412S	agC	agT	1	1	B.1.177.21	0.000076
N	412	S412S	agC	agT	1	1	B.1.177.33	0.001645
N	412	S412S	agC	agT	1	1	B.1.177.43	0.001477
N	412	S412S	agC	agT	1	1	B.1.177.44	0.000519
N	412	S412S	agC	agT	1	1	B.1.177.54	0.000606
N	412	S412S	agC	agT	1	1	B.1.177.57	0.000281
N	412	S412S	agC	agT	1	1	B.1.177.60	0.000218
N	412	S412K	aGC	aAA	1	1	B.1.177.63	0.002703
N	412	S412S	agC	agT	1	1	B.1.177.7	0.000165
N	412	S412R	agC	agA	1	1	B.1.177.73	0.000566
N	412	S412S	agC	agT	1	1	B.1.177.79	0.002342
N	412	S412S	agC	agT	1	1	B.1.177.81	0.000189
N	412	S412N	aGc	aAc	1	1	B.1.177.86	0.000183
N	412	S412G	Agc	Ggc	1	1	B.1.177.86	0.000183
N	412	S412K	aGC	aAG	1	1	B.1.177.86	0.000183
N	412	S412R	agC	agG	1	1	B.1.177.86	0.000183
N	412	S412I	aGc	aTc	1	1	B.1.179	0.003759
N	412	S412N	aGc	aAc	1	1	B.1.182	0.007246
N	412	S412G	Agc	Ggc	1	1	B.1.2	0.000009
N	412	S412del	AGC	---	1	1	B.1.2	0.000009
N	412	S412S	agC	agT	1	1	B.1.206	0.000816
N	412	S412S	agC	agT	1	1	B.1.214.2	0.0006
N	412	S412G	Agc	Ggc	1	1	B.1.221	0.000071
N	412	S412C	Agc	Tgc	1	1	B.1.221	0.000071
N	412	S412I	aGc	aTc	1	1	B.1.234	0.000132
N	412	S412S	agC	agT	1	1	B.1.240	0.000216
N	412	S412N	aGc	aAc	1	1	B.1.241	0.000812
N	412	S412del	AGC	---	1	1	B.1.258.16	0.001637
N	412	S412G	Agc	Ggc	1	1	B.1.284	0.013158
N	412	S412I	aGc	aTc	1	1	B.1.346	0.001311
N	412	S412N	aGc	aAc	1	1	B.1.351	0.00003
N	412	S412S	agC	agT	1	1	B.1.351.5	0.0006
N	412	S412N	aGc	aAc	1	1	B.1.36.1	0.00114
N	412	S412I	aGc	aTc	1	1	B.1.36.17	0.000494
N	412	S412S	agC	agT	1	1	B.1.36.18	0.00042
N	412	S412R	Agc	Cgc	1	1	B.1.36.18	0.00042
N	412	S412N	aGc	aAc	1	1	B.1.36.29	0.000517
N	412	S412S	agC	agT	1	1	B.1.36.8	0.001
N	412	S412S	agC	agT	1	1	B.1.362	0.001541
N	412	S412I	aGc	aTc	1	1	B.1.362	0.001541
N	412	S412N	aGc	aAc	1	1	B.1.391	0.001127
N	412	S412N	aGc	aAc	1	1	B.1.396	0.000706
N	412	S412del	AGC	---	1	1	B.1.415	0.014286
N	412	S412del	AGC	---	1	1	B.1.427	0.00005
N	412	S412S	agC	agT	1	1	B.1.428	0.00102
N	412	S412S	agC	agT	1	1	B.1.436	0.001029
N	412	S412del	AGC	---	1	1	B.1.438.1	0.000107
N	412	S412G	Agc	Ggc	1	1	B.1.456	0.003268
N	412	S412S	agC	agT	1	1	B.1.469	0.00361
N	412	S412S	agC	agT	1	1	B.1.470	0.001404
N	412	S412S	agC	agT	1	1	B.1.485	0.014925
N	412	S412S	agC	agT	1	1	B.1.509	0.000866
N	412	S412N	aGc	aAc	1	1	B.1.517	0.000427
N	412	S412del	AGC	---	1	1	B.1.526	0.000024
N	412	S412S	agC	agT	1	1	B.1.546	0.003704
N	412	S412S	agC	agT	1	1	B.1.564	0.000426
N	412	S412S	agC	agT	1	1	B.1.580	0.004065
N	412	S412S	agC	agT	1	1	B.1.586	0.010989
N	412	S412del	AGC	---	1	1	B.1.596	0.000087
N	412	S412S	agC	agT	1	1	B.1.600	0.005848
N	412	S412R	Agc	Cgc	1	1	B.1.604	0.017241
N	412	S412N	aGc	aAc	1	1	B.1.609	0.000479
N	412	S412S	agC	agT	1	1	B.1.617.1	0.000129
N	412	S412G	Agc	Ggc	1	1	B.1.617.1	0.000129
N	412	S412C	Agc	Tgc	1	1	B.1.617.2	0.000004
N	412	S412D	AGC	GAT	1	1	B.1.617.2	0.000004
N	412	S412S	agC	agT	1	1	B.1.620	0.000946
N	412	S412N	aGc	aAc	1	1	B.1.621	0.000089
N	412	S412I	aGc	aTc	1	1	B.1.621	0.000089
N	412	S412S	agC	agT	1	1	B.1.623	0.000536
N	412	S412S	agC	agT	1	1	B.1.625	0.002353
N	412	S412N	aGc	aAc	1	1	B.1.637	0.000073
N	412	S412I	aGc	aTc	1	1	B.1.637	0.000073
N	412	S412S	agC	agT	1	1	B.1.637	0.000073
N	412	S412S	agC	agT	1	1	B.1.78	0.008547
N	412	S412S	agC	agT	1	1	B.1.8	0.001972
N	412	S412S	agC	agT	1	1	B.28	0.003279
N	412	S412T	aGc	aCc	1	1	B.3	0.000831
N	412	S412S	agC	agT	1	1	B.4	0.002208
N	412	S412S	agC	agT	1	1	B.40	0.000364
N	412	S412R	Agc	Cgc	1	1	B.40	0.000364
N	412	S412S	agC	agT	1	1	B.52	0.010101
N	412	S412N	aGc	aAc	1	1	B.55	0.00295
N	412	S412I	aGC	aTT	1	1	C.1	0.002392
N	412	S412S	agC	agT	1	1	C.1.1	0.076923
N	412	S412S	agC	agT	1	1	C.18	0.002591
N	412	S412G	Agc	Ggc	1	1	C.35	0.000774
N	412	S412G	Agc	Ggc	1	1	C.36	0.000911
N	412	S412R	agC	agA	1	1	C.36.3	0.000567
N	412	S412N	aGc	aAc	1	1	C.37	0.000116
N	412	S412S	agC	agT	1	1	N.5	0.001767
N	412	S412del2	aGC	a--	1	1	P.1	0.000016
N	412	S412G	Agc	Ggc	1	1	P.1	0.000016
N	412	S412I	aGc	aTc	1	1	P.1.11	0.010204
N	412	S412N	aGc	aAc	1	1	P.1.12	0.000484
N	412	S412N	aGc	aAc	1	1	P.1.13	0.000898
N	412	S412N	aGc	aAc	1	1	P.1.14	0.000048
N	412	S412S	agC	agT	1	1	P.1.14	0.000048
N	412	S412G	Agc	Ggc	1	1	P.1.14	0.000048
N	412	S412S	agC	agT	1	1	P.1.15	0.000232
N	412	S412S	agC	agT	1	1	P.1.4	0.000977
N	412	S412R	agC	agA	1	1	P.2	0.000187
N	412	S412I	aGc	aTc	1	1	Q.3	0.000145
N	412	S412S	agC	agT	1	1	Q.5	0.016949
N	412	S412N	aGc	aAc	1	1	Q.8	0.000165
N	412	S412R	agC	agA	1	1	Q.8	0.000165
N	412	S412S	agC	agT	1	1	R.1	0.00009

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.