CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 32

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	32	F32F		syn	ttC	ttT	9321	9321	1	21656-21658
S	32	F32L		nonsyn	Ttc	Ctc	619	502	0.810985	21656-21658
S	32	F32L		nonsyn	ttC	ttG	619	65	0.105008	21656-21658
S	32	F32L		nonsyn	ttC	ttA	619	49	0.0791599	21656-21658
S	32	F32L		nonsyn	TtC	CtT	619	3	0.00484653	21656-21658
S	32	F32del		del	TTC	---	83	83	1	21656-21658
S	32	F32Y		nonsyn	tTc	tAc	82	80	0.97561	21656-21658
S	32	F32Y		nonsyn	tTC	tAT	82	2	0.0243902	21656-21658
S	32	F32S		nonsyn	tTc	tCc	68	67	0.985294	21656-21658
S	32	F32S		nonsyn	tTC	tCA	68	1	0.0147059	21656-21658
S	32	F32V		nonsyn	Ttc	Gtc	24	24	1	21656-21658
S	32	F32del2		del	tTC	t--	13	9	0.692308	21656-21658
S	32	F32del2		del	TTC	--A	13	2	0.153846	21656-21658
S	32	F32del2		del	TTc	--c	13	1	0.0769231	21656-21658
S	32	F32del2		del	TTC	--N	13	1	0.0769231	21656-21658
S	32	F32del1		del	ttC	tt-	12	10	0.833333	21656-21658
S	32	F32del1		del	Ttc	-tc	12	2	0.166667	21656-21658
S	32	F32I		nonsyn	Ttc	Atc	11	11	1	21656-21658
S	32	F32X		nonsyn	tTC	tAA	6	4	0.666667	21656-21658
S	32	F32X		nonsyn	tTC	tAG	6	2	0.333333	21656-21658
S	32	F32C		nonsyn	tTc	tGc	5	4	0.8	21656-21658
S	32	F32C		nonsyn	tTC	tGT	5	1	0.2	21656-21658
S	32	F32M		nonsyn	TtC	AtG	3	3	1	21656-21658
S	32	F32P		nonsyn	TTC	CCT	3	2	0.666667	21656-21658
S	32	F32P		nonsyn	TTc	CCc	3	1	0.333333	21656-21658
S	32	F32K		nonsyn	TTC	AAG	2	2	1	21656-21658
S	32	F32N		nonsyn	TTc	AAc	2	2	1	21656-21658
S	32	F32E		nonsyn	TTC	GAA	1	1	1	21656-21658

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	32	F32F	ttC	ttT	9321	9321	All	0.001783
S	32	F32F	ttC	ttT	2543	2543	B.1.1.7	0.002277
S	32	F32F	ttC	ttT	1607	1607	B.1.526	0.037772
S	32	F32L	Ttc	Ctc	502	619	All	0.000096
S	32	F32L	ttC	ttG	65	619	All	0.000012
S	32	F32L	ttC	ttA	49	619	All	0.000009
S	32	F32L	TtC	CtT	3	619	All	0.000001
S	32	F32F	ttC	ttT	546	546	AY.43	0.002419
S	32	F32F	ttC	ttT	504	504	AY.4	0.000784
S	32	F32F	ttC	ttT	225	225	AY.44	0.00137
S	32	F32F	ttC	ttT	213	213	B.1.617.2	0.000802
S	32	F32F	ttC	ttT	198	198	AY.25	0.001191
S	32	F32F	ttC	ttT	198	198	AY.3	0.001969
S	32	F32L	Ttc	Ctc	184	194	B.1.2	0.00162
S	32	F32L	ttC	ttA	7	194	B.1.2	0.000062
S	32	F32L	ttC	ttG	3	194	B.1.2	0.000026
S	32	F32F	ttC	ttT	181	181	B.1.2	0.001594
S	32	F32F	ttC	ttT	167	167	AY.103	0.001037
S	32	F32F	ttC	ttT	149	149	B.1.1.519	0.005917
S	32	F32F	ttC	ttT	143	143	B.1	0.00131
S	32	F32L	Ttc	Ctc	131	131	B.1.632	0.879195
S	32	F32F	ttC	ttT	130	130	B.1.177	0.001712
S	32	F32F	ttC	ttT	114	114	A.27	0.188742
S	32	F32F	ttC	ttT	90	90	P.1	0.001418
S	32	F32del	TTC	---	83	83	All	0.000016
S	32	F32Y	tTc	tAc	80	82	All	0.000015
S	32	F32Y	tTC	tAT	2	82	All	0
S	32	F32F	ttC	ttT	80	80	B.1.1.517	0.544218
S	32	F32F	ttC	ttT	77	77	B.1.258.17	0.008006
S	32	F32F	ttC	ttT	76	76	B.1.221.3	0.063333
S	32	F32F	ttC	ttT	73	73	P.1.10	0.019671
S	32	F32S	tTc	tCc	67	68	All	0.000013
S	32	F32S	tTC	tCA	1	68	All	0
S	32	F32F	ttC	ttT	67	67	B.1.1	0.001215
S	32	F32L	Ttc	Ctc	42	62	B.1.1.7	0.000038
S	32	F32L	ttC	ttG	15	62	B.1.1.7	0.000013
S	32	F32L	ttC	ttA	5	62	B.1.1.7	0.000004
S	32	F32F	ttC	ttT	59	59	AY.26	0.00167
S	32	F32F	ttC	ttT	59	59	B.1.637	0.004311
S	32	F32F	ttC	ttT	58	58	B.1.429	0.001365
S	32	F32F	ttC	ttT	57	57	B.1.609	0.027325
S	32	F32F	ttC	ttT	56	56	B.1.1.25	0.031836
S	32	F32F	ttC	ttT	54	54	B.1.160	0.001684
S	32	F32F	ttC	ttT	47	47	AY.4.2	0.001019
S	32	F32F	ttC	ttT	45	45	B.1.351	0.001338
S	32	F32F	ttC	ttT	44	44	AY.39	0.001087
S	32	F32F	ttC	ttT	44	44	B.1.1.343	0.916667
S	32	F32Y	tTc	tAc	42	42	AY.13	0.006761
S	32	F32F	ttC	ttT	41	41	AY.61	0.004296
S	32	F32F	ttC	ttT	41	41	AY.98.1	0.001986
S	32	F32F	ttC	ttT	35	35	AY.20	0.00136
S	32	F32F	ttC	ttT	30	30	B.1.258	0.001996
S	32	F32F	ttC	ttT	27	27	AY.5	0.000558
S	32	F32F	ttC	ttT	27	27	AY.5.3	0.009109
S	32	F32F	ttC	ttT	26	26	AY.100	0.001196
S	32	F32F	ttC	ttT	25	25	AY.39.1	0.00099
S	32	F32L	Ttc	Ctc	16	25	AY.4	0.000025
S	32	F32L	ttC	ttG	6	25	AY.4	0.000009
S	32	F32L	ttC	ttA	3	25	AY.4	0.000005
S	32	F32V	Ttc	Gtc	24	24	All	0.000005
S	32	F32F	ttC	ttT	24	24	B.1.1.214	0.001331
S	32	F32Y	tTc	tAc	24	24	B.1.1.7	0.000021
S	32	F32F	ttC	ttT	24	24	B.1.177.77	0.017429
S	32	F32F	ttC	ttT	24	24	B.1.427	0.001212
S	32	F32F	ttC	ttT	23	23	P.2	0.004293
S	32	F32F	ttC	ttT	22	22	AY.16	0.008352
S	32	F32F	ttC	ttT	22	22	AY.54	0.002098
S	32	F32F	ttC	ttT	22	22	B.1.36	0.00321
S	32	F32F	ttC	ttT	22	22	B.1.628	0.007752
S	32	F32F	ttC	ttT	21	21	AY.102	0.000557
S	32	F32F	ttC	ttT	21	21	AY.29	0.000331
S	32	F32L	Ttc	Ctc	11	20	B.1	0.000101
S	32	F32L	ttC	ttA	5	20	B.1	0.000046
S	32	F32L	ttC	ttG	4	20	B.1	0.000037
S	32	F32F	ttC	ttT	20	20	R.1	0.0018
S	32	F32F	ttC	ttT	18	18	A	0.006966
S	32	F32L	Ttc	Ctc	18	18	AY.25	0.000108
S	32	F32F	ttC	ttT	17	17	AY.46.6	0.001228
S	32	F32F	ttC	ttT	17	17	B.1.433	0.054313
S	32	F32F	ttC	ttT	16	16	B.1.621	0.001416
S	32	F32F	ttC	ttT	15	15	AY.116.1	0.004671
S	32	F32del	TTC	---	15	15	B.1.1.7	0.000013
S	32	F32F	ttC	ttT	15	15	B.4	0.033113
S	32	F32F	ttC	ttT	15	15	C.37	0.001741
S	32	F32F	ttC	ttT	15	15	P.1.14	0.000717
S	32	F32F	ttC	ttT	14	14	AY.101	0.006866
S	32	F32L	Ttc	Ctc	11	14	AY.44	0.000067
S	32	F32L	ttC	ttG	2	14	AY.44	0.000012
S	32	F32L	TtC	CtT	1	14	AY.44	0.000006
S	32	F32F	ttC	ttT	14	14	AY.9.2	0.000514
S	32	F32L	Ttc	Ctc	10	14	B.1.617.2	0.000038
S	32	F32L	ttC	ttG	4	14	B.1.617.2	0.000015
S	32	F32del2	tTC	t--	9	13	All	0.000002
S	32	F32del2	TTC	--A	2	13	All	0
S	32	F32del2	TTc	--c	1	13	All	0
S	32	F32del2	TTC	--N	1	13	All	0
S	32	F32F	ttC	ttT	13	13	B.1.1.1	0.004247
S	32	F32F	ttC	ttT	13	13	B.1.1.311	0.004656
S	32	F32del1	ttC	tt-	10	12	All	0.000002
S	32	F32del1	Ttc	-tc	2	12	All	0
S	32	F32F	ttC	ttT	12	12	AY.119	0.000424
S	32	F32F	ttC	ttT	12	12	AY.120	0.000446
S	32	F32F	ttC	ttT	12	12	B.1.1.420	0.012072
S	32	F32F	ttC	ttT	12	12	B.1.232	0.006448
S	32	F32L	Ttc	Ctc	12	12	B.1.390	0.12766
S	32	F32F	ttC	ttT	12	12	B.1.568	0.013333
S	32	F32I	Ttc	Atc	11	11	All	0.000002
S	32	F32F	ttC	ttT	11	11	AZ.1	0.00954
S	32	F32S	tTc	tCc	11	11	B.1.1.7	0.00001
S	32	F32F	ttC	ttT	11	11	P.1.16	0.004115
S	32	F32F	ttC	ttT	10	10	AY.33	0.000668
S	32	F32F	ttC	ttT	10	10	AY.6	0.000411
S	32	F32F	ttC	ttT	9	9	AY.117	0.000761
S	32	F32S	tTc	tCc	9	9	AY.4	0.000014
S	32	F32F	ttC	ttT	9	9	AY.7	0.001764
S	32	F32F	ttC	ttT	9	9	B.1.177.20	0.013657
S	32	F32F	ttC	ttT	9	9	B.1.438.1	0.000965
S	32	F32F	ttC	ttT	9	9	B.1.525	0.001018
S	32	F32F	ttC	ttT	9	9	B.1.596	0.000784
S	32	F32L	Ttc	Ctc	9	9	B.1.627	0.018182
S	32	F32F	ttC	ttT	9	9	B.1.638	0.473684
S	32	F32F	ttC	ttT	9	9	B.4.5	0.107143
S	32	F32F	ttC	ttT	8	8	AY.110	0.000902
S	32	F32F	ttC	ttT	8	8	AY.23	0.000558
S	32	F32del	TTC	---	8	8	AY.33	0.000534
S	32	F32F	ttC	ttT	8	8	AY.47	0.000249
S	32	F32F	ttC	ttT	8	8	AY.98	0.000632
S	32	F32F	ttC	ttT	8	8	B.1.1.33	0.003367
S	32	F32F	ttC	ttT	8	8	B.1.36.10	0.038278
S	32	F32F	ttC	ttT	8	8	C.35	0.006192
S	32	F32F	ttC	ttT	8	8	D.2	0.0006
S	32	F32F	ttC	ttT	7	7	B.1.1.70	0.002387
S	32	F32del	TTC	---	7	7	B.1.177	0.000092
S	32	F32F	ttC	ttT	7	7	B.1.221	0.000497
S	32	F32F	ttC	ttT	7	7	B.1.243	0.000487
S	32	F32F	ttC	ttT	7	7	B.1.351.3	0.006135
S	32	F32F	ttC	ttT	7	7	B.1.36.29	0.003621
S	32	F32X	tTC	tAA	4	6	All	0.000001
S	32	F32X	tTC	tAG	2	6	All	0
S	32	F32F	ttC	ttT	6	6	AY.109	0.004438
S	32	F32F	ttC	ttT	6	6	AY.27	0.000388
S	32	F32F	ttC	ttT	6	6	AY.3.1	0.000512
S	32	F32L	ttC	ttG	3	6	AY.43	0.000013
S	32	F32L	Ttc	Ctc	2	6	AY.43	0.000009
S	32	F32L	ttC	ttA	1	6	AY.43	0.000004
S	32	F32S	tTc	tCc	6	6	AY.44	0.000037
S	32	F32F	ttC	ttT	6	6	AY.46.4	0.000987
S	32	F32F	ttC	ttT	6	6	AY.75	0.000336
S	32	F32F	ttC	ttT	6	6	B	0.000767
S	32	F32F	ttC	ttT	6	6	B.1.1.28	0.001867
S	32	F32F	ttC	ttT	6	6	B.1.160.14	0.012712
S	32	F32F	ttC	ttT	6	6	B.1.36.8	0.006
S	32	F32S	tTc	tCc	6	6	B.1.617.1	0.000774
S	32	F32F	ttC	ttT	6	6	Q.8	0.000989
S	32	F32C	tTc	tGc	4	5	All	0.000001
S	32	F32C	tTC	tGT	1	5	All	0
S	32	F32L	ttC	ttA	5	5	AY.119	0.000177
S	32	F32F	ttC	ttT	5	5	AY.32	0.002662
S	32	F32del	TTC	---	5	5	AY.43	0.000022
S	32	F32F	ttC	ttT	5	5	AY.88	0.004421
S	32	F32del	TTC	---	5	5	B.1.1	0.000091
S	32	F32V	Ttc	Gtc	5	5	B.1.1.7	0.000004
S	32	F32L	ttC	ttG	5	5	B.1.422	0.004062
S	32	F32F	ttC	ttT	5	5	B.1.470	0.007022
S	32	F32F	ttC	ttT	5	5	B.1.617.1	0.000645
S	32	F32F	ttC	ttT	5	5	B.1.620	0.00473
S	32	F32L	ttC	ttA	3	4	AY.103	0.000019
S	32	F32L	Ttc	Ctc	1	4	AY.103	0.000006
S	32	F32F	ttC	ttT	4	4	AY.12	0.001264
S	32	F32F	ttC	ttT	4	4	AY.14	0.000352
S	32	F32F	ttC	ttT	4	4	AY.37	0.001264
S	32	F32F	ttC	ttT	4	4	AY.42	0.000161
S	32	F32V	Ttc	Gtc	4	4	AY.43	0.000018
S	32	F32F	ttC	ttT	4	4	AY.74	0.000463
S	32	F32Y	tTc	tAc	4	4	B.1	0.000037
S	32	F32F	ttC	ttT	4	4	B.1.1.258	0.013029
S	32	F32I	Ttc	Atc	4	4	B.1.1.7	0.000004
S	32	F32F	ttC	ttT	4	4	B.1.177.44	0.002076
S	32	F32F	ttC	ttT	4	4	B.1.177.81	0.000757
S	32	F32F	ttC	ttT	4	4	B.1.177.83	0.005926
S	32	F32F	ttC	ttT	4	4	B.1.409	0.003125
S	32	F32F	ttC	ttT	4	4	B.1.70	0.097561
S	32	F32Y	tTc	tAc	3	3		0.166667
S	32	F32F	ttC	ttT	3	3	A.2.5	0.001497
S	32	F32F	ttC	ttT	3	3	A.29	0.015957
S	32	F32M	TtC	AtG	3	3	All	0.000001
S	32	F32P	TTC	CCT	2	3	All	0
S	32	F32P	TTc	CCc	1	3	All	0
S	32	F32S	tTc	tCc	3	3	AY.101	0.001471
S	32	F32F	ttC	ttT	3	3	AY.113	0.000427
S	32	F32L	Ttc	Ctc	3	3	AY.118	0.000188
S	32	F32F	ttC	ttT	3	3	AY.120.1	0.000963
S	32	F32F	ttC	ttT	3	3	AY.121	0.000406
S	32	F32F	ttC	ttT	3	3	AY.19	0.003421
S	32	F32del	TTC	---	3	3	AY.25	0.000018
S	32	F32S	tTc	tCc	3	3	AY.25	0.000018
S	32	F32del2	tTC	t--	3	3	AY.3	0.00003
S	32	F32del	TTC	---	3	3	AY.4	0.000005
S	32	F32del1	ttC	tt-	2	3	AY.4	0.000003
S	32	F32del1	Ttc	-tc	1	3	AY.4	0.000002
S	32	F32S	tTc	tCc	3	3	AY.43	0.000013
S	32	F32F	ttC	ttT	3	3	AY.45	0.000365
S	32	F32F	ttC	ttT	3	3	AY.5.4	0.00083
S	32	F32F	ttC	ttT	3	3	AY.51	0.002727
S	32	F32F	ttC	ttT	3	3	AY.63	0.001161
S	32	F32L	Ttc	Ctc	3	3	AY.65	0.001599
S	32	F32F	ttC	ttT	3	3	AY.75.1	0.000541
S	32	F32F	ttC	ttT	3	3	AY.78	0.004622
S	32	F32F	ttC	ttT	3	3	AY.9	0.000203
S	32	F32del	TTC	---	3	3	B.1	0.000027
S	32	F32L	ttC	ttA	2	3	B.1.1	0.000036
S	32	F32L	Ttc	Ctc	1	3	B.1.1	0.000018
S	32	F32F	ttC	ttT	3	3	B.1.1.222	0.000612
S	32	F32F	ttC	ttT	3	3	B.1.1.225	0.021583
S	32	F32F	ttC	ttT	3	3	B.1.1.277	0.002276
S	32	F32P	TTC	CCT	2	3	B.1.1.7	0.000002
S	32	F32P	TTc	CCc	1	3	B.1.1.7	0.000001
S	32	F32L	Ttc	Ctc	2	3	B.1.160	0.000062
S	32	F32L	ttC	ttA	1	3	B.1.160	0.000031
S	32	F32L	Ttc	Ctc	3	3	B.1.160.26	0.007264
S	32	F32L	Ttc	Ctc	2	3	B.1.177	0.000026
S	32	F32L	ttC	ttG	1	3	B.1.177	0.000013
S	32	F32F	ttC	ttT	3	3	B.1.177.62	0.003576
S	32	F32del1	ttC	tt-	3	3	B.1.2	0.000026
S	32	F32L	ttC	ttG	3	3	B.1.36.17	0.001482
S	32	F32F	ttC	ttT	3	3	B.1.36.18	0.001261
S	32	F32F	ttC	ttT	3	3	B.1.369	0.000856
S	32	F32F	ttC	ttT	3	3	B.1.371	0.003367
S	32	F32L	ttC	ttG	2	3	B.1.429	0.000047
S	32	F32L	Ttc	Ctc	1	3	B.1.429	0.000024
S	32	F32F	ttC	ttT	3	3	B.1.466.2	0.001174
S	32	F32F	ttC	ttT	3	3	B.1.517	0.001281
S	32	F32F	ttC	ttT	3	3	B.1.539	0.052632
S	32	F32F	ttC	ttT	3	3	B.1.575	0.00091
S	32	F32F	ttC	ttT	3	3	B.1.595	0.000783
S	32	F32L	Ttc	Ctc	1	3	B.1.595	0.000261
S	32	F32L	ttC	ttA	1	3	B.1.595	0.000261
S	32	F32L	TtC	CtT	1	3	B.1.595	0.000261
S	32	F32L	ttC	ttA	1	3	B.1.596	0.000087
S	32	F32L	ttC	ttG	1	3	B.1.596	0.000087
S	32	F32L	Ttc	Ctc	1	3	B.1.596	0.000087
S	32	F32F	ttC	ttT	3	3	N.5	0.0053
S	32	F32F	ttC	ttT	3	3	N.9	0.017857
S	32	F32F	ttC	ttT	3	3	P.1.15	0.000697
S	32	F32F	ttC	ttT	3	3	W.2	0.014493
S	32	F32X	tTC	tAG	2	2		0.111111
S	32	F32F	ttC	ttT	2	2		0.111111
S	32	F32L	ttC	ttG	2	2		0.111111
S	32	F32K	TTC	AAG	2	2		0.111111
S	32	F32N	TTc	AAc	2	2		0.111111
S	32	F32I	Ttc	Atc	2	2		0.111111
S	32	F32M	TtC	AtG	2	2		0.111111
S	32	F32F	ttC	ttT	2	2	A.1	0.000564
S	32	F32Y	tTc	tAc	2	2	A.2	0.001324
S	32	F32F	ttC	ttT	2	2	A.2	0.001324
S	32	F32F	ttC	ttT	2	2	AD.2	0.000438
S	32	F32K	TTC	AAG	2	2	All	0
S	32	F32N	TTc	AAc	2	2	All	0
S	32	F32L	Ttc	Ctc	2	2	AY.100	0.000092
S	32	F32del	TTC	---	2	2	AY.100	0.000092
S	32	F32del	TTC	---	2	2	AY.102	0.000053
S	32	F32del	TTC	---	2	2	AY.103	0.000012
S	32	F32F	ttC	ttT	2	2	AY.105	0.001286
S	32	F32F	ttC	ttT	2	2	AY.106	0.00067
S	32	F32F	ttC	ttT	2	2	AY.116	0.000574
S	32	F32F	ttC	ttT	2	2	AY.22	0.004184
S	32	F32L	ttC	ttA	2	2	AY.26	0.000057
S	32	F32S	tTc	tCc	2	2	AY.3.1	0.000171
S	32	F32L	Ttc	Ctc	2	2	AY.3.1	0.000171
S	32	F32L	Ttc	Ctc	2	2	AY.30	0.000791
S	32	F32L	ttC	ttA	2	2	AY.32	0.001065
S	32	F32F	ttC	ttT	2	2	AY.34	0.000194
S	32	F32del	TTC	---	2	2	AY.34.1	0.00102
S	32	F32F	ttC	ttT	2	2	AY.34.1	0.00102
S	32	F32V	Ttc	Gtc	2	2	AY.4.2	0.000043
S	32	F32F	ttC	ttT	2	2	AY.4.5	0.000215
S	32	F32del	TTC	---	2	2	AY.44	0.000012
S	32	F32L	Ttc	Ctc	2	2	AY.46	0.000208
S	32	F32F	ttC	ttT	2	2	AY.46.2	0.001271
S	32	F32S	tTc	tCc	2	2	AY.47	0.000062
S	32	F32F	ttC	ttT	2	2	AY.49	0.00639
S	32	F32V	Ttc	Gtc	2	2	AY.59	0.001059
S	32	F32F	ttC	ttT	2	2	AY.62	0.000871
S	32	F32L	ttC	ttG	2	2	AY.67	0.000929
S	32	F32F	ttC	ttT	2	2	AY.67	0.000929
S	32	F32F	ttC	ttT	2	2	AY.70	0.000417
S	32	F32S	tTc	tCc	2	2	AY.75	0.000112
S	32	F32F	ttC	ttT	2	2	AY.9.1	0.000167
S	32	F32F	ttC	ttT	2	2	AY.93	0.000546
S	32	F32F	ttC	ttT	2	2	AY.95	0.001522
S	32	F32F	ttC	ttT	2	2	AY.99.2	0.000184
S	32	F32L	Ttc	Ctc	1	2	B	0.000128
S	32	F32L	ttC	ttA	1	2	B	0.000128
S	32	F32F	ttC	ttT	2	2	B.1.1.109	0.08
S	32	F32F	ttC	ttT	2	2	B.1.1.171	0.007353
S	32	F32F	ttC	ttT	2	2	B.1.1.216	0.001781
S	32	F32F	ttC	ttT	2	2	B.1.1.265	0.006309
S	32	F32F	ttC	ttT	2	2	B.1.1.284	0.000215
S	32	F32F	ttC	ttT	2	2	B.1.1.291	0.001485
S	32	F32F	ttC	ttT	2	2	B.1.1.317	0.000823
S	32	F32F	ttC	ttT	2	2	B.1.1.348	0.001592
S	32	F32F	ttC	ttT	2	2	B.1.1.369	0.000892
S	32	F32F	ttC	ttT	2	2	B.1.1.37	0.000386
S	32	F32F	ttC	ttT	2	2	B.1.1.39	0.001019
S	32	F32F	ttC	ttT	2	2	B.1.1.398	0.006452
S	32	F32Y	tTC	tAT	2	2	B.1.1.46	0.008734
S	32	F32F	ttC	ttT	2	2	B.1.1.50	0.001358
S	32	F32F	ttC	ttT	2	2	B.1.128	0.001271
S	32	F32F	ttC	ttT	2	2	B.1.160.22	0.013514
S	32	F32F	ttC	ttT	2	2	B.1.177.12	0.000303
S	32	F32F	ttC	ttT	2	2	B.1.177.33	0.003289
S	32	F32F	ttC	ttT	2	2	B.1.177.54	0.001213
S	32	F32F	ttC	ttT	2	2	B.1.177.60	0.000437
S	32	F32F	ttC	ttT	2	2	B.1.177.7	0.00033
S	32	F32F	ttC	ttT	2	2	B.1.177.86	0.000367
S	32	F32Y	tTc	tAc	2	2	B.1.2	0.000018
S	32	F32V	Ttc	Gtc	2	2	B.1.2	0.000018
S	32	F32F	ttC	ttT	2	2	B.1.219	0.018868
S	32	F32L	ttC	ttG	1	2	B.1.221	0.000071
S	32	F32L	Ttc	Ctc	1	2	B.1.221	0.000071
S	32	F32F	ttC	ttT	2	2	B.1.240	0.000431
S	32	F32F	ttC	ttT	2	2	B.1.241	0.001623
S	32	F32F	ttC	ttT	2	2	B.1.260	0.006689
S	32	F32L	ttC	ttG	2	2	B.1.268	0.020833
S	32	F32F	ttC	ttT	2	2	B.1.320	0.002491
S	32	F32F	ttC	ttT	2	2	B.1.36.36	0.001204
S	32	F32F	ttC	ttT	2	2	B.1.361	0.002577
S	32	F32F	ttC	ttT	2	2	B.1.404	0.002604
S	32	F32F	ttC	ttT	2	2	B.1.422	0.001625
S	32	F32F	ttC	ttT	2	2	B.1.426	0.002018
S	32	F32S	tTc	tCc	2	2	B.1.427	0.000101
S	32	F32del	TTC	---	2	2	B.1.525	0.000226
S	32	F32L	Ttc	Ctc	2	2	B.1.526	0.000047
S	32	F32L	Ttc	Ctc	1	2	B.1.589	0.007576
S	32	F32L	TtC	CtT	1	2	B.1.589	0.007576
S	32	F32del1	ttC	tt-	2	2	B.1.617.2	0.000008
S	32	F32del	TTC	---	2	2	B.1.617.2	0.000008
S	32	F32L	Ttc	Ctc	2	2	B.1.623	0.001073
S	32	F32F	ttC	ttT	2	2	B.1.625	0.004706
S	32	F32F	ttC	ttT	2	2	B.1.634	0.006849
S	32	F32F	ttC	ttT	2	2	B.1.9.4	0.01227
S	32	F32F	ttC	ttT	2	2	B.1.9.5	0.011364
S	32	F32F	ttC	ttT	2	2	B.40	0.000729
S	32	F32F	ttC	ttT	2	2	C.36	0.001821
S	32	F32del2	TTC	--A	2	2	P.1	0.000032
S	32	F32L	Ttc	Ctc	2	2	P.1	0.000032
S	32	F32L	ttC	ttA	2	2	P.1.12	0.000968
S	32	F32S	tTc	tCc	1	1		0.055556
S	32	F32I	Ttc	Atc	1	1	A	0.000387
S	32	F32L	Ttc	Ctc	1	1	A.2	0.000662
S	32	F32S	tTc	tCc	1	1	A.2.4	0.003367
S	32	F32del	TTC	---	1	1	A.2.4	0.003367
S	32	F32F	ttC	ttT	1	1	AA.2	0.007692
S	32	F32F	ttC	ttT	1	1	AE.8	0.000489
S	32	F32E	TTC	GAA	1	1	All	0
S	32	F32F	ttC	ttT	1	1	AY.1	0.000396
S	32	F32del1	ttC	tt-	1	1	AY.100	0.000046
S	32	F32del	TTC	---	1	1	AY.101	0.00049
S	32	F32I	Ttc	Atc	1	1	AY.103	0.000006
S	32	F32S	tTc	tCc	1	1	AY.103	0.000006
S	32	F32L	Ttc	Ctc	1	1	AY.108	0.001103
S	32	F32del	TTC	---	1	1	AY.108	0.001103
S	32	F32L	Ttc	Ctc	1	1	AY.109	0.00074
S	32	F32F	ttC	ttT	1	1	AY.111	0.000183
S	32	F32L	ttC	ttA	1	1	AY.117	0.000085
S	32	F32S	tTc	tCc	1	1	AY.117	0.000085
S	32	F32F	ttC	ttT	1	1	AY.118	0.000063
S	32	F32del2	tTC	t--	1	1	AY.13	0.000161
S	32	F32F	ttC	ttT	1	1	AY.17	0.008197
S	32	F32F	ttC	ttT	1	1	AY.2	0.000356
S	32	F32L	ttC	ttG	1	1	AY.2	0.000356
S	32	F32L	Ttc	Ctc	1	1	AY.23	0.00007
S	32	F32F	ttC	ttT	1	1	AY.23.1	0.000417
S	32	F32S	tTc	tCc	1	1	AY.23.1	0.000417
S	32	F32F	ttC	ttT	1	1	AY.24	0.000431
S	32	F32V	Ttc	Gtc	1	1	AY.26	0.000028
S	32	F32C	tTc	tGc	1	1	AY.3	0.00001
S	32	F32L	ttC	ttG	1	1	AY.3	0.00001
S	32	F32S	tTc	tCc	1	1	AY.3	0.00001
S	32	F32del	TTC	---	1	1	AY.3	0.00001
S	32	F32del2	TTC	--N	1	1	AY.33	0.000067
S	32	F32F	ttC	ttT	1	1	AY.36	0.000148
S	32	F32del2	tTC	t--	1	1	AY.39	0.000025
S	32	F32V	Ttc	Gtc	1	1	AY.39	0.000025
S	32	F32C	tTc	tGc	1	1	AY.4	0.000002
S	32	F32F	ttC	ttT	1	1	AY.4.2.1	0.000149
S	32	F32F	ttC	ttT	1	1	AY.4.3	0.000842
S	32	F32del	TTC	---	1	1	AY.4.5	0.000107
S	32	F32F	ttC	ttT	1	1	AY.40	0.000964
S	32	F32F	ttC	ttT	1	1	AY.41	0.000294
S	32	F32del	TTC	---	1	1	AY.42	0.00004
S	32	F32S	tTC	tCA	1	1	AY.42	0.00004
S	32	F32del2	tTC	t--	1	1	AY.43	0.000004
S	32	F32F	ttC	ttT	1	1	AY.46	0.000104
S	32	F32del	TTC	---	1	1	AY.46.1	0.001027
S	32	F32S	tTc	tCc	1	1	AY.46.4	0.000165
S	32	F32C	tTc	tGc	1	1	AY.47	0.000031
S	32	F32I	Ttc	Atc	1	1	AY.47	0.000031
S	32	F32F	ttC	ttT	1	1	AY.48	0.000465
S	32	F32F	ttC	ttT	1	1	AY.5.1	0.003759
S	32	F32L	ttC	ttG	1	1	AY.5.3	0.000337
S	32	F32L	Ttc	Ctc	1	1	AY.54	0.000095
S	32	F32F	ttC	ttT	1	1	AY.55	0.000917
S	32	F32F	ttC	ttT	1	1	AY.57	0.000656
S	32	F32F	ttC	ttT	1	1	AY.60	0.000938
S	32	F32F	ttC	ttT	1	1	AY.64	0.000595
S	32	F32del	TTC	---	1	1	AY.68	0.000274
S	32	F32F	ttC	ttT	1	1	AY.68	0.000274
S	32	F32F	ttC	ttT	1	1	AY.69	0.000187
S	32	F32Y	tTc	tAc	1	1	AY.7	0.000196
S	32	F32L	ttC	ttG	1	1	AY.7	0.000196
S	32	F32F	ttC	ttT	1	1	AY.71	0.000475
S	32	F32F	ttC	ttT	1	1	AY.73	0.000665
S	32	F32L	ttC	ttA	1	1	AY.75.1	0.00018
S	32	F32F	ttC	ttT	1	1	AY.85	0.000427
S	32	F32L	Ttc	Ctc	1	1	AY.9.1	0.000084
S	32	F32F	ttC	ttT	1	1	AY.96	0.002075
S	32	F32S	tTc	tCc	1	1	AY.98	0.000079
S	32	F32I	Ttc	Atc	1	1	B	0.000128
S	32	F32V	Ttc	Gtc	1	1	B	0.000128
S	32	F32S	tTc	tCc	1	1	B	0.000128
S	32	F32X	tTC	tAA	1	1	B.1	0.000009
S	32	F32del1	ttC	tt-	1	1	B.1	0.000009
S	32	F32S	tTc	tCc	1	1	B.1	0.000009
S	32	F32X	tTC	tAA	1	1	B.1.1	0.000018
S	32	F32del2	tTC	t--	1	1	B.1.1	0.000018
S	32	F32Y	tTc	tAc	1	1	B.1.1	0.000018
S	32	F32F	ttC	ttT	1	1	B.1.1.101	0.01
S	32	F32del2	TTc	--c	1	1	B.1.1.118	0.010204
S	32	F32F	ttC	ttT	1	1	B.1.1.157	0.000913
S	32	F32F	ttC	ttT	1	1	B.1.1.165	0.015385
S	32	F32F	ttC	ttT	1	1	B.1.1.176	0.000439
S	32	F32F	ttC	ttT	1	1	B.1.1.186	0.003436
S	32	F32F	ttC	ttT	1	1	B.1.1.218	0.007692
S	32	F32F	ttC	ttT	1	1	B.1.1.241	0.00207
S	32	F32L	Ttc	Ctc	1	1	B.1.1.25	0.000569
S	32	F32F	ttC	ttT	1	1	B.1.1.266	0.012195
S	32	F32L	ttC	ttA	1	1	B.1.1.28	0.000311
S	32	F32L	Ttc	Ctc	1	1	B.1.1.284	0.000107
S	32	F32F	ttC	ttT	1	1	B.1.1.294	0.001266
S	32	F32F	ttC	ttT	1	1	B.1.1.301	0.001179
S	32	F32F	ttC	ttT	1	1	B.1.1.306	0.000438
S	32	F32del	TTC	---	1	1	B.1.1.306	0.000438
S	32	F32C	tTC	tGT	1	1	B.1.1.306	0.000438
S	32	F32del2	tTC	t--	1	1	B.1.1.311	0.000358
S	32	F32F	ttC	ttT	1	1	B.1.1.312	0.001912
S	32	F32F	ttC	ttT	1	1	B.1.1.316	0.000925
S	32	F32F	ttC	ttT	1	1	B.1.1.326	0.001761
S	32	F32F	ttC	ttT	1	1	B.1.1.347	0.018182
S	32	F32F	ttC	ttT	1	1	B.1.1.349	0.010309
S	32	F32F	ttC	ttT	1	1	B.1.1.370	0.012658
S	32	F32L	ttC	ttG	1	1	B.1.1.389	0.006061
S	32	F32L	Ttc	Ctc	1	1	B.1.1.409	0.002833
S	32	F32F	ttC	ttT	1	1	B.1.1.409	0.002833
S	32	F32F	ttC	ttT	1	1	B.1.1.417	0.002703
S	32	F32F	ttC	ttT	1	1	B.1.1.43	0.014925
S	32	F32L	Ttc	Ctc	1	1	B.1.1.432	0.001266
S	32	F32F	ttC	ttT	1	1	B.1.1.432	0.001266
S	32	F32del	TTC	---	1	1	B.1.1.46	0.004367
S	32	F32F	ttC	ttT	1	1	B.1.1.464	0.001473
S	32	F32F	ttC	ttT	1	1	B.1.1.47	0.005348
S	32	F32V	Ttc	Gtc	1	1	B.1.1.50	0.000679
S	32	F32F	ttC	ttT	1	1	B.1.1.513	0.012346
S	32	F32L	ttC	ttA	1	1	B.1.1.517	0.006803
S	32	F32F	ttC	ttT	1	1	B.1.1.523	0.001563
S	32	F32F	ttC	ttT	1	1	B.1.1.524	0.020833
S	32	F32F	ttC	ttT	1	1	B.1.1.63	0.000386
S	32	F32L	ttC	ttA	1	1	B.1.1.70	0.000341
S	32	F32F	ttC	ttT	1	1	B.1.160.16	0.000929
S	32	F32S	tTc	tCc	1	1	B.1.160.23	0.004831
S	32	F32F	ttC	ttT	1	1	B.1.160.31	0.008065
S	32	F32F	ttC	ttT	1	1	B.1.160.33	0.004425
S	32	F32F	ttC	ttT	1	1	B.1.160.7	0.002079
S	32	F32V	Ttc	Gtc	1	1	B.1.177	0.000013
S	32	F32del1	Ttc	-tc	1	1	B.1.177	0.000013
S	32	F32S	tTc	tCc	1	1	B.1.177	0.000013
S	32	F32F	ttC	ttT	1	1	B.1.177.10	0.000878
S	32	F32del	TTC	---	1	1	B.1.177.17	0.000821
S	32	F32F	ttC	ttT	1	1	B.1.177.18	0.00116
S	32	F32L	Ttc	Ctc	1	1	B.1.177.21	0.000076
S	32	F32F	ttC	ttT	1	1	B.1.177.21	0.000076
S	32	F32F	ttC	ttT	1	1	B.1.177.26	0.006993
S	32	F32L	Ttc	Ctc	1	1	B.1.177.31	0.011494
S	32	F32F	ttC	ttT	1	1	B.1.177.32	0.00135
S	32	F32F	ttC	ttT	1	1	B.1.177.52	0.001757
S	32	F32F	ttC	ttT	1	1	B.1.177.56	0.000668
S	32	F32F	ttC	ttT	1	1	B.1.177.58	0.001332
S	32	F32del	TTC	---	1	1	B.1.177.68	0.015152
S	32	F32F	ttC	ttT	1	1	B.1.177.69	0.001484
S	32	F32del	TTC	---	1	1	B.1.177.7	0.000165
S	32	F32F	ttC	ttT	1	1	B.1.177.75	0.001041
S	32	F32X	tTC	tAA	1	1	B.1.177.78	0.009709
S	32	F32F	ttC	ttT	1	1	B.1.177.8	0.000752
S	32	F32del	TTC	---	1	1	B.1.177.83	0.001481
S	32	F32C	tTc	tGc	1	1	B.1.177.86	0.000183
S	32	F32F	ttC	ttT	1	1	B.1.177.9	0.001332
S	32	F32F	ttC	ttT	1	1	B.1.182	0.007246
S	32	F32del	TTC	---	1	1	B.1.2	0.000009
S	32	F32F	ttC	ttT	1	1	B.1.210	0.002132
S	32	F32F	ttC	ttT	1	1	B.1.22	0.001318
S	32	F32F	ttC	ttT	1	1	B.1.221.2	0.004016
S	32	F32F	ttC	ttT	1	1	B.1.23	0.006061
S	32	F32F	ttC	ttT	1	1	B.1.237	0.004975
S	32	F32F	ttC	ttT	1	1	B.1.247	0.014925
S	32	F32F	ttC	ttT	1	1	B.1.268	0.010417
S	32	F32L	Ttc	Ctc	1	1	B.1.281	0.021739
S	32	F32F	ttC	ttT	1	1	B.1.305	0.002151
S	32	F32F	ttC	ttT	1	1	B.1.311	0.000275
S	32	F32S	tTc	tCc	1	1	B.1.326	0.007576
S	32	F32X	tTC	tAA	1	1	B.1.351.2	0.000303
S	32	F32F	ttC	ttT	1	1	B.1.351.2	0.000303
S	32	F32F	ttC	ttT	1	1	B.1.351.5	0.0006
S	32	F32F	ttC	ttT	1	1	B.1.356	0.001727
S	32	F32S	tTc	tCc	1	1	B.1.36.1	0.00114
S	32	F32F	ttC	ttT	1	1	B.1.36.16	0.001425
S	32	F32F	ttC	ttT	1	1	B.1.36.17	0.000494
S	32	F32F	ttC	ttT	1	1	B.1.36.22	0.001208
S	32	F32F	ttC	ttT	1	1	B.1.36.24	0.006173
S	32	F32F	ttC	ttT	1	1	B.1.36.28	0.005747
S	32	F32F	ttC	ttT	1	1	B.1.36.31	0.001751
S	32	F32del2	tTC	t--	1	1	B.1.36.8	0.001
S	32	F32F	ttC	ttT	1	1	B.1.362	0.001541
S	32	F32F	ttC	ttT	1	1	B.1.398	0.002976
S	32	F32F	ttC	ttT	1	1	B.1.425	0.002994
S	32	F32F	ttC	ttT	1	1	B.1.428	0.00102
S	32	F32F	ttC	ttT	1	1	B.1.428.2	0.033333
S	32	F32S	tTc	tCc	1	1	B.1.429	0.000024
S	32	F32F	ttC	ttT	1	1	B.1.459	0.004082
S	32	F32F	ttC	ttT	1	1	B.1.462	0.007246
S	32	F32F	ttC	ttT	1	1	B.1.468	0.005714
S	32	F32F	ttC	ttT	1	1	B.1.469	0.00361
S	32	F32L	Ttc	Ctc	1	1	B.1.470	0.001404
S	32	F32F	ttC	ttT	1	1	B.1.478	0.011765
S	32	F32F	ttC	ttT	1	1	B.1.497	0.000315
S	32	F32L	ttC	ttG	1	1	B.1.499	0.00105
S	32	F32F	ttC	ttT	1	1	B.1.499	0.00105
S	32	F32F	ttC	ttT	1	1	B.1.515	0.014493
S	32	F32F	ttC	ttT	1	1	B.1.521	0.004975
S	32	F32F	ttC	ttT	1	1	B.1.524	0.001406
S	32	F32del	TTC	---	1	1	B.1.524	0.001406
S	32	F32F	ttC	ttT	1	1	B.1.530	0.007143
S	32	F32F	ttC	ttT	1	1	B.1.533	0.009615
S	32	F32L	Ttc	Ctc	1	1	B.1.533	0.009615
S	32	F32F	ttC	ttT	1	1	B.1.534	0.0125
S	32	F32L	Ttc	Ctc	1	1	B.1.548	0.035714
S	32	F32F	ttC	ttT	1	1	B.1.560	0.00463
S	32	F32F	ttC	ttT	1	1	B.1.575.2	0.004808
S	32	F32F	ttC	ttT	1	1	B.1.588	0.00091
S	32	F32F	ttC	ttT	1	1	B.1.589	0.007576
S	32	F32F	ttC	ttT	1	1	B.1.595.4	0.007299
S	32	F32L	Ttc	Ctc	1	1	B.1.597	0.00463
S	32	F32F	ttC	ttT	1	1	B.1.600	0.005848
S	32	F32F	ttC	ttT	1	1	B.1.604	0.017241
S	32	F32F	ttC	ttT	1	1	B.1.605	0.005952
S	32	F32F	ttC	ttT	1	1	B.1.612	0.002653
S	32	F32del1	ttC	tt-	1	1	B.1.612	0.002653
S	32	F32V	Ttc	Gtc	1	1	B.1.617.1	0.000129
S	32	F32S	tTc	tCc	1	1	B.1.617.2	0.000004
S	32	F32V	Ttc	Gtc	1	1	B.1.617.2	0.000004
S	32	F32F	ttC	ttT	1	1	B.1.619	0.000871
S	32	F32del	TTC	---	1	1	B.1.620	0.000946
S	32	F32L	Ttc	Ctc	1	1	B.1.621	0.000089
S	32	F32del	TTC	---	1	1	B.1.621	0.000089
S	32	F32F	ttC	ttT	1	1	B.1.627	0.00202
S	32	F32L	ttC	ttA	1	1	B.1.637	0.000073
S	32	F32F	ttC	ttT	1	1	B.1.78	0.008547
S	32	F32V	Ttc	Gtc	1	1	B.1.93	0.000934
S	32	F32F	ttC	ttT	1	1	B.1.94	0.027027
S	32	F32F	ttC	ttT	1	1	B.10	0.008264
S	32	F32F	ttC	ttT	1	1	B.28	0.003279
S	32	F32F	ttC	ttT	1	1	B.3	0.000831
S	32	F32L	ttC	ttG	1	1	B.40	0.000364
S	32	F32L	Ttc	Ctc	1	1	B.55	0.00295
S	32	F32F	ttC	ttT	1	1	B.6.1	0.026316
S	32	F32L	ttC	ttA	1	1	B.6.6	0.000889
S	32	F32F	ttC	ttT	1	1	B.6.6	0.000889
S	32	F32S	tTc	tCc	1	1	C.1	0.002392
S	32	F32F	ttC	ttT	1	1	C.16	0.00106
S	32	F32F	ttC	ttT	1	1	C.36.3	0.000567
S	32	F32L	ttC	ttG	1	1	D.2	0.000075
S	32	F32F	ttC	ttT	1	1	K.1	0.02381
S	32	F32F	ttC	ttT	1	1	L.2	0.011364
S	32	F32V	Ttc	Gtc	1	1	P.1	0.000016
S	32	F32E	TTC	GAA	1	1	P.1	0.000016
S	32	F32del	TTC	---	1	1	P.1	0.000016
S	32	F32L	ttC	ttA	1	1	P.1.1	0.000318
S	32	F32F	ttC	ttT	1	1	P.1.1	0.000318
S	32	F32L	Ttc	Ctc	1	1	P.1.14	0.000048
S	32	F32I	Ttc	Atc	1	1	P.1.14	0.000048
S	32	F32F	ttC	ttT	1	1	P.1.17	0.000162
S	32	F32M	TtC	AtG	1	1	P.1.17	0.000162
S	32	F32F	ttC	ttT	1	1	P.1.8	0.004785
S	32	F32Y	tTc	tAc	1	1	P.2	0.000187
S	32	F32del	TTC	---	1	1	Q.1	0.000126
S	32	F32F	ttC	ttT	1	1	Q.3	0.000145
S	32	F32S	tTc	tCc	1	1	Q.4	0.000455
S	32	F32L	ttC	ttG	1	1	Q.8	0.000165
S	32	F32L	Ttc	Ctc	1	1	R.1	0.00009
S	32	F32F	ttC	ttT	1	1	W.3	0.005263
S	32	F32F	ttC	ttT	1	1	Z.1	0.00289

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.