CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 100

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
M	100	F100F		syn	ttC	ttT	8300	8300	1	26820-26822
M	100	F100L		nonsyn	Ttc	Ctc	306	176	0.575163	26820-26822
M	100	F100L		nonsyn	ttC	ttA	306	84	0.27451	26820-26822
M	100	F100L		nonsyn	ttC	ttG	306	46	0.150327	26820-26822
M	100	F100del		del	TTC	---	209	209	1	26820-26822
M	100	F100S		nonsyn	tTc	tCc	92	89	0.967391	26820-26822
M	100	F100S		nonsyn	tTC	tCA	92	1	0.0108696	26820-26822
M	100	F100S		nonsyn	tTC	tCT	92	1	0.0108696	26820-26822
M	100	F100S		nonsyn	TTC	AGT	92	1	0.0108696	26820-26822
M	100	F100C		nonsyn	tTc	tGc	77	77	1	26820-26822
M	100	F100I		nonsyn	Ttc	Atc	37	37	1	26820-26822
M	100	F100del1		del	Ttc	-tc	19	16	0.842105	26820-26822
M	100	F100del1		del	ttC	tt-	19	3	0.157895	26820-26822
M	100	F100V		nonsyn	Ttc	Gtc	12	11	0.916667	26820-26822
M	100	F100V		nonsyn	TtC	GtT	12	1	0.0833333	26820-26822
M	100	F100del2		del	TTc	--c	5	3	0.6	26820-26822
M	100	F100del2		del	tTC	t--	5	2	0.4	26820-26822
M	100	F100Y		nonsyn	tTc	tAc	2	2	1	26820-26822
M	100	F100K		nonsyn	TTC	AAA	1	1	1	26820-26822
M	100	F100G		nonsyn	TTc	GGc	1	1	1	26820-26822

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
M	100	F100F	ttC	ttT	8300	8300	All	0.001587
M	100	F100F	ttC	ttT	2511	2511	AY.4	0.003908
M	100	F100F	ttC	ttT	1125	1125	B.1.1.7	0.001007
M	100	F100F	ttC	ttT	782	782	AY.75	0.04381
M	100	F100F	ttC	ttT	694	694	B.1.617.2	0.002613
M	100	F100F	ttC	ttT	547	547	B.1.2	0.004817
M	100	F100L	Ttc	Ctc	176	306	All	0.000034
M	100	F100L	ttC	ttA	84	306	All	0.000016
M	100	F100L	ttC	ttG	46	306	All	0.000009
M	100	F100F	ttC	ttT	280	280	AY.5	0.005782
M	100	F100del	TTC	---	209	209	All	0.00004
M	100	F100F	ttC	ttT	124	124	P.1	0.001953
M	100	F100F	ttC	ttT	123	123	B.1.243	0.008559
M	100	F100F	ttC	ttT	118	118	AY.44	0.000718
M	100	F100L	ttC	ttA	78	100	B.1.1.7	0.00007
M	100	F100L	Ttc	Ctc	11	100	B.1.1.7	0.00001
M	100	F100L	ttC	ttG	11	100	B.1.1.7	0.00001
M	100	F100S	tTc	tCc	89	92	All	0.000017
M	100	F100S	tTC	tCT	1	92	All	0
M	100	F100S	tTC	tCA	1	92	All	0
M	100	F100S	TTC	AGT	1	92	All	0
M	100	F100F	ttC	ttT	88	88	B.1.177	0.001159
M	100	F100F	ttC	ttT	78	78	AY.46	0.008118
M	100	F100C	tTc	tGc	77	77	All	0.000015
M	100	F100C	tTc	tGc	71	71	AY.4	0.000111
M	100	F100F	ttC	ttT	71	71	AY.43	0.000315
M	100	F100del	TTC	---	69	69	B.1.1.7	0.000062
M	100	F100F	ttC	ttT	67	67	B.1	0.000614
M	100	F100F	ttC	ttT	66	66	B.1.429	0.001553
M	100	F100F	ttC	ttT	65	65	AY.103	0.000404
M	100	F100L	Ttc	Ctc	63	63	AY.121	0.008525
M	100	F100F	ttC	ttT	62	62	AY.3	0.000617
M	100	F100del	TTC	---	62	62	B.1.177.21	0.004741
M	100	F100F	ttC	ttT	59	59	AY.113	0.008401
M	100	F100F	ttC	ttT	58	58	AY.100	0.002668
M	100	F100F	ttC	ttT	49	49	AY.20	0.001904
M	100	F100F	ttC	ttT	49	49	B.1.177.80	0.09369
M	100	F100F	ttC	ttT	48	48	B.1.427	0.002424
M	100	F100F	ttC	ttT	47	47	AY.25	0.000283
M	100	F100L	Ttc	Ctc	43	44	B.1.617.2	0.000162
M	100	F100L	ttC	ttG	1	44	B.1.617.2	0.000004
M	100	F100F	ttC	ttT	43	43	AY.39	0.001063
M	100	F100F	ttC	ttT	43	43	B.1.1	0.00078
M	100	F100F	ttC	ttT	38	38	AY.33	0.002538
M	100	F100I	Ttc	Atc	37	37	All	0.000007
M	100	F100F	ttC	ttT	31	31	AY.108	0.034179
M	100	F100I	Ttc	Atc	28	28	B.1.1.7	0.000025
M	100	F100F	ttC	ttT	26	26	B.1.594	0.8125
M	100	F100F	ttC	ttT	26	26	C.37	0.003018
M	100	F100F	ttC	ttT	24	24	AY.70	0.005004
M	100	F100F	ttC	ttT	24	24	B.1.210	0.051173
M	100	F100F	ttC	ttT	22	22	C.16	0.02333
M	100	F100F	ttC	ttT	20	20	AY.102	0.00053
M	100	F100del1	Ttc	-tc	16	19	All	0.000003
M	100	F100del1	ttC	tt-	3	19	All	0.000001
M	100	F100F	ttC	ttT	19	19	AY.4.2	0.000412
M	100	F100F	ttC	ttT	19	19	B.1.637	0.001388
M	100	F100F	ttC	ttT	18	18	AY.26	0.00051
M	100	F100S	tTc	tCc	17	17	B.1.2	0.00015
M	100	F100F	ttC	ttT	17	17	B.1.497	0.005351
M	100	F100F	ttC	ttT	16	16	B.1.1.288	0.030651
M	100	F100F	ttC	ttT	16	16	B.1.351	0.000476
M	100	F100F	ttC	ttT	15	15	B.1.1.434	0.005228
M	100	F100F	ttC	ttT	15	15	B.1.36	0.002189
M	100	F100F	ttC	ttT	15	15	B.1.526	0.000353
M	100	F100F	ttC	ttT	14	14	B.1.160.17	0.02381
M	100	F100F	ttC	ttT	14	14	B.1.239	0.017094
M	100	F100F	ttC	ttT	14	14	B.1.438.1	0.001502
M	100	F100F	ttC	ttT	14	14	Q.1	0.001769
M	100	F100F	ttC	ttT	13	13	AY.119	0.000459
M	100	F100F	ttC	ttT	13	13	B.1.1.28	0.004046
M	100	F100S	tTc	tCc	13	13	B.1.1.7	0.000012
M	100	F100F	ttC	ttT	13	13	B.1.621	0.001151
M	100	F100V	Ttc	Gtc	11	12	All	0.000002
M	100	F100V	TtC	GtT	1	12	All	0
M	100	F100F	ttC	ttT	12	12	AU.1	0.01519
M	100	F100S	tTc	tCc	11	12	AY.4	0.000017
M	100	F100S	TTC	AGT	1	12	AY.4	0.000002
M	100	F100F	ttC	ttT	12	12	AY.45	0.00146
M	100	F100F	ttC	ttT	12	12	B.1.160	0.000374
M	100	F100F	ttC	ttT	12	12	B.1.36.1	0.013683
M	100	F100F	ttC	ttT	11	11	B.1.177.65	0.007319
M	100	F100F	ttC	ttT	11	11	B.1.311	0.00302
M	100	F100F	ttC	ttT	11	11	P.1.2	0.012717
M	100	F100del	TTC	---	10	10	AY.25	0.00006
M	100	F100F	ttC	ttT	10	10	AY.39.1	0.000396
M	100	F100F	ttC	ttT	10	10	AY.67	0.004643
M	100	F100F	ttC	ttT	10	10	B.1.1.519	0.000397
M	100	F100F	ttC	ttT	10	10	B.1.596	0.000871
M	100	F100F	ttC	ttT	10	10	P.1.17	0.001618
M	100	F100F	ttC	ttT	10	10	R.1	0.0009
M	100	F100F	ttC	ttT	9	9	AY.29	0.000142
M	100	F100L	ttC	ttG	6	9	AY.4	0.000009
M	100	F100L	Ttc	Ctc	3	9	AY.4	0.000005
M	100	F100F	ttC	ttT	9	9	AY.6	0.00037
M	100	F100F	ttC	ttT	9	9	B.1.1.258	0.029316
M	100	F100L	Ttc	Ctc	5	9	B.1.177	0.000066
M	100	F100L	ttC	ttG	3	9	B.1.177	0.00004
M	100	F100L	ttC	ttA	1	9	B.1.177	0.000013
M	100	F100del1	Ttc	-tc	8	8	B.1	0.000073
M	100	F100F	ttC	ttT	8	8	B.1.111	0.009401
M	100	F100F	ttC	ttT	8	8	B.1.602	0.052288
M	100	F100F	ttC	ttT	8	8	B.4	0.01766
M	100	F100F	ttC	ttT	7	7	AY.117	0.000592
M	100	F100F	ttC	ttT	7	7	AY.88	0.006189
M	100	F100F	ttC	ttT	7	7	B.1.1.214	0.000388
M	100	F100F	ttC	ttT	7	7	B.1.1.416	0.006335
M	100	F100F	ttC	ttT	7	7	B.1.220	0.076087
M	100	F100F	ttC	ttT	7	7	B.1.221	0.000497
M	100	F100F	ttC	ttT	7	7	B.1.258.17	0.000728
M	100	F100L	Ttc	Ctc	7	7	B.1.621	0.00062
M	100	F100F	ttC	ttT	7	7	B.1.623	0.003755
M	100	F100F	ttC	ttT	7	7	B.1.627	0.014141
M	100	F100F	ttC	ttT	7	7	P.1.1	0.002224
M	100	F100F	ttC	ttT	7	7	P.2	0.001306
M	100	F100F	ttC	ttT	6	6	AA.8	0.133333
M	100	F100F	ttC	ttT	6	6	AY.23	0.000418
M	100	F100F	ttC	ttT	6	6	AY.97	0.010204
M	100	F100del	TTC	---	6	6	B.1	0.000055
M	100	F100F	ttC	ttT	6	6	B.1.1.273	0.040541
M	100	F100F	ttC	ttT	6	6	B.1.1.464	0.008837
M	100	F100L	ttC	ttG	6	6	B.1.234	0.000792
M	100	F100F	ttC	ttT	6	6	B.1.258	0.000399
M	100	F100V	Ttc	Gtc	6	6	B.1.526	0.000141
M	100	F100S	tTc	tCc	6	6	B.1.596	0.000523
M	100	F100S	tTc	tCc	6	6	B.1.617.2	0.000023
M	100	F100F	ttC	ttT	6	6	B.1.628	0.002114
M	100	F100del2	TTc	--c	3	5	All	0.000001
M	100	F100del2	tTC	t--	2	5	All	0
M	100	F100L	Ttc	Ctc	5	5	AY.103	0.000031
M	100	F100F	ttC	ttT	5	5	AY.120	0.000186
M	100	F100F	ttC	ttT	5	5	AY.37	0.00158
M	100	F100F	ttC	ttT	5	5	AY.53	0.001438
M	100	F100F	ttC	ttT	5	5	AY.61	0.000524
M	100	F100F	ttC	ttT	5	5	B	0.000639
M	100	F100F	ttC	ttT	5	5	B.1.1.277	0.003794
M	100	F100del1	ttC	tt-	3	5	B.1.1.7	0.000003
M	100	F100del1	Ttc	-tc	2	5	B.1.1.7	0.000002
M	100	F100F	ttC	ttT	5	5	B.1.177.21	0.000382
M	100	F100F	ttC	ttT	5	5	B.1.177.86	0.000917
M	100	F100F	ttC	ttT	5	5	B.1.306	0.028571
M	100	F100F	ttC	ttT	5	5	B.1.36.29	0.002587
M	100	F100F	ttC	ttT	5	5	B.1.369	0.001426
M	100	F100F	ttC	ttT	5	5	N.5	0.008834
M	100	F100F	ttC	ttT	5	5	Q.8	0.000825
M	100	F100F	ttC	ttT	4	4	A.2.5	0.001996
M	100	F100F	ttC	ttT	4	4	AY.110	0.000451
M	100	F100F	ttC	ttT	4	4	AY.121	0.000541
M	100	F100del	TTC	---	4	4	AY.43	0.000018
M	100	F100L	Ttc	Ctc	3	4	AY.43	0.000013
M	100	F100L	ttC	ttG	1	4	AY.43	0.000004
M	100	F100L	Ttc	Ctc	4	4	AY.44	0.000024
M	100	F100F	ttC	ttT	4	4	AY.47	0.000124
M	100	F100F	ttC	ttT	4	4	AY.7	0.000784
M	100	F100F	ttC	ttT	4	4	AY.77	0.00451
M	100	F100F	ttC	ttT	4	4	AY.9	0.00027
M	100	F100F	ttC	ttT	4	4	AY.98.1	0.000194
M	100	F100S	tTc	tCc	2	4	B.1.1	0.000036
M	100	F100S	tTC	tCT	1	4	B.1.1	0.000018
M	100	F100S	tTC	tCA	1	4	B.1.1	0.000018
M	100	F100F	ttC	ttT	4	4	B.1.1.153	0.004381
M	100	F100F	ttC	ttT	4	4	B.1.1.176	0.001757
M	100	F100F	ttC	ttT	4	4	B.1.1.222	0.000816
M	100	F100F	ttC	ttT	4	4	B.1.177.7	0.000659
M	100	F100del	TTC	---	4	4	B.1.2	0.000035
M	100	F100F	ttC	ttT	4	4	B.1.240	0.000862
M	100	F100L	Ttc	Ctc	4	4	B.1.390	0.042553
M	100	F100F	ttC	ttT	4	4	B.1.425	0.011976
M	100	F100F	ttC	ttT	4	4	B.1.595	0.001044
M	100	F100F	ttC	ttT	4	4	P.1.10	0.001078
M	100	F100S	tTc	tCc	4	4	P.1.14	0.000191
M	100	F100F	ttC	ttT	3	3	AD.2	0.000657
M	100	F100F	ttC	ttT	3	3	AE.8	0.001467
M	100	F100F	ttC	ttT	3	3	AY.118	0.000188
M	100	F100L	Ttc	Ctc	2	3	AY.119	0.000071
M	100	F100L	ttC	ttA	1	3	AY.119	0.000035
M	100	F100S	tTc	tCc	3	3	AY.3	0.00003
M	100	F100F	ttC	ttT	3	3	AY.30	0.001187
M	100	F100F	ttC	ttT	3	3	AY.4.5	0.000322
M	100	F100F	ttC	ttT	3	3	AY.46.4	0.000494
M	100	F100F	ttC	ttT	3	3	AY.9.1	0.000251
M	100	F100F	ttC	ttT	3	3	AY.9.2	0.00011
M	100	F100L	ttC	ttA	2	3	B.1	0.000018
M	100	F100L	Ttc	Ctc	1	3	B.1	0.000009
M	100	F100L	Ttc	Ctc	3	3	B.1.1	0.000054
M	100	F100S	tTc	tCc	3	3	B.1.1.216	0.002671
M	100	F100F	ttC	ttT	3	3	B.1.110.3	0.002155
M	100	F100del	TTC	---	3	3	B.1.160	0.000094
M	100	F100F	ttC	ttT	3	3	B.1.160.16	0.002788
M	100	F100C	tTc	tGc	3	3	B.1.177	0.00004
M	100	F100S	tTc	tCc	3	3	B.1.258.17	0.000312
M	100	F100F	ttC	ttT	3	3	B.1.446	0.06
M	100	F100del	TTC	---	3	3	B.1.617.2	0.000011
M	100	F100F	ttC	ttT	3	3	B.1.618	0.012097
M	100	F100F	ttC	ttT	3	3	P.1.14	0.000143
M	100	F100F	ttC	ttT	3	3	P.1.15	0.000697
M	100	F100F	ttC	ttT	3	3	P.1.7	0.000958
M	100	F100del	TTC	---	2	2		0.111111
M	100	F100F	ttC	ttT	2	2		0.111111
M	100	F100S	tTc	tCc	2	2		0.111111
M	100	F100L	Ttc	Ctc	2	2		0.111111
M	100	F100V	TtC	GtT	1	2		0.055556
M	100	F100V	Ttc	Gtc	1	2		0.055556
M	100	F100Y	tTc	tAc	2	2	All	0
M	100	F100F	ttC	ttT	2	2	AY.101	0.000981
M	100	F100F	ttC	ttT	2	2	AY.105	0.001286
M	100	F100F	ttC	ttT	2	2	AY.111	0.000366
M	100	F100L	ttC	ttG	1	2	AY.118	0.000063
M	100	F100L	Ttc	Ctc	1	2	AY.118	0.000063
M	100	F100F	ttC	ttT	2	2	AY.16	0.000759
M	100	F100F	ttC	ttT	2	2	AY.2	0.000712
M	100	F100F	ttC	ttT	2	2	AY.27	0.000129
M	100	F100F	ttC	ttT	2	2	AY.34	0.000194
M	100	F100L	ttC	ttG	2	2	AY.39.1	0.000079
M	100	F100del	TTC	---	2	2	AY.4	0.000003
M	100	F100F	ttC	ttT	2	2	AY.4.2.1	0.000298
M	100	F100F	ttC	ttT	2	2	AY.46.1	0.002053
M	100	F100F	ttC	ttT	2	2	AY.54	0.000191
M	100	F100F	ttC	ttT	2	2	AY.62	0.000871
M	100	F100F	ttC	ttT	2	2	AY.65	0.001066
M	100	F100F	ttC	ttT	2	2	AY.69	0.000373
M	100	F100del	TTC	---	2	2	AY.75.1	0.000361
M	100	F100F	ttC	ttT	2	2	AY.75.1	0.000361
M	100	F100L	Ttc	Ctc	2	2	AY.84	0.000875
M	100	F100F	ttC	ttT	2	2	AY.98	0.000158
M	100	F100F	ttC	ttT	2	2	AY.99.2	0.000184
M	100	F100F	ttC	ttT	2	2	AZ.1	0.001735
M	100	F100S	tTc	tCc	2	2	B.1	0.000018
M	100	F100del2	TTc	--c	2	2	B.1	0.000018
M	100	F100F	ttC	ttT	2	2	B.1.1.192	0.004619
M	100	F100F	ttC	ttT	2	2	B.1.128	0.001271
M	100	F100del	TTC	---	2	2	B.1.177	0.000026
M	100	F100F	ttC	ttT	2	2	B.1.177.42	0.001789
M	100	F100F	ttC	ttT	2	2	B.1.177.54	0.001213
M	100	F100F	ttC	ttT	2	2	B.1.184	0.117647
M	100	F100L	ttC	ttG	1	2	B.1.2	0.000009
M	100	F100L	Ttc	Ctc	1	2	B.1.2	0.000009
M	100	F100S	tTc	tCc	2	2	B.1.240	0.000431
M	100	F100L	Ttc	Ctc	2	2	B.1.351	0.000059
M	100	F100del	TTC	---	2	2	B.1.351.5	0.001199
M	100	F100L	Ttc	Ctc	2	2	B.1.36	0.000292
M	100	F100F	ttC	ttT	2	2	B.1.36.18	0.00084
M	100	F100F	ttC	ttT	2	2	B.1.36.7	0.008
M	100	F100F	ttC	ttT	2	2	B.1.36.8	0.002
M	100	F100F	ttC	ttT	2	2	B.1.396	0.001411
M	100	F100F	ttC	ttT	2	2	B.1.404	0.002604
M	100	F100L	Ttc	Ctc	2	2	B.1.427	0.000101
M	100	F100L	ttC	ttG	2	2	B.1.429	0.000047
M	100	F100F	ttC	ttT	2	2	B.1.525	0.000226
M	100	F100F	ttC	ttT	2	2	B.1.577	0.001375
M	100	F100F	ttC	ttT	2	2	B.1.617.1	0.000258
M	100	F100F	ttC	ttT	2	2	B.1.621.1	0.001012
M	100	F100F	ttC	ttT	2	2	C.1	0.004785
M	100	F100F	ttC	ttT	2	2	C.36.3	0.001134
M	100	F100F	ttC	ttT	2	2	D.2	0.00015
M	100	F100del	TTC	---	2	2	D.2	0.00015
M	100	F100S	tTc	tCc	2	2	P.1	0.000032
M	100	F100L	ttC	ttG	2	2	P.1	0.000032
M	100	F100F	ttC	ttT	1	1	A	0.000387
M	100	F100S	tTc	tCc	1	1	A.2.5	0.000499
M	100	F100F	ttC	ttT	1	1	A.3	0.002096
M	100	F100G	TTc	GGc	1	1	All	0
M	100	F100K	TTC	AAA	1	1	All	0
M	100	F100F	ttC	ttT	1	1	AY.10	0.00053
M	100	F100del	TTC	---	1	1	AY.100	0.000046
M	100	F100I	Ttc	Atc	1	1	AY.103	0.000006
M	100	F100F	ttC	ttT	1	1	AY.106	0.000335
M	100	F100L	ttC	ttG	1	1	AY.116	0.000287
M	100	F100S	tTc	tCc	1	1	AY.117	0.000085
M	100	F100del	TTC	---	1	1	AY.118	0.000063
M	100	F100del1	Ttc	-tc	1	1	AY.118	0.000063
M	100	F100F	ttC	ttT	1	1	AY.12	0.000316
M	100	F100del	TTC	---	1	1	AY.120	0.000037
M	100	F100L	ttC	ttG	1	1	AY.120.1	0.000321
M	100	F100F	ttC	ttT	1	1	AY.13	0.000161
M	100	F100del	TTC	---	1	1	AY.13	0.000161
M	100	F100S	tTc	tCc	1	1	AY.14	0.000088
M	100	F100S	tTc	tCc	1	1	AY.2	0.000356
M	100	F100I	Ttc	Atc	1	1	AY.23	0.00007
M	100	F100F	ttC	ttT	1	1	AY.23.1	0.000417
M	100	F100F	ttC	ttT	1	1	AY.24	0.000431
M	100	F100I	Ttc	Atc	1	1	AY.25	0.000006
M	100	F100V	Ttc	Gtc	1	1	AY.25	0.000006
M	100	F100del	TTC	---	1	1	AY.26	0.000028
M	100	F100del	TTC	---	1	1	AY.29	0.000016
M	100	F100S	tTc	tCc	1	1	AY.29	0.000016
M	100	F100L	ttC	ttG	1	1	AY.3	0.00001
M	100	F100del	TTC	---	1	1	AY.3.1	0.000085
M	100	F100L	ttC	ttG	1	1	AY.33	0.000067
M	100	F100F	ttC	ttT	1	1	AY.35	0.000233
M	100	F100F	ttC	ttT	1	1	AY.36	0.000148
M	100	F100F	ttC	ttT	1	1	AY.38	0.000499
M	100	F100del	TTC	---	1	1	AY.39	0.000025
M	100	F100I	Ttc	Atc	1	1	AY.4	0.000002
M	100	F100S	tTc	tCc	1	1	AY.4.2	0.000022
M	100	F100L	ttC	ttG	1	1	AY.4.2	0.000022
M	100	F100F	ttC	ttT	1	1	AY.4.3	0.000842
M	100	F100F	ttC	ttT	1	1	AY.42	0.00004
M	100	F100C	tTc	tGc	1	1	AY.43	0.000004
M	100	F100S	tTc	tCc	1	1	AY.43	0.000004
M	100	F100V	Ttc	Gtc	1	1	AY.43	0.000004
M	100	F100S	tTc	tCc	1	1	AY.44	0.000006
M	100	F100del	TTC	---	1	1	AY.44	0.000006
M	100	F100I	Ttc	Atc	1	1	AY.44	0.000006
M	100	F100L	Ttc	Ctc	1	1	AY.45	0.000122
M	100	F100del	TTC	---	1	1	AY.47	0.000031
M	100	F100S	tTc	tCc	1	1	AY.47	0.000031
M	100	F100L	Ttc	Ctc	1	1	AY.47	0.000031
M	100	F100C	tTc	tGc	1	1	AY.47	0.000031
M	100	F100F	ttC	ttT	1	1	AY.48	0.000465
M	100	F100F	ttC	ttT	1	1	AY.49	0.003195
M	100	F100F	ttC	ttT	1	1	AY.5.3	0.000337
M	100	F100F	ttC	ttT	1	1	AY.5.4	0.000277
M	100	F100F	ttC	ttT	1	1	AY.56	0.001605
M	100	F100F	ttC	ttT	1	1	AY.58	0.000907
M	100	F100L	Ttc	Ctc	1	1	AY.6	0.000041
M	100	F100G	TTc	GGc	1	1	AY.60	0.000938
M	100	F100F	ttC	ttT	1	1	AY.64	0.000595
M	100	F100I	Ttc	Atc	1	1	AY.65	0.000533
M	100	F100del	TTC	---	1	1	AY.67	0.000464
M	100	F100F	ttC	ttT	1	1	AY.7.1	0.000113
M	100	F100L	Ttc	Ctc	1	1	AY.75.1	0.00018
M	100	F100C	tTc	tGc	1	1	AY.84	0.000437
M	100	F100F	ttC	ttT	1	1	AY.87	0.000833
M	100	F100del	TTC	---	1	1	AY.9	0.000068
M	100	F100F	ttC	ttT	1	1	AY.95	0.000761
M	100	F100del1	Ttc	-tc	1	1	AY.99.2	0.000092
M	100	F100L	ttC	ttA	1	1	B	0.000128
M	100	F100del	TTC	---	1	1	B.1.1	0.000018
M	100	F100F	ttC	ttT	1	1	B.1.1.10	0.001115
M	100	F100F	ttC	ttT	1	1	B.1.1.117	0.009709
M	100	F100F	ttC	ttT	1	1	B.1.1.123	0.017857
M	100	F100F	ttC	ttT	1	1	B.1.1.165	0.015385
M	100	F100F	ttC	ttT	1	1	B.1.1.189	0.001513
M	100	F100F	ttC	ttT	1	1	B.1.1.194	0.00495
M	100	F100del	TTC	---	1	1	B.1.1.207	0.001182
M	100	F100F	ttC	ttT	1	1	B.1.1.216	0.00089
M	100	F100del	TTC	---	1	1	B.1.1.221	0.010101
M	100	F100S	tTc	tCc	1	1	B.1.1.222	0.000204
M	100	F100I	Ttc	Atc	1	1	B.1.1.229	0.005747
M	100	F100L	ttC	ttG	1	1	B.1.1.231	0.003096
M	100	F100F	ttC	ttT	1	1	B.1.1.261	0.008621
M	100	F100L	Ttc	Ctc	1	1	B.1.1.275	0.011236
M	100	F100F	ttC	ttT	1	1	B.1.1.279	0.001121
M	100	F100del	TTC	---	1	1	B.1.1.288	0.001916
M	100	F100F	ttC	ttT	1	1	B.1.1.306	0.000438
M	100	F100S	tTc	tCc	1	1	B.1.1.306	0.000438
M	100	F100F	ttC	ttT	1	1	B.1.1.307	0.002532
M	100	F100S	tTc	tCc	1	1	B.1.1.317	0.000412
M	100	F100F	ttC	ttT	1	1	B.1.1.317	0.000412
M	100	F100F	ttC	ttT	1	1	B.1.1.318	0.000302
M	100	F100S	tTc	tCc	1	1	B.1.1.33	0.000421
M	100	F100F	ttC	ttT	1	1	B.1.1.33	0.000421
M	100	F100del1	Ttc	-tc	1	1	B.1.1.343	0.020833
M	100	F100F	ttC	ttT	1	1	B.1.1.368	0.003086
M	100	F100F	ttC	ttT	1	1	B.1.1.371	0.010417
M	100	F100del	TTC	---	1	1	B.1.1.372	0.000689
M	100	F100F	ttC	ttT	1	1	B.1.1.389	0.006061
M	100	F100F	ttC	ttT	1	1	B.1.1.393	0.111111
M	100	F100V	Ttc	Gtc	1	1	B.1.1.398	0.003226
M	100	F100F	ttC	ttT	1	1	B.1.1.461	0.012048
M	100	F100del	TTC	---	1	1	B.1.1.519	0.00004
M	100	F100L	Ttc	Ctc	1	1	B.1.1.519	0.00004
M	100	F100F	ttC	ttT	1	1	B.1.1.523	0.001563
M	100	F100F	ttC	ttT	1	1	B.1.1.67	0.004566
M	100	F100V	Ttc	Gtc	1	1	B.1.1.7	0.000001
M	100	F100del1	Ttc	-tc	1	1	B.1.1.70	0.000341
M	100	F100F	ttC	ttT	1	1	B.1.153	0.018868
M	100	F100Y	tTc	tAc	1	1	B.1.160	0.000031
M	100	F100F	ttC	ttT	1	1	B.1.160.11	0.005714
M	100	F100F	ttC	ttT	1	1	B.1.160.9	0.007194
M	100	F100del	TTC	---	1	1	B.1.161	0.017241
M	100	F100F	ttC	ttT	1	1	B.1.177.10	0.000878
M	100	F100F	ttC	ttT	1	1	B.1.177.16	0.000664
M	100	F100F	ttC	ttT	1	1	B.1.177.17	0.000821
M	100	F100K	TTC	AAA	1	1	B.1.177.21	0.000076
M	100	F100F	ttC	ttT	1	1	B.1.177.23	0.003236
M	100	F100F	ttC	ttT	1	1	B.1.177.28	0.007407
M	100	F100F	ttC	ttT	1	1	B.1.177.45	0.000381
M	100	F100F	ttC	ttT	1	1	B.1.177.60	0.000218
M	100	F100F	ttC	ttT	1	1	B.1.177.73	0.000566
M	100	F100F	ttC	ttT	1	1	B.1.177.81	0.000189
M	100	F100F	ttC	ttT	1	1	B.1.177.83	0.001481
M	100	F100F	ttC	ttT	1	1	B.1.177.87	0.000728
M	100	F100del1	Ttc	-tc	1	1	B.1.2	0.000009
M	100	F100Y	tTc	tAc	1	1	B.1.2	0.000009
M	100	F100F	ttC	ttT	1	1	B.1.201	0.005682
M	100	F100L	Ttc	Ctc	1	1	B.1.221	0.000071
M	100	F100L	Ttc	Ctc	1	1	B.1.238	0.014925
M	100	F100F	ttC	ttT	1	1	B.1.247	0.014925
M	100	F100F	ttC	ttT	1	1	B.1.252	0.006623
M	100	F100L	Ttc	Ctc	1	1	B.1.258	0.000067
M	100	F100del	TTC	---	1	1	B.1.258	0.000067
M	100	F100del	TTC	---	1	1	B.1.258.11	0.000396
M	100	F100L	Ttc	Ctc	1	1	B.1.258.3	0.001675
M	100	F100del	TTC	---	1	1	B.1.265	0.001271
M	100	F100F	ttC	ttT	1	1	B.1.279	0.000514
M	100	F100del	TTC	---	1	1	B.1.351	0.00003
M	100	F100F	ttC	ttT	1	1	B.1.351.2	0.000303
M	100	F100F	ttC	ttT	1	1	B.1.351.3	0.000876
M	100	F100del2	tTC	t--	1	1	B.1.351.5	0.0006
M	100	F100F	ttC	ttT	1	1	B.1.36.10	0.004785
M	100	F100F	ttC	ttT	1	1	B.1.36.22	0.001208
M	100	F100del	TTC	---	1	1	B.1.36.29	0.000517
M	100	F100L	ttC	ttG	1	1	B.1.367	0.000792
M	100	F100F	ttC	ttT	1	1	B.1.380	0.006623
M	100	F100F	ttC	ttT	1	1	B.1.399	0.001934
M	100	F100del1	Ttc	-tc	1	1	B.1.400	0.000429
M	100	F100F	ttC	ttT	1	1	B.1.416	0.001269
M	100	F100F	ttC	ttT	1	1	B.1.417	0.028571
M	100	F100F	ttC	ttT	1	1	B.1.422	0.000812
M	100	F100del	TTC	---	1	1	B.1.427	0.00005
M	100	F100del	TTC	---	1	1	B.1.429	0.000024
M	100	F100F	ttC	ttT	1	1	B.1.443	0.004673
M	100	F100F	ttC	ttT	1	1	B.1.456	0.003268
M	100	F100F	ttC	ttT	1	1	B.1.466.2	0.000391
M	100	F100F	ttC	ttT	1	1	B.1.468	0.005714
M	100	F100F	ttC	ttT	1	1	B.1.523	0.002451
M	100	F100F	ttC	ttT	1	1	B.1.560	0.00463
M	100	F100F	ttC	ttT	1	1	B.1.561	0.000397
M	100	F100del	TTC	---	1	1	B.1.561	0.000397
M	100	F100F	ttC	ttT	1	1	B.1.564	0.000426
M	100	F100F	ttC	ttT	1	1	B.1.576	0.000907
M	100	F100del	TTC	---	1	1	B.1.596	0.000087
M	100	F100I	Ttc	Atc	1	1	B.1.596	0.000087
M	100	F100F	ttC	ttT	1	1	B.1.600	0.005848
M	100	F100L	ttC	ttG	1	1	B.1.617.1	0.000129
M	100	F100del	TTC	---	1	1	B.1.617.1	0.000129
M	100	F100F	ttC	ttT	1	1	B.1.619	0.000871
M	100	F100F	ttC	ttT	1	1	B.1.620	0.000946
M	100	F100del	TTC	---	1	1	B.1.621	0.000089
M	100	F100del	TTC	---	1	1	B.1.627	0.00202
M	100	F100F	ttC	ttT	1	1	B.1.634	0.003425
M	100	F100F	ttC	ttT	1	1	B.1.78	0.008547
M	100	F100del2	TTc	--c	1	1	B.1.91	0.002075
M	100	F100del	TTC	---	1	1	B.30	0.014706
M	100	F100F	ttC	ttT	1	1	B.40	0.000364
M	100	F100F	ttC	ttT	1	1	C.26	0.007353
M	100	F100F	ttC	ttT	1	1	C.30	0.001727
M	100	F100F	ttC	ttT	1	1	C.36	0.000911
M	100	F100L	ttC	ttG	1	1	C.36.3	0.000567
M	100	F100F	ttC	ttT	1	1	K.3	0.006173
M	100	F100del	TTC	---	1	1	P.1	0.000016
M	100	F100del	TTC	---	1	1	P.1.1	0.000318
M	100	F100F	ttC	ttT	1	1	P.1.12	0.000484
M	100	F100del	TTC	---	1	1	P.1.15	0.000232
M	100	F100F	ttC	ttT	1	1	P.1.16	0.000374
M	100	F100L	ttC	ttG	1	1	P.1.7	0.000319
M	100	F100L	ttC	ttA	1	1	P.2	0.000187
M	100	F100I	Ttc	Atc	1	1	Q.1	0.000126
M	100	F100del	TTC	---	1	1	Q.2	0.000613
M	100	F100del2	tTC	t--	1	1	Q.4	0.000455

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.