CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1528

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
ORF1ab/nsp3	1528	I1528I	I2346I	syn	atC	atT	5583	5443	0.974924	7301-7303
ORF1ab/nsp3	1528	I1528I	I2346I	syn	atC	atA	5583	140	0.0250761	7301-7303
ORF1ab/nsp3	1528	I1528V	I2346V	nonsyn	Atc	Gtc	809	808	0.998764	7301-7303
ORF1ab/nsp3	1528	I1528V	I2346V	nonsyn	AtC	GtT	809	1	0.00123609	7301-7303
ORF1ab/nsp3	1528	I1528T	I2346T	nonsyn	aTc	aCc	363	360	0.991736	7301-7303
ORF1ab/nsp3	1528	I1528T	I2346T	nonsyn	aTC	aCA	363	3	0.00826446	7301-7303
ORF1ab/nsp3	1528	I1528del	I2346del	del	ATC	---	148	148	1	7301-7303
ORF1ab/nsp3	1528	I1528S	I2346S	nonsyn	aTc	aGc	26	24	0.923077	7301-7303
ORF1ab/nsp3	1528	I1528S	I2346S	nonsyn	aTC	aGT	26	1	0.0384615	7301-7303
ORF1ab/nsp3	1528	I1528S	I2346S	nonsyn	ATC	TCA	26	1	0.0384615	7301-7303
ORF1ab/nsp3	1528	I1528L	I2346L	nonsyn	Atc	Ctc	24	19	0.791667	7301-7303
ORF1ab/nsp3	1528	I1528L	I2346L	nonsyn	AtC	CtT	24	2	0.0833333	7301-7303
ORF1ab/nsp3	1528	I1528L	I2346L	nonsyn	AtC	TtG	24	2	0.0833333	7301-7303
ORF1ab/nsp3	1528	I1528L	I2346L	nonsyn	AtC	CtG	24	1	0.0416667	7301-7303
ORF1ab/nsp3	1528	I1528del1	I2346del1	del	aTc	a-c	14	5	0.357143	7301-7303
ORF1ab/nsp3	1528	I1528del1	I2346del1	del	atC	at-	14	2	0.142857	7301-7303
ORF1ab/nsp3	1528	I1528del1	I2346del1	del	aTC	aC-	14	2	0.142857	7301-7303
ORF1ab/nsp3	1528	I1528del1	I2346del1	del	ATc	-Ac	14	2	0.142857	7301-7303
ORF1ab/nsp3	1528	I1528del1	I2346del1	del	Atc	-tc	14	2	0.142857	7301-7303
ORF1ab/nsp3	1528	I1528del1	I2346del1	del	aTC	a-A	14	1	0.0714286	7301-7303
ORF1ab/nsp3	1528	I1528N	I2346N	nonsyn	aTc	aAc	13	9	0.692308	7301-7303
ORF1ab/nsp3	1528	I1528N	I2346N	nonsyn	aTC	aAT	13	4	0.307692	7301-7303
ORF1ab/nsp3	1528	I1528F	I2346F	nonsyn	Atc	Ttc	9	8	0.888889	7301-7303
ORF1ab/nsp3	1528	I1528del2	I2346del2	del	aTC	a--	9	6	0.666667	7301-7303
ORF1ab/nsp3	1528	I1528del2	I2346del2	del	ATc	--c	9	3	0.333333	7301-7303
ORF1ab/nsp3	1528	I1528F	I2346F	nonsyn	AtC	TtT	9	1	0.111111	7301-7303
ORF1ab/nsp3	1528	I1528R	I2346R	nonsyn	aTC	aGG	8	3	0.375	7301-7303
ORF1ab/nsp3	1528	I1528R	I2346R	nonsyn	ATC	CGG	8	2	0.25	7301-7303
ORF1ab/nsp3	1528	I1528R	I2346R	nonsyn	ATC	CGT	8	1	0.125	7301-7303
ORF1ab/nsp3	1528	I1528R	I2346R	nonsyn	aTC	aGA	8	1	0.125	7301-7303
ORF1ab/nsp3	1528	I1528R	I2346R	nonsyn	ATc	CGc	8	1	0.125	7301-7303
ORF1ab/nsp3	1528	I1528M	I2346M	nonsyn	atC	atG	7	7	1	7301-7303
ORF1ab/nsp3	1528	I1528K	I2346K	nonsyn	aTC	aAG	6	4	0.666667	7301-7303
ORF1ab/nsp3	1528	I1528K	I2346K	nonsyn	aTC	aAA	6	2	0.333333	7301-7303
ORF1ab/nsp3	1528	I1528Y	I2346Y	nonsyn	ATc	TAc	4	3	0.75	7301-7303
ORF1ab/nsp3	1528	I1528Y	I2346Y	nonsyn	ATC	TAT	4	1	0.25	7301-7303
ORF1ab/nsp3	1528	I1528A	I2346A	nonsyn	ATc	GCc	2	2	1	7301-7303
ORF1ab/nsp3	1528	I1528X	I2346X	nonsyn	ATC	TAG	2	2	1	7301-7303
ORF1ab/nsp3	1528	I1528H	I2346H	nonsyn	ATC	CAT	1	1	1	7301-7303
ORF1ab/nsp3	1528	I1528Q	I2346Q	nonsyn	ATC	CAG	1	1	1	7301-7303

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
ORF1ab/nsp3	1528	I1528I	atC	atT	5443	5583	All	0.001041
ORF1ab/nsp3	1528	I1528I	atC	atA	140	5583	All	0.000027
ORF1ab/nsp3	1528	I1528I	atC	atT	1610	1610	B.1.2	0.014177
ORF1ab/nsp3	1528	I1528I	atC	atT	1091	1091	B.1.367	0.864501
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	808	809	All	0.000155
ORF1ab/nsp3	1528	I1528V	AtC	GtT	1	809	All	0
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	674	674	AY.103	0.004185
ORF1ab/nsp3	1528	I1528I	atC	atT	429	432	B.1.1.7	0.000384
ORF1ab/nsp3	1528	I1528I	atC	atA	3	432	B.1.1.7	0.000003
ORF1ab/nsp3	1528	I1528T	aTc	aCc	360	363	All	0.000069
ORF1ab/nsp3	1528	I1528T	aTC	aCA	3	363	All	0.000001
ORF1ab/nsp3	1528	I1528I	atC	atT	209	210	AY.4	0.000325
ORF1ab/nsp3	1528	I1528I	atC	atA	1	210	AY.4	0.000002
ORF1ab/nsp3	1528	I1528I	atC	atT	206	207	B.1.617.2	0.000776
ORF1ab/nsp3	1528	I1528I	atC	atA	1	207	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528I	atC	atA	106	157	B.1.160	0.003306
ORF1ab/nsp3	1528	I1528I	atC	atT	51	157	B.1.160	0.001591
ORF1ab/nsp3	1528	I1528I	atC	atT	151	151	B.1.1.519	0.005996
ORF1ab/nsp3	1528	I1528del	ATC	---	148	148	All	0.000028
ORF1ab/nsp3	1528	I1528I	atC	atT	143	147	B.1	0.00131
ORF1ab/nsp3	1528	I1528I	atC	atA	4	147	B.1	0.000037
ORF1ab/nsp3	1528	I1528T	aTc	aCc	125	125	AY.4	0.000195
ORF1ab/nsp3	1528	I1528I	atC	atT	125	125	B.1.1.406	0.811688
ORF1ab/nsp3	1528	I1528I	atC	atT	123	124	AY.103	0.000764
ORF1ab/nsp3	1528	I1528I	atC	atA	1	124	AY.103	0.000006
ORF1ab/nsp3	1528	I1528I	atC	atT	106	106	B.1.351	0.003151
ORF1ab/nsp3	1528	I1528I	atC	atT	99	99	B.1.1	0.001796
ORF1ab/nsp3	1528	I1528I	atC	atT	72	73	AY.61	0.007544
ORF1ab/nsp3	1528	I1528I	atC	atA	1	73	AY.61	0.000105
ORF1ab/nsp3	1528	I1528I	atC	atT	55	55	B.1.177	0.000724
ORF1ab/nsp3	1528	I1528T	aTc	aCc	44	44	B.1.617.2	0.000166
ORF1ab/nsp3	1528	I1528I	atC	atT	40	40	P.1	0.00063
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	39	39	B.1.1.7	0.000035
ORF1ab/nsp3	1528	I1528I	atC	atT	38	38	AY.43	0.000168
ORF1ab/nsp3	1528	I1528I	atC	atT	33	37	AY.3	0.000328
ORF1ab/nsp3	1528	I1528I	atC	atA	4	37	AY.3	0.00004
ORF1ab/nsp3	1528	I1528I	atC	atT	36	36	AY.120	0.001338
ORF1ab/nsp3	1528	I1528I	atC	atT	33	36	AY.20	0.001283
ORF1ab/nsp3	1528	I1528I	atC	atA	3	36	AY.20	0.000117
ORF1ab/nsp3	1528	I1528I	atC	atT	35	36	AY.25	0.000211
ORF1ab/nsp3	1528	I1528I	atC	atA	1	36	AY.25	0.000006
ORF1ab/nsp3	1528	I1528I	atC	atT	35	36	AY.44	0.000213
ORF1ab/nsp3	1528	I1528I	atC	atA	1	36	AY.44	0.000006
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	33	33	AY.4	0.000051
ORF1ab/nsp3	1528	I1528del	ATC	---	32	32	B.1.1.7	0.000029
ORF1ab/nsp3	1528	I1528I	atC	atT	31	31	B.1.429	0.000729
ORF1ab/nsp3	1528	I1528T	aTc	aCc	30	30	AY.103	0.000186
ORF1ab/nsp3	1528	I1528S	aTc	aGc	24	26	All	0.000005
ORF1ab/nsp3	1528	I1528S	ATC	TCA	1	26	All	0
ORF1ab/nsp3	1528	I1528S	aTC	aGT	1	26	All	0
ORF1ab/nsp3	1528	I1528I	atC	atT	26	26	B.1.177.60	0.005679
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	19	24	All	0.000004
ORF1ab/nsp3	1528	I1528L	AtC	TtG	2	24	All	0
ORF1ab/nsp3	1528	I1528L	AtC	CtT	2	24	All	0
ORF1ab/nsp3	1528	I1528L	AtC	CtG	1	24	All	0
ORF1ab/nsp3	1528	I1528T	aTc	aCc	22	22	AY.43	0.000097
ORF1ab/nsp3	1528	I1528I	atC	atT	21	21	AY.75.1	0.003787
ORF1ab/nsp3	1528	I1528I	atC	atT	19	19	AY.29.1	0.00419
ORF1ab/nsp3	1528	I1528T	aTc	aCc	18	19	B.1.1.7	0.000016
ORF1ab/nsp3	1528	I1528T	aTC	aCA	1	19	B.1.1.7	0.000001
ORF1ab/nsp3	1528	I1528I	atC	atT	18	18	AY.5.4	0.004981
ORF1ab/nsp3	1528	I1528I	atC	atT	17	17	AY.26	0.000481
ORF1ab/nsp3	1528	I1528I	atC	atT	17	17	B.1.1.309	0.099415
ORF1ab/nsp3	1528	I1528I	atC	atT	16	16	AY.9.2	0.000588
ORF1ab/nsp3	1528	I1528I	atC	atT	16	16	B.1.258	0.001065
ORF1ab/nsp3	1528	I1528I	atC	atT	16	16	B.1.311	0.004393
ORF1ab/nsp3	1528	I1528I	atC	atT	16	16	B.1.596	0.001394
ORF1ab/nsp3	1528	I1528I	atC	atT	16	16	R.1	0.00144
ORF1ab/nsp3	1528	I1528I	atC	atT	15	15	AY.46.6	0.001083
ORF1ab/nsp3	1528	I1528del1	aTc	a-c	5	14	All	0.000001
ORF1ab/nsp3	1528	I1528del1	atC	at-	2	14	All	0
ORF1ab/nsp3	1528	I1528del1	Atc	-tc	2	14	All	0
ORF1ab/nsp3	1528	I1528del1	ATc	-Ac	2	14	All	0
ORF1ab/nsp3	1528	I1528del1	aTC	aC-	2	14	All	0
ORF1ab/nsp3	1528	I1528del1	aTC	a-A	1	14	All	0
ORF1ab/nsp3	1528	I1528I	atC	atT	14	14	AY.4.5	0.001505
ORF1ab/nsp3	1528	I1528del	ATC	---	14	14	AY.43	0.000062
ORF1ab/nsp3	1528	I1528I	atC	atT	14	14	B.1.177.4	0.002955
ORF1ab/nsp3	1528	I1528I	atC	atT	14	14	B.1.497	0.004407
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	13	14	B.1.617.2	0.000049
ORF1ab/nsp3	1528	I1528V	AtC	GtT	1	14	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528I	atC	atT	14	14	B.1.621	0.001239
ORF1ab/nsp3	1528	I1528N	aTc	aAc	9	13	All	0.000002
ORF1ab/nsp3	1528	I1528N	aTC	aAT	4	13	All	0.000001
ORF1ab/nsp3	1528	I1528I	atC	atT	13	13	AY.98.1	0.00063
ORF1ab/nsp3	1528	I1528I	atC	atT	12	12	AY.38	0.005991
ORF1ab/nsp3	1528	I1528I	atC	atA	7	12	AY.39	0.000173
ORF1ab/nsp3	1528	I1528I	atC	atT	5	12	AY.39	0.000124
ORF1ab/nsp3	1528	I1528I	atC	atT	12	12	AY.5	0.000248
ORF1ab/nsp3	1528	I1528I	atC	atT	11	11	AY.4.2	0.000239
ORF1ab/nsp3	1528	I1528T	aTc	aCc	11	11	B.1	0.000101
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	8	9	All	0.000002
ORF1ab/nsp3	1528	I1528del2	aTC	a--	6	9	All	0.000001
ORF1ab/nsp3	1528	I1528del2	ATc	--c	3	9	All	0.000001
ORF1ab/nsp3	1528	I1528F	AtC	TtT	1	9	All	0
ORF1ab/nsp3	1528	I1528I	atC	atT	7	9	AY.102	0.000186
ORF1ab/nsp3	1528	I1528I	atC	atA	2	9	AY.102	0.000053
ORF1ab/nsp3	1528	I1528T	aTc	aCc	9	9	AY.3	0.00009
ORF1ab/nsp3	1528	I1528T	aTc	aCc	9	9	AY.9.2.1	0.017787
ORF1ab/nsp3	1528	I1528I	atC	atT	9	9	B	0.00115
ORF1ab/nsp3	1528	I1528I	atC	atT	9	9	B.1.526	0.000212
ORF1ab/nsp3	1528	I1528del	ATC	---	9	9	B.1.617.2	0.000034
ORF1ab/nsp3	1528	I1528R	aTC	aGG	3	8	All	0.000001
ORF1ab/nsp3	1528	I1528R	ATC	CGG	2	8	All	0
ORF1ab/nsp3	1528	I1528R	ATc	CGc	1	8	All	0
ORF1ab/nsp3	1528	I1528R	ATC	CGT	1	8	All	0
ORF1ab/nsp3	1528	I1528R	aTC	aGA	1	8	All	0
ORF1ab/nsp3	1528	I1528I	atC	atT	7	8	AY.119	0.000247
ORF1ab/nsp3	1528	I1528I	atC	atA	1	8	AY.119	0.000035
ORF1ab/nsp3	1528	I1528T	aTc	aCc	8	8	AY.26	0.000226
ORF1ab/nsp3	1528	I1528S	aTc	aGc	8	8	AY.4	0.000012
ORF1ab/nsp3	1528	I1528T	aTc	aCc	8	8	C.37	0.000929
ORF1ab/nsp3	1528	I1528M	atC	atG	7	7	All	0.000001
ORF1ab/nsp3	1528	I1528I	atC	atT	7	7	AY.100	0.000322
ORF1ab/nsp3	1528	I1528I	atC	atT	7	7	AY.114	0.001618
ORF1ab/nsp3	1528	I1528del	ATC	---	7	7	AY.25	0.000042
ORF1ab/nsp3	1528	I1528I	atC	atT	7	7	AY.47	0.000218
ORF1ab/nsp3	1528	I1528T	aTc	aCc	7	7	B.1.2	0.000062
ORF1ab/nsp3	1528	I1528I	atC	atT	7	7	B.1.240	0.001509
ORF1ab/nsp3	1528	I1528I	atC	atT	7	7	B.1.36	0.001021
ORF1ab/nsp3	1528	I1528I	atC	atT	7	7	B.1.561	0.002779
ORF1ab/nsp3	1528	I1528I	atC	atT	7	7	P.1.14	0.000335
ORF1ab/nsp3	1528	I1528K	aTC	aAG	4	6	All	0.000001
ORF1ab/nsp3	1528	I1528K	aTC	aAA	2	6	All	0
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	AY.113	0.000854
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	6	6	AY.20	0.000233
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	AY.27	0.000388
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	AY.29	0.000095
ORF1ab/nsp3	1528	I1528T	aTc	aCc	6	6	AY.39	0.000148
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	AY.42	0.000241
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	AY.54	0.000572
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	AY.95	0.004566
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	B.1.1.241	0.012422
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	B.1.1.351	0.01676
ORF1ab/nsp3	1528	I1528S	aTc	aGc	5	6	B.1.1.7	0.000004
ORF1ab/nsp3	1528	I1528S	ATC	TCA	1	6	B.1.1.7	0.000001
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	B.1.243	0.000418
ORF1ab/nsp3	1528	I1528I	atC	atT	6	6	B.1.630	0.031414
ORF1ab/nsp3	1528	I1528I	atC	atT	5	5	AY.109	0.003698
ORF1ab/nsp3	1528	I1528I	atC	atT	5	5	AY.71	0.002375
ORF1ab/nsp3	1528	I1528del	ATC	---	5	5	B.1	0.000046
ORF1ab/nsp3	1528	I1528del	ATC	---	5	5	B.1.1	0.000091
ORF1ab/nsp3	1528	I1528I	atC	atT	5	5	B.1.1.1	0.001633
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	5	5	B.1.1.7	0.000004
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	5	5	B.1.2	0.000044
ORF1ab/nsp3	1528	I1528I	atC	atT	5	5	B.1.258.17	0.00052
ORF1ab/nsp3	1528	I1528I	atC	atT	5	5	B.1.564	0.002129
ORF1ab/nsp3	1528	I1528I	atC	atT	5	5	B.1.625	0.011765
ORF1ab/nsp3	1528	I1528Y	ATc	TAc	3	4	All	0.000001
ORF1ab/nsp3	1528	I1528Y	ATC	TAT	1	4	All	0
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	4	4	AY.102	0.000106
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	4	4	AY.103	0.000025
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	4	4	AY.44	0.000024
ORF1ab/nsp3	1528	I1528I	atC	atT	4	4	AY.7.1	0.000451
ORF1ab/nsp3	1528	I1528T	aTc	aCc	4	4	B.1.1.157	0.003653
ORF1ab/nsp3	1528	I1528T	aTc	aCc	4	4	B.1.160.23	0.019324
ORF1ab/nsp3	1528	I1528I	atC	atT	4	4	B.1.369	0.001141
ORF1ab/nsp3	1528	I1528T	aTc	aCc	4	4	B.1.400	0.001716
ORF1ab/nsp3	1528	I1528I	atC	atT	4	4	B.1.469	0.01444
ORF1ab/nsp3	1528	I1528K	aTC	aAG	2	4	B.1.617.2	0.000008
ORF1ab/nsp3	1528	I1528K	aTC	aAA	2	4	B.1.617.2	0.000008
ORF1ab/nsp3	1528	I1528I	atC	atT	4	4	D.2	0.0003
ORF1ab/nsp3	1528	I1528I	atC	atT	4	4	P.1.7	0.001277
ORF1ab/nsp3	1528	I1528I	atC	atT	4	4	Q.3	0.00058
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	A.21	0.00831
ORF1ab/nsp3	1528	I1528T	aTc	aCc	3	3	AY.102	0.00008
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	AY.104	0.005952
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	AY.118	0.000188
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	AY.13	0.000483
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	AY.3.1	0.000256
ORF1ab/nsp3	1528	I1528del	ATC	---	3	3	AY.4	0.000005
ORF1ab/nsp3	1528	I1528del	ATC	---	3	3	AY.42	0.000121
ORF1ab/nsp3	1528	I1528T	aTc	aCc	3	3	AY.44	0.000018
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	AY.75	0.000168
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	AY.83	0.005172
ORF1ab/nsp3	1528	I1528R	aTC	aGG	1	3	AY.9.2	0.000037
ORF1ab/nsp3	1528	I1528R	ATc	CGc	1	3	AY.9.2	0.000037
ORF1ab/nsp3	1528	I1528R	ATC	CGG	1	3	AY.9.2	0.000037
ORF1ab/nsp3	1528	I1528N	aTc	aAc	2	3	B.1	0.000018
ORF1ab/nsp3	1528	I1528N	aTC	aAT	1	3	B.1	0.000009
ORF1ab/nsp3	1528	I1528R	aTC	aGG	1	3	B.1	0.000009
ORF1ab/nsp3	1528	I1528R	ATC	CGG	1	3	B.1	0.000009
ORF1ab/nsp3	1528	I1528R	ATC	CGT	1	3	B.1	0.000009
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	3	3	B.1.1	0.000054
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.1.1.192	0.006928
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.1.1.214	0.000166
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.1.1.216	0.002671
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.1.1.317	0.001235
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.1.1.333	0.003229
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.1.36.29	0.001552
ORF1ab/nsp3	1528	I1528del	ATC	---	3	3	B.1.617.1	0.000387
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.1.617.1	0.000387
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	1	3	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528L	AtC	CtT	1	3	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528L	AtC	TtG	1	3	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	B.6.6	0.002667
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	C.14	0.012987
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	C.37	0.000348
ORF1ab/nsp3	1528	I1528I	atC	atT	2	3	P.1.15	0.000465
ORF1ab/nsp3	1528	I1528I	atC	atA	1	3	P.1.15	0.000232
ORF1ab/nsp3	1528	I1528I	atC	atT	3	3	P.2	0.00056
ORF1ab/nsp3	1528	I1528del1	ATc	-Ac	2	2		0.111111
ORF1ab/nsp3	1528	I1528del2	ATc	--c	2	2		0.111111
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2		0.111111
ORF1ab/nsp3	1528	I1528N	aTc	aAc	1	2		0.055556
ORF1ab/nsp3	1528	I1528N	aTC	aAT	1	2		0.055556
ORF1ab/nsp3	1528	I1528Y	ATc	TAc	1	2		0.055556
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	1	2		0.055556
ORF1ab/nsp3	1528	I1528F	AtC	TtT	1	2		0.055556
ORF1ab/nsp3	1528	I1528Y	ATC	TAT	1	2		0.055556
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AE.3	0.064516
ORF1ab/nsp3	1528	I1528A	ATc	GCc	2	2	All	0
ORF1ab/nsp3	1528	I1528X	ATC	TAG	2	2	All	0
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.10	0.00106
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	AY.111	0.000366
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.117	0.000169
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	AY.120.2	0.002571
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.14	0.000176
ORF1ab/nsp3	1528	I1528I	atC	atA	1	2	AY.23	0.00007
ORF1ab/nsp3	1528	I1528I	atC	atT	1	2	AY.23	0.00007
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	AY.25	0.000012
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.32	0.001065
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	AY.32	0.001065
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.34	0.000194
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	AY.36	0.000296
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	2	2	AY.39	0.000049
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	2	2	AY.4	0.000003
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	2	2	AY.4	0.000003
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.41	0.000588
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.45	0.000243
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.46	0.000208
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	AY.46.6	0.000144
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	AY.5	0.000041
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.5.3	0.000675
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.55	0.001835
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	1	2	AY.59	0.00053
ORF1ab/nsp3	1528	I1528L	AtC	TtG	1	2	AY.59	0.00053
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.69	0.000373
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.74	0.000231
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	AY.78	0.003082
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	AY.9.2	0.000073
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	AY.9.2	0.000073
ORF1ab/nsp3	1528	I1528L	AtC	CtG	1	2	AY.9.2	0.000037
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	1	2	AY.9.2	0.000037
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	AY.99.2	0.000184
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	2	B.1	0.000009
ORF1ab/nsp3	1528	I1528S	aTC	aGT	1	2	B.1	0.000009
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.1.117	0.019417
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.1.37	0.000386
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.1.372	0.001377
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.1.434	0.000697
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	2	2	B.1.1.519	0.000079
ORF1ab/nsp3	1528	I1528del2	aTC	a--	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	B.1.177	0.000026
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	B.1.177	0.000026
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.177.87	0.001456
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.210	0.004264
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	2	2	B.1.221	0.000142
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.234	0.000264
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	B.1.258	0.000133
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	B.1.336	0.004878
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.351.2	0.000605
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	B.1.351.3	0.001753
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	B.1.36.1	0.002281
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.36.17	0.000988
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	B.1.411	0.007407
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	B.1.470	0.002809
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	B.1.497	0.00063
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	B.1.525	0.000226
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	2	2	B.1.617.1	0.000258
ORF1ab/nsp3	1528	I1528del1	aTc	a-c	1	2	B.1.617.1	0.000129
ORF1ab/nsp3	1528	I1528del1	atC	at-	1	2	B.1.617.1	0.000129
ORF1ab/nsp3	1528	I1528Y	ATc	TAc	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1528	I1528N	aTc	aAc	1	2	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528N	aTC	aAT	1	2	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	B.1.621	0.000177
ORF1ab/nsp3	1528	I1528del	ATC	---	2	2	B.1.628	0.000705
ORF1ab/nsp3	1528	I1528N	aTc	aAc	1	2	B.60	0.015873
ORF1ab/nsp3	1528	I1528N	aTC	aAT	1	2	B.60	0.015873
ORF1ab/nsp3	1528	I1528I	atC	atT	2	2	C.35	0.001548
ORF1ab/nsp3	1528	I1528T	aTc	aCc	2	2	P.1	0.000032
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	2	2	Q.1	0.000253
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1		0.055556
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	A.19	0.009434
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	A.2	0.000662
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	A.2.5	0.000499
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	A.27	0.001656
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	A.28	0.002646
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	A.28	0.002646
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AD.2	0.000219
ORF1ab/nsp3	1528	I1528H	ATC	CAT	1	1	All	0
ORF1ab/nsp3	1528	I1528Q	ATC	CAG	1	1	All	0
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AW.1	0.003049
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.101	0.00049
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	AY.102	0.000027
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.103	0.000006
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	AY.103	0.000006
ORF1ab/nsp3	1528	I1528R	aTC	aGG	1	1	AY.107	0.000466
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	1	1	AY.108	0.001103
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.110	0.000113
ORF1ab/nsp3	1528	I1528T	aTC	aCA	1	1	AY.116	0.000287
ORF1ab/nsp3	1528	I1528K	aTC	aAG	1	1	AY.119	0.000035
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	AY.119	0.000035
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.119	0.000035
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.120	0.000037
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.120	0.000037
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.121	0.000135
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.24	0.000431
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.24	0.000431
ORF1ab/nsp3	1528	I1528del2	aTC	a--	1	1	AY.25	0.000006
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.25	0.000006
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.29	0.000016
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.29.1	0.000221
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.3	0.00001
ORF1ab/nsp3	1528	I1528M	atC	atG	1	1	AY.3	0.00001
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.30	0.000396
ORF1ab/nsp3	1528	I1528N	aTc	aAc	1	1	AY.30	0.000396
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.33	0.000067
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.33	0.000067
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.34.1	0.00051
ORF1ab/nsp3	1528	I1528del1	aTC	aC-	1	1	AY.35	0.000233
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.36	0.000148
ORF1ab/nsp3	1528	I1528T	aTC	aCA	1	1	AY.38	0.000499
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.39.1	0.00004
ORF1ab/nsp3	1528	I1528del2	aTC	a--	1	1	AY.4	0.000002
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.4.3	0.000842
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.4.3	0.000842
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.43	0.000004
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	AY.43	0.000004
ORF1ab/nsp3	1528	I1528del2	aTC	a--	1	1	AY.44	0.000006
ORF1ab/nsp3	1528	I1528del1	aTC	a-A	1	1	AY.44	0.000006
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.44	0.000006
ORF1ab/nsp3	1528	I1528del2	ATc	--c	1	1	AY.46	0.000104
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.46.4	0.000165
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.46.6	0.000072
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.47	0.000031
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.5	0.000021
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.51	0.000909
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.56	0.001605
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	1	1	AY.59	0.00053
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.6	0.000041
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.60	0.000938
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.62	0.000436
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.63	0.000387
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.67	0.000464
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.67	0.000464
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.68	0.000274
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	1	1	AY.68	0.000274
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	1	1	AY.69	0.000187
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.7	0.000196
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.7.1	0.000113
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.7.2	0.000559
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.74	0.000116
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.75	0.000056
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	AY.75	0.000056
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.75.1	0.00018
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.76	0.004831
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.84	0.000437
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.9	0.000068
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.9.1	0.000084
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	AY.9.2	0.000037
ORF1ab/nsp3	1528	I1528M	atC	atG	1	1	AY.9.2	0.000037
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.94	0.000443
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.98	0.000079
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.98.1	0.000048
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	AY.99	0.001049
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	AY.99.2	0.000092
ORF1ab/nsp3	1528	I1528K	aTC	aAG	1	1	B.1	0.000009
ORF1ab/nsp3	1528	I1528H	ATC	CAT	1	1	B.1	0.000009
ORF1ab/nsp3	1528	I1528Q	ATC	CAG	1	1	B.1	0.000009
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	1	1	B.1	0.000009
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	B.1	0.000009
ORF1ab/nsp3	1528	I1528M	atC	atG	1	1	B.1.1	0.000018
ORF1ab/nsp3	1528	I1528del1	aTc	a-c	1	1	B.1.1	0.000018
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	B.1.1	0.000018
ORF1ab/nsp3	1528	I1528A	ATc	GCc	1	1	B.1.1	0.000018
ORF1ab/nsp3	1528	I1528del1	aTc	a-c	1	1	B.1.1.101	0.01
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.128	0.007092
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.138	0.006061
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.1.159	0.004673
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.172	0.018182
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.189	0.001513
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	B.1.1.189	0.001513
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.207	0.001182
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.1.221	0.010101
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.270	0.010309
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.277	0.000759
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.284	0.000107
ORF1ab/nsp3	1528	I1528M	atC	atG	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1528	I1528del1	aTC	aC-	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.1.354	0.004386
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.1.46	0.004367
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	B.1.1.486	0.001577
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.507	0.008696
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.526	0.003546
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.1.83	0.00271
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.115	0.021739
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.127	0.002198
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.128	0.000635
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.146	0.004237
ORF1ab/nsp3	1528	I1528I	atC	atA	1	1	B.1.157	0.002985
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.160.7	0.002079
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.161	0.017241
ORF1ab/nsp3	1528	I1528A	ATc	GCc	1	1	B.1.177	0.000013
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	1528	I1528M	atC	atG	1	1	B.1.177.35	0.000691
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.177.45	0.000381
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.177.62	0.001192
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	1528	I1528del1	aTc	a-c	1	1	B.1.2	0.000009
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.2	0.000009
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.206	0.000816
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.210	0.002132
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.221	0.000071
ORF1ab/nsp3	1528	I1528N	aTc	aAc	1	1	B.1.221	0.000071
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	B.1.240	0.000216
ORF1ab/nsp3	1528	I1528X	ATC	TAG	1	1	B.1.258	0.000067
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.258.14	0.00098
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	B.1.258.17	0.000104
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.265	0.001271
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	B.1.311	0.000275
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.351	0.00003
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	B.1.36.31	0.001751
ORF1ab/nsp3	1528	I1528del1	aTc	a-c	1	1	B.1.36.8	0.001
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.375	0.00082
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.397	0.004854
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.409	0.000781
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.415	0.014286
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	B.1.433	0.003195
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	B.1.452	0.013699
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.453	0.003236
ORF1ab/nsp3	1528	I1528R	aTC	aGA	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	1528	I1528M	atC	atG	1	1	B.1.497	0.000315
ORF1ab/nsp3	1528	I1528V	Atc	Gtc	1	1	B.1.499	0.00105
ORF1ab/nsp3	1528	I1528del1	Atc	-tc	1	1	B.1.526	0.000024
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	B.1.526	0.000024
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	B.1.526	0.000024
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.530	0.007143
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.575.1	0.002439
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.576	0.000907
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.581	0.009434
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.582	0.000491
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.595	0.000261
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.597	0.00463
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.604	0.017241
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.612	0.002653
ORF1ab/nsp3	1528	I1528L	Atc	Ctc	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528X	ATC	TAG	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528M	atC	atG	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528del1	Atc	-tc	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1528	I1528del1	atC	at-	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	1528	I1528I	atC	atA	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.1.620	0.000946
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1528	I1528N	aTc	aAc	1	1	B.1.621	0.000089
ORF1ab/nsp3	1528	I1528del2	aTC	a--	1	1	B.1.628	0.000352
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	B.1.628	0.000352
ORF1ab/nsp3	1528	I1528S	aTc	aGc	1	1	B.40	0.000364
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	B.60	0.015873
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	C.35	0.000774
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	C.36.1	0.004149
ORF1ab/nsp3	1528	I1528F	Atc	Ttc	1	1	D.2	0.000075
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	D.2	0.000075
ORF1ab/nsp3	1528	I1528N	aTc	aAc	1	1	D.2	0.000075
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	K.1	0.02381
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	P.1	0.000016
ORF1ab/nsp3	1528	I1528L	AtC	CtT	1	1	P.1	0.000016
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	P.1.1	0.000318
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	P.1.1	0.000318
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	P.1.12	0.000484
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	P.1.15	0.000232
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	P.1.17	0.000162
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	Q.2	0.000613
ORF1ab/nsp3	1528	I1528I	atC	atT	1	1	Q.2	0.000613
ORF1ab/nsp3	1528	I1528del	ATC	---	1	1	Q.8	0.000165
ORF1ab/nsp3	1528	I1528T	aTc	aCc	1	1	Q.8	0.000165

CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.