CoV-GLUE Mutations

CoV-GLUE | Mutations

CoV-GLUE Mutations: Lineage = All

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Lineage:

ORF:

Mutation type:

Min count:

Min prop:

Lineage = All ; ORF = All
Mutation Type = nonsyn ; Min count = 1 ; Min prop = 0.01

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Lineage	ORF	CodonNum	Mutation	ORF1ab	MutType	C1	C2	C3	RefCodon	MutCodon	Count	Proportion
All	S	614	D614G		nonsyn	23402	23403	23404	gAt	gGt	5182511	0.991216
All	ORF1ab/nsp12	323	P323L	P4715L	nonsyn	14407	14408	14409	cCt	cTt	5144375	0.983923
All	S	452	L452R		nonsyn	22916	22917	22918	cTg	cGg	2772069	0.530191
All	M	82	I82T		nonsyn	26766	26767	26768	aTc	aCc	2769241	0.52965
All	S	681	P681R		nonsyn	23603	23604	23605	cCt	cGt	2762560	0.528372
All	ORF3a	26	S26L		nonsyn	25468	25469	25470	tCa	tTa	2758877	0.527668
All	N	377	D377Y		nonsyn	29402	29403	29404	Gat	Tat	2747198	0.525434
All	ORF1ab/nsp13	77	P77L	P5401L	nonsyn	16465	16466	16467	cCa	cTa	2737605	0.523599
All	N	203	R203M		nonsyn	28880	28881	28882	aGg	aTg	2734740	0.523051
All	S	19	T19R		nonsyn	21617	21618	21619	aCa	aGa	2719065	0.520053
All	ORF1ab/nsp12	671	G671S	G5063S	nonsyn	15451	15452	15453	Ggt	Agt	2718826	0.520008
All	S	478	T478K		nonsyn	22994	22995	22996	aCa	aAa	2709160	0.518159
All	N	63	D63G		nonsyn	28460	28461	28462	gAc	gGc	2684161	0.513378
All	S	950	D950N		nonsyn	24410	24411	24412	Gat	Aat	2681700	0.512907
All	ORF7a	120	T120I		nonsyn	27751	27752	27753	aCa	aTa	2638678	0.504678
All	ORF7a	82	V82A		nonsyn	27637	27638	27639	gTt	gCt	2596239	0.496561
All	S	158	R158G		nonsyn	22034	22035	22036	Aga	Gga	2519550	0.481894
All	ORF1ab/nsp4	492	T492I	T3255I	nonsyn	10028	10029	10030	aCc	aTc	2468093	0.472052
All	ORF1ab/nsp6	77	T77A	T3646A	nonsyn	11201	11202	11203	Act	Gct	2426563	0.464109
All	ORF1ab/nsp14A2-B	394	A394V	A6319V	nonsyn	19219	19220	19221	gCt	gTt	2422977	0.463423
All	ORF1ab/nsp4	167	V167L	V2930L	nonsyn	9053	9054	9055	Gta	Tta	2417358	0.462348
All	ORF1ab/nsp3	1228	P1228L	P2046L	nonsyn	6401	6402	6403	cCa	cTa	2409735	0.46089
All	N	215	G215C		nonsyn	28916	28917	28918	Ggt	Tgt	2395920	0.458248
All	ORF1ab/nsp3	488	A488S	A1306S	nonsyn	4181	4182	4183	Gct	Tct	2394155	0.45791
All	ORF7b	40	T40I		nonsyn	27873	27874	27875	aCt	aTt	2381370	0.455465
All	ORF1ab/nsp3	1469	P1469S	P2287S	nonsyn	7124	7125	7126	Cct	Tct	2364296	0.4522
All	S	142	G142D		nonsyn	21986	21987	21988	gGt	gAt	1762111	0.337025
All	N	203	R203K		nonsyn	28880	28881	28882	aGG	aAA	1521802	0.291063
All	N	204	G204R		nonsyn	28883	28884	28885	Gga	Cga	1440956	0.2756
All	S	501	N501Y		nonsyn	23063	23064	23065	Aat	Tat	1292878	0.247278
All	S	681	P681H		nonsyn	23603	23604	23605	cCt	cAt	1223473	0.234004
All	ORF1ab/nsp3	183	T183I	T1001I	nonsyn	3266	3267	3268	aCt	aTt	1151925	0.220319
All	S	716	T716I		nonsyn	23708	23709	23710	aCa	aTa	1147179	0.219412
All	S	570	A570D		nonsyn	23270	23271	23272	gCt	gAt	1144583	0.218915
All	S	1118	D1118H		nonsyn	24914	24915	24916	Gac	Cac	1144377	0.218876
All	ORF1ab/nsp3	890	A890D	A1708D	nonsyn	5387	5388	5389	gCt	gAt	1142651	0.218546
All	ORF8	27	Q27X		nonsyn	27972	27973	27974	Caa	Taa	1141607	0.218346
All	ORF8	73	Y73C		nonsyn	28110	28111	28112	tAc	tGc	1141306	0.218288
All	N	235	S235F		nonsyn	28976	28977	28978	tCt	tTt	1140362	0.218108
All	ORF8	52	R52I		nonsyn	28047	28048	28049	aGa	aTa	1139702	0.217981
All	S	982	S982A		nonsyn	24506	24507	24508	Tca	Gca	1139418	0.217927
All	N	3	D3L		nonsyn	28280	28281	28282	GAT	CTA	1129900	0.216107
All	ORF1ab/nsp3	1412	I1412T	I2230T	nonsyn	6953	6954	6955	aTa	aCa	1122427	0.214677
All	S	95	T95I		nonsyn	21845	21846	21847	aCt	aTt	1102245	0.210817
All	ORF1ab/nsp3	1711	A1711V	A2529V	nonsyn	7850	7851	7852	gCt	gTt	719774	0.137665
All	ORF3a	57	Q57H		nonsyn	25561	25562	25563	caG	caT	514139	0.098335
All	S	222	A222V		nonsyn	22226	22227	22228	gCt	gTt	455853	0.087187
All	ORF8	68	K68X		nonsyn	28095	28096	28097	Aaa	Taa	405457	0.077548
All	ORF1ab/nsp2	85	T85I	T265I	nonsyn	1058	1059	1060	aCc	aTc	399347	0.07638
All	ORF1ab/nsp4	446	A446V	A3209V	nonsyn	9890	9891	9892	gCt	gTt	327958	0.062726
All	ORF1ab/nsp3	822	P822L	P1640L	nonsyn	5183	5184	5185	cCt	cTt	321544	0.061499
All	ORF1ab/nsp6	149	V149A	V3718A	nonsyn	11417	11418	11419	gTt	gCt	296085	0.05663
All	ORF1ab/nsp13	460	K460R	K5784R	nonsyn	17614	17615	17616	aAg	aGg	243524	0.046577
All	ORF1ab/nsp6	181	T181I	T3750I	nonsyn	11513	11514	11515	aCt	aTt	239955	0.045894
All	S	484	E484K		nonsyn	23012	23013	23014	Gaa	Aaa	229757	0.043944
All	S	18	L18F		nonsyn	21614	21615	21616	Ctt	Ttt	222267	0.042511
All	ORF10	30	V30L		nonsyn	29645	29646	29647	Gta	Tta	177133	0.033879
All	N	220	A220V		nonsyn	28931	28932	28933	gCt	gTt	174671	0.033408
All	ORF1ab/nsp13	334	I334V	I5658V	nonsyn	17236	17237	17238	Ata	Gta	174140	0.033306
All	ORF1ab/nsp12	227	P227L	P4619L	nonsyn	14119	14120	14121	cCa	cTa	172986	0.033086
All	N	199	P199L		nonsyn	28868	28869	28870	cCa	cTa	170770	0.032662
All	ORF3a	239	E239Q		nonsyn	26107	26108	26109	Gag	Cag	165718	0.031696
All	N	205	T205I		nonsyn	28886	28887	28888	aCt	aTt	165671	0.031687
All	ORF1ab/nsp12	192	F192V	F4584V	nonsyn	14014	14015	14016	Ttc	Gtc	164557	0.031473
All	ORF1ab/nsp12	838	L838I	L5230I	nonsyn	15952	15953	15954	Cta	Ata	157138	0.030055
All	N	9	Q9L		nonsyn	28298	28299	28300	cAg	cTg	156199	0.029875
All	ORF1ab/nsp3	1736	A1736V	A2554V	nonsyn	7925	7926	7927	gCa	gTa	154157	0.029484
All	ORF8	24	S24L		nonsyn	27963	27964	27965	tCa	tTa	141602	0.027083
All	S	5	L5F		nonsyn	21575	21576	21577	Ctt	Ttt	140051	0.026786
All	ORF1ab/nsp5A-B	89	L89F	L3352F	nonsyn	10319	10320	10321	Ctt	Ttt	136471	0.026102
All	ORF1ab/nsp6	37	L37F	L3606F	nonsyn	11081	11082	11083	ttG	ttT	133400	0.025514
All	S	1176	V1176F		nonsyn	25088	25089	25090	Gtt	Ttt	130343	0.02493
All	ORF3a	172	G172V		nonsyn	25906	25907	25908	gGt	gTt	129015	0.024676
All	ORF1ab/nsp14A2-B	129	N129D	N6054D	nonsyn	18424	18425	18426	Aat	Gat	126719	0.024237
All	N	67	P67S		nonsyn	28472	28473	28474	Cct	Tct	126441	0.024183
All	S	26	P26S		nonsyn	21638	21639	21640	Cct	Tct	124884	0.023886
All	ORF1ab/nsp13	341	E341D	E5665D	nonsyn	17257	17258	17259	gaG	gaT	124506	0.023813
All	S	1027	T1027I		nonsyn	24641	24642	24643	aCt	aTt	123272	0.023577
All	ORF1ab/nsp2	81	K81N	K261N	nonsyn	1046	1047	1048	aaG	aaT	123249	0.023573
All	S	138	D138Y		nonsyn	21974	21975	21976	Gat	Tat	122978	0.023521
All	S	655	H655Y		nonsyn	23525	23526	23527	Cat	Tat	122823	0.023491
All	ORF1ab/nsp12	694	F694Y	F5086Y	nonsyn	15520	15521	15522	tTt	tAt	121421	0.023223
All	ORF1ab/nsp3	370	S370L	S1188L	nonsyn	3827	3828	3829	tCa	tTa	119870	0.022927
All	ORF1ab/nsp6	162	I162V	I3731V	nonsyn	11456	11457	11458	Att	Gtt	118533	0.022671
All	ORF1ab/nsp5A-B	90	K90R	K3353R	nonsyn	10322	10323	10324	aAg	aGg	117758	0.022523
All	ORF8	92	E92K		nonsyn	28167	28168	28169	Gaa	Aaa	115968	0.02218
All	ORF1ab/nsp16	216	R216C	R7014C	nonsyn	21304	21305	21306	Cgc	Tgc	115537	0.022098
All	ORF1ab/nsp3	977	K977Q	K1795Q	nonsyn	5648	5649	5650	Aaa	Caa	115002	0.021995
All	ORF3a	253	S253P		nonsyn	26149	26150	26151	Tcc	Ccc	114966	0.021989
All	N	80	P80R		nonsyn	28511	28512	28513	cCa	cGa	114772	0.021952
All	S	20	T20N		nonsyn	21620	21621	21622	aCc	aAc	112270	0.021473
All	S	417	K417T		nonsyn	22811	22812	22813	aAg	aCg	110908	0.021212
All	S	190	R190S		nonsyn	22130	22131	22132	agG	agT	108611	0.020773
All	N	194	S194L		nonsyn	28853	28854	28855	tCa	tTa	98184	0.018779
All	ORF1ab/nsp2	129	P129L	P309L	nonsyn	1190	1191	1192	cCa	cTa	97476	0.018643
All	ORF1ab/nsp13	164	H164Y	H5488Y	nonsyn	16726	16727	16728	Cat	Tat	96730	0.018501
All	ORF1ab/nsp16	160	K160R	K6958R	nonsyn	21136	21137	21138	aAg	aGg	89882	0.017191
All	ORF1ab/nsp2	550	L550F	L730F	nonsyn	2453	2454	2455	Ctc	Ttc	87092	0.016657
All	N	204	G204P		nonsyn	28883	28884	28885	GGa	CCa	83275	0.015927
All	ORF1ab/nsp6	197	C197F	C3766F	nonsyn	11561	11562	11563	tGc	tTc	77973	0.014913
All	ORF1ab/nsp13	261	E261D	E5585D	nonsyn	17017	17018	17019	gaG	gaT	76970	0.014721
All	S	701	A701V		nonsyn	23663	23664	23665	gCa	gTa	76446	0.014621
All	ORF7a	116	L116F		nonsyn	27739	27740	27741	Ctc	Ttc	75670	0.014473
All	ORF1ab/nsp3	1307	H1307Y	H2125Y	nonsyn	6638	6639	6640	Cat	Tat	73794	0.014114
All	N	234	M234I		nonsyn	28973	28974	28975	atG	atT	73337	0.014027
All	ORF1ab/nsp4	94	V94A	V2857A	nonsyn	8834	8835	8836	gTc	gCc	73320	0.014023
All	S	477	S477N		nonsyn	22991	22992	22993	aGc	aAc	71987	0.013768
All	ORF1ab/nsp3	1441	M1441I	M2259I	nonsyn	7040	7041	7042	atG	atT	70849	0.013551
All	ORF1ab/nsp3	410	D410G	D1228G	nonsyn	3947	3948	3949	gAt	gGt	70817	0.013545
All	ORF7a	45	P45L		nonsyn	27526	27527	27528	cCa	cTa	70702	0.013523
All	ORF1ab/nsp8	24	Q24R	Q3966R	nonsyn	12161	12162	12163	cAg	cGg	70177	0.013422
All	ORF8	60	L60F		nonsyn	28071	28072	28073	ttG	ttT	69235	0.013242
All	ORF1ab/nsp3	932	V932A	V1750A	nonsyn	5513	5514	5515	gTg	gCg	68589	0.013118
All	ORF1ab/nsp4	438	L438P	L3201P	nonsyn	9866	9867	9868	cTt	cCt	67797	0.012967
All	ORF1ab/nsp13	260	D260Y	D5584Y	nonsyn	17014	17015	17016	Gat	Tat	66389	0.012698
All	ORF3a	131	W131C		nonsyn	25783	25784	25785	tgG	tgT	64322	0.012302
All	ORF3a	42	P42L		nonsyn	25516	25517	25518	cCt	cTt	64111	0.012262
All	S	13	S13I		nonsyn	21599	21600	21601	aGt	aTt	62027	0.011863
All	S	1264	V1264L		nonsyn	25352	25353	25354	Gtg	Ttg	61539	0.01177
All	ORF1ab/nsp13	296	A296S	A5620S	nonsyn	17122	17123	17124	Gct	Tct	61405	0.011744
All	S	152	W152C		nonsyn	22016	22017	22018	tgG	tgT	60968	0.011661
All	ORF1ab/nsp14A2-B	46	P46L	P5971L	nonsyn	18175	18176	18177	cCt	cTt	60648	0.0116
All	S	1214	W1214G		nonsyn	25202	25203	25204	Tgg	Ggg	60474	0.011566
All	ORF1ab/nsp16	238	Q238H	Q7036H	nonsyn	21370	21371	21372	caG	caT	59532	0.011386
All	N	327	S327L		nonsyn	29252	29253	29254	tCg	tTg	59444	0.011369
All	ORF3a	171	S171L		nonsyn	25903	25904	25905	tCa	tTa	59122	0.011308
All	ORF8	11	T11I		nonsyn	27924	27925	27926	aCa	aTa	58427	0.011175
All	ORF7a	71	V71I		nonsyn	27604	27605	27606	Gta	Ata	55662	0.010646
All	S	145	Y145H		nonsyn	21995	21996	21997	Tac	Cac	54591	0.010441
All	ORF1ab/nsp2	339	G339S	G519S	nonsyn	1820	1821	1822	Ggt	Agt	53617	0.010255
All	ORF1ab/nsp3	1788	M1788I	M2606I	nonsyn	8081	8082	8083	atG	atA	52693	0.010078

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.