mutation	lineage	mutation_count	lineage_count	gene	ref_aa	alt_aa	codon_num	codon_end	type	prevalence	grouping_lineage	count_lineages	count_groupinglineages	unique_to_groupinglineage	unique_to_lineage
S:D614G	B.1.1.7	979861	987142	S	D	G	614	None	substitution	0.992624161	B.1.1.7	115	75	FALSE	FALSE
S:D1118H	B.1.1.7	978489	987142	S	D	H	1118	None	substitution	0.991234291	B.1.1.7	1	1	TRUE	TRUE
ORF1A:T1001I	B.1.1.7	978354	987142	ORF1a	T	I	1001	None	substitution	0.991097532	B.1.1.7	1	1	TRUE	TRUE
S:A570D	B.1.1.7	977290	987142	S	A	D	570	None	substitution	0.990019673	B.1.1.7	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.7	975836	987142	ORF1b	P	L	314	None	substitution	0.988546734	B.1.1.7	113	73	FALSE	FALSE
ORF1A:A1708D	B.1.1.7	975386	987142	ORF1a	A	D	1708	None	substitution	0.988090872	B.1.1.7	1	1	TRUE	TRUE
ORF8:Y73C	B.1.1.7	973014	987142	ORF8	Y	C	73	None	substitution	0.985687976	B.1.1.7	1	1	TRUE	TRUE
S:S982A	B.1.1.7	972539	987142	S	S	A	982	None	substitution	0.985206789	B.1.1.7	1	1	TRUE	TRUE
S:T716I	B.1.1.7	971993	987142	S	T	I	716	None	substitution	0.984653677	B.1.1.7	3	3	FALSE	FALSE
ORF8:Q27*	B.1.1.7	971988	987142	ORF8	Q	*	27	None	substitution	0.984648612	B.1.1.7	1	1	TRUE	TRUE
N:S235F	B.1.1.7	971463	987142	N	S	F	235	None	substitution	0.984116773	B.1.1.7	1	1	TRUE	TRUE
S:P681H	B.1.1.7	970386	987142	S	P	H	681	None	substitution	0.983025745	B.1.1.7	6	6	FALSE	FALSE
ORF8:R52I	B.1.1.7	969092	987142	ORF8	R	I	52	None	substitution	0.98171489	B.1.1.7	1	1	TRUE	TRUE
N:R203K	B.1.1.7	964080	987142	N	R	K	203	None	substitution	0.976637606	B.1.1.7	44	39	FALSE	FALSE
N:D3L	B.1.1.7	964077	987142	N	D	L	3	None	substitution	0.976634567	B.1.1.7	1	1	TRUE	TRUE
S:N501Y	B.1.1.7	962783	987142	S	N	Y	501	None	substitution	0.975323712	B.1.1.7	6	4	FALSE	FALSE
ORF1A:I2230T	B.1.1.7	960463	987142	ORF1a	I	T	2230	None	substitution	0.972973493	B.1.1.7	1	1	TRUE	TRUE
S:DEL69/70	B.1.1.7	957230	987142	S	S:DEL69/70	DEL69/70	69	70	deletion	0.969698382	B.1.1.7	6	4	FALSE	FALSE
ORF1A:DEL3675/3677	B.1.1.7	955167	987142	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.96760851	B.1.1.7	8	6	FALSE	FALSE
S:DEL144/145	B.1.1.7	936958	987142	S	S:DEL144/145	DEL144/145	144	145	deletion	0.949162329	B.1.1.7	3	3	FALSE	FALSE
N:G204R	B.1.1.7	889925	987142	N	G	R	204	None	substitution	0.901516702	B.1.1.7	44	39	FALSE	FALSE
S:D614G	B.1.351	27398	28053	S	D	G	614	None	substitution	0.976651339	B.1.351	115	75	FALSE	FALSE
ORF1A:T265I	B.1.351	27237	28053	ORF1a	T	I	265	None	substitution	0.970912202	B.1.351	8	7	FALSE	FALSE
ORF1A:K3353R	B.1.351	27064	28053	ORF1a	K	R	3353	None	substitution	0.964745304	B.1.351	4	3	FALSE	FALSE
S:D80A	B.1.351	26942	28053	S	D	A	80	None	substitution	0.960396393	B.1.351	2	1	TRUE	FALSE
E:P71L	B.1.351	26754	28053	E	P	L	71	None	substitution	0.953694792	B.1.351	2	1	TRUE	FALSE
ORF3A:Q57H	B.1.351	26574	28053	ORF3a	Q	H	57	None	substitution	0.947278366	B.1.351	21	12	FALSE	FALSE
N:T205I	B.1.351	26532	28053	N	T	I	205	None	substitution	0.9457812	B.1.351	7	6	FALSE	FALSE
S:A701V	B.1.351	26493	28053	S	A	V	701	None	substitution	0.944390974	B.1.351	2	1	TRUE	FALSE
S:D215G	B.1.351	25821	28053	S	D	G	215	None	substitution	0.920436317	B.1.351	2	1	TRUE	FALSE
S:K417N	B.1.351	25394	28053	S	K	N	417	None	substitution	0.905215129	B.1.351	2	1	TRUE	FALSE
ORF1A:DEL3675/3677	B.1.351	25372	28053	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.904430899	B.1.351	8	6	FALSE	FALSE
ORF1A:K1655N	B.1.351	25261	28053	ORF1a	K	N	1655	None	substitution	0.900474103	B.1.351	2	1	TRUE	FALSE
ORF1B:P314L	B.1.351	25244	28053	ORF1b	P	L	314	None	substitution	0.899868107	B.1.351	113	73	FALSE	FALSE
ORF3A:S171L	B.1.351	24670	28053	ORF3a	S	L	171	None	substitution	0.879406837	B.1.351	3	2	FALSE	FALSE
S:N501Y	B.1.351	24289	28053	S	N	Y	501	None	substitution	0.865825402	B.1.351	6	4	FALSE	FALSE
S:E484K	B.1.351	24044	28053	S	E	K	484	None	substitution	0.857091933	B.1.351	9	6	FALSE	FALSE
ORF1A:K1795Q	P.1	50867	51330	ORF1a	K	Q	1795	None	substitution	0.990979934	P	2	1	TRUE	FALSE
S:D614G	P.1	50856	51330	S	D	G	614	None	substitution	0.990765634	P	115	75	FALSE	FALSE
S:V1176F	P.1	50786	51330	S	V	F	1176	None	substitution	0.989401909	P	3	2	FALSE	FALSE
ORF1B:P314L	P.1	50759	51330	ORF1b	P	L	314	None	substitution	0.988875901	P	113	73	FALSE	FALSE
N:P80R	P.1	50710	51330	N	P	R	80	None	substitution	0.987921294	P	2	1	TRUE	FALSE
ORF1B:E1264D	P.1	50705	51330	ORF1b	E	D	1264	None	substitution	0.987823885	P	2	1	TRUE	FALSE
ORF3A:S253P	P.1	50659	51330	ORF3a	S	P	253	None	substitution	0.986927723	P	2	1	TRUE	FALSE
S:H655Y	P.1	50471	51330	S	H	Y	655	None	substitution	0.983265147	P	4	2	FALSE	FALSE
ORF1A:S1188L	P.1	50450	51330	ORF1a	S	L	1188	None	substitution	0.98285603	P	2	1	TRUE	FALSE
ORF8:E92K	P.1	50368	51330	ORF8	E	K	92	None	substitution	0.981258523	P	2	1	TRUE	FALSE
S:L18F	P.1	50206	51330	S	L	F	18	None	substitution	0.978102474	P	6	5	FALSE	FALSE
S:P26S	P.1	50184	51330	S	P	S	26	None	substitution	0.977673875	P	2	1	TRUE	FALSE
S:T20N	P.1	50032	51330	S	T	N	20	None	substitution	0.974712644	P	2	1	TRUE	FALSE
N:G204R	P.1	49623	51330	N	G	R	204	None	substitution	0.966744594	P	44	39	FALSE	FALSE
ORF1A:DEL3675/3677	P.1	49607	51330	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.966432885	P	8	6	FALSE	FALSE
N:R203K	P.1	49553	51330	N	R	K	203	None	substitution	0.965380869	P	44	39	FALSE	FALSE
S:N501Y	P.1	49412	51330	S	N	Y	501	None	substitution	0.962633937	P	6	4	FALSE	FALSE
S:D138Y	P.1	49366	51330	S	D	Y	138	None	substitution	0.961737775	P	3	2	FALSE	FALSE
S:T1027I	P.1	49344	51330	S	T	I	1027	None	substitution	0.961309176	P	3	2	FALSE	FALSE
S:E484K	P.1	49277	51330	S	E	K	484	None	substitution	0.960003896	P	9	6	FALSE	FALSE
S:K417T	P.1	48747	51330	S	K	T	417	None	substitution	0.949678551	P	2	1	TRUE	FALSE
S:R190S	P.1	47459	51330	S	R	S	190	None	substitution	0.924586012	P	2	1	TRUE	FALSE
S:D614G	B.1.525	7102	7184	S	D	G	614	None	substitution	0.988585746	B.1.525	115	75	FALSE	FALSE
M:I82T	B.1.525	7075	7184	M	I	T	82	None	substitution	0.984827394	B.1.525	6	6	FALSE	FALSE
ORF1B:P314F	B.1.525	7057	7184	ORF1b	P	F	314	None	substitution	0.982321826	B.1.525	1	1	TRUE	TRUE
ORF1A:T2007I	B.1.525	7023	7184	ORF1a	T	I	2007	None	substitution	0.977589087	B.1.525	1	1	TRUE	TRUE
S:Q677H	B.1.525	7023	7184	S	Q	H	677	None	substitution	0.977589087	B.1.525	3	2	FALSE	FALSE
S:E484K	B.1.525	6977	7184	S	E	K	484	None	substitution	0.971185969	B.1.525	9	6	FALSE	FALSE
S:F888L	B.1.525	6958	7184	S	F	L	888	None	substitution	0.968541203	B.1.525	1	1	TRUE	TRUE
ORF6:DEL2/3	B.1.525	6889	7184	ORF6	ORF6:DEL2/3	DEL2/3	2	3	deletion	0.958936526	B.1.525	1	1	TRUE	TRUE
ORF1A:DEL3675/3677	B.1.525	6871	7184	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.956430958	B.1.525	8	6	FALSE	FALSE
S:A67V	B.1.525	6860	7184	S	A	V	67	None	substitution	0.954899777	B.1.525	1	1	TRUE	TRUE
S:DEL69/70	B.1.525	6726	7184	S	S:DEL69/70	DEL69/70	69	70	deletion	0.936247216	B.1.525	6	4	FALSE	FALSE
S:DEL144/145	B.1.525	6649	7184	S	S:DEL144/145	DEL144/145	144	145	deletion	0.925528953	B.1.525	3	3	FALSE	FALSE
N:A12G	B.1.525	6620	7184	N	A	G	12	None	substitution	0.921492205	B.1.525	1	1	TRUE	TRUE
N:DEL3	B.1.525	6569	7184	N	N:DEL3	DEL3	3	None	deletion	0.914393096	B.1.525	1	1	TRUE	TRUE
N:T205I	B.1.525	6565	7184	N	T	I	205	None	substitution	0.913836303	B.1.525	7	6	FALSE	FALSE
S:Q52R	B.1.525	6094	7184	S	Q	R	52	None	substitution	0.848273942	B.1.525	1	1	TRUE	TRUE
E:L21F	B.1.525	6046	7184	E	L	F	21	None	substitution	0.841592428	B.1.525	1	1	TRUE	TRUE
ORF1A:DEL3675/3677	B.1.619	1696	1702	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.996474736	B.1.619	8	6	FALSE	FALSE
ORF1B:P314L	B.1.619	1678	1702	ORF1b	P	L	314	None	substitution	0.985898942	B.1.619	113	73	FALSE	FALSE
S:D614G	B.1.619	1678	1702	S	D	G	614	None	substitution	0.985898942	B.1.619	115	75	FALSE	FALSE
S:E484K	B.1.619	1487	1702	S	E	K	484	None	substitution	0.873678026	B.1.619	9	6	FALSE	FALSE
N:P13L	B.1.619	1485	1702	N	P	L	13	None	substitution	0.872502938	B.1.619	1	1	TRUE	TRUE
ORF1A:A2123V	B.1.619	1482	1702	ORF1a	A	V	2123	None	substitution	0.870740306	B.1.619	1	1	TRUE	TRUE
M:I82T	B.1.619	1481	1702	M	I	T	82	None	substitution	0.870152761	B.1.619	6	6	FALSE	FALSE
S:I210T	B.1.619	1478	1702	S	I	T	210	None	substitution	0.868390129	B.1.619	1	1	TRUE	TRUE
S:D936N	B.1.619	1477	1702	S	D	N	936	None	substitution	0.867802585	B.1.619	1	1	TRUE	TRUE
S:S939F	B.1.619	1475	1702	S	S	F	939	None	substitution	0.866627497	B.1.619	1	1	TRUE	TRUE
S:T1027I	B.1.619	1474	1702	S	T	I	1027	None	substitution	0.866039953	B.1.619	3	2	FALSE	FALSE
N:S201I	B.1.619	1470	1702	N	S	I	201	None	substitution	0.863689777	B.1.619	1	1	TRUE	TRUE
N:T205I	B.1.619	1470	1702	N	T	I	205	None	substitution	0.863689777	B.1.619	7	6	FALSE	FALSE
ORF1A:E2607K	B.1.619	1469	1702	ORF1a	E	K	2607	None	substitution	0.863102233	B.1.619	1	1	TRUE	TRUE
ORF1A:M3752I	B.1.619	1458	1702	ORF1a	M	I	3752	None	substitution	0.856639248	B.1.619	1	1	TRUE	TRUE
ORF7A:E22D	B.1.619	1418	1702	ORF7a	E	D	22	None	substitution	0.833137485	B.1.619	1	1	TRUE	TRUE
S:D614G	B.1.617.1	5829	5913	S	D	G	614	None	substitution	0.985794013	B.1.617	115	75	FALSE	FALSE
ORF1B:P314L	B.1.617.1	5784	5913	ORF1b	P	L	314	None	substitution	0.978183663	B.1.617	113	73	FALSE	FALSE
S:P681R	B.1.617.1	5717	5913	S	P	R	681	None	substitution	0.966852697	B.1.617	2	1	TRUE	FALSE
ORF3A:S26L	B.1.617.1	5675	5913	ORF3a	S	L	26	None	substitution	0.959749704	B.1.617	2	1	TRUE	FALSE
ORF1B:M1352I	B.1.617.1	5612	5913	ORF1b	M	I	1352	None	substitution	0.949095214	B.1.617	1	1	TRUE	TRUE
ORF1A:T3646A	B.1.617.1	5604	5913	ORF1a	T	A	3646	None	substitution	0.947742263	B.1.617	1	1	TRUE	TRUE
S:L452R	B.1.617.1	5589	5913	S	L	R	452	None	substitution	0.945205479	B.1.617	7	4	FALSE	FALSE
N:R203M	B.1.617.1	5550	5913	N	R	M	203	None	substitution	0.938609843	B.1.617	2	1	TRUE	FALSE
ORF1A:T1567I	B.1.617.1	5506	5913	ORF1a	T	I	1567	None	substitution	0.931168612	B.1.617	1	1	TRUE	TRUE
S:E484Q	B.1.617.1	5464	5913	S	E	Q	484	None	substitution	0.924065618	B.1.617	1	1	TRUE	TRUE
ORF1B:K2310R	B.1.617.1	5418	5913	ORF1b	K	R	2310	None	substitution	0.916286149	B.1.617	1	1	TRUE	TRUE
N:D377Y	B.1.617.1	5284	5913	N	D	Y	377	None	substitution	0.893624218	B.1.617	2	1	TRUE	FALSE
ORF7A:V82A	B.1.617.1	5098	5913	ORF7a	V	A	82	None	substitution	0.862168104	B.1.617	2	1	TRUE	FALSE
N:G204R	B.1.1.420	876	878	N	G	R	204	None	substitution	0.997722096	B.1.1.420	44	39	FALSE	FALSE
N:R203K	B.1.1.420	875	878	N	R	K	203	None	substitution	0.996583144	B.1.1.420	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.420	875	878	ORF1b	P	L	314	None	substitution	0.996583144	B.1.1.420	113	73	FALSE	FALSE
S:D614G	B.1.1.420	874	878	S	D	G	614	None	substitution	0.995444191	B.1.1.420	115	75	FALSE	FALSE
ORF1A:Q3729R	B.1.1.420	873	878	ORF1a	Q	R	3729	None	substitution	0.994305239	B.1.1.420	1	1	TRUE	TRUE
N:P13S	B.1.1.420	871	878	N	P	S	13	None	substitution	0.992027335	B.1.1.420	1	1	TRUE	TRUE
N:S197T	B.1.1.420	868	878	N	S	T	197	None	substitution	0.988610478	B.1.1.420	1	1	TRUE	TRUE
ORF1B:T76I	B.1.1.420	860	878	ORF1b	T	I	76	None	substitution	0.979498861	B.1.1.420	1	1	TRUE	TRUE
ORF3A:W149C	B.1.1.420	855	878	ORF3a	W	C	149	None	substitution	0.9738041	B.1.1.420	1	1	TRUE	TRUE
ORF1A:T1638I	B.1.1.420	854	878	ORF1a	T	I	1638	None	substitution	0.972665148	B.1.1.420	1	1	TRUE	TRUE
S:L18F	B.1.1.420	844	878	S	L	F	18	None	substitution	0.961275626	B.1.1.420	6	5	FALSE	FALSE
S:D614G	B.1.177.81	4356	4369	S	D	G	614	None	substitution	0.997024491	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177.81	4352	4369	ORF1b	P	L	314	None	substitution	0.996108949	B.1.177	113	73	FALSE	FALSE
ORF3A:S166L	B.1.177.81	4352	4369	ORF3a	S	L	166	None	substitution	0.996108949	B.1.177	1	1	TRUE	TRUE
N:A220V	B.1.177.81	4328	4369	N	A	V	220	None	substitution	0.990615702	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.81	4306	4369	S	A	V	222	None	substitution	0.985580224	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.81	4291	4369	ORF10	V	L	30	None	substitution	0.982146944	B.1.177	20	3	FALSE	FALSE
ORF1A:P3952S	B.1.177.81	4158	4369	ORF1a	P	S	3952	None	substitution	0.951705196	B.1.177	1	1	TRUE	TRUE
S:D614G	B.1	81721	84098	S	D	G	614	None	substitution	0.971735356	B.1	115	75	FALSE	FALSE
ORF1B:P314L	B.1	81010	84098	ORF1b	P	L	314	None	substitution	0.963280934	B.1	113	73	FALSE	FALSE
ORF1B:P314L	B.1.94	35	35	ORF1b	P	L	314	None	substitution	1	B.1.94	113	73	FALSE	FALSE
S:D614G	B.1.94	35	35	S	D	G	614	None	substitution	1	B.1.94	115	75	FALSE	FALSE
ORF1A:Y118C	B.1.211	39	39	ORF1a	Y	C	118	None	substitution	1	B.1.211	1	1	TRUE	TRUE
ORF1B:P314L	B.1.211	39	39	ORF1b	P	L	314	None	substitution	1	B.1.211	113	73	FALSE	FALSE
S:D614G	B.1.211	39	39	S	D	G	614	None	substitution	1	B.1.211	115	75	FALSE	FALSE
ORF1A:A1352V	B.1.12	121	121	ORF1a	A	V	1352	None	substitution	1	B.1.12	1	1	TRUE	TRUE
ORF1A:T265I	B.1.12	121	121	ORF1a	T	I	265	None	substitution	1	B.1.12	8	7	FALSE	FALSE
ORF1B:P314L	B.1.12	121	121	ORF1b	P	L	314	None	substitution	1	B.1.12	113	73	FALSE	FALSE
S:D614G	B.1.12	121	121	S	D	G	614	None	substitution	1	B.1.12	115	75	FALSE	FALSE
ORF3A:Q57H	B.1.12	120	121	ORF3a	Q	H	57	None	substitution	0.991735537	B.1.12	21	12	FALSE	FALSE
ORF3A:A99V	B.1.12	105	121	ORF3a	A	V	99	None	substitution	0.867768595	B.1.12	2	2	FALSE	FALSE
ORF1B:P314L	B.1.93	1050	1050	ORF1b	P	L	314	None	substitution	1	B.1.93	113	73	FALSE	FALSE
S:D614G	B.1.93	1048	1050	S	D	G	614	None	substitution	0.998095238	B.1.93	115	75	FALSE	FALSE
N:S188L	B.1.93	1044	1050	N	S	L	188	None	substitution	0.994285714	B.1.93	1	1	TRUE	TRUE
ORF1B:T132I	B.1.93	1041	1050	ORF1b	T	I	132	None	substitution	0.991428571	B.1.93	1	1	TRUE	TRUE
S:D614G	B.1.1	46825	47591	S	D	G	614	None	substitution	0.98390452	B.1.1	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1	46358	47591	ORF1b	P	L	314	None	substitution	0.97409174	B.1.1	113	73	FALSE	FALSE
N:R203K	B.1.1	45896	47591	N	R	K	203	None	substitution	0.964384022	B.1.1	44	39	FALSE	FALSE
N:G204R	B.1.1	45139	47591	N	G	R	204	None	substitution	0.948477653	B.1.1	44	39	FALSE	FALSE
ORF1B:P314L	C.35	1192	1194	ORF1b	P	L	314	None	substitution	0.998324958	C	113	73	FALSE	FALSE
S:D614G	C.35	1191	1194	S	D	G	614	None	substitution	0.997487437	C	115	75	FALSE	FALSE
ORF1B:V2089F	C.35	1186	1194	ORF1b	V	F	2089	None	substitution	0.993299832	C	1	1	TRUE	TRUE
N:R203K	C.35	1177	1194	N	R	K	203	None	substitution	0.985762144	C	44	39	FALSE	FALSE
ORF1A:T1246I	C.35	1177	1194	ORF1a	T	I	1246	None	substitution	0.985762144	C	6	2	FALSE	FALSE
N:G204R	C.35	1170	1194	N	G	R	204	None	substitution	0.979899497	C	44	39	FALSE	FALSE
ORF1A:G3278S	C.35	1075	1194	ORF1a	G	S	3278	None	substitution	0.900335008	C	5	2	FALSE	FALSE
ORF1A:K1895N	C.35	1020	1194	ORF1a	K	N	1895	None	substitution	0.854271357	C	1	1	TRUE	TRUE
S:D614G	B.1.177	71965	72482	S	D	G	614	None	substitution	0.992867195	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177	71879	72482	ORF1b	P	L	314	None	substitution	0.991680693	B.1.177	113	73	FALSE	FALSE
N:A220V	B.1.177	70617	72482	N	A	V	220	None	substitution	0.974269474	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177	70599	72482	S	A	V	222	None	substitution	0.974021136	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177	69728	72482	ORF10	V	L	30	None	substitution	0.96200436	B.1.177	20	3	FALSE	FALSE
ORF1B:P314L	B.1.177.32	714	714	ORF1b	P	L	314	None	substitution	1	B.1.177	113	73	FALSE	FALSE
S:D614G	B.1.177.32	714	714	S	D	G	614	None	substitution	1	B.1.177	115	75	FALSE	FALSE
ORF1A:A1812V	B.1.177.32	712	714	ORF1a	A	V	1812	None	substitution	0.99719888	B.1.177	1	1	TRUE	TRUE
N:A220V	B.1.177.32	711	714	N	A	V	220	None	substitution	0.995798319	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.32	707	714	ORF10	V	L	30	None	substitution	0.990196078	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.32	704	714	S	A	V	222	None	substitution	0.985994398	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.160	25643	25910	S	D	G	614	None	substitution	0.989695098	B.1.160	115	75	FALSE	FALSE
ORF1B:P314L	B.1.160	25597	25910	ORF1b	P	L	314	None	substitution	0.987919722	B.1.160	113	73	FALSE	FALSE
ORF1B:V767L	B.1.160	24908	25910	ORF1b	V	L	767	None	substitution	0.961327673	B.1.160	7	1	TRUE	FALSE
ORF3A:Q57H	B.1.160	24898	25910	ORF3a	Q	H	57	None	substitution	0.960941721	B.1.160	21	12	FALSE	FALSE
ORF1B:A176S	B.1.160	24880	25910	ORF1b	A	S	176	None	substitution	0.960247009	B.1.160	7	1	TRUE	FALSE
ORF1A:M3087I	B.1.160	24822	25910	ORF1a	M	I	3087	None	substitution	0.958008491	B.1.160	7	1	TRUE	FALSE
ORF1B:K1141R	B.1.160	24799	25910	ORF1b	K	R	1141	None	substitution	0.957120803	B.1.160	7	1	TRUE	FALSE
ORF1B:E1184D	B.1.160	24798	25910	ORF1b	E	D	1184	None	substitution	0.957082208	B.1.160	7	1	TRUE	FALSE
N:M234I	B.1.160	24619	25910	N	M	I	234	None	substitution	0.950173678	B.1.160	10	4	FALSE	FALSE
S:S477N	B.1.160	24575	25910	S	S	N	477	None	substitution	0.948475492	B.1.160	7	1	TRUE	FALSE
N:A376T	B.1.160	24260	25910	N	A	T	376	None	substitution	0.936318024	B.1.160	7	1	TRUE	FALSE
ORF1B:P314L	B.1.221	13203	13261	ORF1b	P	L	314	None	substitution	0.995626273	B.1.221	113	73	FALSE	FALSE
S:D614G	B.1.221	13191	13261	S	D	G	614	None	substitution	0.994721363	B.1.221	115	75	FALSE	FALSE
ORF3A:Q38R	B.1.221	12934	13261	ORF3a	Q	R	38	None	substitution	0.975341226	B.1.221	4	1	TRUE	FALSE
S:S98F	B.1.221	12877	13261	S	S	F	98	None	substitution	0.971042908	B.1.221	4	1	TRUE	FALSE
N:P199L	B.1.221	12849	13261	N	P	L	199	None	substitution	0.968931453	B.1.221	5	2	FALSE	FALSE
ORF3A:V202L	B.1.221	12814	13261	ORF3a	V	L	202	None	substitution	0.966292135	B.1.221	4	1	TRUE	FALSE
ORF1A:H1113Y	B.1.221	12225	13261	ORF1a	H	Y	1113	None	substitution	0.921876178	B.1.221	4	1	TRUE	FALSE
ORF3A:G172R	B.1.221	12171	13261	ORF3a	G	R	172	None	substitution	0.917804087	B.1.221	3	1	TRUE	FALSE
N:G204R	B.1.1.297	397	397	N	G	R	204	None	substitution	1	B.1.1.297	44	39	FALSE	FALSE
N:R203K	B.1.1.297	397	397	N	R	K	203	None	substitution	1	B.1.1.297	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.297	397	397	ORF1b	P	L	314	None	substitution	1	B.1.1.297	113	73	FALSE	FALSE
ORF1B:Q2425H	B.1.1.297	397	397	ORF1b	Q	H	2425	None	substitution	1	B.1.1.297	1	1	TRUE	TRUE
S:D614G	B.1.1.297	397	397	S	D	G	614	None	substitution	1	B.1.1.297	115	75	FALSE	FALSE
ORF8:I10T	B.1.1.297	396	397	ORF8	I	T	10	None	substitution	0.997481108	B.1.1.297	1	1	TRUE	TRUE
ORF1B:P314L	B.1.236	805	810	ORF1b	P	L	314	None	substitution	0.99382716	B.1.236	113	73	FALSE	FALSE
S:D614G	B.1.236	805	810	S	D	G	614	None	substitution	0.99382716	B.1.236	115	75	FALSE	FALSE
N:S194L	B.1.236	777	810	N	S	L	194	None	substitution	0.959259259	B.1.236	5	3	FALSE	FALSE
ORF3A:Q57H	B.1.160.28	326	330	ORF3a	Q	H	57	None	substitution	0.987878788	B.1.160	21	12	FALSE	FALSE
S:D614G	B.1.160.28	326	330	S	D	G	614	None	substitution	0.987878788	B.1.160	115	75	FALSE	FALSE
N:M234I	B.1.160.28	325	330	N	M	I	234	None	substitution	0.984848485	B.1.160	10	4	FALSE	FALSE
ORF1B:E1184D	B.1.160.28	325	330	ORF1b	E	D	1184	None	substitution	0.984848485	B.1.160	7	1	TRUE	FALSE
ORF1B:K1141R	B.1.160.28	325	330	ORF1b	K	R	1141	None	substitution	0.984848485	B.1.160	7	1	TRUE	FALSE
ORF1B:P314L	B.1.160.28	325	330	ORF1b	P	L	314	None	substitution	0.984848485	B.1.160	113	73	FALSE	FALSE
ORF1B:V767L	B.1.160.28	324	330	ORF1b	V	L	767	None	substitution	0.981818182	B.1.160	7	1	TRUE	FALSE
S:S477N	B.1.160.28	324	330	S	S	N	477	None	substitution	0.981818182	B.1.160	7	1	TRUE	FALSE
N:A376T	B.1.160.28	323	330	N	A	T	376	None	substitution	0.978787879	B.1.160	7	1	TRUE	FALSE
ORF1A:M3087I	B.1.160.28	322	330	ORF1a	M	I	3087	None	substitution	0.975757576	B.1.160	7	1	TRUE	FALSE
N:G25C	B.1.160.28	319	330	N	G	C	25	None	substitution	0.966666667	B.1.160	1	1	TRUE	TRUE
ORF1B:A176S	B.1.160.28	313	330	ORF1b	A	S	176	None	substitution	0.948484848	B.1.160	7	1	TRUE	FALSE
S:D614G	B.1.177.77	1331	1333	S	D	G	614	None	substitution	0.998499625	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177.77	1329	1333	ORF1b	P	L	314	None	substitution	0.99699925	B.1.177	113	73	FALSE	FALSE
N:A220V	B.1.177.77	1326	1333	N	A	V	220	None	substitution	0.994748687	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.77	1315	1333	S	A	V	222	None	substitution	0.986496624	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.77	1277	1333	ORF10	V	L	30	None	substitution	0.957989497	B.1.177	20	3	FALSE	FALSE
ORF1B:T17I	B.1.177.77	1275	1333	ORF1b	T	I	17	None	substitution	0.956489122	B.1.177	1	1	TRUE	TRUE
ORF1B:P314L	B.1.258	13791	13904	ORF1b	P	L	314	None	substitution	0.991872842	B.1.258	113	73	FALSE	FALSE
S:D614G	B.1.258	13741	13904	S	D	G	614	None	substitution	0.988276755	B.1.258	115	75	FALSE	FALSE
ORF1B:H1213Y	B.1.258	13659	13904	ORF1b	H	Y	1213	None	substitution	0.982379171	B.1.258	4	1	TRUE	FALSE
ORF1A:I2501T	B.1.258	13464	13904	ORF1a	I	T	2501	None	substitution	0.96835443	B.1.258	4	1	TRUE	FALSE
S:N439K	B.1.258	13325	13904	S	N	K	439	None	substitution	0.958357307	B.1.258	4	1	TRUE	FALSE
S:D614G	B.1.1.198	656	656	S	D	G	614	None	substitution	1	B.1.1.198	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.198	651	656	ORF1b	P	L	314	None	substitution	0.992378049	B.1.1.198	113	73	FALSE	FALSE
ORF1A:T999I	B.1.1.198	650	656	ORF1a	T	I	999	None	substitution	0.990853659	B.1.1.198	1	1	TRUE	TRUE
N:G204R	B.1.1.198	649	656	N	G	R	204	None	substitution	0.989329268	B.1.1.198	44	39	FALSE	FALSE
N:R203K	B.1.1.198	649	656	N	R	K	203	None	substitution	0.989329268	B.1.1.198	44	39	FALSE	FALSE
S:D614G	B.1.177.44	1770	1793	S	D	G	614	None	substitution	0.987172337	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177.44	1768	1793	ORF1b	P	L	314	None	substitution	0.986056888	B.1.177	113	73	FALSE	FALSE
N:A220V	B.1.177.44	1629	1793	N	A	V	220	None	substitution	0.908533185	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.44	1620	1793	S	A	V	222	None	substitution	0.903513664	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.44	1581	1793	ORF10	V	L	30	None	substitution	0.881762409	B.1.177	20	3	FALSE	FALSE
ORF1B:M2667I	B.1.177.44	1516	1793	ORF1b	M	I	2667	None	substitution	0.845510318	B.1.177	1	1	TRUE	TRUE
N:A220V	B.1.177.72	278	279	N	A	V	220	None	substitution	0.996415771	B.1.177	20	3	FALSE	FALSE
ORF1B:L820F	B.1.177.72	278	279	ORF1b	L	F	820	None	substitution	0.996415771	B.1.177	1	1	TRUE	TRUE
ORF1B:P314L	B.1.177.72	278	279	ORF1b	P	L	314	None	substitution	0.996415771	B.1.177	113	73	FALSE	FALSE
S:A222V	B.1.177.72	277	279	S	A	V	222	None	substitution	0.992831541	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.177.72	277	279	S	D	G	614	None	substitution	0.992831541	B.1.177	115	75	FALSE	FALSE
ORF10:V30L	B.1.177.72	275	279	ORF10	V	L	30	None	substitution	0.985663082	B.1.177	20	3	FALSE	FALSE
M:H125Y	B.1.177.72	256	279	M	H	Y	125	None	substitution	0.917562724	B.1.177	2	2	FALSE	FALSE
ORF1B:P314L	B.1.221.4	216	216	ORF1b	P	L	314	None	substitution	1	B.1.221	113	73	FALSE	FALSE
ORF3A:Q38R	B.1.221.4	216	216	ORF3a	Q	R	38	None	substitution	1	B.1.221	4	1	TRUE	FALSE
ORF3A:G172R	B.1.221.4	215	216	ORF3a	G	R	172	None	substitution	0.99537037	B.1.221	3	1	TRUE	FALSE
ORF3A:V202L	B.1.221.4	215	216	ORF3a	V	L	202	None	substitution	0.99537037	B.1.221	4	1	TRUE	FALSE
S:S98F	B.1.221.4	215	216	S	S	F	98	None	substitution	0.99537037	B.1.221	4	1	TRUE	FALSE
ORF1A:H1113Y	B.1.221.4	214	216	ORF1a	H	Y	1113	None	substitution	0.990740741	B.1.221	4	1	TRUE	FALSE
S:D614G	B.1.221.4	214	216	S	D	G	614	None	substitution	0.990740741	B.1.221	115	75	FALSE	FALSE
N:P199L	B.1.221.4	213	216	N	P	L	199	None	substitution	0.986111111	B.1.221	5	2	FALSE	FALSE
N:Q9H	B.1.221.4	212	216	N	Q	H	9	None	substitution	0.981481481	B.1.221	1	1	TRUE	TRUE
N:S193I	B.1.221.4	212	216	N	S	I	193	None	substitution	0.981481481	B.1.221	1	1	TRUE	TRUE
ORF1B:G2610C	B.1.221.4	210	216	ORF1b	G	C	2610	None	substitution	0.972222222	B.1.221	1	1	TRUE	TRUE
ORF1A:H1160Y	B.1.221.4	186	216	ORF1a	H	Y	1160	None	substitution	0.861111111	B.1.221	1	1	TRUE	TRUE
ORF1B:P314L	B.1.213	62	62	ORF1b	P	L	314	None	substitution	1	B.1.213	113	73	FALSE	FALSE
S:D614G	B.1.213	62	62	S	D	G	614	None	substitution	1	B.1.213	115	75	FALSE	FALSE
ORF1A:N2256D	B.1.213	55	62	ORF1a	N	D	2256	None	substitution	0.887096774	B.1.213	1	1	TRUE	TRUE
ORF1B:K50N	B.1.213	51	62	ORF1b	K	N	50	None	substitution	0.822580645	B.1.213	1	1	TRUE	TRUE
ORF1A:I2501T	B.1.258.20	59	59	ORF1a	I	T	2501	None	substitution	1	B.1.258	4	1	TRUE	FALSE
ORF1A:M4241I	B.1.258.20	59	59	ORF1a	M	I	4241	None	substitution	1	B.1.258	3	1	TRUE	FALSE
ORF1B:A1521S	B.1.258.20	59	59	ORF1b	A	S	1521	None	substitution	1	B.1.258	3	1	TRUE	FALSE
ORF1B:H1213Y	B.1.258.20	59	59	ORF1b	H	Y	1213	None	substitution	1	B.1.258	4	1	TRUE	FALSE
ORF1B:P314L	B.1.258.20	59	59	ORF1b	P	L	314	None	substitution	1	B.1.258	113	73	FALSE	FALSE
ORF1B:V711I	B.1.258.20	59	59	ORF1b	V	I	711	None	substitution	1	B.1.258	3	1	TRUE	FALSE
S:D614G	B.1.258.20	59	59	S	D	G	614	None	substitution	1	B.1.258	115	75	FALSE	FALSE
S:N439K	B.1.258.20	59	59	S	N	K	439	None	substitution	1	B.1.258	4	1	TRUE	FALSE
ORF3A:G172D	B.1.258.20	57	59	ORF3a	G	D	172	None	substitution	0.966101695	B.1.258	1	1	TRUE	TRUE
ORF3A:K67N	B.1.258.20	57	59	ORF3a	K	N	67	None	substitution	0.966101695	B.1.258	1	1	TRUE	TRUE
S:DEL69/70	B.1.258.20	57	59	S	S:DEL69/70	DEL69/70	69	70	deletion	0.966101695	B.1.258	6	4	FALSE	FALSE
ORF1B:T2432I	B.1.258.20	55	59	ORF1b	T	I	2432	None	substitution	0.93220339	B.1.258	1	1	TRUE	TRUE
ORF1B:P314L	B.1.474	482	482	ORF1b	P	L	314	None	substitution	1	B.1.474	113	73	FALSE	FALSE
S:D614G	B.1.474	482	482	S	D	G	614	None	substitution	1	B.1.474	115	75	FALSE	FALSE
S:P681H	B.1.474	481	482	S	P	H	681	None	substitution	0.997925311	B.1.474	6	6	FALSE	FALSE
ORF1A:L92F	B.1.474	480	482	ORF1a	L	F	92	None	substitution	0.995850622	B.1.474	1	1	TRUE	TRUE
ORF3A:Q57H	B.1.474	480	482	ORF3a	Q	H	57	None	substitution	0.995850622	B.1.474	21	12	FALSE	FALSE
ORF3A:S216P	B.1.474	479	482	ORF3a	S	P	216	None	substitution	0.993775934	B.1.474	1	1	TRUE	TRUE
ORF8:T26N	B.1.474	478	482	ORF8	T	N	26	None	substitution	0.991701245	B.1.474	1	1	TRUE	TRUE
ORF1B:V1149L	B.1.474	477	482	ORF1b	V	L	1149	None	substitution	0.989626556	B.1.474	1	1	TRUE	TRUE
N:T205I	B.1.474	472	482	N	T	I	205	None	substitution	0.979253112	B.1.474	7	6	FALSE	FALSE
S:D796Y	B.1.474	470	482	S	D	Y	796	None	substitution	0.975103734	B.1.474	2	2	FALSE	FALSE
ORF1A:A2785T	B.1.474	453	482	ORF1a	A	T	2785	None	substitution	0.939834025	B.1.474	1	1	TRUE	TRUE
ORF1A:L3606F	B.1.474	418	482	ORF1a	L	F	3606	None	substitution	0.867219917	B.1.474	2	2	FALSE	FALSE
S:D614G	B.1.1.37	5075	5077	S	D	G	614	None	substitution	0.999606067	B.1.1.37	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.37	5041	5077	ORF1b	P	L	314	None	substitution	0.992909198	B.1.1.37	113	73	FALSE	FALSE
N:R203K	B.1.1.37	5039	5077	N	R	K	203	None	substitution	0.992515265	B.1.1.37	44	39	FALSE	FALSE
N:G204R	B.1.1.37	4978	5077	N	G	R	204	None	substitution	0.980500295	B.1.1.37	44	39	FALSE	FALSE
ORF1A:A1082T	B.1.177.85	179	180	ORF1a	A	T	1082	None	substitution	0.994444444	B.1.177	1	1	TRUE	TRUE
ORF1B:P314L	B.1.177.85	179	180	ORF1b	P	L	314	None	substitution	0.994444444	B.1.177	113	73	FALSE	FALSE
S:A222V	B.1.177.85	179	180	S	A	V	222	None	substitution	0.994444444	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.177.85	179	180	S	D	G	614	None	substitution	0.994444444	B.1.177	115	75	FALSE	FALSE
N:A220V	B.1.177.85	178	180	N	A	V	220	None	substitution	0.988888889	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.85	177	180	ORF10	V	L	30	None	substitution	0.983333333	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.1.70	2666	2675	S	D	G	614	None	substitution	0.996635514	B.1.1.70	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.70	2656	2675	ORF1b	P	L	314	None	substitution	0.992897196	B.1.1.70	113	73	FALSE	FALSE
N:G204R	B.1.1.70	2595	2675	N	G	R	204	None	substitution	0.970093458	B.1.1.70	44	39	FALSE	FALSE
N:R203K	B.1.1.70	2594	2675	N	R	K	203	None	substitution	0.969719626	B.1.1.70	44	39	FALSE	FALSE
ORF1B:T2084I	B.1.1.70	2559	2675	ORF1b	T	I	2084	None	substitution	0.956635514	B.1.1.70	2	2	FALSE	FALSE
ORF1A:G3334S	B.1.1.70	2554	2675	ORF1a	G	S	3334	None	substitution	0.954766355	B.1.1.70	1	1	TRUE	TRUE
N:A220V	W.1	101	101	N	A	V	220	None	substitution	1	W	20	3	FALSE	FALSE
ORF1B:P314L	W.1	101	101	ORF1b	P	L	314	None	substitution	1	W	113	73	FALSE	FALSE
S:A222V	W.1	101	101	S	A	V	222	None	substitution	1	W	20	3	FALSE	FALSE
ORF10:V30L	W.1	100	101	ORF10	V	L	30	None	substitution	0.99009901	W	20	3	FALSE	FALSE
ORF3A:W131C	W.1	100	101	ORF3a	W	C	131	None	substitution	0.99009901	W	1	1	TRUE	TRUE
S:D614G	W.1	100	101	S	D	G	614	None	substitution	0.99009901	W	115	75	FALSE	FALSE
ORF1A:A903V	W.1	93	101	ORF1a	A	V	903	None	substitution	0.920792079	W	2	1	TRUE	FALSE
N:R203K	C.5	11	11	N	R	K	203	None	substitution	1	C	44	39	FALSE	FALSE
ORF1A:E910D	C.5	11	11	ORF1a	E	D	910	None	substitution	1	C	1	1	TRUE	TRUE
ORF1A:L2062F	C.5	11	11	ORF1a	L	F	2062	None	substitution	1	C	1	1	TRUE	TRUE
ORF1A:T1246I	C.5	11	11	ORF1a	T	I	1246	None	substitution	1	C	6	2	FALSE	FALSE
ORF1A:Y1536H	C.5	11	11	ORF1a	Y	H	1536	None	substitution	1	C	1	1	TRUE	TRUE
ORF1B:P314L	C.5	11	11	ORF1b	P	L	314	None	substitution	1	C	113	73	FALSE	FALSE
ORF7B:L18P	C.5	11	11	ORF7b	L	P	18	None	substitution	1	C	1	1	TRUE	TRUE
S:D614G	C.5	11	11	S	D	G	614	None	substitution	1	C	115	75	FALSE	FALSE
N:G204R	C.5	10	11	N	G	R	204	None	substitution	0.909090909	C	44	39	FALSE	FALSE
ORF1B:P1967S	C.5	10	11	ORF1b	P	S	1967	None	substitution	0.909090909	C	1	1	TRUE	TRUE
S:D614G	AN.1	51	51	S	D	G	614	None	substitution	1	AN	115	75	FALSE	FALSE
N:G204R	AN.1	50	51	N	G	R	204	None	substitution	0.980392157	AN	44	39	FALSE	FALSE
N:R203K	AN.1	50	51	N	R	K	203	None	substitution	0.980392157	AN	44	39	FALSE	FALSE
ORF1A:DEL445/446	AN.1	50	51	ORF1a	ORF1A:DEL445/446	DEL445/446	445	446	deletion	0.980392157	AN	1	1	TRUE	TRUE
ORF1A:V1211F	AN.1	50	51	ORF1a	V	F	1211	None	substitution	0.980392157	AN	1	1	TRUE	TRUE
ORF1B:P314L	AN.1	50	51	ORF1b	P	L	314	None	substitution	0.980392157	AN	113	73	FALSE	FALSE
ORF1A:L3951F	AN.1	45	51	ORF1a	L	F	3951	None	substitution	0.882352941	AN	1	1	TRUE	TRUE
ORF1A:L2146F	AN.1	42	51	ORF1a	L	F	2146	None	substitution	0.823529412	AN	1	1	TRUE	TRUE
N:G215V	B.1.146	187	188	N	G	V	215	None	substitution	0.994680851	B.1.146	1	1	TRUE	TRUE
ORF1B:P314L	B.1.146	187	188	ORF1b	P	L	314	None	substitution	0.994680851	B.1.146	113	73	FALSE	FALSE
S:D614G	B.1.146	185	188	S	D	G	614	None	substitution	0.984042553	B.1.146	115	75	FALSE	FALSE
ORF1A:A3523V	B.1.146	183	188	ORF1a	A	V	3523	None	substitution	0.973404255	B.1.146	1	1	TRUE	TRUE
N:M234I	B.1.160.21	46	46	N	M	I	234	None	substitution	1	B.1.160	10	4	FALSE	FALSE
ORF1A:M3087I	B.1.160.21	46	46	ORF1a	M	I	3087	None	substitution	1	B.1.160	7	1	TRUE	FALSE
ORF1B:A176S	B.1.160.21	46	46	ORF1b	A	S	176	None	substitution	1	B.1.160	7	1	TRUE	FALSE
ORF1B:E1184D	B.1.160.21	46	46	ORF1b	E	D	1184	None	substitution	1	B.1.160	7	1	TRUE	FALSE
ORF1B:K1141R	B.1.160.21	46	46	ORF1b	K	R	1141	None	substitution	1	B.1.160	7	1	TRUE	FALSE
ORF1B:P314L	B.1.160.21	46	46	ORF1b	P	L	314	None	substitution	1	B.1.160	113	73	FALSE	FALSE
ORF1B:V767L	B.1.160.21	46	46	ORF1b	V	L	767	None	substitution	1	B.1.160	7	1	TRUE	FALSE
ORF3A:Q57H	B.1.160.21	46	46	ORF3a	Q	H	57	None	substitution	1	B.1.160	21	12	FALSE	FALSE
S:D614G	B.1.160.21	46	46	S	D	G	614	None	substitution	1	B.1.160	115	75	FALSE	FALSE
S:S477N	B.1.160.21	46	46	S	S	N	477	None	substitution	1	B.1.160	7	1	TRUE	FALSE
S:V622A	B.1.160.21	46	46	S	V	A	622	None	substitution	1	B.1.160	1	1	TRUE	TRUE
ORF1A:E102K	B.1.160.21	45	46	ORF1a	E	K	102	None	substitution	0.97826087	B.1.160	2	2	FALSE	FALSE
ORF1A:K1233R	B.1.160.21	45	46	ORF1a	K	R	1233	None	substitution	0.97826087	B.1.160	1	1	TRUE	TRUE
ORF1A:T2106I	B.1.160.21	45	46	ORF1a	T	I	2106	None	substitution	0.97826087	B.1.160	1	1	TRUE	TRUE
ORF1A:V1583F	B.1.160.21	45	46	ORF1a	V	F	1583	None	substitution	0.97826087	B.1.160	1	1	TRUE	TRUE
N:A376T	B.1.160.21	43	46	N	A	T	376	None	substitution	0.934782609	B.1.160	7	1	TRUE	FALSE
S:D614G	B.1.177.83	542	543	S	D	G	614	None	substitution	0.998158379	B.1.177	115	75	FALSE	FALSE
S:P272L	B.1.177.83	542	543	S	P	L	272	None	substitution	0.998158379	B.1.177	2	1	TRUE	FALSE
ORF1B:P314L	B.1.177.83	541	543	ORF1b	P	L	314	None	substitution	0.996316759	B.1.177	113	73	FALSE	FALSE
N:A220V	B.1.177.83	540	543	N	A	V	220	None	substitution	0.994475138	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.83	535	543	S	A	V	222	None	substitution	0.985267035	B.1.177	20	3	FALSE	FALSE
S:A262S	B.1.177.83	515	543	S	A	S	262	None	substitution	0.948434622	B.1.177	2	1	TRUE	FALSE
ORF10:V30L	B.1.177.83	500	543	ORF10	V	L	30	None	substitution	0.920810313	B.1.177	20	3	FALSE	FALSE
ORF1B:P314L	W.2	195	195	ORF1b	P	L	314	None	substitution	1	W	113	73	FALSE	FALSE
S:D614G	W.2	195	195	S	D	G	614	None	substitution	1	W	115	75	FALSE	FALSE
N:A220V	W.2	194	195	N	A	V	220	None	substitution	0.994871795	W	20	3	FALSE	FALSE
ORF1A:A903V	W.2	194	195	ORF1a	A	V	903	None	substitution	0.994871795	W	2	1	TRUE	FALSE
ORF1A:A2529V	W.2	192	195	ORF1a	A	V	2529	None	substitution	0.984615385	W	1	1	TRUE	TRUE
ORF1B:P1727L	W.2	191	195	ORF1b	P	L	1727	None	substitution	0.979487179	W	1	1	TRUE	TRUE
ORF10:V30L	W.2	190	195	ORF10	V	L	30	None	substitution	0.974358974	W	20	3	FALSE	FALSE
S:A222V	W.2	183	195	S	A	V	222	None	substitution	0.938461538	W	20	3	FALSE	FALSE
ORF1B:P314L	B.1.1.39	1720	1738	ORF1b	P	L	314	None	substitution	0.989643268	B.1.1.39	113	73	FALSE	FALSE
S:D614G	B.1.1.39	1705	1738	S	D	G	614	None	substitution	0.981012658	B.1.1.39	115	75	FALSE	FALSE
N:P199S	B.1.1.39	1640	1738	N	P	S	199	None	substitution	0.943613349	B.1.1.39	1	1	TRUE	TRUE
N:G204R	B.1.1.39	1633	1738	N	G	R	204	None	substitution	0.939585731	B.1.1.39	44	39	FALSE	FALSE
N:R203K	B.1.1.39	1631	1738	N	R	K	203	None	substitution	0.938434983	B.1.1.39	44	39	FALSE	FALSE
N:V72I	B.1.1.39	1600	1738	N	V	I	72	None	substitution	0.920598389	B.1.1.39	1	1	TRUE	TRUE
N:R203K	B.1.1.159	183	183	N	R	K	203	None	substitution	1	B.1.1.159	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.159	183	183	ORF1b	P	L	314	None	substitution	1	B.1.1.159	113	73	FALSE	FALSE
S:D614G	B.1.1.159	183	183	S	D	G	614	None	substitution	1	B.1.1.159	115	75	FALSE	FALSE
N:G204R	B.1.1.159	182	183	N	G	R	204	None	substitution	0.994535519	B.1.1.159	44	39	FALSE	FALSE
ORF1A:D2980A	B.1.1.159	181	183	ORF1a	D	A	2980	None	substitution	0.989071038	B.1.1.159	1	1	TRUE	TRUE
ORF1A:T2952I	B.1.1.159	181	183	ORF1a	T	I	2952	None	substitution	0.989071038	B.1.1.159	1	1	TRUE	TRUE
N:P6L	B.1.1.159	178	183	N	P	L	6	None	substitution	0.972677596	B.1.1.159	1	1	TRUE	TRUE
ORF1A:K2200N	B.1.1.159	175	183	ORF1a	K	N	2200	None	substitution	0.956284153	B.1.1.159	1	1	TRUE	TRUE
S:D614G	B.1.389	761	761	S	D	G	614	None	substitution	1	B.1.389	115	75	FALSE	FALSE
ORF1A:Q2702H	B.1.389	760	761	ORF1a	Q	H	2702	None	substitution	0.99868594	B.1.389	1	1	TRUE	TRUE
ORF1B:P314L	B.1.389	760	761	ORF1b	P	L	314	None	substitution	0.99868594	B.1.389	113	73	FALSE	FALSE
ORF3A:Q57H	B.1.389	760	761	ORF3a	Q	H	57	None	substitution	0.99868594	B.1.389	21	12	FALSE	FALSE
S:T723I	B.1.389	760	761	S	T	I	723	None	substitution	0.99868594	B.1.389	1	1	TRUE	TRUE
ORF1B:D2386F	B.1.389	751	761	ORF1b	D	F	2386	None	substitution	0.986859396	B.1.389	1	1	TRUE	TRUE
ORF1B:K2385N	B.1.389	751	761	ORF1b	K	N	2385	None	substitution	0.986859396	B.1.389	1	1	TRUE	TRUE
ORF1B:A1643V	B.1.389	745	761	ORF1b	A	V	1643	None	substitution	0.978975033	B.1.389	1	1	TRUE	TRUE
N:S194L	B.1.389	665	761	N	S	L	194	None	substitution	0.873850197	B.1.389	5	3	FALSE	FALSE
N:G204R	B.1.1.269	514	517	N	G	R	204	None	substitution	0.994197292	B.1.1.269	44	39	FALSE	FALSE
S:D614G	B.1.1.269	513	517	S	D	G	614	None	substitution	0.992263056	B.1.1.269	115	75	FALSE	FALSE
N:R203K	B.1.1.269	512	517	N	R	K	203	None	substitution	0.99032882	B.1.1.269	44	39	FALSE	FALSE
ORF1A:M3862I	B.1.1.269	512	517	ORF1a	M	I	3862	None	substitution	0.99032882	B.1.1.269	1	1	TRUE	TRUE
ORF1A:T1597I	B.1.1.269	511	517	ORF1a	T	I	1597	None	substitution	0.988394584	B.1.1.269	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.269	510	517	ORF1b	P	L	314	None	substitution	0.986460348	B.1.1.269	113	73	FALSE	FALSE
S:D1084Y	B.1.1.269	508	517	S	D	Y	1084	None	substitution	0.982591876	B.1.1.269	1	1	TRUE	TRUE
M:H125Y	B.1.1.269	428	517	M	H	Y	125	None	substitution	0.827852998	B.1.1.269	2	2	FALSE	FALSE
ORF1B:P314L	B.1.160.26	411	413	ORF1b	P	L	314	None	substitution	0.995157385	B.1.160	113	73	FALSE	FALSE
ORF1B:A176S	B.1.160.26	409	413	ORF1b	A	S	176	None	substitution	0.99031477	B.1.160	7	1	TRUE	FALSE
ORF1B:V767L	B.1.160.26	409	413	ORF1b	V	L	767	None	substitution	0.99031477	B.1.160	7	1	TRUE	FALSE
S:D614G	B.1.160.26	409	413	S	D	G	614	None	substitution	0.99031477	B.1.160	115	75	FALSE	FALSE
ORF1A:M3087I	B.1.160.26	408	413	ORF1a	M	I	3087	None	substitution	0.987893462	B.1.160	7	1	TRUE	FALSE
ORF1B:E1184D	B.1.160.26	407	413	ORF1b	E	D	1184	None	substitution	0.985472155	B.1.160	7	1	TRUE	FALSE
ORF1B:K1141R	B.1.160.26	406	413	ORF1b	K	R	1141	None	substitution	0.983050847	B.1.160	7	1	TRUE	FALSE
ORF3A:T151I	B.1.160.26	406	413	ORF3a	T	I	151	None	substitution	0.983050847	B.1.160	1	1	TRUE	TRUE
ORF3A:Q57H	B.1.160.26	405	413	ORF3a	Q	H	57	None	substitution	0.98062954	B.1.160	21	12	FALSE	FALSE
ORF7B:C41F	B.1.160.26	405	413	ORF7b	C	F	41	None	substitution	0.98062954	B.1.160	1	1	TRUE	TRUE
N:M234I	B.1.160.26	404	413	N	M	I	234	None	substitution	0.978208232	B.1.160	10	4	FALSE	FALSE
N:A376T	B.1.160.26	396	413	N	A	T	376	None	substitution	0.958837772	B.1.160	7	1	TRUE	FALSE
S:S477N	B.1.160.26	395	413	S	S	N	477	None	substitution	0.956416465	B.1.160	7	1	TRUE	FALSE
ORF1A:V3593I	B.1.160.26	346	413	ORF1a	V	I	3593	None	substitution	0.837772397	B.1.160	1	1	TRUE	TRUE
S:H655Y	A.28	363	363	S	H	Y	655	None	substitution	1	A	4	2	FALSE	FALSE
S:N501T	A.28	363	363	S	N	T	501	None	substitution	1	A	1	1	TRUE	TRUE
ORF8:L84S	A.28	361	363	ORF8	L	S	84	None	substitution	0.994490358	A	4	1	TRUE	FALSE
ORF1B:D1183Y	A.28	356	363	ORF1b	D	Y	1183	None	substitution	0.980716253	A	1	1	TRUE	TRUE
ORF1A:A3529T	A.28	355	363	ORF1a	A	T	3529	None	substitution	0.977961433	A	1	1	TRUE	TRUE
ORF1B:A975V	A.28	354	363	ORF1b	A	V	975	None	substitution	0.975206612	A	1	1	TRUE	TRUE
N:A35V	A.28	353	363	N	A	V	35	None	substitution	0.972451791	A	1	1	TRUE	TRUE
ORF3A:S171L	A.28	347	363	ORF3a	S	L	171	None	substitution	0.955922865	A	3	2	FALSE	FALSE
ORF1A:V86F	A.28	343	363	ORF1a	V	F	86	None	substitution	0.944903581	A	1	1	TRUE	TRUE
N:S202N	A.28	337	363	N	S	N	202	None	substitution	0.928374656	A	2	1	TRUE	FALSE
S:DEL69/70	A.28	333	363	S	S:DEL69/70	DEL69/70	69	70	deletion	0.917355372	A	6	4	FALSE	FALSE
N:G204R	B.1.1.25	1647	1661	N	G	R	204	None	substitution	0.991571343	B.1.1.25	44	39	FALSE	FALSE
N:R203K	B.1.1.25	1647	1661	N	R	K	203	None	substitution	0.991571343	B.1.1.25	44	39	FALSE	FALSE
S:D614G	B.1.1.25	1639	1661	S	D	G	614	None	substitution	0.986754967	B.1.1.25	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.25	1619	1661	ORF1b	P	L	314	None	substitution	0.974714028	B.1.1.25	113	73	FALSE	FALSE
ORF1A:I300F	B.1.1.25	1608	1661	ORF1a	I	F	300	None	substitution	0.968091511	B.1.1.25	2	2	FALSE	FALSE
N:G204R	B.1.1.519	21587	21640	N	G	R	204	None	substitution	0.997550832	B.1.1.519	44	39	FALSE	FALSE
S:P681H	B.1.1.519	21553	21640	S	P	H	681	None	substitution	0.995979667	B.1.1.519	6	6	FALSE	FALSE
S:D614G	B.1.1.519	21539	21640	S	D	G	614	None	substitution	0.995332717	B.1.1.519	115	75	FALSE	FALSE
S:T732A	B.1.1.519	21538	21640	S	T	A	732	None	substitution	0.995286506	B.1.1.519	2	2	FALSE	FALSE
ORF1B:P314L	B.1.1.519	21495	21640	ORF1b	P	L	314	None	substitution	0.993299445	B.1.1.519	113	73	FALSE	FALSE
ORF1A:T3255I	B.1.1.519	21484	21640	ORF1a	T	I	3255	None	substitution	0.992791128	B.1.1.519	3	3	FALSE	FALSE
ORF1A:P959S	B.1.1.519	21465	21640	ORF1a	P	S	959	None	substitution	0.991913124	B.1.1.519	1	1	TRUE	TRUE
ORF1A:I3618V	B.1.1.519	21448	21640	ORF1a	I	V	3618	None	substitution	0.991127542	B.1.1.519	1	1	TRUE	TRUE
N:R203K	B.1.1.519	21435	21640	N	R	K	203	None	substitution	0.990526802	B.1.1.519	44	39	FALSE	FALSE
ORF1A:T4175I	B.1.1.519	20746	21640	ORF1a	T	I	4175	None	substitution	0.958687616	B.1.1.519	2	2	FALSE	FALSE
S:T478K	B.1.1.519	20461	21640	S	T	K	478	None	substitution	0.94551756	B.1.1.519	3	3	FALSE	FALSE
S:D614G	P.2	4452	4483	S	D	G	614	None	substitution	0.993084988	P	115	75	FALSE	FALSE
ORF1A:L3930F	P.2	4447	4483	ORF1a	L	F	3930	None	substitution	0.991969663	P	1	1	TRUE	TRUE
S:V1176F	P.2	4434	4483	S	V	F	1176	None	substitution	0.989069819	P	3	2	FALSE	FALSE
N:A119S	P.2	4421	4483	N	A	S	119	None	substitution	0.986169975	P	1	1	TRUE	TRUE
ORF1B:P314L	P.2	4417	4483	ORF1b	P	L	314	None	substitution	0.985277716	P	113	73	FALSE	FALSE
N:M234I	P.2	4407	4483	N	M	I	234	None	substitution	0.983047067	P	10	4	FALSE	FALSE
N:R203K	P.2	4402	4483	N	R	K	203	None	substitution	0.981931742	P	44	39	FALSE	FALSE
N:G204R	P.2	4393	4483	N	G	R	204	None	substitution	0.979924158	P	44	39	FALSE	FALSE
ORF1A:L3468V	P.2	4323	4483	ORF1a	L	V	3468	None	substitution	0.964309614	P	1	1	TRUE	TRUE
S:E484K	P.2	4301	4483	S	E	K	484	None	substitution	0.959402186	P	9	6	FALSE	FALSE
ORF1B:P314L	B.1.258.11	2501	2508	ORF1b	P	L	314	None	substitution	0.997208931	B.1.258	113	73	FALSE	FALSE
S:D614G	B.1.258.11	2500	2508	S	D	G	614	None	substitution	0.996810207	B.1.258	115	75	FALSE	FALSE
ORF1B:H1213Y	B.1.258.11	2478	2508	ORF1b	H	Y	1213	None	substitution	0.988038278	B.1.258	4	1	TRUE	FALSE
ORF1A:I2501T	B.1.258.11	2475	2508	ORF1a	I	T	2501	None	substitution	0.986842105	B.1.258	4	1	TRUE	FALSE
ORF1B:V711I	B.1.258.11	2471	2508	ORF1b	V	I	711	None	substitution	0.985247209	B.1.258	3	1	TRUE	FALSE
ORF1B:A1521S	B.1.258.11	2464	2508	ORF1b	A	S	1521	None	substitution	0.98245614	B.1.258	3	1	TRUE	FALSE
S:N439K	B.1.258.11	2462	2508	S	N	K	439	None	substitution	0.981658692	B.1.258	4	1	TRUE	FALSE
ORF1A:L4064F	B.1.258.11	2454	2508	ORF1a	L	F	4064	None	substitution	0.9784689	B.1.258	1	1	TRUE	TRUE
S:DEL69/70	B.1.258.11	2454	2508	S	S:DEL69/70	DEL69/70	69	70	deletion	0.9784689	B.1.258	6	4	FALSE	FALSE
ORF1A:M4241I	B.1.258.11	2418	2508	ORF1a	M	I	4241	None	substitution	0.964114833	B.1.258	3	1	TRUE	FALSE
S:D614G	B.1.2	95717	96147	S	D	G	614	None	substitution	0.995527682	B.1.2	115	75	FALSE	FALSE
ORF3A:Q57H	B.1.2	94686	96147	ORF3a	Q	H	57	None	substitution	0.984804518	B.1.2	21	12	FALSE	FALSE
ORF1A:T265I	B.1.2	94614	96147	ORF1a	T	I	265	None	substitution	0.984055665	B.1.2	8	7	FALSE	FALSE
ORF1B:P314L	B.1.2	94191	96147	ORF1b	P	L	314	None	substitution	0.979656152	B.1.2	113	73	FALSE	FALSE
ORF1A:L3352F	B.1.2	94143	96147	ORF1a	L	F	3352	None	substitution	0.979156916	B.1.2	1	1	TRUE	TRUE
ORF1B:N1653D	B.1.2	93952	96147	ORF1b	N	D	1653	None	substitution	0.977170375	B.1.2	1	1	TRUE	TRUE
N:P199L	B.1.2	92937	96147	N	P	L	199	None	substitution	0.966613623	B.1.2	5	2	FALSE	FALSE
N:P67S	B.1.2	92757	96147	N	P	S	67	None	substitution	0.96474149	B.1.2	1	1	TRUE	TRUE
ORF8:S24L	B.1.2	92742	96147	ORF8	S	L	24	None	substitution	0.964585478	B.1.2	2	2	FALSE	FALSE
ORF3A:G172V	B.1.2	91244	96147	ORF3a	G	V	172	None	substitution	0.949005169	B.1.2	1	1	TRUE	TRUE
ORF1B:R2613C	B.1.2	83940	96147	ORF1b	R	C	2613	None	substitution	0.87303816	B.1.2	1	1	TRUE	TRUE
ORF1B:P314L	B.1.36	5914	6011	ORF1b	P	L	314	None	substitution	0.983862918	B.1.36	113	73	FALSE	FALSE
N:S194L	B.1.36	5912	6011	N	S	L	194	None	substitution	0.983530195	B.1.36	5	3	FALSE	FALSE
ORF3A:Q57H	B.1.36	5905	6011	ORF3a	Q	H	57	None	substitution	0.982365663	B.1.36	21	12	FALSE	FALSE
S:D614G	B.1.36	5905	6011	S	D	G	614	None	substitution	0.982365663	B.1.36	115	75	FALSE	FALSE
ORF1B:P314L	C.16	862	870	ORF1b	P	L	314	None	substitution	0.990804598	C	113	73	FALSE	FALSE
ORF1A:E1013K	C.16	860	870	ORF1a	E	K	1013	None	substitution	0.988505747	C	1	1	TRUE	TRUE
S:D614G	C.16	860	870	S	D	G	614	None	substitution	0.988505747	C	115	75	FALSE	FALSE
ORF1A:A3143V	C.16	859	870	ORF1a	A	V	3143	None	substitution	0.987356322	C	1	1	TRUE	TRUE
ORF1A:T1246I	C.16	857	870	ORF1a	T	I	1246	None	substitution	0.985057471	C	6	2	FALSE	FALSE
ORF1A:G3278S	C.16	830	870	ORF1a	G	S	3278	None	substitution	0.954022989	C	5	2	FALSE	FALSE
S:L452R	C.16	822	870	S	L	R	452	None	substitution	0.944827586	C	7	4	FALSE	FALSE
N:G204R	C.16	819	870	N	G	R	204	None	substitution	0.94137931	C	44	39	FALSE	FALSE
N:R203K	C.16	818	870	N	R	K	203	None	substitution	0.940229885	C	44	39	FALSE	FALSE
ORF1A:T4175I	C.16	808	870	ORF1a	T	I	4175	None	substitution	0.928735632	C	2	2	FALSE	FALSE
S:V1176F	B.1.1.28	3003	3063	S	V	F	1176	None	substitution	0.980411361	B.1.1.28	3	2	FALSE	FALSE
N:R203K	B.1.1.28	2996	3063	N	R	K	203	None	substitution	0.97812602	B.1.1.28	44	39	FALSE	FALSE
N:G204R	B.1.1.28	2995	3063	N	G	R	204	None	substitution	0.977799543	B.1.1.28	44	39	FALSE	FALSE
S:D614G	B.1.1.28	2978	3063	S	D	G	614	None	substitution	0.972249429	B.1.1.28	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.28	2960	3063	ORF1b	P	L	314	None	substitution	0.966372837	B.1.1.28	113	73	FALSE	FALSE
N:R203K	B.1.1.1	2724	2736	N	R	K	203	None	substitution	0.995614035	B.1.1.1	44	39	FALSE	FALSE
N:G204R	B.1.1.1	2722	2736	N	G	R	204	None	substitution	0.994883041	B.1.1.1	44	39	FALSE	FALSE
S:D614G	B.1.1.1	2719	2736	S	D	G	614	None	substitution	0.99378655	B.1.1.1	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.1	2702	2736	ORF1b	P	L	314	None	substitution	0.987573099	B.1.1.1	113	73	FALSE	FALSE
ORF1A:T1246I	B.1.1.1	2626	2736	ORF1a	T	I	1246	None	substitution	0.959795322	B.1.1.1	6	2	FALSE	FALSE
ORF1A:G3278S	B.1.1.1	2613	2736	ORF1a	G	S	3278	None	substitution	0.95504386	B.1.1.1	5	2	FALSE	FALSE
S:D614G	B.1.177.52	529	533	S	D	G	614	None	substitution	0.99249531	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177.52	528	533	ORF1b	P	L	314	None	substitution	0.990619137	B.1.177	113	73	FALSE	FALSE
S:A222V	B.1.177.52	527	533	S	A	V	222	None	substitution	0.988742964	B.1.177	20	3	FALSE	FALSE
N:A220V	B.1.177.52	523	533	N	A	V	220	None	substitution	0.981238274	B.1.177	20	3	FALSE	FALSE
ORF1A:M1586I	B.1.177.52	519	533	ORF1a	M	I	1586	None	substitution	0.973733583	B.1.177	2	2	FALSE	FALSE
S:P1162R	B.1.177.52	519	533	S	P	R	1162	None	substitution	0.973733583	B.1.177	2	2	FALSE	FALSE
ORF10:V30L	B.1.177.52	511	533	ORF10	V	L	30	None	substitution	0.958724203	B.1.177	20	3	FALSE	FALSE
ORF1B:P314L	B.1.597	127	127	ORF1b	P	L	314	None	substitution	1	B.1.597	113	73	FALSE	FALSE
S:D614G	B.1.597	126	127	S	D	G	614	None	substitution	0.992125984	B.1.597	115	75	FALSE	FALSE
ORF3A:Q57H	B.1.597	125	127	ORF3a	Q	H	57	None	substitution	0.984251969	B.1.597	21	12	FALSE	FALSE
N:S186Y	B.1.597	124	127	N	S	Y	186	None	substitution	0.976377953	B.1.597	1	1	TRUE	TRUE
ORF1A:T265I	B.1.597	124	127	ORF1a	T	I	265	None	substitution	0.976377953	B.1.597	8	7	FALSE	FALSE
S:D614G	B.1.258.17	7237	7262	S	D	G	614	None	substitution	0.996557422	B.1.258	115	75	FALSE	FALSE
ORF1B:P1570L	B.1.258.17	7234	7262	ORF1b	P	L	1570	None	substitution	0.996144313	B.1.258	1	1	TRUE	TRUE
ORF1B:H1213Y	B.1.258.17	7228	7262	ORF1b	H	Y	1213	None	substitution	0.995318094	B.1.258	4	1	TRUE	FALSE
ORF1A:M4241I	B.1.258.17	7223	7262	ORF1a	M	I	4241	None	substitution	0.994629579	B.1.258	3	1	TRUE	FALSE
ORF1B:A1521S	B.1.258.17	7209	7262	ORF1b	A	S	1521	None	substitution	0.992701735	B.1.258	3	1	TRUE	FALSE
ORF1B:P314L	B.1.258.17	7208	7262	ORF1b	P	L	314	None	substitution	0.992564032	B.1.258	113	73	FALSE	FALSE
ORF1B:V711I	B.1.258.17	7205	7262	ORF1b	V	I	711	None	substitution	0.992150923	B.1.258	3	1	TRUE	FALSE
ORF3A:Q185H	B.1.258.17	7187	7262	ORF3a	Q	H	185	None	substitution	0.989672267	B.1.258	1	1	TRUE	TRUE
S:V772I	B.1.258.17	7178	7262	S	V	I	772	None	substitution	0.988432939	B.1.258	1	1	TRUE	TRUE
S:L189F	B.1.258.17	7163	7262	S	L	F	189	None	substitution	0.986367392	B.1.258	1	1	TRUE	TRUE
ORF1B:P976L	B.1.258.17	7108	7262	ORF1b	P	L	976	None	substitution	0.978793721	B.1.258	1	1	TRUE	TRUE
ORF1A:I2501T	B.1.258.17	7060	7262	ORF1a	I	T	2501	None	substitution	0.972183971	B.1.258	4	1	TRUE	FALSE
ORF1B:E1977D	B.1.258.17	7046	7262	ORF1b	E	D	1977	None	substitution	0.970256128	B.1.258	1	1	TRUE	TRUE
S:DEL69/70	B.1.258.17	6933	7262	S	S:DEL69/70	DEL69/70	69	70	deletion	0.954695676	B.1.258	6	4	FALSE	FALSE
S:N439K	B.1.258.17	6871	7262	S	N	K	439	None	substitution	0.946158083	B.1.258	4	1	TRUE	FALSE
ORF8:E64*	B.1.258.17	6073	7262	ORF8	E	*	64	None	substitution	0.836271	B.1.258	1	1	TRUE	TRUE
S:D614G	B.1.1.318	4149	4186	S	D	G	614	None	substitution	0.991161013	B.1.1.318	115	75	FALSE	FALSE
M:I82T	B.1.1.318	4140	4186	M	I	T	82	None	substitution	0.989010989	B.1.1.318	6	6	FALSE	FALSE
ORF1A:A3209V	B.1.1.318	4138	4186	ORF1a	A	V	3209	None	substitution	0.988533206	B.1.1.318	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.318	4134	4186	ORF1b	P	L	314	None	substitution	0.98757764	B.1.1.318	113	73	FALSE	FALSE
ORF1A:T2936I	B.1.1.318	4128	4186	ORF1a	T	I	2936	None	substitution	0.98614429	B.1.1.318	1	1	TRUE	TRUE
S:P681H	B.1.1.318	4126	4186	S	P	H	681	None	substitution	0.985666507	B.1.1.318	6	6	FALSE	FALSE
ORF8:E106*	B.1.1.318	4115	4186	ORF8	E	*	106	None	substitution	0.9830387	B.1.1.318	1	1	TRUE	TRUE
S:D796H	B.1.1.318	4097	4186	S	D	H	796	None	substitution	0.978738653	B.1.1.318	1	1	TRUE	TRUE
S:T95I	B.1.1.318	4095	4186	S	T	I	95	None	substitution	0.97826087	B.1.1.318	2	2	FALSE	FALSE
S:E484K	B.1.1.318	4090	4186	S	E	K	484	None	substitution	0.977066412	B.1.1.318	9	6	FALSE	FALSE
ORF1A:K2511N	B.1.1.318	4069	4186	ORF1a	K	N	2511	None	substitution	0.972049689	B.1.1.318	1	1	TRUE	TRUE
ORF1A:DEL3675/3677	B.1.1.318	4027	4186	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.962016245	B.1.1.318	8	6	FALSE	FALSE
N:DEL209	B.1.1.318	4011	4186	N	N:DEL209	DEL209	209	None	deletion	0.95819398	B.1.1.318	1	1	TRUE	TRUE
N:G204R	B.1.1.318	4002	4186	N	G	R	204	None	substitution	0.956043956	B.1.1.318	44	39	FALSE	FALSE
N:R203K	B.1.1.318	3990	4186	N	R	K	203	None	substitution	0.953177258	B.1.1.318	44	39	FALSE	FALSE
ORF1B:V2371M	B.1.1.318	3982	4186	ORF1b	V	M	2371	None	substitution	0.951266125	B.1.1.318	1	1	TRUE	TRUE
ORF1A:T3284I	B.1.1.318	3721	4186	ORF1a	T	I	3284	None	substitution	0.888915432	B.1.1.318	1	1	TRUE	TRUE
S:DEL144/145	B.1.1.318	3594	4186	S	S:DEL144/145	DEL144/145	144	145	deletion	0.858576206	B.1.1.318	3	3	FALSE	FALSE
ORF1A:E1196V	B.1.1.318	3498	4186	ORF1a	E	V	1196	None	substitution	0.835642618	B.1.1.318	1	1	TRUE	TRUE
S:D614G	B.1.177.18	819	820	S	D	G	614	None	substitution	0.998780488	B.1.177	115	75	FALSE	FALSE
S:E583D	B.1.177.18	818	820	S	E	D	583	None	substitution	0.997560976	B.1.177	1	1	TRUE	TRUE
ORF1B:P314L	B.1.177.18	817	820	ORF1b	P	L	314	None	substitution	0.996341463	B.1.177	113	73	FALSE	FALSE
ORF3A:K16N	B.1.177.18	814	820	ORF3a	K	N	16	None	substitution	0.992682927	B.1.177	1	1	TRUE	TRUE
S:A222V	B.1.177.18	813	820	S	A	V	222	None	substitution	0.991463415	B.1.177	20	3	FALSE	FALSE
N:A220V	B.1.177.18	808	820	N	A	V	220	None	substitution	0.985365854	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.18	808	820	ORF10	V	L	30	None	substitution	0.985365854	B.1.177	20	3	FALSE	FALSE
ORF1A:K3353R	B.1.177.18	790	820	ORF1a	K	R	3353	None	substitution	0.963414634	B.1.177	4	3	FALSE	FALSE
ORF7A:T120I	B.1.177.18	725	820	ORF7a	T	I	120	None	substitution	0.884146341	B.1.177	2	2	FALSE	FALSE
N:G204R	B.1.1.219	202	202	N	G	R	204	None	substitution	1	B.1.1.219	44	39	FALSE	FALSE
N:R203K	B.1.1.219	202	202	N	R	K	203	None	substitution	1	B.1.1.219	44	39	FALSE	FALSE
ORF1A:C3059G	B.1.1.219	202	202	ORF1a	C	G	3059	None	substitution	1	B.1.1.219	1	1	TRUE	TRUE
S:D614G	B.1.1.219	202	202	S	D	G	614	None	substitution	1	B.1.1.219	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.219	201	202	ORF1b	P	L	314	None	substitution	0.995049505	B.1.1.219	113	73	FALSE	FALSE
ORF3A:W128C	B.1.1.219	200	202	ORF3a	W	C	128	None	substitution	0.99009901	B.1.1.219	1	1	TRUE	TRUE
ORF1A:Q2034L	B.1.1.219	193	202	ORF1a	Q	L	2034	None	substitution	0.955445545	B.1.1.219	1	1	TRUE	TRUE
ORF1A:M1769I	B.1.1.219	187	202	ORF1a	M	I	1769	None	substitution	0.925742574	B.1.1.219	1	1	TRUE	TRUE
N:G204R	B.1.1.221	108	110	N	G	R	204	None	substitution	0.981818182	B.1.1.221	44	39	FALSE	FALSE
N:R203K	B.1.1.221	108	110	N	R	K	203	None	substitution	0.981818182	B.1.1.221	44	39	FALSE	FALSE
S:D614G	B.1.1.221	108	110	S	D	G	614	None	substitution	0.981818182	B.1.1.221	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.221	107	110	ORF1b	P	L	314	None	substitution	0.972727273	B.1.1.221	113	73	FALSE	FALSE
S:D614G	B.1.36.8	911	919	S	D	G	614	None	substitution	0.991294886	B.1.36	115	75	FALSE	FALSE
ORF1B:P314L	B.1.36.8	895	919	ORF1b	P	L	314	None	substitution	0.973884657	B.1.36	113	73	FALSE	FALSE
ORF3A:Q57H	B.1.36.8	868	919	ORF3a	Q	H	57	None	substitution	0.944504897	B.1.36	21	12	FALSE	FALSE
N:S194L	B.1.36.8	856	919	N	S	L	194	None	substitution	0.931447225	B.1.36	5	3	FALSE	FALSE
S:A222V	B.1.177.82	1912	1914	S	A	V	222	None	substitution	0.998955068	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.177.82	1911	1914	S	D	G	614	None	substitution	0.998432602	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177.82	1910	1914	ORF1b	P	L	314	None	substitution	0.997910136	B.1.177	113	73	FALSE	FALSE
S:P272L	B.1.177.82	1891	1914	S	P	L	272	None	substitution	0.987983281	B.1.177	2	1	TRUE	FALSE
N:A220V	B.1.177.82	1889	1914	N	A	V	220	None	substitution	0.986938349	B.1.177	20	3	FALSE	FALSE
S:A262S	B.1.177.82	1778	1914	S	A	S	262	None	substitution	0.928944619	B.1.177	2	1	TRUE	FALSE
ORF10:V30L	B.1.177.82	1742	1914	ORF10	V	L	30	None	substitution	0.910135841	B.1.177	20	3	FALSE	FALSE
ORF1B:P314L	B.1.177.75	783	784	ORF1b	P	L	314	None	substitution	0.99872449	B.1.177	113	73	FALSE	FALSE
N:A220V	B.1.177.75	778	784	N	A	V	220	None	substitution	0.992346939	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.75	778	784	S	A	V	222	None	substitution	0.992346939	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.177.75	778	784	S	D	G	614	None	substitution	0.992346939	B.1.177	115	75	FALSE	FALSE
ORF10:V30L	B.1.177.75	766	784	ORF10	V	L	30	None	substitution	0.977040816	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.1.294	748	750	S	D	G	614	None	substitution	0.997333333	B.1.1.294	115	75	FALSE	FALSE
N:R203K	B.1.1.294	744	750	N	R	K	203	None	substitution	0.992	B.1.1.294	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.294	743	750	ORF1b	P	L	314	None	substitution	0.990666667	B.1.1.294	113	73	FALSE	FALSE
N:G204R	B.1.1.294	742	750	N	G	R	204	None	substitution	0.989333333	B.1.1.294	44	39	FALSE	FALSE
ORF1A:D1036E	B.1.1.294	728	750	ORF1a	D	E	1036	None	substitution	0.970666667	B.1.1.294	1	1	TRUE	TRUE
S:D614G	B.1.617.2	177575	178149	S	D	G	614	None	substitution	0.996777978	B.1.617	115	75	FALSE	FALSE
M:I82T	B.1.617.2	177337	178149	M	I	T	82	None	substitution	0.995442018	B.1.617	6	6	FALSE	FALSE
S:P681R	B.1.617.2	177178	178149	S	P	R	681	None	substitution	0.994549506	B.1.617	2	1	TRUE	FALSE
ORF3A:S26L	B.1.617.2	177159	178149	ORF3a	S	L	26	None	substitution	0.994442854	B.1.617	2	1	TRUE	FALSE
ORF1B:P314L	B.1.617.2	176536	178149	ORF1b	P	L	314	None	substitution	0.990945781	B.1.617	113	73	FALSE	FALSE
N:R203M	B.1.617.2	175772	178149	N	R	M	203	None	substitution	0.986657236	B.1.617	2	1	TRUE	FALSE
S:T19R	B.1.617.2	175438	178149	S	T	R	19	None	substitution	0.984782401	B.1.617	1	1	TRUE	TRUE
N:D63G	B.1.617.2	175168	178149	N	D	G	63	None	substitution	0.983266816	B.1.617	1	1	TRUE	TRUE
N:D377Y	B.1.617.2	174921	178149	N	D	Y	377	None	substitution	0.981880336	B.1.617	2	1	TRUE	FALSE
ORF1B:P1000L	B.1.617.2	174693	178149	ORF1b	P	L	1000	None	substitution	0.980600509	B.1.617	3	2	FALSE	FALSE
ORF1B:G662S	B.1.617.2	174533	178149	ORF1b	G	S	662	None	substitution	0.979702384	B.1.617	1	1	TRUE	TRUE
S:L452R	B.1.617.2	173885	178149	S	L	R	452	None	substitution	0.976064979	B.1.617	7	4	FALSE	FALSE
S:T478K	B.1.617.2	173800	178149	S	T	K	478	None	substitution	0.975587851	B.1.617	3	3	FALSE	FALSE
ORF7A:T120I	B.1.617.2	170718	178149	ORF7a	T	I	120	None	substitution	0.958287725	B.1.617	2	2	FALSE	FALSE
S:D950N	B.1.617.2	169827	178149	S	D	N	950	None	substitution	0.953286294	B.1.617	1	1	TRUE	TRUE
ORF7A:V82A	B.1.617.2	169221	178149	ORF7a	V	A	82	None	substitution	0.949884647	B.1.617	2	1	TRUE	FALSE
ORF8:DEL119/120	B.1.617.2	168067	178149	ORF8	ORF8:DEL119/120	DEL119/120	119	120	deletion	0.943406923	B.1.617	2	2	FALSE	FALSE
S:DEL157/158	B.1.617.2	158728	178149	S	S:DEL157/158	DEL157/158	157	158	deletion	0.890984513	B.1.617	1	1	TRUE	TRUE
N:G204R	B.1.1.435	28	28	N	G	R	204	None	substitution	1	B.1.1.435	44	39	FALSE	FALSE
N:G214S	B.1.1.435	28	28	N	G	S	214	None	substitution	1	B.1.1.435	1	1	TRUE	TRUE
N:R203K	B.1.1.435	28	28	N	R	K	203	None	substitution	1	B.1.1.435	44	39	FALSE	FALSE
N:T205A	B.1.1.435	28	28	N	T	A	205	None	substitution	1	B.1.1.435	1	1	TRUE	TRUE
ORF1A:I431M	B.1.1.435	28	28	ORF1a	I	M	431	None	substitution	1	B.1.1.435	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.435	28	28	ORF1b	P	L	314	None	substitution	1	B.1.1.435	113	73	FALSE	FALSE
S:D614G	B.1.1.435	28	28	S	D	G	614	None	substitution	1	B.1.1.435	115	75	FALSE	FALSE
ORF1A:I300F	AD.2	4488	4488	ORF1a	I	F	300	None	substitution	1	AD	2	2	FALSE	FALSE
S:D614G	AD.2	4487	4488	S	D	G	614	None	substitution	0.999777184	AD	115	75	FALSE	FALSE
ORF1B:E245D	AD.2	4483	4488	ORF1b	E	D	245	None	substitution	0.998885918	AD	1	1	TRUE	TRUE
ORF1B:T2084I	AD.2	4482	4488	ORF1b	T	I	2084	None	substitution	0.998663102	AD	2	2	FALSE	FALSE
N:G204R	AD.2	4474	4488	N	G	R	204	None	substitution	0.99688057	AD	44	39	FALSE	FALSE
N:R203K	AD.2	4473	4488	N	R	K	203	None	substitution	0.996657754	AD	44	39	FALSE	FALSE
ORF1A:P1786L	AD.2	4473	4488	ORF1a	P	L	1786	None	substitution	0.996657754	AD	1	1	TRUE	TRUE
ORF1B:P314L	AD.2	4470	4488	ORF1b	P	L	314	None	substitution	0.995989305	AD	113	73	FALSE	FALSE
ORF3A:T223I	AD.2	4465	4488	ORF3a	T	I	223	None	substitution	0.994875223	AD	1	1	TRUE	TRUE
N:A398V	AD.2	4437	4488	N	A	V	398	None	substitution	0.988636364	AD	1	1	TRUE	TRUE
ORF1B:M2025I	AD.2	4200	4488	ORF1b	M	I	2025	None	substitution	0.935828877	AD	1	1	TRUE	TRUE
N:G204R	B.1.1.241	322	324	N	G	R	204	None	substitution	0.99382716	B.1.1.241	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.241	322	324	ORF1b	P	L	314	None	substitution	0.99382716	B.1.1.241	113	73	FALSE	FALSE
N:R203K	B.1.1.241	321	324	N	R	K	203	None	substitution	0.990740741	B.1.1.241	44	39	FALSE	FALSE
S:D614G	B.1.1.241	320	324	S	D	G	614	None	substitution	0.987654321	B.1.1.241	115	75	FALSE	FALSE
S:L5F	B.1.1.241	311	324	S	L	F	5	None	substitution	0.959876543	B.1.1.241	1	1	TRUE	TRUE
S:V3G	B.1.1.241	299	324	S	V	G	3	None	substitution	0.922839506	B.1.1.241	1	1	TRUE	TRUE
N:G204R	B.1.1.404	53	54	N	G	R	204	None	substitution	0.981481481	B.1.1.404	44	39	FALSE	FALSE
N:R203K	B.1.1.404	53	54	N	R	K	203	None	substitution	0.981481481	B.1.1.404	44	39	FALSE	FALSE
ORF1B:D2361Y	B.1.1.404	53	54	ORF1b	D	Y	2361	None	substitution	0.981481481	B.1.1.404	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.404	53	54	ORF1b	P	L	314	None	substitution	0.981481481	B.1.1.404	113	73	FALSE	FALSE
S:D614G	B.1.1.404	53	54	S	D	G	614	None	substitution	0.981481481	B.1.1.404	115	75	FALSE	FALSE
N:G204R	B.1.1.204	232	232	N	G	R	204	None	substitution	1	B.1.1.204	44	39	FALSE	FALSE
N:R203K	B.1.1.204	232	232	N	R	K	203	None	substitution	1	B.1.1.204	44	39	FALSE	FALSE
ORF1A:I1203T	B.1.1.204	232	232	ORF1a	I	T	1203	None	substitution	1	B.1.1.204	1	1	TRUE	TRUE
ORF1A:N2603D	B.1.1.204	232	232	ORF1a	N	D	2603	None	substitution	1	B.1.1.204	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.204	232	232	ORF1b	P	L	314	None	substitution	1	B.1.1.204	113	73	FALSE	FALSE
S:D614G	B.1.1.204	232	232	S	D	G	614	None	substitution	1	B.1.1.204	115	75	FALSE	FALSE
S:D614G	B.1.438	109	109	S	D	G	614	None	substitution	1	B.1.438	115	75	FALSE	FALSE
ORF1B:P314L	B.1.438	108	109	ORF1b	P	L	314	None	substitution	0.990825688	B.1.438	113	73	FALSE	FALSE
ORF3A:Q57H	B.1.438	108	109	ORF3a	Q	H	57	None	substitution	0.990825688	B.1.438	21	12	FALSE	FALSE
ORF1A:M297V	B.1.438	107	109	ORF1a	M	V	297	None	substitution	0.981651376	B.1.438	1	1	TRUE	TRUE
N:D401Y	B.1.438	104	109	N	D	Y	401	None	substitution	0.95412844	B.1.438	1	1	TRUE	TRUE
S:D614G	B.1.177.50	521	522	S	D	G	614	None	substitution	0.998084291	B.1.177	115	75	FALSE	FALSE
N:A220V	B.1.177.50	516	522	N	A	V	220	None	substitution	0.988505747	B.1.177	20	3	FALSE	FALSE
ORF1B:P314L	B.1.177.50	516	522	ORF1b	P	L	314	None	substitution	0.988505747	B.1.177	113	73	FALSE	FALSE
ORF10:V30L	B.1.177.50	507	522	ORF10	V	L	30	None	substitution	0.971264368	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.50	502	522	S	A	V	222	None	substitution	0.961685824	B.1.177	20	3	FALSE	FALSE
ORF8:L84S	A.27	467	472	ORF8	L	S	84	None	substitution	0.98940678	A	4	1	TRUE	FALSE
S:H655Y	A.27	465	472	S	H	Y	655	None	substitution	0.985169492	A	4	2	FALSE	FALSE
S:N501Y	A.27	465	472	S	N	Y	501	None	substitution	0.985169492	A	6	4	FALSE	FALSE
ORF1A:N3651S	A.27	463	472	ORF1a	N	S	3651	None	substitution	0.980932203	A	1	1	TRUE	TRUE
ORF1A:P286L	A.27	463	472	ORF1a	P	L	286	None	substitution	0.980932203	A	1	1	TRUE	TRUE
S:G1219V	A.27	463	472	S	G	V	1219	None	substitution	0.980932203	A	1	1	TRUE	TRUE
N:S202N	A.27	462	472	N	S	N	202	None	substitution	0.978813559	A	2	1	TRUE	FALSE
ORF3A:V50A	A.27	462	472	ORF3a	V	A	50	None	substitution	0.978813559	A	1	1	TRUE	TRUE
ORF1A:D2980G	A.27	460	472	ORF1a	D	G	2980	None	substitution	0.974576271	A	1	1	TRUE	TRUE
S:L452R	A.27	458	472	S	L	R	452	None	substitution	0.970338983	A	7	4	FALSE	FALSE
ORF1B:P1000L	A.27	457	472	ORF1b	P	L	1000	None	substitution	0.968220339	A	3	2	FALSE	FALSE
S:A653V	A.27	456	472	S	A	V	653	None	substitution	0.966101695	A	1	1	TRUE	TRUE
S:D796Y	A.27	455	472	S	D	Y	796	None	substitution	0.963983051	A	2	2	FALSE	FALSE
S:L18F	A.27	453	472	S	L	F	18	None	substitution	0.959745763	A	6	5	FALSE	FALSE
ORF8:DEL119/120	A.27	447	472	ORF8	ORF8:DEL119/120	DEL119/120	119	120	deletion	0.947033898	A	2	2	FALSE	FALSE
ORF3A:DEL257/258	A.27	395	472	ORF3a	ORF3A:DEL257/258	DEL257/258	257	258	deletion	0.836864407	A	1	1	TRUE	TRUE
ORF6:DEL63	A.27	379	472	ORF6	ORF6:DEL63	DEL63	63	None	deletion	0.802966102	A	1	1	TRUE	TRUE
N:G204R	B.1.1.397	444	444	N	G	R	204	None	substitution	1	B.1.1.397	44	39	FALSE	FALSE
N:R203K	B.1.1.397	443	444	N	R	K	203	None	substitution	0.997747748	B.1.1.397	44	39	FALSE	FALSE
S:D614G	B.1.1.397	443	444	S	D	G	614	None	substitution	0.997747748	B.1.1.397	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.397	428	444	ORF1b	P	L	314	None	substitution	0.963963964	B.1.1.397	113	73	FALSE	FALSE
S:M153T	B.1.1.397	415	444	S	M	T	153	None	substitution	0.934684685	B.1.1.397	2	2	FALSE	FALSE
ORF8:V62L	B.1.1.397	402	444	ORF8	V	L	62	None	substitution	0.905405405	B.1.1.397	1	1	TRUE	TRUE
S:D138Y	B.1.1.397	391	444	S	D	Y	138	None	substitution	0.880630631	B.1.1.397	3	2	FALSE	FALSE
N:M234I	B.1.1.397	386	444	N	M	I	234	None	substitution	0.869369369	B.1.1.397	10	4	FALSE	FALSE
S:D614G	B.1.210	395	397	S	D	G	614	None	substitution	0.994962217	B.1.210	115	75	FALSE	FALSE
ORF1B:P314L	B.1.210	393	397	ORF1b	P	L	314	None	substitution	0.989924433	B.1.210	113	73	FALSE	FALSE
S:D614G	B.1.541	215	215	S	D	G	614	None	substitution	1	B.1.541	115	75	FALSE	FALSE
ORF1B:P314L	B.1.541	213	215	ORF1b	P	L	314	None	substitution	0.990697674	B.1.541	113	73	FALSE	FALSE
N:S187L	B.1.541	210	215	N	S	L	187	None	substitution	0.976744186	B.1.541	2	2	FALSE	FALSE
ORF3A:Q57H	B.1.541	206	215	ORF3a	Q	H	57	None	substitution	0.958139535	B.1.541	21	12	FALSE	FALSE
ORF1A:T265I	B.1.541	203	215	ORF1a	T	I	265	None	substitution	0.944186047	B.1.541	8	7	FALSE	FALSE
ORF1B:M1499I	B.1.541	201	215	ORF1b	M	I	1499	None	substitution	0.934883721	B.1.541	1	1	TRUE	TRUE
ORF1B:G1450R	B.1.1.351	330	330	ORF1b	G	R	1450	None	substitution	1	B.1.1.351	1	1	TRUE	TRUE
N:G204R	B.1.1.351	329	330	N	G	R	204	None	substitution	0.996969697	B.1.1.351	44	39	FALSE	FALSE
N:R203K	B.1.1.351	329	330	N	R	K	203	None	substitution	0.996969697	B.1.1.351	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.351	329	330	ORF1b	P	L	314	None	substitution	0.996969697	B.1.1.351	113	73	FALSE	FALSE
ORF1B:T1064I	B.1.1.351	329	330	ORF1b	T	I	1064	None	substitution	0.996969697	B.1.1.351	1	1	TRUE	TRUE
S:P681H	B.1.1.351	325	330	S	P	H	681	None	substitution	0.984848485	B.1.1.351	6	6	FALSE	FALSE
ORF1B:K134Q	B.1.1.351	319	330	ORF1b	K	Q	134	None	substitution	0.966666667	B.1.1.351	1	1	TRUE	TRUE
ORF1A:K3162E	B.1.1.351	317	330	ORF1a	K	E	3162	None	substitution	0.960606061	B.1.1.351	1	1	TRUE	TRUE
S:D614G	B.1.1.351	317	330	S	D	G	614	None	substitution	0.960606061	B.1.1.351	115	75	FALSE	FALSE
ORF1A:P3504H	B.1.1.351	289	330	ORF1a	P	H	3504	None	substitution	0.875757576	B.1.1.351	1	1	TRUE	TRUE
ORF1A:E1413D	B.1.221.2	250	250	ORF1a	E	D	1413	None	substitution	1	B.1.221	1	1	TRUE	TRUE
ORF1B:P314L	B.1.221.2	250	250	ORF1b	P	L	314	None	substitution	1	B.1.221	113	73	FALSE	FALSE
ORF3A:Q38R	B.1.221.2	250	250	ORF3a	Q	R	38	None	substitution	1	B.1.221	4	1	TRUE	FALSE
S:D614G	B.1.221.2	250	250	S	D	G	614	None	substitution	1	B.1.221	115	75	FALSE	FALSE
ORF1A:H1113Y	B.1.221.2	248	250	ORF1a	H	Y	1113	None	substitution	0.992	B.1.221	4	1	TRUE	FALSE
N:P199L	B.1.221.2	247	250	N	P	L	199	None	substitution	0.988	B.1.221	5	2	FALSE	FALSE
ORF3A:V202L	B.1.221.2	246	250	ORF3a	V	L	202	None	substitution	0.984	B.1.221	4	1	TRUE	FALSE
S:S98F	B.1.221.2	246	250	S	S	F	98	None	substitution	0.984	B.1.221	4	1	TRUE	FALSE
E:L73F	B.1.221.2	244	250	E	L	F	73	None	substitution	0.976	B.1.221	1	1	TRUE	TRUE
ORF1A:K3832N	B.1.221.2	244	250	ORF1a	K	N	3832	None	substitution	0.976	B.1.221	1	1	TRUE	TRUE
N:R203K	B.1.1.141	481	485	N	R	K	203	None	substitution	0.991752577	B.1.1.141	44	39	FALSE	FALSE
ORF3A:D222Y	B.1.1.141	481	485	ORF3a	D	Y	222	None	substitution	0.991752577	B.1.1.141	1	1	TRUE	TRUE
N:G204R	B.1.1.141	480	485	N	G	R	204	None	substitution	0.989690722	B.1.1.141	44	39	FALSE	FALSE
S:D614G	B.1.1.141	480	485	S	D	G	614	None	substitution	0.989690722	B.1.1.141	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.141	474	485	ORF1b	P	L	314	None	substitution	0.977319588	B.1.1.141	113	73	FALSE	FALSE
S:M153T	B.1.1.141	459	485	S	M	T	153	None	substitution	0.946391753	B.1.1.141	2	2	FALSE	FALSE
ORF1B:P314L	Y.1	77	77	ORF1b	P	L	314	None	substitution	1	Y	113	73	FALSE	FALSE
S:A222V	Y.1	77	77	S	A	V	222	None	substitution	1	Y	20	3	FALSE	FALSE
S:D614G	Y.1	77	77	S	D	G	614	None	substitution	1	Y	115	75	FALSE	FALSE
S:P1162R	Y.1	77	77	S	P	R	1162	None	substitution	1	Y	2	2	FALSE	FALSE
N:A220V	Y.1	76	77	N	A	V	220	None	substitution	0.987012987	Y	20	3	FALSE	FALSE
ORF10:V30L	Y.1	76	77	ORF10	V	L	30	None	substitution	0.987012987	Y	20	3	FALSE	FALSE
ORF1A:M1586I	Y.1	76	77	ORF1a	M	I	1586	None	substitution	0.987012987	Y	2	2	FALSE	FALSE
ORF1A:T1665I	Y.1	75	77	ORF1a	T	I	1665	None	substitution	0.974025974	Y	1	1	TRUE	TRUE
N:G204R	B.1.1.47	177	177	N	G	R	204	None	substitution	1	B.1.1.47	44	39	FALSE	FALSE
N:R203K	B.1.1.47	177	177	N	R	K	203	None	substitution	1	B.1.1.47	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.47	176	177	ORF1b	P	L	314	None	substitution	0.994350282	B.1.1.47	113	73	FALSE	FALSE
ORF1B:T2099I	B.1.1.47	175	177	ORF1b	T	I	2099	None	substitution	0.988700565	B.1.1.47	1	1	TRUE	TRUE
S:D614G	B.1.1.47	175	177	S	D	G	614	None	substitution	0.988700565	B.1.1.47	115	75	FALSE	FALSE
S:D614G	B.1.177.33	371	373	S	D	G	614	None	substitution	0.99463807	B.1.177	115	75	FALSE	FALSE
N:A220V	B.1.177.33	370	373	N	A	V	220	None	substitution	0.991957105	B.1.177	20	3	FALSE	FALSE
ORF1B:P314L	B.1.177.33	368	373	ORF1b	P	L	314	None	substitution	0.986595174	B.1.177	113	73	FALSE	FALSE
ORF10:V30L	B.1.177.33	367	373	ORF10	V	L	30	None	substitution	0.983914209	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.33	363	373	S	A	V	222	None	substitution	0.973190349	B.1.177	20	3	FALSE	FALSE
S:G639S	B.1.177.33	363	373	S	G	S	639	None	substitution	0.973190349	B.1.177	1	1	TRUE	TRUE
ORF1A:T2274I	B.1.177.33	359	373	ORF1a	T	I	2274	None	substitution	0.962466488	B.1.177	1	1	TRUE	TRUE
N:P365S	B.1.177.33	325	373	N	P	S	365	None	substitution	0.871313673	B.1.177	2	1	TRUE	FALSE
N:G204R	B.1.1.222	3565	3575	N	G	R	204	None	substitution	0.997202797	B.1.1.222	44	39	FALSE	FALSE
S:T732A	B.1.1.222	3564	3575	S	T	A	732	None	substitution	0.996923077	B.1.1.222	2	2	FALSE	FALSE
S:D614G	B.1.1.222	3556	3575	S	D	G	614	None	substitution	0.994685315	B.1.1.222	115	75	FALSE	FALSE
N:R203K	B.1.1.222	3521	3575	N	R	K	203	None	substitution	0.984895105	B.1.1.222	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.222	3503	3575	ORF1b	P	L	314	None	substitution	0.97986014	B.1.1.222	113	73	FALSE	FALSE
S:D614G	C.36	949	953	S	D	G	614	None	substitution	0.995802728	C	115	75	FALSE	FALSE
ORF1A:T1246I	C.36	943	953	ORF1a	T	I	1246	None	substitution	0.989506821	C	6	2	FALSE	FALSE
N:G212V	C.36	942	953	N	G	V	212	None	substitution	0.988457503	C	2	1	TRUE	FALSE
N:R203K	C.36	942	953	N	R	K	203	None	substitution	0.988457503	C	44	39	FALSE	FALSE
ORF1B:P314L	C.36	941	953	ORF1b	P	L	314	None	substitution	0.987408185	C	113	73	FALSE	FALSE
ORF1A:G3278S	C.36	874	953	ORF1a	G	S	3278	None	substitution	0.917103882	C	5	2	FALSE	FALSE
N:G204R	C.36	821	953	N	G	R	204	None	substitution	0.861490031	C	44	39	FALSE	FALSE
S:Q677H	C.36	785	953	S	Q	H	677	None	substitution	0.823714586	C	3	2	FALSE	FALSE
S:D614G	B.1.575.1	367	367	S	D	G	614	None	substitution	1	B.1.575	115	75	FALSE	FALSE
N:T205I	B.1.575.1	366	367	N	T	I	205	None	substitution	0.997275204	B.1.575	7	6	FALSE	FALSE
S:P681H	B.1.575.1	366	367	S	P	H	681	None	substitution	0.997275204	B.1.575	6	6	FALSE	FALSE
ORF1A:T265I	B.1.575.1	365	367	ORF1a	T	I	265	None	substitution	0.994550409	B.1.575	8	7	FALSE	FALSE
ORF1A:T3255I	B.1.575.1	365	367	ORF1a	T	I	3255	None	substitution	0.994550409	B.1.575	3	3	FALSE	FALSE
ORF3A:Q57H	B.1.575.1	365	367	ORF3a	Q	H	57	None	substitution	0.994550409	B.1.575	21	12	FALSE	FALSE
S:T716I	B.1.575.1	365	367	S	T	I	716	None	substitution	0.994550409	B.1.575	3	3	FALSE	FALSE
M:I82T	B.1.575.1	364	367	M	I	T	82	None	substitution	0.991825613	B.1.575	6	6	FALSE	FALSE
ORF1B:P314L	B.1.575.1	364	367	ORF1b	P	L	314	None	substitution	0.991825613	B.1.575	113	73	FALSE	FALSE
N:A414S	B.1.575.1	363	367	N	A	S	414	None	substitution	0.989100817	B.1.575	1	1	TRUE	TRUE
ORF1B:P970S	B.1.575.1	363	367	ORF1b	P	S	970	None	substitution	0.989100817	B.1.575	1	1	TRUE	TRUE
S:S494P	B.1.575.1	363	367	S	S	P	494	None	substitution	0.989100817	B.1.575	1	1	TRUE	TRUE
ORF1A:T3750I	B.1.575.1	355	367	ORF1a	T	I	3750	None	substitution	0.967302452	B.1.575	1	1	TRUE	TRUE
N:G204R	L.3	242	246	N	G	R	204	None	substitution	0.983739837	L	44	39	FALSE	FALSE
N:R203K	L.3	242	246	N	R	K	203	None	substitution	0.983739837	L	44	39	FALSE	FALSE
S:D614G	L.3	242	246	S	D	G	614	None	substitution	0.983739837	L	115	75	FALSE	FALSE
ORF1B:P314L	L.3	239	246	ORF1b	P	L	314	None	substitution	0.971544715	L	113	73	FALSE	FALSE
S:Y1155F	L.3	233	246	S	Y	F	1155	None	substitution	0.947154472	L	1	1	TRUE	TRUE
ORF1A:P2739L	L.3	223	246	ORF1a	P	L	2739	None	substitution	0.906504065	L	1	1	TRUE	TRUE
ORF1A:M1378I	L.3	222	246	ORF1a	M	I	1378	None	substitution	0.902439024	L	1	1	TRUE	TRUE
S:L452R	L.3	222	246	S	L	R	452	None	substitution	0.902439024	L	7	4	FALSE	FALSE
ORF1A:L446F	L.3	221	246	ORF1a	L	F	446	None	substitution	0.898373984	L	1	1	TRUE	TRUE
S:V1228L	L.3	221	246	S	V	L	1228	None	substitution	0.898373984	L	1	1	TRUE	TRUE
ORF1A:P3767L	L.3	218	246	ORF1a	P	L	3767	None	substitution	0.886178862	L	1	1	TRUE	TRUE
ORF1A:Y3063S	L.3	215	246	ORF1a	Y	S	3063	None	substitution	0.87398374	L	1	1	TRUE	TRUE
S:D614G	B.1.1.170	753	756	S	D	G	614	None	substitution	0.996031746	B.1.1.170	115	75	FALSE	FALSE
N:G204R	B.1.1.170	751	756	N	G	R	204	None	substitution	0.993386243	B.1.1.170	44	39	FALSE	FALSE
N:R203K	B.1.1.170	751	756	N	R	K	203	None	substitution	0.993386243	B.1.1.170	44	39	FALSE	FALSE
ORF1A:P1640H	B.1.1.170	751	756	ORF1a	P	H	1640	None	substitution	0.993386243	B.1.1.170	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.170	750	756	ORF1b	P	L	314	None	substitution	0.992063492	B.1.1.170	113	73	FALSE	FALSE
ORF1A:M3087I	B.1.160.29	229	230	ORF1a	M	I	3087	None	substitution	0.995652174	B.1.160	7	1	TRUE	FALSE
ORF1B:E1184D	B.1.160.29	229	230	ORF1b	E	D	1184	None	substitution	0.995652174	B.1.160	7	1	TRUE	FALSE
ORF1B:K1141R	B.1.160.29	229	230	ORF1b	K	R	1141	None	substitution	0.995652174	B.1.160	7	1	TRUE	FALSE
ORF1B:V767L	B.1.160.29	229	230	ORF1b	V	L	767	None	substitution	0.995652174	B.1.160	7	1	TRUE	FALSE
ORF3A:Q57H	B.1.160.29	229	230	ORF3a	Q	H	57	None	substitution	0.995652174	B.1.160	21	12	FALSE	FALSE
ORF1B:P314L	B.1.160.29	228	230	ORF1b	P	L	314	None	substitution	0.991304348	B.1.160	113	73	FALSE	FALSE
ORF3A:E239D	B.1.160.29	228	230	ORF3a	E	D	239	None	substitution	0.991304348	B.1.160	1	1	TRUE	TRUE
S:D614G	B.1.160.29	228	230	S	D	G	614	None	substitution	0.991304348	B.1.160	115	75	FALSE	FALSE
ORF1B:A176S	B.1.160.29	226	230	ORF1b	A	S	176	None	substitution	0.982608696	B.1.160	7	1	TRUE	FALSE
ORF1B:V1639F	B.1.160.29	226	230	ORF1b	V	F	1639	None	substitution	0.982608696	B.1.160	1	1	TRUE	TRUE
N:M234I	B.1.160.29	224	230	N	M	I	234	None	substitution	0.973913043	B.1.160	10	4	FALSE	FALSE
N:A376T	B.1.160.29	220	230	N	A	T	376	None	substitution	0.956521739	B.1.160	7	1	TRUE	FALSE
S:S477N	B.1.160.29	220	230	S	S	N	477	None	substitution	0.956521739	B.1.160	7	1	TRUE	FALSE
ORF1B:E1184D	B.1.160.15	203	205	ORF1b	E	D	1184	None	substitution	0.990243902	B.1.160	7	1	TRUE	FALSE
ORF1B:K1141R	B.1.160.15	203	205	ORF1b	K	R	1141	None	substitution	0.990243902	B.1.160	7	1	TRUE	FALSE
ORF1B:V767L	B.1.160.15	203	205	ORF1b	V	L	767	None	substitution	0.990243902	B.1.160	7	1	TRUE	FALSE
S:D614G	B.1.160.15	203	205	S	D	G	614	None	substitution	0.990243902	B.1.160	115	75	FALSE	FALSE
ORF1B:A176S	B.1.160.15	202	205	ORF1b	A	S	176	None	substitution	0.985365854	B.1.160	7	1	TRUE	FALSE
ORF1B:P314L	B.1.160.15	202	205	ORF1b	P	L	314	None	substitution	0.985365854	B.1.160	113	73	FALSE	FALSE
ORF3A:Q57H	B.1.160.15	202	205	ORF3a	Q	H	57	None	substitution	0.985365854	B.1.160	21	12	FALSE	FALSE
ORF1A:M3087I	B.1.160.15	200	205	ORF1a	M	I	3087	None	substitution	0.975609756	B.1.160	7	1	TRUE	FALSE
N:A376T	B.1.160.15	196	205	N	A	T	376	None	substitution	0.956097561	B.1.160	7	1	TRUE	FALSE
N:M234I	B.1.160.15	195	205	N	M	I	234	None	substitution	0.951219512	B.1.160	10	4	FALSE	FALSE
ORF7A:T14I	B.1.160.15	191	205	ORF7a	T	I	14	None	substitution	0.931707317	B.1.160	2	1	TRUE	FALSE
S:S477N	B.1.160.15	188	205	S	S	N	477	None	substitution	0.917073171	B.1.160	7	1	TRUE	FALSE
S:D614G	B.1.157	203	203	S	D	G	614	None	substitution	1	B.1.157	115	75	FALSE	FALSE
ORF1B:P314L	B.1.157	202	203	ORF1b	P	L	314	None	substitution	0.995073892	B.1.157	113	73	FALSE	FALSE
ORF1B:L1220P	B.1.157	201	203	ORF1b	L	P	1220	None	substitution	0.990147783	B.1.157	1	1	TRUE	TRUE
N:G204R	B.1.1.16	21	21	N	G	R	204	None	substitution	1	B.1.1.16	44	39	FALSE	FALSE
N:R203K	B.1.1.16	21	21	N	R	K	203	None	substitution	1	B.1.1.16	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.16	21	21	ORF1b	P	L	314	None	substitution	1	B.1.1.16	113	73	FALSE	FALSE
S:A892S	B.1.1.16	21	21	S	A	S	892	None	substitution	1	B.1.1.16	1	1	TRUE	TRUE
S:D614G	B.1.1.16	21	21	S	D	G	614	None	substitution	1	B.1.1.16	115	75	FALSE	FALSE
ORF1B:P314L	B.1.356	534	534	ORF1b	P	L	314	None	substitution	1	B.1.356	113	73	FALSE	FALSE
S:D614G	B.1.356	533	534	S	D	G	614	None	substitution	0.998127341	B.1.356	115	75	FALSE	FALSE
ORF3A:Q57H	B.1.356	530	534	ORF3a	Q	H	57	None	substitution	0.992509363	B.1.356	21	12	FALSE	FALSE
ORF3A:A99V	B.1.356	528	534	ORF3a	A	V	99	None	substitution	0.988764045	B.1.356	2	2	FALSE	FALSE
ORF1A:T265I	B.1.356	525	534	ORF1a	T	I	265	None	substitution	0.983146067	B.1.356	8	7	FALSE	FALSE
ORF1A:G392D	B.3	1115	1147	ORF1a	G	D	392	None	substitution	0.972101133	B.3	1	1	TRUE	TRUE
ORF1A:A876T	B.3	953	1147	ORF1a	A	T	876	None	substitution	0.830863121	B.3	1	1	TRUE	TRUE
ORF1B:P314L	B.1.384	351	357	ORF1b	P	L	314	None	substitution	0.983193277	B.1.384	113	73	FALSE	FALSE
S:D614G	B.1.384	350	357	S	D	G	614	None	substitution	0.980392157	B.1.384	115	75	FALSE	FALSE
ORF8:L84S	A.2	1464	1482	ORF8	L	S	84	None	substitution	0.987854251	A	4	1	TRUE	FALSE
N:S197L	A.2	1449	1482	N	S	L	197	None	substitution	0.977732794	A	2	1	TRUE	FALSE
ORF1A:F3071Y	A.2	1447	1482	ORF1a	F	Y	3071	None	substitution	0.976383266	A	2	1	TRUE	FALSE
ORF3A:G196V	A.2	1247	1482	ORF3a	G	V	196	None	substitution	0.841430499	A	2	1	TRUE	FALSE
N:G204R	B.1.1.71	152	152	N	G	R	204	None	substitution	1	B.1.1.71	44	39	FALSE	FALSE
N:R203K	B.1.1.71	152	152	N	R	K	203	None	substitution	1	B.1.1.71	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.71	151	152	ORF1b	P	L	314	None	substitution	0.993421053	B.1.1.71	113	73	FALSE	FALSE
S:D614G	B.1.1.71	151	152	S	D	G	614	None	substitution	0.993421053	B.1.1.71	115	75	FALSE	FALSE
ORF1B:P314L	B.1.201	170	170	ORF1b	P	L	314	None	substitution	1	B.1.201	113	73	FALSE	FALSE
S:D614G	B.1.201	170	170	S	D	G	614	None	substitution	1	B.1.201	115	75	FALSE	FALSE
ORF1A:P892L	B.1.201	169	170	ORF1a	P	L	892	None	substitution	0.994117647	B.1.201	1	1	TRUE	TRUE
ORF1B:P314L	B.1.143	47	47	ORF1b	P	L	314	None	substitution	1	B.1.143	113	73	FALSE	FALSE
S:D614G	B.1.143	47	47	S	D	G	614	None	substitution	1	B.1.143	115	75	FALSE	FALSE
S:D614G	B.1.147	1206	1211	S	D	G	614	None	substitution	0.995871181	B.1.147	115	75	FALSE	FALSE
ORF3A:T14I	B.1.147	1205	1211	ORF3a	T	I	14	None	substitution	0.995045417	B.1.147	1	1	TRUE	TRUE
ORF1B:P314L	B.1.147	1196	1211	ORF1b	P	L	314	None	substitution	0.987613543	B.1.147	113	73	FALSE	FALSE
ORF1B:P314L	B.1.160.16	935	945	ORF1b	P	L	314	None	substitution	0.989417989	B.1.160	113	73	FALSE	FALSE
S:D614G	B.1.160.16	932	945	S	D	G	614	None	substitution	0.986243386	B.1.160	115	75	FALSE	FALSE
ORF1B:K1141R	B.1.160.16	919	945	ORF1b	K	R	1141	None	substitution	0.972486772	B.1.160	7	1	TRUE	FALSE
ORF1B:E1184D	B.1.160.16	918	945	ORF1b	E	D	1184	None	substitution	0.971428571	B.1.160	7	1	TRUE	FALSE
ORF1B:V767L	B.1.160.16	918	945	ORF1b	V	L	767	None	substitution	0.971428571	B.1.160	7	1	TRUE	FALSE
ORF7A:T14I	B.1.160.16	918	945	ORF7a	T	I	14	None	substitution	0.971428571	B.1.160	2	1	TRUE	FALSE
ORF8:S24L	B.1.160.16	916	945	ORF8	S	L	24	None	substitution	0.969312169	B.1.160	2	2	FALSE	FALSE
ORF3A:Q57H	B.1.160.16	914	945	ORF3a	Q	H	57	None	substitution	0.967195767	B.1.160	21	12	FALSE	FALSE
N:M234I	B.1.160.16	913	945	N	M	I	234	None	substitution	0.966137566	B.1.160	10	4	FALSE	FALSE
ORF1A:M3087I	B.1.160.16	910	945	ORF1a	M	I	3087	None	substitution	0.962962963	B.1.160	7	1	TRUE	FALSE
N:A376T	B.1.160.16	906	945	N	A	T	376	None	substitution	0.958730159	B.1.160	7	1	TRUE	FALSE
ORF1B:A176S	B.1.160.16	905	945	ORF1b	A	S	176	None	substitution	0.957671958	B.1.160	7	1	TRUE	FALSE
S:S477N	B.1.160.16	879	945	S	S	N	477	None	substitution	0.93015873	B.1.160	7	1	TRUE	FALSE
S:D614G	B.1.177.86	5299	5319	S	D	G	614	None	substitution	0.996239895	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177.86	5293	5319	ORF1b	P	L	314	None	substitution	0.995111863	B.1.177	113	73	FALSE	FALSE
ORF7B:E39*	B.1.177.86	5284	5319	ORF7b	E	*	39	None	substitution	0.993419816	B.1.177	1	1	TRUE	TRUE
S:A222V	B.1.177.86	5241	5319	S	A	V	222	None	substitution	0.985335589	B.1.177	20	3	FALSE	FALSE
N:A220V	B.1.177.86	5234	5319	N	A	V	220	None	substitution	0.984019553	B.1.177	20	3	FALSE	FALSE
S:L18F	B.1.177.86	5214	5319	S	L	F	18	None	substitution	0.980259447	B.1.177	6	5	FALSE	FALSE
ORF10:V30L	B.1.177.86	4899	5319	ORF10	V	L	30	None	substitution	0.921037789	B.1.177	20	3	FALSE	FALSE
S:D614G	B.1.177.43	581	584	S	D	G	614	None	substitution	0.994863014	B.1.177	115	75	FALSE	FALSE
ORF1B:P314L	B.1.177.43	576	584	ORF1b	P	L	314	None	substitution	0.98630137	B.1.177	113	73	FALSE	FALSE
ORF1B:I1539T	B.1.177.43	562	584	ORF1b	I	T	1539	None	substitution	0.962328767	B.1.177	1	1	TRUE	TRUE
N:A220V	B.1.177.43	559	584	N	A	V	220	None	substitution	0.957191781	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.43	553	584	ORF10	V	L	30	None	substitution	0.946917808	B.1.177	20	3	FALSE	FALSE
S:A222V	B.1.177.43	550	584	S	A	V	222	None	substitution	0.941780822	B.1.177	20	3	FALSE	FALSE
ORF1A:H1113Y	B.1.221.1	331	331	ORF1a	H	Y	1113	None	substitution	1	B.1.221	4	1	TRUE	FALSE
ORF1A:V1393L	B.1.221.1	331	331	ORF1a	V	L	1393	None	substitution	1	B.1.221	1	1	TRUE	TRUE
ORF3A:Q38R	B.1.221.1	331	331	ORF3a	Q	R	38	None	substitution	1	B.1.221	4	1	TRUE	FALSE
S:D614G	B.1.221.1	331	331	S	D	G	614	None	substitution	1	B.1.221	115	75	FALSE	FALSE
S:S98F	B.1.221.1	331	331	S	S	F	98	None	substitution	1	B.1.221	4	1	TRUE	FALSE
N:P199L	B.1.221.1	330	331	N	P	L	199	None	substitution	0.996978852	B.1.221	5	2	FALSE	FALSE
ORF1A:T2087I	B.1.221.1	330	331	ORF1a	T	I	2087	None	substitution	0.996978852	B.1.221	1	1	TRUE	TRUE
ORF1B:P314L	B.1.221.1	328	331	ORF1b	P	L	314	None	substitution	0.990936556	B.1.221	113	73	FALSE	FALSE
ORF3A:G172R	B.1.221.1	328	331	ORF3a	G	R	172	None	substitution	0.990936556	B.1.221	3	1	TRUE	FALSE
ORF3A:V202L	B.1.221.1	328	331	ORF3a	V	L	202	None	substitution	0.990936556	B.1.221	4	1	TRUE	FALSE
N:T205I	B.1.214.3	109	110	N	T	I	205	None	substitution	0.990909091	B.1.214	7	6	FALSE	FALSE
S:D614G	B.1.214.3	109	110	S	D	G	614	None	substitution	0.990909091	B.1.214	115	75	FALSE	FALSE
S:T716I	B.1.214.3	109	110	S	T	I	716	None	substitution	0.990909091	B.1.214	3	3	FALSE	FALSE
ORF1A:A4016V	B.1.214.3	107	110	ORF1a	A	V	4016	None	substitution	0.972727273	B.1.214	1	1	TRUE	TRUE
S:T95I	B.1.214.3	107	110	S	T	I	95	None	substitution	0.972727273	B.1.214	2	2	FALSE	FALSE
ORF1A:I1398V	B.1.214.3	106	110	ORF1a	I	V	1398	None	substitution	0.963636364	B.1.214	1	1	TRUE	TRUE
ORF1A:T1881I	B.1.214.3	106	110	ORF1a	T	I	1881	None	substitution	0.963636364	B.1.214	1	1	TRUE	TRUE
ORF1B:P314L	B.1.214.3	106	110	ORF1b	P	L	314	None	substitution	0.963636364	B.1.214	113	73	FALSE	FALSE
ORF1A:Y3722C	B.1.214.3	101	110	ORF1a	Y	C	3722	None	substitution	0.918181818	B.1.214	1	1	TRUE	TRUE
S:T478K	B.1.214.3	96	110	S	T	K	478	None	substitution	0.872727273	B.1.214	3	3	FALSE	FALSE
ORF1A:DEL3674/3676	B.1.214.3	94	110	ORF1a	ORF1A:DEL3674/3676	DEL3674/3676	3674	3676	deletion	0.854545455	B.1.214	1	1	TRUE	TRUE
ORF1B:R574G	B.1.214.3	94	110	ORF1b	R	G	574	None	substitution	0.854545455	B.1.214	1	1	TRUE	TRUE
N:G204R	B.1.1.451	32	32	N	G	R	204	None	substitution	1	B.1.1.451	44	39	FALSE	FALSE
N:R203K	B.1.1.451	32	32	N	R	K	203	None	substitution	1	B.1.1.451	44	39	FALSE	FALSE
ORF1B:P314L	B.1.1.451	32	32	ORF1b	P	L	314	None	substitution	1	B.1.1.451	113	73	FALSE	FALSE
S:D614G	B.1.1.451	32	32	S	D	G	614	None	substitution	1	B.1.1.451	115	75	FALSE	FALSE
S:D614G	B.1.610	614	615	S	D	G	614	None	substitution	0.998373984	B.1.610	115	75	FALSE	FALSE
ORF1B:P314L	B.1.610	609	615	ORF1b	P	L	314	None	substitution	0.990243902	B.1.610	113	73	FALSE	FALSE
N:G204R	B.1.1.410	22	22	N	G	R	204	None	substitution	1	B.1.1.410	44	39	FALSE	FALSE
N:R203K	B.1.1.410	22	22	N	R	K	203	None	substitution	1	B.1.1.410	44	39	FALSE	FALSE
ORF1B:M2414I	B.1.1.410	22	22	ORF1b	M	I	2414	None	substitution	1	B.1.1.410	1	1	TRUE	TRUE
ORF1B:P314L	B.1.1.410	22	22	ORF1b	P	L	314	None	substitution	1	B.1.1.410	113	73	FALSE	FALSE
S:D614G	B.1.1.410	22	22	S	D	G	614	None	substitution	1	B.1.1.410	115	75	FALSE	FALSE
N:G204R	B.1.1.385	208	208	N	G	R	204	None	substitution	1	B.1.1.385	44	39	FALSE	FALSE
N:R203K	B.1.1.385	208	208	N	R	K	203	None	substitution	1	B.1.1.385	44	39	FALSE	FALSE
ORF3A:A23S	B.1.1.385	208	208	ORF3a	A	S	23	None	substitution	1	B.1.1.385	1	1	TRUE	TRUE
S:D614G	B.1.1.385	208	208	S	D	G	614	None	substitution	1	B.1.1.385	115	75	FALSE	FALSE
ORF1B:P314L	B.1.1.385	207	208	ORF1b	P	L	314	None	substitution	0.995192308	B.1.1.385	113	73	FALSE	FALSE
ORF7A:A8S	B.1.1.385	207	208	ORF7a	A	S	8	None	substitution	0.995192308	B.1.1.385	1	1	TRUE	TRUE
S:Q675H	B.1.1.385	205	208	S	Q	H	675	None	substitution	0.985576923	B.1.1.385	1	1	TRUE	TRUE
ORF1A:H417R	B.39	405	408	ORF1a	H	R	417	None	substitution	0.992647059	B.39	1	1	TRUE	TRUE
ORF3A:G251V	B.39	400	408	ORF3a	G	V	251	None	substitution	0.980392157	B.39	1	1	TRUE	TRUE
ORF1A:L3606F	B.39	391	408	ORF1a	L	F	3606	None	substitution	0.958333333	B.39	2	2	FALSE	FALSE
ORF1B:P314L	B.1.177.40	200	200	ORF1b	P	L	314	None	substitution	1	B.1.177	113	73	FALSE	FALSE
S:D614G	B.1.177.40	200	200	S	D	G	614	None	substitution	1	B.1.177	115	75	FALSE	FALSE
S:A222V	B.1.177.40	197	200	S	A	V	222	None	substitution	0.985	B.1.177	20	3	FALSE	FALSE
N:A220V	B.1.177.40	196	200	N	A	V	220	None	substitution	0.98	B.1.177	20	3	FALSE	FALSE
ORF10:V30L	B.1.177.40	194	200	ORF10	V	L	30	None	substitution	0.97	B.1.177	20	3	FALSE	FALSE
N:P365S	B.1.177.40	165	200	N	P	S	365	None	substitution	0.825	B.1.177	2	1	TRUE	FALSE
ORF1B:P314L	B.1.160.32	211	211	ORF1b	P	L	314	None	substitution	1	B.1.160	113	73	FALSE	FALSE
S:D614G	B.1.160.32	210	211	S	D	G	614	None	substitution	0.995260664	B.1.160	115	75	FALSE	FALSE
ORF1A:T3255I	A.2.5	1039	1058	ORF1a	T	I	3255	None	substitution	0.982041588	A	3	3	FALSE	FALSE
ORF1A:F3071Y	A.2.5	1035	1058	ORF1a	F	Y	3071	None	substitution	0.97826087	A	2	1	TRUE	FALSE
ORF8:L84S	A.2.5	1032	1058	ORF8	L	S	84	None	substitution	0.975425331	A	4	1	TRUE	FALSE
N:S197L	A.2.5	1030	1058	N	S	L	197	None	substitution	0.973534972	A	2	1	TRUE	FALSE
ORF3A:S74F	A.2.5	1030	1058	ORF3a	S	F	74	None	substitution	0.973534972	A	1	1	TRUE	TRUE
N:M234I	A.2.5	1025	1058	N	M	I	234	None	substitution	0.968809074	A	10	4	FALSE	FALSE
ORF1B:P1000L	A.2.5	1025	1058	ORF1b	P	L	1000	None	substitution	0.968809074	A	3	2	FALSE	FALSE
ORF1A:L4F	A.2.5	1018	1058	ORF1a	L	F	4	None	substitution	0.962192817	A	1	1	TRUE	TRUE
ORF3A:G196V	A.2.5	1009	1058	ORF3a	G	V	196	None	substitution	0.9536862	A	2	1	TRUE	FALSE
ORF1A:H3580Q	A.2.5	1000	1058	ORF1a	H	Q	3580	None	substitution	0.945179584	A	1	1	TRUE	TRUE
S:D614G	A.2.5	994	1058	S	D	G	614	None	substitution	0.939508507	A	115	75	FALSE	FALSE
ORF1A:K1657E	A.2.5	982	1058	ORF1a	K	E	1657	None	substitution	0.928166352	A	1	1	TRUE	TRUE
S:L452R	A.2.5	946	1058	S	L	R	452	None	substitution	0.894139887	A	7	4	FALSE	FALSE
N:P383L	A.2.5	925	1058	N	P	L	383	None	substitution	0.874291115	A	1	1	TRUE	TRUE
ORF1A:DEL3675/3677	P.1.1	3919	3981	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.984426024	P	8	6	FALSE	FALSE
ORF1B:P314L	P.1.1	3880	3981	ORF1b	P	L	314	None	substitution	0.97462949	P	113	73	FALSE	FALSE
S:D614G	P.1.1	3873	3981	S	D	G	614	None	substitution	0.972871138	P	115	75	FALSE	FALSE
S:H655Y	P.1.1	3856	3981	S	H	Y	655	None	substitution	0.968600854	P	4	2	FALSE	FALSE
ORF1A:K1795Q	P.1.1	3848	3981	ORF1a	K	Q	1795	None	substitution	0.966591309	P	2	1	TRUE	FALSE
ORF1B:E1264D	P.1.1	3818	3981	ORF1b	E	D	1264	None	substitution	0.959055514	P	2	1	TRUE	FALSE
N:P80R	P.1.1	3797	3981	N	P	R	80	None	substitution	0.953780457	P	2	1	TRUE	FALSE
S:D138Y	P.1.1	3796	3981	S	D	Y	138	None	substitution	0.953529264	P	3	2	FALSE	FALSE
ORF1A:S1188L	P.1.1	3784	3981	ORF1a	S	L	1188	None	substitution	0.950514946	P	2	1	TRUE	FALSE
S:T20N	P.1.1	3768	3981	S	T	N	20	None	substitution	0.946495855	P	2	1	TRUE	FALSE
S:E484K	P.1.1	3756	3981	S	E	K	484	None	substitution	0.943481537	P	9	6	FALSE	FALSE
S:N501Y	P.1.1	3752	3981	S	N	Y	501	None	substitution	0.942476765	P	6	4	FALSE	FALSE
S:P26S	P.1.1	3750	3981	S	P	S	26	None	substitution	0.941974378	P	2	1	TRUE	FALSE
ORF3A:S253P	P.1.1	3734	3981	ORF3a	S	P	253	None	substitution	0.937955288	P	2	1	TRUE	FALSE
S:K417T	P.1.1	3731	3981	S	K	T	417	None	substitution	0.937201708	P	2	1	TRUE	FALSE
S:L18F	P.1.1	3711	3981	S	L	F	18	None	substitution	0.932177845	P	6	5	FALSE	FALSE
ORF8:E92K	P.1.1	3683	3981	ORF8	E	K	92	None	substitution	0.925144436	P	2	1	TRUE	FALSE
S:R190S	P.1.1	3572	3981	S	R	S	190	None	substitution	0.897261994	P	2	1	TRUE	FALSE
S:T1027I	P.1.1	3482	3981	S	T	I	1027	None	substitution	0.874654609	P	3	2	FALSE	FALSE
N:G204R	R.1	9960	9964	N	G	R	204	None	substitution	0.999598555	R	44	39	FALSE	FALSE
ORF1B:G1362R	R.1	9960	9964	ORF1b	G	R	1362	None	substitution	0.999598555	R	1	1	TRUE	TRUE
S:E484K	R.1	9960	9964	S	E	K	484	None	substitution	0.999598555	R	9	6	FALSE	FALSE
S:D614G	R.1	9958	9964	S	D	G	614	None	substitution	0.999397832	R	115	75	FALSE	FALSE
N:S187L	R.1	9953	9964	N	S	L	187	None	substitution	0.998896026	R	2	2	FALSE	FALSE
N:R203K	R.1	9952	9964	N	R	K	203	None	substitution	0.998795664	R	44	39	FALSE	FALSE
M:F28L	R.1	9941	9964	M	F	L	28	None	substitution	0.99769169	R	1	1	TRUE	TRUE
ORF1B:P314L	R.1	9940	9964	ORF1b	P	L	314	None	substitution	0.997591329	R	113	73	FALSE	FALSE
N:Q418H	R.1	9935	9964	N	Q	H	418	None	substitution	0.997089522	R	1	1	TRUE	TRUE
S:W152L	R.1	9877	9964	S	W	L	152	None	substitution	0.991268567	R	1	1	TRUE	TRUE
S:G769V	R.1	9793	9964	S	G	V	769	None	substitution	0.982838218	R	1	1	TRUE	TRUE
ORF1B:P1936H	R.1	9640	9964	ORF1b	P	H	1936	None	substitution	0.967482939	R	1	1	TRUE	TRUE
N:G204R	C.36.3	1371	1375	N	G	R	204	None	substitution	0.997090909	C	44	39	FALSE	FALSE
ORF1A:T1246I	C.36.3	1371	1375	ORF1a	T	I	1246	None	substitution	0.997090909	C	6	2	FALSE	FALSE
ORF1A:L3691S	C.36.3	1370	1375	ORF1a	L	S	3691	None	substitution	0.996363636	C	1	1	TRUE	TRUE
S:Q677H	C.36.3	1370	1375	S	Q	H	677	None	substitution	0.996363636	C	3	2	FALSE	FALSE
N:R203K	C.36.3	1369	1375	N	R	K	203	None	substitution	0.995636364	C	44	39	FALSE	FALSE
ORF1A:D3222N	C.36.3	1369	1375	ORF1a	D	N	3222	None	substitution	0.995636364	C	1	1	TRUE	TRUE
S:A899S	C.36.3	1369	1375	S	A	S	899	None	substitution	0.995636364	C	1	1	TRUE	TRUE
ORF1B:P314L	C.36.3	1366	1375	ORF1b	P	L	314	None	substitution	0.993454545	C	113	73	FALSE	FALSE
S:D614G	C.36.3	1362	1375	S	D	G	614	None	substitution	0.990545455	C	115	75	FALSE	FALSE
S:R346S	C.36.3	1362	1375	S	R	S	346	None	substitution	0.990545455	C	1	1	TRUE	TRUE
ORF1A:D2980N	C.36.3	1361	1375	ORF1a	D	N	2980	None	substitution	0.989818182	C	1	1	TRUE	TRUE
N:G212V	C.36.3	1358	1375	N	G	V	212	None	substitution	0.987636364	C	2	1	TRUE	FALSE
ORF1A:S3687L	C.36.3	1358	1375	ORF1a	S	L	3687	None	substitution	0.987636364	C	1	1	TRUE	TRUE
ORF1B:D1028Y	C.36.3	1358	1375	ORF1b	D	Y	1028	None	substitution	0.987636364	C	1	1	TRUE	TRUE
M:I82T	C.36.3	1353	1375	M	I	T	82	None	substitution	0.984	C	6	6	FALSE	FALSE
S:L452R	C.36.3	1346	1375	S	L	R	452	None	substitution	0.978909091	C	7	4	FALSE	FALSE
S:W152R	C.36.3	1338	1375	S	W	R	152	None	substitution	0.973090909	C	1	1	TRUE	TRUE
ORF1A:E102K	C.36.3	1334	1375	ORF1a	E	K	102	None	substitution	0.970181818	C	2	2	FALSE	FALSE
ORF1A:P2287S	C.36.3	1334	1375	ORF1a	P	S	2287	None	substitution	0.970181818	C	1	1	TRUE	TRUE
ORF7B:A43S	C.36.3	1329	1375	ORF7b	A	S	43	None	substitution	0.966545455	C	1	1	TRUE	TRUE
ORF1A:G3278S	C.36.3	1328	1375	ORF1a	G	S	3278	None	substitution	0.965818182	C	5	2	FALSE	FALSE
ORF1A:T4090I	C.36.3	1324	1375	ORF1a	T	I	4090	None	substitution	0.962909091	C	1	1	TRUE	TRUE
S:S12F	C.36.3	1324	1375	S	S	F	12	None	substitution	0.962909091	C	1	1	TRUE	TRUE
ORF1A:D1639N	C.36.3	1319	1375	ORF1a	D	N	1639	None	substitution	0.959272727	C	1	1	TRUE	TRUE
ORF1A:A859V	C.36.3	1310	1375	ORF1a	A	V	859	None	substitution	0.952727273	C	1	1	TRUE	TRUE
ORF1B:P314L	B.1.36.22	780	781	ORF1b	P	L	314	None	substitution	0.99871959	B.1.36	113	73	FALSE	FALSE
ORF1A:K3353R	B.1.36.22	779	781	ORF1a	K	R	3353	None	substitution	0.997439181	B.1.36	4	3	FALSE	FALSE
ORF3A:Q57H	B.1.36.22	775	781	ORF3a	Q	H	57	None	substitution	0.992317542	B.1.36	21	12	FALSE	FALSE
N:S194L	B.1.36.22	770	781	N	S	L	194	None	substitution	0.985915493	B.1.36	5	3	FALSE	FALSE
S:D614G	B.1.36.22	768	781	S	D	G	614	None	substitution	0.983354673	B.1.36	115	75	FALSE	FALSE
S:D80A	B.1.351.3	1019	1020	S	D	A	80	None	substitution	0.999019608	B.1.351	2	1	TRUE	FALSE
ORF1B:I1074V	B.1.351.3	1018	1020	ORF1b	I	V	1074	None	substitution	0.998039216	B.1.351	1	1	TRUE	TRUE
ORF1A:K3353R	B.1.351.3	1017	1020	ORF1a	K	R	3353	None	substitution	0.997058824	B.1.351	4	3	FALSE	FALSE
S:D614G	B.1.351.3	1017	1020	S	D	G	614	None	substitution	0.997058824	B.1.351	115	75	FALSE	FALSE
ORF1A:T265I	B.1.351.3	1013	1020	ORF1a	T	I	265	None	substitution	0.993137255	B.1.351	8	7	FALSE	FALSE
ORF1B:P314L	B.1.351.3	1011	1020	ORF1b	P	L	314	None	substitution	0.991176471	B.1.351	113	73	FALSE	FALSE
ORF1A:P2046L	B.1.351.3	1010	1020	ORF1a	P	L	2046	None	substitution	0.990196078	B.1.351	1	1	TRUE	TRUE
ORF3A:Q57H	B.1.351.3	1009	1020	ORF3a	Q	H	57	None	substitution	0.989215686	B.1.351	21	12	FALSE	FALSE
N:T205I	B.1.351.3	1006	1020	N	T	I	205	None	substitution	0.98627451	B.1.351	7	6	FALSE	FALSE
S:A701V	B.1.351.3	1005	1020	S	A	V	701	None	substitution	0.985294118	B.1.351	2	1	TRUE	FALSE
E:P71L	B.1.351.3	1004	1020	E	P	L	71	None	substitution	0.984313725	B.1.351	2	1	TRUE	FALSE
S:L18F	B.1.351.3	1004	1020	S	L	F	18	None	substitution	0.984313725	B.1.351	6	5	FALSE	FALSE
S:D215G	B.1.351.3	1003	1020	S	D	G	215	None	substitution	0.983333333	B.1.351	2	1	TRUE	FALSE
S:K417N	B.1.351.3	1001	1020	S	K	N	417	None	substitution	0.981372549	B.1.351	2	1	TRUE	FALSE
ORF3A:S171L	B.1.351.3	994	1020	ORF3a	S	L	171	None	substitution	0.974509804	B.1.351	3	2	FALSE	FALSE
ORF1A:N2596S	B.1.351.3	992	1020	ORF1a	N	S	2596	None	substitution	0.97254902	B.1.351	1	1	TRUE	TRUE
ORF1A:DEL3675/3677	B.1.351.3	982	1020	ORF1a	ORF1A:DEL3675/3677	DEL3675/3677	3675	3677	deletion	0.962745098	B.1.351	8	6	FALSE	FALSE
ORF1A:K1655N	B.1.351.3	962	1020	ORF1a	K	N	1655	None	substitution	0.943137255	B.1.351	2	1	TRUE	FALSE
S:N501Y	B.1.351.3	927	1020	S	N	Y	501	None	substitution	0.908823529	B.1.351	6	4	FALSE	FALSE
S:E484K	B.1.351.3	913	1020	S	E	K	484	None	substitution	0.895098039	B.1.351	9	6	FALSE	FALSE
