Table 1.

SNPs with high F_ST ( > 0.8) that differentiate P. vivax isolates from South East Asia (SEA), East Africa and South Asia regions.

Region	Chr.	Position	Ref.	Alt	Effect*	AA change	Gene name	FST**
SEA	2	155305	G	T	Non Syn	L1207I	pvmrp1	0.83
SEA	2	156287	C	A	Syn	V879	pvmrp1	0.82
SEA	2	158223	G	A	Non Syn	T234M	pvmrp1	0.81
SEA	14	1070933	A	T	Non Syn	S310R	pvdmt1	0.86
SEA	14	1071214	C	T	Non Syn	V217I	pvdmt1	0.90
South Asia	5	286241	A	T	Non Syn	I83F	PDI8	0.83
South Asia	5	618291	T	G	Non Syn	F165V	PVP01_0514700	0.95
South Asia	6	668360	G	T	Non Syn	T65K	P28	0.83
South Asia	12	323703	G	C	Non Syn	S57T	P47	0.81
South Asia	13	336960	C	A	Non Syn	T1455K	CRMP3	0.81
East Africa	4	308246	A	G	Intron	–	CDPK1	0.83
East Africa	4	401595	C	T	Syn	Y670	ACS9	0.81
East Africa	4	401608	T	C	Syn	L675	ACS9	0.85
East Africa	4	401622	C	T	Syn	N679	ACS9	0.90
East Africa	5	722792	T	G	Non Syn	I172L	PVP01_0517200	0.86
East Africa	5	1067476	C	T	Non Syn	E158K	PVP01_0526300	0.87
East Africa	5	1071079	T	G	Intron	–	PVP01_0526400	0.92
East Africa	6	646355	C	T	Non Syn	M236I	CLAMP	0.96
East Africa	6	646864	C	T	Non Syn	D67N	CLAMP	0.88
East Africa	6	661527	C	G	Non Syn	S273C	RPN9	0.85
East Africa	7	499047	T	G	Non Syn	I1234S	CRMP1	0.93
East Africa	7	507890	T	A	Syn	P582	PVP01_0709900	0.90
East Africa	7	509284	C	T	Non Syn	D118N	PVP01_0709900	0.96
East Africa	7	509311	A	G	Non Syn	Y109H	PVP01_0709900	0.95
East Africa	7	509312	G	A	Syn	L108	PVP01_0709900	0.95
East Africa	7	514538	A	G	Syn	L14	PVP01_0710100	0.91
East Africa	7	525785	T	C	Syn	A1270	PVP01_0710500	0.80
East Africa	7	556907	C	G	Non Syn	M709I	PVP01_0711500	0.89
East Africa	11	917226	A	T	Non Syn	F1138L	PK4	0.87
East Africa	11	1075544	C	G	Non Syn	S455R	PVP01_1124700	0.88
East Africa	12	1869662	T	C	Non Syn	V414A	PVP01_1245200	0.84
East Africa	13	334457	A	G	Non Syn	K621E	CRMP3	0.86
East Africa	13	334917	T	G	Non Syn	M774R	CRMP3	0.90
East Africa	13	610100	C	A	Non Syn	K841N	PVP01_1313400	0.89
East Africa	14	1296340	T	C	Syn	S205	PPM5	0.81
East Africa	14	1923223	G	A	Non Syn	P504S	PVP01_1444400	0.81
East Africa	14	1923997	T	G	Non Syn	M246L	PVP01_1444400	0.91
East Africa	14	1923998	C	G	Syn	T245	PVP01_1444400	0.91
East Africa	14	1924051	T	C	Non Syn	T228A	PVP01_1444400	0.91
East Africa	14	1924658	C	T	Syn	E25	PVP01_1444400	0.85

AA amino acid, *Non Syn non-synonymous mutation, Syn synonymous mutation, Inter intergenic region, Start lost start codon lost.

**Within Region vs. other isolates.

See Supplementary Data 3 for all regional comparisons.