Table S7.

Limited copy-number variation in P. vivax and P. falciparum clinical isolates

Species	Gene(s)	GeneID	Breakpoints* (Chr:start-end)	Copy number	Frequency
P. vivax	Duffy-binding protein (dbp)	PVX_110810	Chr06	2×	16/70
			974,753 (± 3)
			982,117 (± 1)
				4×	1/70
P. vivax	Cytoadherence-linked asexual protein (clag); exported protein, unknown function	PVX_094265; PVX_094270	Chr08	0׆	6/70
			73,105 (± 2)
			82,397 (± 6)
P. falciparum	Multidrug-resistance protein 1 (pfmdr1)	PF3D7_0523000	Chr05	2×	5/80
			946,536 (± 3124)
			967,973 (± 3065)
				3×	5/80
				4×	2/80
P. falciparum	Plasmepsin II	PF3D7_1408000	Chr14	2×	16/80
			289,558 (± 34)
			298,819 (± 16)
				3×	16/80

Copy-number duplication events are reported where detected by two methodologically distinct copy-number–calling software programs.

^*Breakpoints were predicted probabilistically for each sample and in some cases differ among isolates. It is currently unclear whether these differences represent unique duplication events or imperfect accuracy in predicting breakpoints. Mean breakpoints with SDs are reported.

^†A copy number of zero indicates a deletion.