Table S2.

P. falciparum nuclear reads

Sample	Total reads	Mapped reads	Unique reads	Nuclear coverage
CA depletion	41,669,177	90,132	80,570	0.0182
CM depletion	36,781,114	9,516	4,784	0.0130
POS depletion	47,712,546	6,653	4,965	0.0157
CA capture	52,310,688	24,196,904	132,642	0.4290
CM capture	32,441,831	78,769	3,559	0.0100
POS capture	32,323,796	489,464	2,792	0.0100