Table S1.

P. vivax nuclear reads

Sample	Total reads	Mapped reads	Unique reads	Nuclear coverage
CA depletion	41,669,177	8,939	3,036	0.0000
CM depletion	36,781,114	40,047	35,072	0.0889
POS depletion	47,712,546	2,348	710	0.0000
CA capture	52,310,688	8,388	2,600	0.0053
CM capture	32,441,831	13,940	10,678	0.0259
POS capture	32,323,796	2,013	547	0.0010