Table 1.

Whole-genome sequencing statistics

Experiment ID	Data source	Background strain	# of genomes	Resistance	Gene conferring resistance
Dd2 (parent)	[6,10-12]	n/a	1	Chloroquine, Mefloquine, Pyrimethamine	n/a
3D7 (parent)	[12]	n/a	1	Sulfadoxine	n/a
KAD707 and 458	[12]	Dd2	4	Imidazolopiperazine	pfcarl
CladoR	[10], this study	Dd2	3	Cladosporin	pfkrs1
NITD609 (KAE609)	[6,11]	Dd2	3	Spiroindolone	pfatp4
NITD678	[6,11]	Dd2	3	Spiroindolone	pfatp4
Evo	[6]	3D7	14	Atovaquone	mal_mito_3

Whole genome sequencing data acquisition statistics from each of the experiments used to validate the pipeline. Note that all of the lines with variants to be called were sub-cloned before sequencing and were sequenced as 70 bp paired end reads, except the KAD (imidazolopiperazines resistant) lines, which were sequenced as 60 bp single end reads. Library preparation details for sequences obtained from previous studies are available in their respective manuscripts. Library preparations for sequences obtained for this study (those resistant to cladosporin), are as follows: 200 bp fragments with 70 bp reads were prepared according to the manufacturers instructions using the Illumina NexTera XT sample preparation kit with accompanying primers and sheared using a Covaris E220x machine.

n/a – not applicable.