Table 1 SNPs associated with antimalarial resistance. SNPs of interest used to optimize target primer design that are covered by primer pools R1.1, R1.2 or R2. The list excludes copy number variation markers, such as plasmepsins 2 and 3 (piperaquine) or mdr1 (mefloquine). A full list of targets with the amino acid ranges they cover in each gene can be found in Supplementary Table 4.

Antimalarial^a	Gene	Amino acids covered
Chloroquine and piperaquine	crt	72–76, 93, 97, 145, 218, 220, 271^b, 326^b, 343, 350, 353, 356
Chloroquine	aat1^b	135^b, 162^b, 185^b, 230^b, 238^b, 380^b
Piperaquine	exo	415
Chloroquine and lumefantrine	mdr1	86, 184, 186, 371, 1034, 1042, 1246
Sulfadoxine	dhps	431, 436, 437, 540, 581, 613
Pyrimethamine and proguanil	dhfr	16, 51, 59, 108, 164
Artemisinin	kelch13	441, 446, 449, 458, 469, 476,481, 493, 515, 527, 537, 538, 539, 543, 553, 561, 568, 574, 580, 622, 675
	coronin	50, 100, 107
	fd	193
	arps10	127, 128
	mdr2	463, 484, 515
	PF3D7_1322700	236
	pib7	1484
	ubp-1	1525
	pph^b	1157^b

^aAntimalarial with validated or candidate markers⁷⁹, or with SNPs identified in GWAS studies⁸⁰.
^bIncluded only in R1.1 and not in R1.2.

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