Genetic linkage by QTL and concentrations of metabolites‡ (µM ± s.d.) observed in parasite extracts from chloroquine sensitive (CQS) and resistant (CQR) transgenic parasites.

Peptides are listed by their standard abbreviations, unknowns are abbreviated as Ukn, and 6PGn indicates 6-phosphogluconate.Threshold LOD scores for genome wide significance, computed by permutation, before and after Bonferroni α correction for multiple comparison testing. Q-value analysis of the original unfiltered mass list established a LOD score of 5.5 as the 5% false discovery threshold.p-values for QTL analysis reflect the genome-wide significance computed by permutation (N = 1000) of the sample genotypes (N = 36); p-values reported for metabolite concentrations observed in the parasite extracts were computed by one-way analysis of variance (N = 9; K = 3).Metabolite levels are reported as µM concentrations present in 1∶4 final dilutions of extracts from packed infected cells (∼90% parasitemia) as measured by single reaction monitoring mass spectrometry. C2 parasites carry the CQS HB3 pfcrt allele, C4 and C6 carry the CQR pfcrt alleles from Dd2 and 7G8, respectively.