Table 1. Summary of SNP verification.
| Chromosome | 5 | 5 | 6 | 8 | 14 |
| SNP Position | 214184 | 214244 | 645035 | 738807 | 721985 |
| Gene ID* | PFE0245c | PFE0245c | PFF0750w | MAL8P1_82 | PF14_0173 |
| 3D7** | T | T | A | T | A |
| Dd2 (new) | T | T | G | T | T |
| Dd2 (old) | A | T | G | A | T |
| C | A | T | G | A | T |
| D | A | T | G | A | T |
| E | A | T | Nd | A | T |
| F | A | T | Nd | A | T |
| NS | T | T | Nd | T | A |
| C53-1 | A | T | G | Nd | T |
| D53-1 | A | T | Nd | A | T |
| D73-1 | A | T | Nd | Nd | T |
| D73-2 | A | T | Nd | A | T |
| C710-1a | A | T | G | A | T |
| C710-2b | A | T | G | A | T |
Regions of the genome where non-synonomous exonic SNPs were detected in whole genome Illumina sequencing (Table S5) were PCR amplified (primers listed in Table S12) and dideoxy-sequenced in multiple parasite clones including 3D7 recently acquired from MR4 (MRA-156, MR4, ATCC Manassas Virginia), Dd2 (new) recently acquired from MR4, Dd2 (old) maintained in the Rathod lab for years, round 1 clones (C, D, E and F), NS clone newly selected from Dd2 (new) at 0.3 µM DSM1 (Fig. S10), and round 2 clones (C53-1, D53-1, D73-1, D73-2, C710-1b, C710-2b). Overall, SNPs at positions 214184, 645035, 738807, and 721985 likely originated in the parent Dd2 clone. This conclusion was based on the presence of the wild type nucleotide in the newly selected clone (NS) and/or the mutant nucleotide in an “old” Dd2 clone (the closest known clone to the parent of these selections). The SNP at position 214244 was not detected at all in this analysis, indicating that it was not important for the phenotype. We do not believe that position 214244 is a miscall because we can observe Illumina reads that contain this SNP; the final call was likely due to repetitive sequence in the region that caused misalignment of reads from the proximal SNP position at 214184.
PlasmoDB gene ID.
Based on 3D7 sequence from PlasmoDB. Loci on chromosome 6, 8 and 14 were also sequenced from a laboratory 3D7 clone.
Nd, not determined.