Table 2.
Top hits in nSL analysis of P. vivax monoclonal infections
| Chr | Focal SNP statistics | Sweep region statistics | |||
| Location | nSL | Closest plausible genetic driver | Gene ID | Distance* | |
| 14 | 797,870 | 6.203 | Transcription factor with AP2 domain(s), putative (apiap2) | PVX_122680 | −4,462 |
| 10 | 351,691 | 4.453 | Multidrug resistance protein 1, putative (MDR1) | PVX_080100 | 10,010 |
| 14 | 1,650,897 | 4.389 | Heterochromatin protein 1 (HP1); H3 lysine methyltransferase (SET10) | PVX_123682; PVX_123685 | 999; 9,918 |
| 04 | 577,543 | 4.215 | Serine-repeat antigen 4 (SERA) | PVX_003825; PVX_003830 | 789; −1,691 |
| Serine-repeat antigen 5 (SERA) | |||||
| 02 | 85,446 | 3.997 | Multidrug resistance-associated protein 1, putative (MRP1) | PVX_097025 | −68,196 |
| 03 | 368,737 | 3.964 | Hypothetical proteins | — | — |
| 13 | 396,427 | 3.805 | ABC transporter B family member 7, putative (ABCB7) | PVX_084521 | −7,326 |
| 11 | 1,900,445 | 3.581 | Transcription factor with AP2 domain(s), putative (apiap2) | PVX_113370 | −31,184 |
| 12 | 2,421,187 | 3.578 | Multidrug resistance protein 2 (MDR2) | PVX_118100 | −4,361 |
| 11 | 749,030 | 3.549 | SET domain containing protein | PVX_114585 | 46,877 |
| 09 | 1,693,066 | 3.527 | Transcription factor with AP2 domain(s), putative (AP2-O) | PVX_092760 | 7,201 |
| 14 | 1,002,439 | 3.515 | Hypothetical proteins | — | — |
| 09 | 1,506,397 | 3.403 | Transcription factor with AP2 domain(s), putative (apiap2) | PVX_092570 | 9,327 |
| 13 | 676,297 | 3.393 | Hypothetical protein | — | — |
| 05 | 1,303,321 | 3.299 | Vir and fam antigens | — | — |
Haplotype-based tests of selection were performed in monoclonal samples to avoid false breakdown of linkage caused by mixed genotypes from sequencing. Results are presented by ranking on absolute normalized nSL score.
*
Distance in bases from focal SNP to the putative driver gene; a negative sign indicates putative driver gene occurs upstream of the focal SNP.