Table 4.
CNVs detected using WGS and genomic microarrays
| Strain | Position (Micr.) | Position (Seq.) | Presumed relevant gene | Copy number (Seq.) | Orientation (Seq.) |
|---|---|---|---|---|---|
| all 3D7 derived lines |
chr12_974243-975980 |
chr12_974276-976007 |
pfgch |
2 |
tandem |
| all Dd2 derived lines |
chr5_892863-968421 |
chr5_892872-968429 |
pfmdr1 |
2 |
tandem |
| all Dd2 derived lines |
chr12_970985-975864 |
chr12_971011-975866 |
pfgch |
2 |
tandem |
| Evo5a/b |
chr1_428540-643352 |
chr1_428538-643350 |
pfmrp1 |
2 |
unknown* |
| CladoR_clone1 |
chr13_1996541-2018534 |
chr13_1996635-2018727 |
pfkrs1 |
3 |
tandem |
| CladoR_clone2 |
chr13_1996668-2055132 |
chr13_1996621-2055107 |
pfkrs1 |
3 |
tandem |
| CladoR_clone3 |
chr13_2001466-2051201 |
chr13_2001482-2051233 |
pfkrs1 |
3 |
tandem |
| NITD678_clone1 | chr12_510069-633784 | chr12_510123-633834 | pfatp4 | 2-3 | tandem |
*Orientation could not be determined as the amplification continued into the telomeric region.
Predicted CNV calls with position from both WGS (Seq.) using Platypus and microarray data (Micr.), with predicted copy number compared to the 3D7 reference and orientation of the amplification as determined by Platypus.