Non-parent copy number forms at a segregating CNV locus. We observed non-parental copy number due to amplification/deamplification at the segregating CNV region in Chr 5, which overlaps the multi-drug resistance gene, pfmdr1. The size and boundaries of the CNV region of the non-parent form remained identical to that of the parent form indicating that all genes within the amplification were amplified or deamplified. (A) Scatter plot of signal intensity ratios for the Dd2 parent (Dd2vs.HB3) hybridization across an 82 kb segregating amplification highlight the presence of the CNV in the Dd2 parent. Fourteen progeny inherit the amplification. (B) Heat map illustrates increased relative probe signal intensities in Dd2 and progeny lines (red) to the reference HB3 parent (amplified region is marked by a grey box). (C) The scatter plot highlights the relative hybridization signal intensities represented as log2 (test/HB3) (amplified region is marked by grey arrow). (C) The progeny exhibit a range of copy number across the amplicon including parent copy number forms as well as non-parent copy numbers reflected by the 3 different groups in the height of the CGH signal intensity across the amplicon. (D) The CNV in the region results in an increase in gene expression (at~18 hrs within the parasite life cycle) in all the multicopy parasites, including the non-parent copy numbers.