Categories of CNVs. Two broad categories of CNVs were identified within the progeny of the HB3 × Dd2 genetic cross: (A) Segregating CNVs are present in a parent clone and are inherited in the progeny, and (B, C) de novo CNVs are detected exclusively in the progeny. For each category, the left panel heatmap displays the CNV region (grey boxed) across the Dd2 parent (column 1) as well as the progeny population; the right panel shows a scatter plot of the relative hybridization signal distribution for selected examples highlighted by red boxes. (A) Segregating CNV (deletion) in Chr 2; (B) singleton de novo CNV (Chr 4, progeny strain 7C170), (C) recurrent de novo CNV detected in Chr 10. In each pair of scatter plots, the left scatter plot shows the signal distribution across the Dd2 parent in comparison with a progeny which carries the CNV (right).