Fig. 2

Peach SV map and hotspots. a The tracks from A to E of the circos plot respectively represent the density of deletions (DEL), insertions (INS), and duplications (DUP) in a 100-kb sliding window, and inversions (INV), and hotspots in the peach SV map. b Size distribution of different types of SVs. In the box plots, central line: median values; bounds of box: 25th and 75th percentiles; whiskers: 1.5 * IQR (IQR: the interquartile range between the 25th and 75th percentile). c The expected and empirical probability distributions of SVs in 30-kb long intervals were estimated assuming a Poisson distribution. A total of 500 intervals with more than 10 SVs in the empirical distribution were considered SV hotspots based if they fell within the 99th percentile or higher of the expected distributions. d Scatter plot of enriched GO terms under the ‘biological process’ category for the genes located within hotspot intervals. p < 0.05, calculated using Fisher’s exact test. Color intensity reflects the significance of enrichment, with darker colors representing lower P values. Circle sizes represent the frequency of each enriched GO term in the Gene Ontology Annotation database (bubbles of more general terms are larger)