Extended Data Fig. 9: Statistical significance of dSNP enrichment in the dSV coupling phase.
From: Leveraging a phased pangenome for haplotype design of hybrid potato
a, Diagram depicting our dSNP accumulation assessment. For calculation purposes, chromosomes were segmented into fragments based on the midpoint between adjacent dSVs (irrespective whether in coupling or repulsion phase). Statistical tests were performed on each 10-kb non-overlapping window within each fragment. b, Statistical significance for the number of dSNPs flanking dSVs using the 10-kb non-overlapping windows between dSV coupling and repulsion phases. The significance threshold of P = 0.05 (two-sided Student’s t-test) is indicated. c, Diagram illustrating the calculation of the distance of a focal dSV to the nearest dSV in coupling phase (Dis-coupling) and to the nearest dSV in repulsion phase (Dis-repulsion). The focal dSV is highlighted in red. d, The frequency distribution of Dis-coupling and Dis-repulsion in potato genomes.
