Statistical difference between the two pools along the genome revealed by three methods.

<p>A: SNP distribution in the genome. B: <i>G</i>′ value profile. The horizontal dotted line shows the significance threshold for FDR≤0.05. The upper longer and lower shorter horizontal bars under each major <i>G</i>′ peak indicate the ranges of the full and the most probable intervals of a putative QTL, respectively. The downward black arrowhead marked as CM within the interval of <i>qCTSS-2</i> indicates the position of centromere on chromosome 2. C: Distribution of differential SNPs in the genome. D: Profile of Nipponbare allele frequency difference.