This module provides a pairwise variant-level comparison that enables users to identify polymorphic positions between two rice cultivars within a user-defined genomic interval. Genotype states at individual variant sites are directly contrasted under a common reference coordinate system, allowing fine-scale inspection of allelic differences between cultivars.
Genotype visualization: For each variant, genotype states of the two selected cultivars are highlighted using a color-coded scheme to facilitate interpretation. Cells with a blue background indicate the major allele, whereas cells with a red background indicate the minor allele. Genotypes not matching either the major or minor allele are displayed without background highlighting.
Usage notes: Only variants located within the specified genomic interval (≤100 kb) are returned. Genotype symbols such as N and DEL represent imputed missing and missing genotypes in high-coverage regions, respectively. Interpretation of genotype differences should consider variant type, local allele frequency, and population context.