ALT The graphic shows how read mapping and the called allele dosage in allo- and autopolyploids differ due to the structure of the reference genome. Reads (gray) are shown aligning the reference genome (black), with alleles for the focal variant in pink or yellow. (A) In an allotetraploid with two subgenomes (subgenome K in light gray and subgenome N in dark gray), reads are mapped to one haplotype of each parental subgenome, and diploid genotypes are called. (B) In an autotetraploid with no preferential pairing, all reads are mapped to a single haplotype. Here, reads are aligned to a haplotype carrying the yellow A allele at the focal variant.