Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Motivation: Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e., the crossovers), and minimized mapping intervals for quantitative-trait locus analysis. LC-NGS data usually need to be imputed. Here we present imputed genotypes for rice chromosome 1 obtained from Illumina whole-genome low-coverage sequencing of an Indica x Japonica rice F2 bi-parental population (n = 222). The parents are IR64 (indica) and Azucena (tropical japonica). The genotypes were called with FreeBayes, using a SnakeMake pipeline.