This page provides a variant genotype query interface for rice, allowing users to examine the genotype composition of specified genetic variants across selected rice accessions. Users can query multiple variant sites simultaneously and retrieve both raw and imputed genotype calls, enabling direct comparison of allelic states among accessions.

Genotype Imputation and Accuracy Assessment: based algorithm, adapted from the method described by Huang et al. (2010). To improve computational efficiency and local haplotype resolution, all variant sites were partitioned into 4,058 genomic intervals, each containing 5,000 variant sites, and genotype imputation was performed independently within each interval. Rare heterozygous genotypes were treated as missing values prior to imputation. To evaluate imputation accuracy, 1% of known genotypes were randomly masked and re-imputed, and the concordance between original and imputed genotypes was assessed. In addition, genotype accuracy was independently evaluated using data from the Illumina Infinium RiceSNP50 array (Chen et al. , 2014). This array contains 41,709 high-quality SNP markers, all of which are covered by RiceVarMap V2. Genotypes obtained from array hybridization were compared with those derived from sequencing, including both raw and imputed calls, to assess overall genotype concordance.