Dr. Chang-Yong Lee earned a B.S. in Computer Science and Statistics from Seoul National University, South Korea, in 1983, and a Ph.D. in Physics from The University of Texas at Austin, USA, in 1995. He served as a Professor at Kongju National University, South Korea, from 1998 to 2025. Since 2025, he has been serving as Professor Emeritus at the same university.

Title: Pangenome-Guided Identification and Elimination of False-Positive Variants in Mixed-Germplasm Variant Calling.                                                                                                                   Abstract: Variant calling in mixed-subspecies rice panels (Indica and Japonica) using a single linear reference inevitably generates substantial false-positive variants due to cross-lineage sequence divergence, confounding downstream genomic interpretations. Recently, graph-based pangenome references have emerged as a viable paradigm to overcome linear mapping limitations and systematically eliminate these reference-induced false positives. While graph pan-genomics offers a theoretical remedy, the quantitative extent of artifact reduction remains under-characterized. In this study, we systematically assess the impact of replacing linear references with a graphical pangenome in mixed-cohort variant calling. Our pangenome-guided pipeline purged approximately 90% of linear-specific false positives. Furthermore, we demonstrate that this performance superiority is strictly independent of the Indica–Japonica mixture ratio, establishing that graph referencing provides a stable, unbiased foundation regardless of cohort composition. Keywords: variant calling, mixed germplasm, graph pangenome, linear reference bias, false positives, rice genomics