Phased haplotype reference panel for genotype imputation in Macaca mulatta: 618 Indian- and Chinese-origin WGS samples, Mmul_10 assembly

This dataset contains a phased haplotype reference panel for genotype imputation in rhesus macaque (Macaca mulatta), built from 618 whole-genome sequencing samples representing both major geographic lineages: 418 individuals of Indian origin (NCBI SRA: PRJNA382404, PRJNA251548) and 200 individuals of Chinese origin (CNGB: CRA014717). Variants were called against the Mmul_10 reference genome (GCF_003339765.1) and phased using SHAPEIT5 v5.1.0. The panel contains 33,457,491 biallelic SNPs passing quality filters (VQSR, MAF ≥ 0.01, call rate ≥ 0.95). The dataset includes per-chromosome phased BCF files with CSI indices for all 20 autosomes (NC_041754.1–NC_041773.1), ready for direct use with GLIMPSE2 for low-coverage WGS imputation. Imputation accuracy was assessed by leave-two-out concordance using GLIMPSE2_concordance on 10 independent samples; R² ≥ 0.90 was achieved at 0.5× coverage for variants with MAF ≥ 5%. To our knowledge, this is the first publicly available phased imputation reference panel for Macaca mulatta combining both Indian- and Chinese-origin individuals and built with current-generation phasing and imputation tools. This resource is intended to support genotype imputation, GWAS, and population genomic studies in rhesus macaque research.