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Chunk #33 — Methods — Quantifying population structure and changes in population size

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The GenomeAsia 100K Project enables genetic discoveries across Asia.
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Analyses of population structure was performed using the quality-control-positive linkage-disequilibrium-pruned set of 1,089,227 autosomal SNPs. Principal component analysis (PCA)18 was conducted across all available populations in EIGENSTRAT v.6.1.4. Results were visualized in Tableau v.9.3. We applied unsupervised hierarchical clustering of individuals using the maximum likelihood method implemented in ADMIXTURE v.1.3.020 using default input parameters. The ‘--cv’ flag was adopted to perform the cross-validation procedure and to calculate the optimal k value.