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Kernel density distributions of minor-allele frequency and site heterozygosity using the different SNP datasets. For each of the six SNP data sets (CLC, GATK, SAMtools, GATK-CLCintersect, SAMtools-GATKintersect, and SAMtools-CLCintersect) we computed the minor-allele frequency (MAF) for the Sumatran (WA) and Bornean (SK) individuals (panels a and b, respectively), and site heterozygosity for WA and SK (panels c and d, respectively).
