2007 ), removing markers with low minor allele frequency (MAF <0.01) and subsequently, those showing a significant excess of heterozygotes compared to that predicted under Hardy–Weinberg equilibrium (HWE) (thresholds of P < 4.59E−7 for autosomal markers and P < 1.80E−5 for X-linked markers, applying Bonferroni correction); regarding deviations from HWE, we made the decision to only exclude markers showing significant excess of heterozygotes since a deficit of heterozygotes may represent a true effect of inbreeding while a highly significant excess of heterozygotes is likely to be an indicator of genotyping errors.
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