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\(j \,=\, 1,\ldots , M\)
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Index over number of SNPs, M
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\(i\,=\, 1,\ldots , N\)
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Index over number of samples, N
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\(r_{ij}, \ n_{ij}\)
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Reference/non-reference read count data in sample i at variant j
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\(d_{ij}\,=\, (r_{ij},n_{ij})\)
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Read count data in sample i at variant j
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\(p_j\) (\(\widehat{p}_j\))
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Population-level non-reference allele frequency for SNP j (estimate)
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\(p_{ij}\),\((\widehat{p}_{ij})\)
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Within-sample non-reference allele frequency for SNP j in sample i (estimate)
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\(f_i\)
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Inbreeding coefficient for sample i
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\(H_o(b,i)\)
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Observed heterozygosity for sample i in bin b
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\(H_e(b)\)
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Expected heterozygosity for bin b
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\(\widehat{f}^{*}_i\)
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Estimator of \(f_i\) by method \(*\).
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\(\ {f}, \ {p}\)
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Vector of \(f_i\) and \(p_j\)’s in Bayesian model
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