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Table 1 Notation for parameters used throughout the manuscript

From: Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data

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