| Variable | Description |
| Index variables | |
| \(h\) | test number (one per test SNP / target region pair) |
| \(i\) | individual |
| \(j\) | target region |
| \(k\) | SNP within target region |
| \(m\) | test SNP |
| Latent variables | |
| \(\alpha_h\) | molecular phenotype level of the reference allele for test \(h\) |
| \(\beta_h\) | molecular phenotype level of the alternative allele for test \(h\) |
| \(p_h\) | fraction of allele-specific reads expected from reference allele \((p_h = \frac{\alpha_h}{\alpha_h + \beta_h})\) |
| \(T^{*}_{i,j}\) | genotype-independent expected total read count for individual \(i\), target region \(j\) |
| \(\lambda_{hi}\) | expected total read count for test \(h\), individual \(i\) |
| \(\Omega_i\) | overdispersion of read counts for individual \(i\) (across all tests) |
| \(\phi_j\) | overdispersion of read counts for test number \(j\) (across all individuals) |
| \(\Upsilon_i\) | overdispersion of allele-specific reads for individual \(i\) |
| Observed variables | |
| \(x_{ij}\) | number of reads for individual \(i\), target region \(j\) |
| \(G_{im}\) | genotype call for individual \(i\), test SNP \(m\) |
| \(T_{i}\) | total number of genome-wide mapped reads for individual \(i\) |
| \(n_{ik}\) | total number of allele-specific reads for individual \(i\), target SNP \(k\) |
| \(y_{ik}\) | number of allele-specific reads from reference haplotype for individual \(i\), target SNP \(k\) |
| \(H_{ik}\) | probability individual \(i\) is heterozygous for target SNP \(k\) |
\label{tab:variables}