Schematic of model for site-specific joint genotypic inference. The philosophy of JGIL is for the model to mirror the experimental design. The founding females and their implicit mates are sampled from a common population that is described by population-level parameters. The experimental design specifies the probabilistic dependency between the genotypes of these initial flies and those of the pooled inbred samples that are ultimately sequenced. Technical and bioinformatic errors are modeled as a site-specific phenomenon that applies equally to all lines. This allows “line effects” (i.e., genotypes) and “nucleotide effects” (i.e., errors) to be disentangled.
