= Phenotype
{wiki}
A <phenotype> is an observable characteristic of an <organism>, arising from its <genotype>, environment and other influences. Seed shape is a <phenotype>; $Aa$ is a <genotype>. The distinction prevents appearance from being mistaken for a complete inherited description. See https://www.genome.gov/genetics-glossary/Phenotype[NHGRI: phenotype].
For a specified binary <phenotype> $T$, let its <penetrance> in <genotype> $g$ be $r_g=P(T\mid g)$. The <law of total probability> gives $P(T)=\sum_g r_gP(g)$. Thus the ideal $Aa\times Aa$ example has $P(T)=r_{AA}/4+r_{Aa}/2+r_{aa}/4$: the familiar $3/4$ follows only when these <penetrances> are $1,1,0$. A <pedigree likelihood> keeps inheritance and the conditional <phenotype> model as separate factors.
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