Table 4.

gSPIM simulation results for the genotype observation model

	$p_C^{het1}$	$p_{AD}^{het1}$	$p_{FA}^{het1}$	$p_C^{het2}$	$p_{AD}^{het2}$	$p_{FA}^{het2}$	$p_C^{hom1}$	$p_{FA}^{hom1}$	$p_C^{hom2}$	$p_{FA}^{hom2}$
True	0.806	0.185	0.009	0.489	0.496	0.015	0.994	0.006	0.999	0.001
SPIM3A	0.806	0.185	0.009	0.486	0.498	0.016	0.993	0.007	0.997	0.003
SPIM2A	0.805	0.185	0.009	0.484	0.500	0.016	0.993	0.007	0.996	0.004
SPIM1A	0.797	0.194	0.010	0.479	0.503	0.018	0.993	0.007	0.989	0.011
SPIM3B	0.806	0.185	0.009	—	—	—	0.994	0.006	—	—
SPIM2B	0.805	0.186	0.009	—	—	—	0.994	0.006	—	—
SPIM1B	0.792	0.198	0.010	—	—	—	0.993	0.007	—	—

Scenarios indicate the model used (SPIM), the number of replicated assignments (1 to 3), and whether the low-quality samples were included (A) or not (B). C, AD, and FA indicate correct, allelic dropout, and false allele probabilities, respectively. Het indicates heterozygous genotypes and hom indicates homozygous genotypes. The high-quality sample parameters are indicated with a “1” and low-quality parameters are indicated with a “2.”