Genotyping error rates among software packages with default settings.

Default minimum read depth; AmpliSAS, 100 reads; Megasat, 50 reads; CHIIMP, 500 reads; MicNeSs, 16 reads. Proportion genotyped, the number of genotypes estimated by each software (Ngenotypes) divided by the total number of reference genotypes per locus across all replicates and samples. Genotyping success, the number of genotypes that coincide with the consensus (Nsuccessful) divided by the total number of genotypes estimated by the software per locus across all replicates and samples (Ngenotypes). Proportion ADO, the number of heterozygote genotypes for which only one of the two alleles could be genotyped (NADO) divided by the number of heterozygote genotypes in the reference. Proportion FA, the number of genotypes including a false allele (NFA) divided by the total number of reference genotypes. Values are shown as mean ± standard error per locus.