Ranking markers

MicroHapDB provides three primary criteria for ranking markers. Phased genotypes for 2,504 individuals from Phase 3 of the 1000 Genomes Project, selected from 26 global population groups, are used to calculate these statistics.

Effective number of alleles (A_e)

The marker’s effective number of alleles (\(A_e\)) is computed individually for 26 population groups. By default, the average of the 26 populations \(A_e\) is shown, but the --ae-pop flag or the microhapdb.set_ae_population function can be used to specify a single population for which to display \(A_e\) values.

The \(A_e\) statistic is a measure of the within-population allelic variation at a locus, which corresponds to the marker’s diagnostic power for identification purposes.

Informativeness (I_n)

Rosenberg’s informativeness for assignment to populations (\(I_n\)) is computed on 26 global population groups.

Fixation index (F_ST)

The fixation index (\(F_{ST}\)) is computed on 26 global population groups.

The \(I_n\) and \(F_{ST}\) statistics measure between-population allelic variation at a locus, which corresponds to the marker’s utility for predicting population of origin.