Abstract: The method described presents a novel method of quantitative estimation of genetic quality of crop for a specific trait using pyrosequencing and next generation sequencing. The method quantitatively estimates the presence of a seed lot with seed of unwanted genetic trait using the allele frequency. The method assesses the genetic purity of a trait quantitatively based on allele frequency of the genetic variation between the desired and the contaminant's locus. Allele frequency is obtained by sequencing amplicons with a sequencing primer binding at the intersection of the site of genetic variation that differentiates between contaminant and the desired trait. The true genetic purity of an unknown seed lot is estimated by substituting the allele frequency value in a regression equation derived from the allele frequencies of several standards used in every sequencing experiment.