Genotyping by polymerase binding

A method for identifying target alleles in a mixture of nucleic acids, comprising

• (a) providing an array of features, wherein different template nucleic acids are attached at different features of the array;
• (b) contacting the array with a plurality of primers, polymerases and nucleotides to form a plurality of stabilized ternary complexes at a plurality of the features, wherein the stabilized ternary complexes at the features each comprises a polymerase, a template nucleic acid attached to a feature of the array and comprising a target allele of a locus, a primer hybridized to the locus, and a next correct nucleotide having a cognate in the locus, wherein either
• (i) the primer is an allele-specific primer comprising a 3′ nucleotide that is a cognate nucleotide for the target allele, or
• (ii) the primer is a locus-specific primer and the next correct nucleotide hybridizes to the target allele;
• and
• (c) detecting stabilized ternary complexes at the features, thereby identifying the target alleles.