A method for identifying target alleles in a mixture of nucleic acids, comprising (a) providing an array of features, wherein different locus-specific primers or different allele-specific primers are attached at different features of the array, or different locus-specific primers are attached at a first subset of the features of the array and different allele-specific primers are attached at a second subset of the features of the array; (b) contacting the array with a plurality of nucleic acid templates, polymerases and nucleotides to form a plurality of stabilized ternary complexes at a plurality of the features, wherein, when different locus-specific primers are attached at different features of the array, the stabilized ternary complexes each comprises a polymerase, template nucleic acid comprising a target allele of a locus, a locus-specific primer of the array hybridized to the locus, and a next correct nucleotide that is a cognate to the target allele, wherein, when different allele-specific primers are attached at different features of the array, the stabilized ternary complexes each comprises a polymerase, template nucleic acid comprising a target allele of a locus, an allele-specific primer of the array hybridized to the locus, and a next correct nucleotide having a cognate in the locus, and wherein, when different locus-specific primers are attached at a first subset of the features of the array and different allele-specific primers are attached at a second subset of the features of the array, the stabilized ternary complexes at the first subset of features each comprises a polymerase, template nucleic acid comprising a target allele of a locus, a locus-specific primer of the array hybridized to the locus, and a next correct nucleotide that is a cognate to the target allele, the stabilized ternary complexes at the second subset of features each comprises a polymerase, template nucleic acid comprising a target allele of a locus, an allele-specific primer of the array hybridized to the locus, and a next correct nucleotide having a cognate in the locus; and (c) detecting stabilized ternary complexes at the features, thereby identifying the target alleles. (a) providing an array of features, wherein different locus-specific primers or different allele-specific primers are attached at different features of the array, or different locus-specific primers are attached at a first subset of the features of the array and different allele-specific primers are attached at a second subset of the features of the array; (b) contacting the array with a plurality of nucleic acid templates, polymerases and nucleotides to form a plurality of stabilized ternary complexes at a plurality of the features, wherein, when different locus-specific primers are attached at different features of the array, the stabilized ternary complexes each comprises a polymerase, template nucleic acid comprising a target allele of a locus, a locus-specific primer of the array hybridized to the locus, and a next correct nucleotide that is a cognate to the target allele, wherein, when different allele-specific primers are attached at different features of the array, the stabilized ternary complexes each comprises a polymerase, template nucleic acid comprising a target allele of a locus, an allele-specific primer of the array hybridized to the locus, and a next correct nucleotide having a cognate in the locus, and wherein, when different locus-specific primers are attached at a first subset of the features of the array and different allele-specific primers are attached at a second subset of the features of the array, the stabilized ternary complexes at the first subset of features each comprises a polymerase, template nucleic acid comprising a target allele of a locus, a locus-specific primer of the array hybridized to the locus, and a next correct nucleotide that is a cognate to the target allele, the stabilized ternary complexes at the second subset of features each comprises a polymerase, template nucleic acid comprising a target allele of a locus, an allele-specific primer of the array hybridized to the locus, and a next correct nucleotide having a cognate in the locus; and (c) detecting stabilized ternary complexes at the features, thereby identifying the target alleles.