Abstract: The present invention provides a variety of methods for determining the identity of a nucleotide present at a variant site in a target nucleic acid. The methods involve conducting partial chain termination sequencing reactions of a target nucleic acid of interest conducted with the four deoxynucleotides but only one to three non-extendible nucleotides (i.e., analogs of dATP, dTTP, dGTP and dCTP that are non-extendible by a polymerase). The non-extendible nucleotide(s) utilized in the sequencing reactions are selected to be complementary to the bases potentially occupying the variant site of a target nucleic acid that serves as a template during sequencing. Analyses can also be performed in multiplex formats.