A method of concurrent determination of nucleotide composition at designated polymorphic sites located within one or more target nucleotide sequences, said target nucleotide sequences comprising a non-designated polymorphism, said method comprising the following steps: (a) providing a set of oligonucleotide primer pairs, each pair capable of annealing with complementary polynucleotide strands to delineate a region of the corresponding target which includes at least one designated polymorphic site; (b) contacting said set of oligonucleotide primers with said targets under conditions allowing formation of amplicons with designated polymorphic sites corresponding to the designated polymorphic sites in corresponding targets, each amplicon comprising an amplicon sense strand corresponding to a target sense strand and an amplicon antisense strand corresponding to a target antisense strand; (c) providing one or more sets of degenerate probes, wherein the set contains degenerate probes capable of annealing to a subsequence of said one or more amplicon sense strand and antisense strand sequences located within a range of proximity to a designated polymorphic site on the sense or antisense strand; (d) contacting the set of probes with said one or more amplicon nucleotide sequences so as to permit formation of hybridization complexes by placing an interrogation site within a probe sequence in direct alignment with the designated polymorphic site on the sense and antisense strand; (e) incubating each hybridization complex with a DNA polymerase capable of extending the probes within the complex: (i) determining the presence of a match between the interrogation site and a designated polymorphic site by probe elongation; and (ii) determining the presence of a mismatch between the interrogation site and a designated polymorphic site by the lack of probe elongation; thereby determining the composition of the designated polymorphic site; wherein the one or more sets of probes are immobilized on encoded microparticles, the encoded microparticles being assembled into a random encoded array. (a) providing a set of oligonucleotide primer pairs, each pair capable of annealing with complementary polynucleotide strands to delineate a region of the corresponding target which includes at least one designated polymorphic site; (b) contacting said set of oligonucleotide primers with said targets under conditions allowing formation of amplicons with designated polymorphic sites corresponding to the designated polymorphic sites in corresponding targets, each amplicon comprising an amplicon sense strand corresponding to a target sense strand and an amplicon antisense strand corresponding to a target antisense strand; (c) providing one or more sets of degenerate probes, wherein the set contains degenerate probes capable of annealing to a subsequence of said one or more amplicon sense strand and antisense strand sequences located within a range of proximity to a designated polymorphic site on the sense or antisense strand; (d) contacting the set of probes with said one or more amplicon nucleotide sequences so as to permit formation of hybridization complexes by placing an interrogation site within a probe sequence in direct alignment with the designated polymorphic site on the sense and antisense strand; (e) incubating each hybridization complex with a DNA polymerase capable of extending the probes within the complex: (i) determining the presence of a match between the interrogation site and a designated polymorphic site by probe elongation; and (ii) determining the presence of a mismatch between the interrogation site and a designated polymorphic site by the lack of probe elongation; thereby determining the composition of the designated polymorphic site; (i) determining the presence of a match between the interrogation site and a designated polymorphic site by probe elongation; and (ii) determining the presence of a mismatch between the interrogation site and a designated polymorphic site by the lack of probe elongation; thereby determining the composition of the designated polymorphic site;