A method for identifying a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of differing target nucleotide sequences comprising: providing a sample potentially containing target nucleotide sequences differing by one or more single-base changes, insertions, deletions, or translocations; providing oligonucleotide probe sets, each set characterized by (a) a first oligonucleotide probe comprising a target-specific portion and a detectable reporter label and (b) a second oligonucleotide probe comprising a target-specific portion and an addressable array-specific portion, wherein the oligonucleotide probes are suitable for ligation together when hybridized on corresponding target nucleotide sequences, wherein the addressable array-specific portion comprises a nucleic acid sequence of greater than 16 nucleotides that differs for each different target-specific portion, wherein the addressable array-specific portions of each set hybridize to their complementary portions under uniform hybridization conditions, and wherein the nucleic acid sequence of a complement to one addressable array-specific portion differs from the nucleic acid sequence of a complement to another addressable array-specific portion, when aligned to each other, by at least 25% to minimize cross-hybridization of one addressable array-specific portion to a complementary portion of another addressable array-specific portion; providing a ligase; blending the sample, the oligonucleotide probe sets, and the ligase to form a ligation detection reaction mixture; subjecting the ligation detection reaction mixture to one or more ligation detection reaction cycles to form a ligated product having a sequence comprising (a) the target-specific portions, (b) the addressable array-specific portion of an oligonucleotide probe set if its target nucleotide sequence is present in the sample, and (c) the detectable reporter label, wherein the addressable array-specific portion is comprised of a nucleotide sequence which is distinct from that of the target-specific portions to prevent hybridization between the target specific portions and the addressable array-specific portion; providing a collection of capture oligonucleotides complementary to the addressable array specific portion, each of said capture oligonucleotides being attached to a solid support; and detecting the ligated product sequences based on hybridization of the addressable array-specific portion and a capture oligonucleotide of the collection in a base-specific manner on the solid support, thereby indicating the presence of one or more target nucleotide sequences in the sample. providing a sample potentially containing target nucleotide sequences differing by one or more single-base changes, insertions, deletions, or translocations; providing oligonucleotide probe sets, each set characterized by (a) a first oligonucleotide probe comprising a target-specific portion and a detectable reporter label and (b) a second oligonucleotide probe comprising a target-specific portion and an addressable array-specific portion, wherein the oligonucleotide probes are suitable for ligation together when hybridized on corresponding target nucleotide sequences, wherein the addressable array-specific portion comprises a nucleic acid sequence of greater than 16 nucleotides that differs for each different target-specific portion, wherein the addressable array-specific portions of each set hybridize to their complementary portions under uniform hybridization conditions, and wherein the nucleic acid sequence of a complement to one addressable array-specific portion differs from the nucleic acid sequence of a complement to another addressable array-specific portion, when aligned to each other, by at least 25% to minimize cross-hybridization of one addressable array-specific portion to a complementary portion of another addressable array-specific portion; providing a ligase; blending the sample, the oligonucleotide probe sets, and the ligase to form a ligation detection reaction mixture; subjecting the ligation detection reaction mixture to one or more ligation detection reaction cycles to form a ligated product having a sequence comprising (a) the target-specific portions, (b) the addressable array-specific portion of an oligonucleotide probe set if its target nucleotide sequence is present in the sample, and (c) the detectable reporter label, wherein the addressable array-specific portion is comprised of a nucleotide sequence which is distinct from that of the target-specific portions to prevent hybridization between the target specific portions and the addressable array-specific portion; providing a collection of capture oligonucleotides complementary to the addressable array specific portion, each of said capture oligonucleotides being attached to a solid support; and detecting the ligated product sequences based on hybridization of the addressable array-specific portion and a capture oligonucleotide of the collection in a base-specific manner on the solid support, thereby indicating the presence of one or more target nucleotide sequences in the sample.