Provided herein is a method of sample analysis. In some embodiments, the method comprises hybridizing fragmented genomic DNA from a test genome with a population of first oligonucleotides of the formula V1-B-V2 in the presence of one or more second oligonucleotides; contacting the product with ligase to join the ends of the fragmented genomic DNA that are hybridized to V1 and V2 to the one or more second oligonucleotides; and subjecting the product to polymerase chain reaction conditions using amplification primers that hybridize to sites that are provided by the one or more second oligonucleotides, wherein production of a product indicates that the test genome contains a chromosomal rearrangement relative to the reference genome.