Abstract: The present teachings relate to methods and kits for detecting one or more target polynucleotide sequences in a sample. In some embodiments of the present teachings, a probe set comprising a target identifying portion is hybridized to a strand of an amplification product and ligated together to form a ligation product. The ligation product can be queried with a mobility probe, and analysis of the mobility probe with a mobility dependent analysis technique is used to determine the target polynucleotide sequence. The present teachings can employ highly multiplexed amplification and ligation reactions to query a variety of target polynucleotide sequences, including single nucleotide polymorphisms.