System, including methods, apparatus, and compositions, for performing a multiplexed digital assay of at least three targets. In an exemplary method, partitions may be formed each including a portion of a same sample. The sample may include a first target that is a reference sequence, a second target that is a variant sequence from a gene of interest, and a third target that is a normal sequence from the gene of interest. The target may be amplified in the partitions and amplification data may be collected. A level of the second target may be determined. A copy number of the third target may be determined from a level of the first target and a level of the third target.