A method for detecting a first and a second allele of a target locus in a plurality of target polynucleotide molecules, comprising: (a) partitioning a sample comprising said target polynucleotide molecules into a plurality of partitions; (b) performing an amplification reaction on said partitions, wherein each of a plurality of reaction volumes of the amplification reaction comprises: (i) a forward primer that is complementary to a first sequence of a first strand of the target polynucleotide molecules, wherein the first sequence is 5' of the target locus; (ii) a reverse primer that is complementary to a second sequence of a second strand of the target polynucleotide molecules, wherein the second sequence is 3' of the target locus; (iii) a single detection probe that is capable of hybridizing to a third sequence of the target polynucleotide molecules that encompasses the target locus, wherein the detection probe comprises a first signal reporter; and (c) determining a number and/or fraction of positive reaction volumes containing a target molecule having the first allele and a number and/or fraction of reaction volumes containing a target molecule having the second allele based on the signal of the first signal reporter released from the reaction volumes; wherein the plurality of reaction volumes of the amplification reaction further comprises (i) a reference forward primer that is complementary to a fourth sequence of the target polynucleotide molecules, wherein the fourth sequence is 5' of a reference locus that does not contain a variant; (ii) a reference reverse primer that is complementary to a fifth sequence of the target polynucleotide molecules, wherein the fifth sequence is 3' of the reference locus; and (iii) a reference probe capable of hybridizing to the reference locus, wherein the reference probe comprises a second signal reporter. (a) partitioning a sample comprising said target polynucleotide molecules into a plurality of partitions; (b) performing an amplification reaction on said partitions, wherein each of a plurality of reaction volumes of the amplification reaction comprises: (i) a forward primer that is complementary to a first sequence of a first strand of the target polynucleotide molecules, wherein the first sequence is 5' of the target locus; (ii) a reverse primer that is complementary to a second sequence of a second strand of the target polynucleotide molecules, wherein the second sequence is 3' of the target locus; (iii) a single detection probe that is capable of hybridizing to a third sequence of the target polynucleotide molecules that encompasses the target locus, wherein the detection probe comprises a first signal reporter; and (i) a forward primer that is complementary to a first sequence of a first strand of the target polynucleotide molecules, wherein the first sequence is 5' of the target locus; (ii) a reverse primer that is complementary to a second sequence of a second strand of the target polynucleotide molecules, wherein the second sequence is 3' of the target locus; (iii) a single detection probe that is capable of hybridizing to a third sequence of the target polynucleotide molecules that encompasses the target locus, wherein the detection probe comprises a first signal reporter; (c) determining a number and/or fraction of positive reaction volumes containing a target molecule having the first allele and a number and/or fraction of reaction volumes containing a target molecule having the second allele based on the signal of the first signal reporter released from the reaction volumes;