Nondiscriminatory detection of rare variants

A detection method comprising:

• (a) partitioning into a plurality of partitions an aqueous sample that comprises a non-target nucleic acid and potentially comprises a plurality of variants of the non-target nucleic acid, wherein the partitions include:
• nucleic acid amplification reagents including a set of primers to amplify at least a portion of each of the plurality of variants;
• a set of probes that detect at least two variants of the plurality of variants, and
• a blocker that inhibits amplification of the non-target nucleic acid;
• (b) subjecting the partitions to conditions that promote nucleic acid amplification, wherein the set of probes comprises:
• at least a first probe that is specific for a first variant of the plurality of variants and produces a first detectable signal upon amplification of the first variant, and
• at least a second probe that is specific for a second variant of the plurality of variants and produces a second detectable signal upon amplification of the second variant;
• and
• (c) detecting a cis or trans configuration of at least the first variant and the second variant in the sample by detecting the presence or absence of the first detectable signal and the second detectable signal in one or more partitions of the plurality of partitions,
• wherein:
• (i) presence of both the first detectable signal and the second detectable signal in one or more partitions of the plurality of partitions indicates that the first variant and the second variant are present in the sample in a cis configuration, and (ii) presence of only the first detectable signal in a first subset of partitions of the plurality of partitions and presence of only the second detectable signal in a second subset of partitions of the plurality of partitions indicates that the first variant and the second variant are present in the sample in a trans configuration.