Noise describes a series of non-reproducible background peaks that occur along the baseline in all samples. A wide variety of factors, including amplified current fluctuations within the electronic circuitry, air bubbles, urea crystals, and sample contamination, can create noise. If large enough (close to the laboratory threshold), they may be confused with an allele or mask alleles.

Trained analysts using a proper analytical threshold should not have difficulty differentiating actual alleles with noise and vice versa; they should be familiar with the signal-to-noise ratio of the instrument and/or the specific data. If unsure, data interpretation may involve viewing both raw and analyzed data to assess the signal-to-noise ratio and distinguish real data from noise. Noise is not reproducible; one way to differentiate alleles from noise is to rerun the sample.

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