Why are there ERCC reads detected in my sample?

ERCC spike-in controls (External RNA Consortium Controls) are a set of 92 standardized RNA transcripts used to measure experimental variability. By comparing observed ERCC Spike-In Mix data to known concentrations and ratios, researchers can assess the dynamic range (the breadth of measurement), lower limit of detection (the smallest detectable signal), and fold-change response (the ability to detect differences in expression levels) of experiments.

The set of standardized ERCC transcripts were designed to mimic natural eukaryotic mRNAs and range from 250 to 2000 nt in length. The transcripts are synthesized from synthetic DNA sequences or DNA derived from the genomes of Bacillus subtilis and the deep-sea vent microbe Methanocaldococcus jannaschii. ERCC transcripts also contain a poly-A+ tail mimic in the DNA template. ERCC sequences do not share homology with eukaryotic genomes based on comparisons against multiple databases. However, the ERCC Spike-In Mix contains some sequences with similarity to B. subtilis and M. jannaschii. If you did not use the ERCC Spike-In Mix during library prep and CZ ID is detecting ERCCs, is likely that the sequences represent Bacillus species present in your samples. Our team has not observed ERCC sequence matches based on poly-A tails. Click here to learn how to find ERCC counts in CZ ID.

Reference:

Lichun Jiang, Felix Schlesinger, Carrie A. Davis, Yu Zhang, Renhua Li, Marc Salit, Thomas R. Gingeras, and Brian Oliver. 2011. Synthetic spike-in standards for RNA-seq experiments. Genome Research 21: 1543-1551; doi:10.1101/gr.121095.111