Figure 1. Graphical output from FastQ Screen after mapping a publicly available RNA-Seq sample (SRR5100711) against several reference genomes.

Reads either i) mapped uniquely to one genome only (light blue), ii) multi-mapped to one genome only (dark blue), iii) mapped uniquely to a given genome and mapped to at least one other genome (light red), or iv) multi-mapped to a given genome and mapped to at least one other genome (dark red). The reads represented by blue shading are significant since these are sequences that align only to one genome, and consequently, if are observed in an unexpected genome they suggest contamination.