Bradysia ocellaris was collected from the Edinburgh Botanical Gardens, UK. Genomic DNA was extracted from an adult male fly using a protocol modified for low-input starting material, developed by C. Laumer at the Wellcome Sanger Institute (dx.doi.org/10.17504/protocols.io.bypypvpw). The samples were quantified and quality-checked with Qubit and Nanodrop (ThermoFisher) and sequenced for 150bp paired-end Illumina reads on the Novaseq 6000 platform. If using this data, note that one sample was split across three sequencing lanes, so all three files should be downloaded. Also note that significant non-metazoan contamination was found in these reads.