Source data for the main figures of the article "Simultaneous identification of viruses and viral variants with programmable DNA nanobait" in Nature Nanotechnology. This dataset includes data for single events, plotting bar charts, and statistic test details. Data were recorded with home-built LabVIEW codes. They represent ionic current measurements over time. From these ionic current measurements, single events that correspond to nanobaits were extracted and used for further analysis and bar charts. , nanobait events were filtered out of raw ionic current traces, then the detection region was determined, and information of the spike’s presence at each specific site was extracted. The plotted displacement efficiency was calculated as a displacement efficiency for a measurement subtracted to a no target control for each site (fifty nanobait events for each of three nanopore recordings) unless stated otherwise. 99.9% confidence intervals for the displacement efficiencies were calculated for all measurements. The statistical significance between two sites without and with the target was tested using a two-sided Student’s T-test.