Validation of using Strand-seq to map unplaced scaffolds to built genomes. To confirm that Bioinformatic Analysis of Inherited Templates (BAIT) can successfully locate orphan scaffolds, the reads were aligned to MGSCv37/mm9, which has 202 orphan scaffolds, of which 60 can be mapped to a specific location in GRCm38/mm10. We used BAIT to locate these scaffolds in MGSCv37/mm9, and then cross-referenced these locations to the actual location in the GRCm38/mm10 assembly version. BAIT correctly located all regions in which there were more than 10 libraries to analyze, and where the percentage concordance was above 68%. Green points indicate correctly mapped fragments, and red points indicate incorrectly mapped fragments. Dashed lines show the minimum number of libraries and minimal concordance needed to make confident calls.