When target and reference sequences diverge (e.g. a UniProt accession that doesn't match MANE Select), the aligner currently handles discrepancies silently — they inform the score but are then discarded. Parse alignment output to explicitly extract mismatch columns where target and reference residues disagree. Store these as structured metadata on the mapping record, including both residues at each discrepant position. Proactively trigger warnings and alerting when potentially troubling mappings arise. Use this during annotation to flag variants that map into or near discrepant regions.
When target and reference sequences diverge (e.g. a UniProt accession that doesn't match MANE Select), the aligner currently handles discrepancies silently — they inform the score but are then discarded. Parse alignment output to explicitly extract mismatch columns where target and reference residues disagree. Store these as structured metadata on the mapping record, including both residues at each discrepant position. Proactively trigger warnings and alerting when potentially troubling mappings arise. Use this during annotation to flag variants that map into or near discrepant regions.