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  "interpretation": {
    "tier": "REVIEW is expected because automatic reporting is disabled and no validated model or compatible PoN was supplied.",
    "support_fraction": "FusionSieve fusion_support_fraction is a support proxy, not tumor allele fraction.",
    "realism": "All BAM-level controls failed the post-hoc realism audit because planted reads lack aligner-derived AS/XS tags.",
    "scope": "Functional software interoperability only; not clinical sensitivity, specificity, LoD, or treatment evidence."
  }
}