{
  "sample_id": "MMMRD_P01",
  "patient_id": "MMMRD_P01",
  "sample_type": "BM",
  "analysis_mode": "mm_mrd",
  "engine_mode": "real_gating_v1_3",
  "panel_id": "ngf_inspired_2t_8c",
  "panel_supported": "yes",
  "anti_cd38_safe": "yes",
  "anti_cd38_flag": "no",
  "events_total": 150000,
  "events_analyzed": 149402,
  "event_qc_flag": "insufficient",
  "total_pc_count": 4505,
  "normal_pc_count": 4488,
  "aberrant_pc_count": 0,
  "uncertain_pc_count": 17,
  "clonality_call": "polyclonal_or_non_informative",
  "clonality_method": "unresolved",
  "standard_clonality_call": "polyclonal_or_non_informative",
  "rescued_clonality_call": "not_attempted",
  "rescue_subset_count": 0,
  "mrd_burden": 0.0,
  "mrd_burden_scientific": "0.00e+00",
  "lod": 0.00013386701650580312,
  "loq": 0.00033466754126450785,
  "mrd_status": "not_detected",
  "hemodilution_flag": "adequate",
  "research_only_flag": "yes",
  "warnings": [
    "Real gating v1.3 active: rule-based plasma-cell gating, sample-adaptive aberrancy scoring, and robust T2 clonality rescue.",
    "Current v1 uses independent T1 and T2 compartment logic; no advanced multi-tube cell-by-cell fusion yet.",
    "Clonality not confidently resolved on T2 with current v1.3 thresholds.",
    "Low-count non-clonal aberrant-like events were suppressed by the v1.1 noise floor."
  ],
  "tube_panel_details": {
    "T1": {
      "present": true,
      "resolved_markers": [
        "CD117",
        "CD138",
        "CD19",
        "CD27",
        "CD38",
        "CD45",
        "CD56",
        "CD81",
        "FSC-A",
        "FSC-H",
        "SSC-A",
        "SSC-H",
        "Time"
      ],
      "missing_required_markers": []
    },
    "T2": {
      "present": true,
      "resolved_markers": [
        "CD117",
        "CD138",
        "CD19",
        "CD38_multiE",
        "CD45",
        "CD56",
        "FSC-A",
        "FSC-H",
        "SSC-A",
        "SSC-H",
        "Time",
        "cyIgK",
        "cyIgL"
      ],
      "missing_required_markers": []
    }
  },
  "source_files": [
    "MMMRD_P01_T1_surface.fcs",
    "MMMRD_P01_T2_cytoplasmic.fcs"
  ],
  "gating_thresholds": {
    "t1_pc": {
      "cd138": 2.9788403511047363,
      "cd38": 5.828839302062988
    },
    "t1_aberrancy": {
      "CD19_low": 4.7913594245910645,
      "CD56_high": 3.563232898712158,
      "CD27_low": 5.909111976623535,
      "CD81_low": 5.740654945373535,
      "CD117_high": 3.933603048324585,
      "active_aberrant_score_min": 3
    },
    "t2_clonality": {
      "CD19_low": 4.78153657913208,
      "CD56_high": 3.565589427947998,
      "CD117_high": 3.9383938312530518
    }
  },
  "t2_clonality_metrics": {
    "final_method": "unresolved",
    "pc_like_count": 4502,
    "aberrant_like_count": 5,
    "kappa_median": null,
    "lambda_median": null,
    "kappa_lambda_ratio": null,
    "standard_call": "polyclonal_or_non_informative",
    "standard_kappa_median": null,
    "standard_lambda_median": null,
    "standard_kappa_lambda_ratio": null,
    "standard_aberrant_like_count": 5,
    "rescued_call": "not_attempted",
    "rescue_used": false,
    "rescue_subset_count": 0,
    "rescue_kappa_median": null,
    "rescue_lambda_median": null,
    "rescue_kappa_lambda_ratio": null,
    "rescue_dominance_fraction": null,
    "broad_hint_ratio": null
  },
  "plot_files": {
    "t1_fsc_ssc": "plot_t1_fsc_ssc.png",
    "t1_cd38_cd138": "plot_t1_cd38_cd138.png",
    "t1_cd19_cd56": "plot_t1_cd19_cd56.png",
    "t1_cd27_cd81": "plot_t1_cd27_cd81.png",
    "t2_cyigk_cyigl": "plot_t2_cyigk_cyigl.png"
  }
}