{
 "schema": "lgasieve.synthetic-software-verification.v2",
 "artifact_type": "synthetic software verification",
 "generated_utc": "2026-07-31T04:33:17.871387Z",
 "runtime_seconds": 70.21,
 "claims_boundary": [
  "Every endpoint is conditional synthetic software verification, not analytical or clinical performance.",
  "Conditional Wilson intervals describe finite simulated draws only and exclude simulator, assay, and transport uncertainty.",
  "Full event truth is never clipped to the caller callable mask; truth-target callability is reported separately.",
  "The locked same-assay stream was not used to select model components or thresholds.",
  "The independent dosage channel tests workflow logic only; it is not evidence about MLPA, aCGH, ddPCR, or clinical confirmation.",
  "Stress and transport-shift findings must be reviewed before the more favorable same-generator results."
 ],
 "stress_and_transport_findings_review_first": {
  "reason": "distribution shift is the principal limitation of a same-generator simulation",
  "transport_shift": {
   "positive_events_intention_to_test": 2400,
   "positive_events_completed": 0,
   "positive_sample_qc_no_calls": 2400,
   "positive_events_not_fully_callable": 437,
   "positive_completion_rate": 0.0,
   "any_reflex_trigger_rate_intention_to_test": 0.0,
   "matched_80pct_reciprocal_overlap_rate_intention_to_test": 0.0,
   "matched_80pct_reciprocal_overlap_rate_completed": null,
   "exact_endpoints_rate_intention_to_test": 0.0,
   "exact_target_set_rate_intention_to_test": 0.0,
   "all_truth_targets_callable_rate": 0.8179166666666666,
   "negative_samples_intention_to_test": 1200,
   "negative_samples_completed": 0,
   "negative_sample_qc_no_calls": 1200,
   "negative_primary_referral_rate_completed": null,
   "negative_no_referral_rate_completed": null
  },
  "within_assay_low_depth_site_mosaic_stress": {
   "positive_events_intention_to_test": 2400,
   "positive_events_completed": 1325,
   "positive_sample_qc_no_calls": 763,
   "positive_events_not_fully_callable": 458,
   "positive_completion_rate": 0.5520833333333334,
   "any_reflex_trigger_rate_intention_to_test": 0.5858333333333333,
   "matched_80pct_reciprocal_overlap_rate_intention_to_test": 0.475,
   "matched_80pct_reciprocal_overlap_rate_completed": 0.8445283018867924,
   "exact_endpoints_rate_intention_to_test": 0.45916666666666667,
   "exact_target_set_rate_intention_to_test": 0.45916666666666667,
   "all_truth_targets_callable_rate": 0.8091666666666667,
   "negative_samples_intention_to_test": 1200,
   "negative_samples_completed": 806,
   "negative_sample_qc_no_calls": 394,
   "negative_primary_referral_rate_completed": 0.03970223325062035,
   "negative_no_referral_rate_completed": 0.9602977667493796
  }
 },
 "design": {
  "base_seed": 20260731,
  "quick": false,
  "sizes": {
   "fit": 1300,
   "calibration": 3000,
   "development_normal": 1200,
   "development_positive": 2400,
   "locked_same_assay_normal": 2000,
   "locked_same_assay_positive": 4000,
   "stress_normal": 1200,
   "stress_positive": 2400,
   "transport_normal": 1200,
   "transport_positive": 2400
  },
  "n_targets": 550,
  "n_control_targets": 500,
  "n_reportable_targets": 50,
  "unstable_reportable_targets": [
   "BRCA2_E01",
   "BRCA2_E09",
   "BRCA2_E11",
   "BRCA2_E15"
  ],
  "component_grid": [
   0,
   4,
   8,
   12
  ],
  "family_alpha_grid": [
   0.01,
   0.02,
   0.05
  ],
  "selected_family_alpha": 0.01,
  "selection_rule": "engineering-only: maximize development gates (completed 80%-reciprocal-overlap rate>=0.98, completed negative referral rate<=0.025, >=90% targets callable, >=85% positive completion), then callable fraction, completion, overlap rate, fewer negative referrals, and fewer components",
  "selection_gates_are_clinical_acceptance_criteria": false,
  "deployment_site_shift": 0.55,
  "locked_same_assay_site_shift": 0.55,
  "verification_seed_offset": 300,
  "intended_site_shifts_in_fit_and_calibration": [
   0.55
  ],
  "transport_shift": {
   "construction": "target-specific efficiency, latent-loading, and instability shift; same target IDs and GC values",
   "seed": 20261231,
   "target_ids_aligned": true,
   "target_ids_sha256": "f0b2dff7532ee26a259803a458333a5681ad895602514ae87c3f3bccdeb2804a",
   "efficiency_log2_ratio_rms": 0.26376771912841945,
   "log_efficiency_correlation": 0.7947082591639596,
   "latent_loading_rms_delta": 0.03831716397516238,
   "latent_loading_correlation": 0.8878081969015317,
   "source_median_instability": 0.035,
   "shifted_median_instability": 0.04586288417385777,
   "forced_unstable_reportable_target_ids": [
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    "BRCA1_E11",
    "BRCA1_E17",
    "BRCA2_E03",
    "BRCA2_E05",
    "BRCA2_E06",
    "BRCA2_E10",
    "BRCA2_E17"
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  "normal_artifact_fraction": 0.015,
  "independent_dosage_channel_workflow_logic_only": {
   "independent_log2_sigma": 0.055,
   "independent_artifact_fraction": 0.002,
   "deletion_threshold": -0.25,
   "duplication_threshold": 0.2,
   "minimum_fraction_of_called_targets": 0.5,
   "scope": "synthetic workflow verification only; not a claim about MLPA or aCGH clinical performance"
  }
 },
 "transport_shift_synthetic_software_verification": {
  "evaluation_label": "synthetic software verification",
  "truth_policy": "full event target IDs are retained and evaluated without intersection with the caller callable mask",
  "population_definitions": {
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   "completed_positive": "sample passed caller QC and every full-truth event target was callable; truth is still not clipped",
   "intention_to_test_negative": "every generated copy-number-negative sample",
   "completed_negative": "copy-number-negative sample passed caller QC"
  },
  "sample_counts": {
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   "positive_events_intention_to_test": 2400,
   "positive_events_completed": 0,
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   "positive_events_not_fully_callable": 437,
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   "negative_samples_completed": 0,
   "negative_sample_qc_no_calls": 1200
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  "caller_callable_reportable_targets": {
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   "primary_reflex_calls_in_completed_samples": 0,
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