{
  "snapshot": "2026-09-30",
  "scope": "Scoped report-backed evidence; retention is not accuracy",
  "controlled": {
    "source": "GCST90018642",
    "selected_source_variants": 100000,
    "scenario_row_evaluations": 180000,
    "pvalue_injected": 5000,
    "pvalue_detected": 5000,
    "pvalue_false_positives": 0,
    "pvalue_false_positive_denominator": 95000,
    "blank_rsid_correct": 4002,
    "blank_rsid_unresolved": 998,
    "blank_rsid_wrong": 0,
    "rsid_conflicts_detected": 5000,
    "rsid_conflicts_injected": 5000,
    "report": "evidence/controlled-report.md"
  },
  "subsets": [
    {
      "name": "FinnGen R13 \u00b7 Type 2 diabetes",
      "context": "Clean biobank subset / GRCh38",
      "input": 99999,
      "retained": 99999,
      "sha256": "abf3a414ed2abbd1b6eaf1ec6fd6efbfe492ca5049fb7fe81dff4ca3a15ea9b5",
      "limitation": "Exact upstream R13 source object and access metadata remain pending. Recorded conflicting rsIDs and incomplete audit trail prevent a submission-ready claim.",
      "report": "evidence/subset-register.md"
    },
    {
      "name": "Neale Lab \u00b7 Standing height",
      "context": "Liftover subset / GRCh37 \u2192 GRCh38",
      "input": 100000,
      "retained": 99829,
      "sha256": "69e8bde0cb41642fbd05da3d6094e1605d5e3d102d03d1b20c143621db4b8f9b",
      "limitation": "Selected-profile readiness was blocked by ambiguous confidence-interval handling and no requested GWAS Catalog schema. The upstream S3 ETag is multipart, not a file checksum.",
      "report": "evidence/subset-register.md"
    },
    {
      "name": "Suzuki \u00b7 Type 2 diabetes, EAS",
      "context": "Ancestry-aware liftover subset / GRCh37 \u2192 GRCh38",
      "input": 100000,
      "retained": 92022,
      "sha256": "baeb0c78194476c0fed43f1f0f1a0ec48e5af4c6944838a28a03ed25b5644f4c",
      "limitation": "Two severe p-value inconsistencies and ambiguous CI handling remain recorded blockers. Resolved upstream URL, byte size and original access timestamp are pending.",
      "report": "evidence/subset-register.md"
    },
    {
      "name": "GWAS Catalog \u00b7 Hypothyroidism",
      "context": "Repository-harmonized control / GCST90018642 / GRCh38",
      "input": 100000,
      "retained": 83382,
      "sha256": "a3a6f876f9395d3aaff111799669bae4c0232c64d61b145d9b5d651d52df585d",
      "limitation": "The archived audit accounts for all 16,618 exclusions: 12,491 unresolved palindromes and 4,127 ambiguous indels. Of those palindromes, 11,679 were outside the 0.42\u20130.58 band; missing compatible orientation evidence drove quarantine. This explains policy-driven loss, not whether each row could be recovered with additional evidence.",
      "report": "evidence/subset-register.md"
    }
  ],
  "coverage": [
    {
      "name": "GCTA fastGWA \u00b7 Standing height",
      "context": "Full-file format coverage / supplemental evidence",
      "input": 8531093,
      "retained": 7861307,
      "sha256": "3e6121eb2bb45b6f0591fa143692f08a8566fa7532dfa5c2332286c7f359330c",
      "limitation": "669,786 quarantined; 7,232 liftover failures. Two source p-value-floor inconsistencies are recorded; this run is not submission-ready.",
      "report": "evidence/format-coverage.md"
    },
    {
      "name": "PLINK2 \u00b7 Standing height, fold 1",
      "context": "Full-file format coverage / training folds are not independent studies",
      "input": 1074448,
      "retained": 1073599,
      "sha256": "19d38fa30bf763be271c189f8bb847211eddb737219c1b1ff4e2e7f4d1c86477",
      "limitation": "849 quarantined; 562 liftover failures; no severe p-value inconsistencies. Complete harmonization audit, but the canonical bundle is not a GWAS Catalog submission package.",
      "report": "evidence/format-coverage.md"
    }
  ]
}