{
  "blockers": [],
  "cache_issue": 269,
  "claim_boundary": "The Borzoi rescue overlap audit is an alignment and feasibility artifact only. It is not a model-quality result, clinical result, deployment-readiness result, broad VEP superiority claim, broad Carbon comparison, useful-planning claim, ground-truth biology claim, or exact fipip overlap claim unless the exact fipip table join is actually run.",
  "contract_issue": 267,
  "decision": "go_traitgym_native_borzoi",
  "epic_issue": 266,
  "fipip_exact_join": {
    "metadata_only": {
      "bucket": "seqnn-share",
      "generation": "1750977790216459",
      "object": "sniff/borzoi_102_annotation_set/sniff_102_annotations.gz",
      "size_bytes": 18670353280
    },
    "reason": "The full fipip table was not staged locally for this run.",
    "status": "not_run_full_table_not_staged"
  },
  "generated_at": "2026-06-11T12:00:00Z",
  "generated_by": "tools.research.fx_borzoi_overlap",
  "manifest": {
    "path": "configs/fx/borzoi_rescue_sources.json",
    "sha256": "sha256:a1a7eb0dfcd06aca753f13279465f9bfb035c71dd1ffd5379862c38ddeea6e99"
  },
  "minimum_usable_rows": 10000,
  "ok_to_build_cache": true,
  "overlap_issue": 268,
  "recommended_issue_actions": [
    {
      "action": "close-completed",
      "issue": 268,
      "reason": "The TraitGym-native row-aligned Borzoi path passes the 10,000-row alignment gate."
    },
    {
      "action": "open-next",
      "issue": 269,
      "reason": "Build the manifest-backed cache from the compact row-aligned Borzoi score vector."
    }
  ],
  "schema_version": "1.0.0",
  "source_inputs": {
    "fipip_borzoi_source": {
      "bucket": "seqnn-share",
      "crc32c": "DPBpaA==",
      "expected_rows": 19534182,
      "generation": "1750977790216459",
      "genome_build": "hg19",
      "md5_hash": "KmaNYQ9EEH+5MQvOfCOaZQ==",
      "object": "sniff/borzoi_102_annotation_set/sniff_102_annotations.gz",
      "repository": "https://github.com/statgen/fipip",
      "score_kind": "Borzoi PCA-derived annotations for autosomal SNPs and indels.",
      "size_bytes": 18670353280,
      "updated": "2025-06-26T22:43:10.246Z"
    },
    "traitgym_borzoi_score": {
      "path": "complex_traits_matched_9/preds/all/Borzoi_L2_L2.plus.all.parquet",
      "repo_id": "songlab/TraitGym",
      "repo_type": "dataset",
      "revision": "1fde19555fe8c0a55b1382bdf4c6f7082209f566",
      "sha256": "sha256:04ecf61997bad7f84c36021cd2ca2d30d6781b2f56d3a22e65e6742b0cac2a3f",
      "size_bytes": 66797
    },
    "traitgym_slice": {
      "path": "complex_traits_matched_9/test.parquet",
      "repo_id": "songlab/TraitGym",
      "repo_type": "dataset",
      "revision": "1fde19555fe8c0a55b1382bdf4c6f7082209f566",
      "sha256": "sha256:068940684e1e6f735a25a1a4418fb65390628023a96188af7f1a15dd17de7036",
      "size_bytes": 411336
    }
  },
  "traitgym_native_alignment": {
    "chromosome_counts": {
      "1": 1000,
      "10": 510,
      "11": 680,
      "12": 590,
      "13": 200,
      "14": 380,
      "15": 390,
      "16": 590,
      "17": 560,
      "18": 290,
      "19": 580,
      "2": 900,
      "20": 530,
      "21": 140,
      "22": 280,
      "3": 650,
      "4": 400,
      "5": 510,
      "6": 780,
      "7": 540,
      "8": 460,
      "9": 440
    },
    "config": "complex_traits",
    "dataset": "songlab/TraitGym",
    "expected_row_count_match": true,
    "expected_traitgym_rows": 11400,
    "label_summary": {
      "both_classes_present": true,
      "negative": 10260,
      "positive": 1140
    },
    "minimum_usable_rows_passed": true,
    "observed_score_rows": 11400,
    "observed_traitgym_rows": 11400,
    "row_count_match": true,
    "row_order_status": "assumed_by_traitgym_matched_slice_artifact_layout",
    "score_column": "score",
    "score_id": "Borzoi_L2_L2.plus.all",
    "score_semantics": "TraitGym-native row-aligned Borzoi L2 score; teacher-derived score, not ground truth.",
    "score_summary": {
      "finite_scores": 11400,
      "max": 388.5757141113281,
      "mean": 13.421279713720606,
      "min": 0.8960618376731873,
      "non_numeric_or_non_finite_scores": 0,
      "null_scores": 0,
      "p50": 8.508103847503662
    },
    "split": "test",
    "split_summary": {
      "holdout_chromosomes": [
        "11",
        "14",
        "16",
        "17",
        "20",
        "3"
      ],
      "holdout_negative": 3051,
      "holdout_positive": 339,
      "holdout_rows": 3390,
      "split_has_both_classes": true,
      "train_negative": 7209,
      "train_positive": 801,
      "train_rows": 8010
    },
    "usable_rows": 11400,
    "variant_key_summary": {
      "duplicate_key_count": 0,
      "duplicate_key_passed": true,
      "unique_keys": 11400
    }
  }
}