{
  "study_id": "STUDY-15-TIER1-ALPHAPROTEO-MITO-EXPLORATORY",
  "tier": 1,
  "tier_label": "Tier 1: Exploratory",
  "prior_beakers": 3,
  "posterior_beakers": 3,
  "total_cohorts": 8,
  "total_taxa": 58,
  "total_alignment_bp": 272000,
  "composite_z_score": 3.46,
  "mean_dnds_core": 0.039,
  "rcfv_raw_aa": 0.136,
  "rickettsiales_lba_1d_ufboot": 84.6,
  "cohorts": [
    {
      "cohort_id": "MITO-T1-01",
      "clade_group": "Alphaproteobacteria / Eukaryota OM",
      "representative_taxon": "Caulobacter vibrioides / Homo sapiens SAM50",
      "ncbi_accession": "NC_011916.1 / PDB 6WUT",
      "functional_pillar": "Pillar 1: Outer Membrane Beta-Barrel Translocase",
      "locus_symbol": "BamA / Omp85 -> SAMM50 (16-Stranded Beta-Barrel)",
      "alignment_length_bp": 34200,
      "taxa_count": 54,
      "gc_fraction": 0.562,
      "dnds_omega": 0.039,
      "ufboot_1d_pct": 92.4,
      "kabsch_rmsd_angstrom": 1.34,
      "z_score": 3.64,
      "beaker_rating": 3,
      "diagnostic_status": "PASS (POTRA-5 retained; POTRA 1-4 truncated in SAM50)"
    },
    {
      "cohort_id": "MITO-T1-02",
      "clade_group": "Alphaproteobacteria / MICOS Cristae",
      "representative_taxon": "Rhodobacter sphaeroides / Homo sapiens Mic60",
      "ncbi_accession": "NC_007493.2 / IMMT",
      "functional_pillar": "Pillar 1: Cristae Junction Remodeling (MICOS)",
      "locus_symbol": "Mic60 (Mitofilin) Coiled-Coil + LBS1/2 Amphipathic Helix",
      "alignment_length_bp": 31800,
      "taxa_count": 54,
      "gc_fraction": 0.584,
      "dnds_omega": 0.044,
      "ufboot_1d_pct": 90.8,
      "kabsch_rmsd_angstrom": 1.42,
      "z_score": 3.51,
      "beaker_rating": 3,
      "diagnostic_status": "PASS (Pre-endosymbiotic ICM cristae curvature domain)"
    },
    {
      "cohort_id": "MITO-T1-03",
      "clade_group": "Eukaryota TOM/TIM23 Import Core",
      "representative_taxon": "Saccharomyces cerevisiae / Homo sapiens TOM40",
      "ncbi_accession": "NM_006114.3 / PDB 7CK6",
      "functional_pillar": "Pillar 1: Protein Import Pore Recruitment",
      "locus_symbol": "TOM40 (19-Stranded Beta-Barrel) + TIM23/TIM17",
      "alignment_length_bp": 29400,
      "taxa_count": 54,
      "gc_fraction": 0.482,
      "dnds_omega": 0.035,
      "ufboot_1d_pct": 93.1,
      "kabsch_rmsd_angstrom": 1.28,
      "z_score": 3.58,
      "beaker_rating": 3,
      "diagnostic_status": "PASS (Acidic inner pore track for presequence import)"
    },
    {
      "cohort_id": "MITO-T1-04",
      "clade_group": "Iodidimonadales / Deep Marine Alpha",
      "representative_taxon": "Iodidimonas muriae C-3 / Marine Alpha Bin",
      "ncbi_accession": "NZ_AP024462.1",
      "functional_pillar": "Pillar 2: Bioenergetic Supermatrix (24 Core Loci)",
      "locus_symbol": "COX1-3 + COB + NAD1-5 + SDHB + ATP6 + RpoB",
      "alignment_length_bp": 48000,
      "taxa_count": 58,
      "gc_fraction": 0.514,
      "dnds_omega": 0.028,
      "ufboot_1d_pct": 84.6,
      "kabsch_rmsd_angstrom": 1.18,
      "z_score": 3.42,
      "beaker_rating": 3,
      "diagnostic_status": "ATTENUATED_1D (AT-rich Rickettsiales LBA RCFV = 0.136)"
    },
    {
      "cohort_id": "MITO-T1-05",
      "clade_group": "Jakobida Ancestral Mitogenomes",
      "representative_taxon": "Reclinomonas americana (67-Protein mtDNA)",
      "ncbi_accession": "NC_001823.1",
      "functional_pillar": "Pillar 2: Ancestral Bacterial-Type mtRNAP (rpoA-D)",
      "locus_symbol": "mt-rpoA + rpoB + rpoC + rpoD + secY + tatC",
      "alignment_length_bp": 42600,
      "taxa_count": 58,
      "gc_fraction": 0.261,
      "dnds_omega": 0.032,
      "ufboot_1d_pct": 86.2,
      "kabsch_rmsd_angstrom": 1.26,
      "z_score": 3.55,
      "beaker_rating": 3,
      "diagnostic_status": "PASS (Retains bacterial multisubunit RNAP & SecY)"
    },
    {
      "cohort_id": "MITO-T1-06",
      "clade_group": "Jakobida -> Metazoa Mitoribosome LSU",
      "representative_taxon": "Reclinomonas / Yeast / Homo sapiens 55S LSU",
      "ncbi_accession": "NC_012920.1 / PDB 3J9M",
      "functional_pillar": "Pillar 3: Mitoribosome rRNA-to-Protein Replacement",
      "locus_symbol": "16S mt-rRNA (MT-RNR2) + Supernumerary mL37-mL66",
      "alignment_length_bp": 39000,
      "taxa_count": 56,
      "gc_fraction": 0.412,
      "dnds_omega": 0.046,
      "ufboot_1d_pct": 91.2,
      "kabsch_rmsd_angstrom": 1.21,
      "z_score": 3.61,
      "beaker_rating": 3,
      "diagnostic_status": "PASS (46.4% rRNA reduction compensated by +28 mRPs)"
    },
    {
      "cohort_id": "MITO-T1-07",
      "clade_group": "Metazoa Mitoribosome Central Protuberance",
      "representative_taxon": "Homo sapiens / Bos taurus 55S Mitoribosome",
      "ncbi_accession": "PDB 3J9M / PDB 5AJ4",
      "functional_pillar": "Pillar 3: Structural mt-tRNA^Val CP Replacement",
      "locus_symbol": "mt-tRNA-Val / mt-tRNA-Phe + mL40 + mL48 Clamp",
      "alignment_length_bp": 27600,
      "taxa_count": 56,
      "gc_fraction": 0.438,
      "dnds_omega": 0.049,
      "ufboot_1d_pct": 89.4,
      "kabsch_rmsd_angstrom": 1.32,
      "z_score": 3.44,
      "beaker_rating": 3,
      "diagnostic_status": "PASS (mt-tRNA replaces deleted bacterial 5S rRNA)"
    },
    {
      "cohort_id": "MITO-T1-08",
      "clade_group": "Negative Control (0-Beaker Boundary)",
      "representative_taxon": "Homo sapiens Chr17p11.2 Nuclear NUMT Pseudogene",
      "ncbi_accession": "NT_010718.17_NUMT",
      "functional_pillar": "Negative Control: Nuclear Mitochondrial Pseudogene",
      "locus_symbol": "MT-CO1 / MT-RNR2 Nuclear Pseudogene Paralog",
      "alignment_length_bp": 19400,
      "taxa_count": 48,
      "gc_fraction": 0.451,
      "dnds_omega": 0.914,
      "ufboot_1d_pct": 38.4,
      "kabsch_rmsd_angstrom": 5.92,
      "z_score": 0.86,
      "beaker_rating": 0,
      "diagnostic_status": "REJECT_0_STAR (In-frame stop codons; neutral omega = 0.914)"
    }
  ],
  "negative_controls_logged": 2,
  "runtime_ms": 18
}