{
  "study_id": "STUDY-15-TIER2-ALPHAPROTEO-MITO-BLIND-DAYHOFF6-VALIDATION",
  "validation_set_id": "VAL-SET-025-ALPHAPROTEO-MITO-ENDOSYMBIOSIS-24COHORT",
  "tier": 2,
  "tier_label": "Tier 2: Validation",
  "prior_beakers": 4,
  "posterior_beakers": 4,
  "total_cohorts": 24,
  "dev_cohorts": 12,
  "reserve_cohorts": 12,
  "total_alignment_bp": 816000,
  "z_dev_split": 4.27,
  "z_reserve_split": 4.24,
  "split_drift_sd": 0.03,
  "composite_z_score": 4.25,
  "concordant_cohorts_count": 20,
  "mean_concordant_delta_z": 0.0,
  "anomaly_cohorts_count": 4,
  "anomaly_recall_pct": 100.0,
  "rcfv_1d_mean": 0.136,
  "rcfv_2d_dayhoff6_mean": 0.021,
  "iodidimonas_marine_sister_ufboot_2d": 99.4,
  "rickettsiales_lba_ufboot_2d": 14.2,
  "dual_pass_rows": [
    {
      "cohort_id": "MITO-V25-01",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-EB277D0DC1",
      "extrapolated_biotype_pass1": "16-Stranded Beta-Barrel Outer Membrane Translocase (SAM50/BamA)",
      "true_repository_label_pass2": "SAMM50 + BamA Core (PDB 6WUT / 5D0O)",
      "z_blind_pass1": 4.32,
      "z_context_pass2": 4.32,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.128,
      "rcfv_after_dayhoff6": 0.019,
      "ufboot_1d_raw": 92.4,
      "ufboot_2d_dayhoff6": 99.5,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-02",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-501AD9AD6D",
      "extrapolated_biotype_pass1": "MICOS Cristae Junction Coiled-Coil + LBS1/2 Helix",
      "true_repository_label_pass2": "Mic60 / Mitofilin Homologs (NC_007493.2)",
      "z_blind_pass1": 4.24,
      "z_context_pass2": 4.24,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.124,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 90.8,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-03",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-0949903C71",
      "extrapolated_biotype_pass1": "19-Stranded Beta-Barrel Presequence Import Channel (TOM40)",
      "true_repository_label_pass2": "TOMM40 Channel Complex (PDB 7CK6)",
      "z_blind_pass1": 4.29,
      "z_context_pass2": 4.29,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.119,
      "rcfv_after_dayhoff6": 0.018,
      "ufboot_1d_raw": 93.1,
      "ufboot_2d_dayhoff6": 99.6,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-04",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-4B4B3D6FA0",
      "extrapolated_biotype_pass1": "Inner Membrane Presequence Translocase Twin-Pore (TIM23/17)",
      "true_repository_label_pass2": "TIMM23 + TIMM17A Core",
      "z_blind_pass1": 4.18,
      "z_context_pass2": 4.18,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.122,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 89.8,
      "ufboot_2d_dayhoff6": 99.2,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-05",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-E3D7B03A9F",
      "extrapolated_biotype_pass1": "Free-Living Aerobic Marine Alphaproteobacteria Sister Clade",
      "true_repository_label_pass2": "Iodidimonas muriae 24-Locus Supermatrix (NZ_AP024462.1)",
      "z_blind_pass1": 4.38,
      "z_context_pass2": 4.38,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.142,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 81.4,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-06",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-DAEA075AD7",
      "extrapolated_biotype_pass1": "Ancestral Jakobid Mitogenome with rpoA-D & secY",
      "true_repository_label_pass2": "Reclinomonas americana mtDNA (NC_001823.1)",
      "z_blind_pass1": 4.35,
      "z_context_pass2": 4.35,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.148,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 86.2,
      "ufboot_2d_dayhoff6": 99.5,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-07",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-F3E7423956",
      "extrapolated_biotype_pass1": "Ancestral Jakobid Bioenergetic Complex I-IV Core",
      "true_repository_label_pass2": "Jakoba libera mtDNA (NC_021127.1)",
      "z_blind_pass1": 4.27,
      "z_context_pass2": 4.27,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.144,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 85.8,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-08",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-3B27ACD5F8",
      "extrapolated_biotype_pass1": "Eroded 16S mt-rRNA + Supernumerary mL37-mL66 Shell",
      "true_repository_label_pass2": "Human 55S Mitoribosome LSU (PDB 3J9M)",
      "z_blind_pass1": 4.31,
      "z_context_pass2": 4.31,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.131,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 91.2,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-09",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-E6D6D588D8",
      "extrapolated_biotype_pass1": "Structural mt-tRNA^Val Central Protuberance Replacement",
      "true_repository_label_pass2": "Bovine 55S Mitoribosome CP (PDB 5AJ4)",
      "z_blind_pass1": 4.21,
      "z_context_pass2": 4.21,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.126,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 89.4,
      "ufboot_2d_dayhoff6": 99.2,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-10",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-8613ED2118",
      "extrapolated_biotype_pass1": "Fungal Mitoribosome Intermediate rRNA/Protein Ratio",
      "true_repository_label_pass2": "Yeast 74S Mitoribosome (PDB 5MRC)",
      "z_blind_pass1": 4.19,
      "z_context_pass2": 4.19,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.129,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 90.1,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-11",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-623B9CD6EB",
      "extrapolated_biotype_pass1": "Convergent AT-Rich FYMINK Long-Branch Attraction Artifact (28% GC)",
      "true_repository_label_pass2": "Raw 1D AA 'Rickettsiales Sister to Mitochondria' Claim",
      "z_blind_pass1": 0.92,
      "z_context_pass2": 4.04,
      "discordance_d_ctx": 3.12,
      "rcfv_before_dayhoff6": 0.174,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 84.6,
      "ufboot_2d_dayhoff6": 14.2,
      "anomaly_detected": true,
      "anomaly_mechanism": "Dayhoff-6 + CAT-GTR recoding collapses false Rickettsiales/SAR11 sisterhood (UFBoot drops 84.6% -> 14.2%), restoring free-living marine Iodidimonadales sister clade (99.4%)"
    },
    {
      "cohort_id": "MITO-V25-12",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-MITO-C7AEB336FA",
      "extrapolated_biotype_pass1": "Nuclear Mitochondrial Pseudogene (NUMT) with Neutral Drift (omega = 0.91)",
      "true_repository_label_pass2": "Mislabelled 'Cryptic Human Mitochondrial Heteroplasmy Lineage'",
      "z_blind_pass1": 0.78,
      "z_context_pass2": 4.1,
      "discordance_d_ctx": 3.32,
      "rcfv_before_dayhoff6": 0.088,
      "rcfv_after_dayhoff6": 0.019,
      "ufboot_1d_raw": 94.2,
      "ufboot_2d_dayhoff6": 22.0,
      "anomaly_detected": true,
      "anomaly_mechanism": "Pass 1 blind scan detects vertebrate-to-standard codon table shift (TGA=Stop vs. Trp) and omega = 0.914, flagging nuclear NUMT pseudogene"
    },
    {
      "cohort_id": "MITO-V25-13",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-6DCE7A80FC",
      "extrapolated_biotype_pass1": "Basal Magnetotactic Alphaproteobacteria Outgroup (MC-1)",
      "true_repository_label_pass2": "Magnetococcus marinus MC-1 (NC_008576.1)",
      "z_blind_pass1": 4.25,
      "z_context_pass2": 4.25,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.13,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 91.6,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-14",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-E86C3A9319",
      "extrapolated_biotype_pass1": "Intracytoplasmic Membrane (ICM) Dimeric F1Fo-ATP Synthase + Mic60",
      "true_repository_label_pass2": "Rhodospirillum rubrum ATCC 11170 (NC_007643.1)",
      "z_blind_pass1": 4.22,
      "z_context_pass2": 4.22,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.127,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 90.4,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-15",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-7DF22C0AEE",
      "extrapolated_biotype_pass1": "Basal Jakobid Mitogenome Conserving secY & rpoA-D",
      "true_repository_label_pass2": "Andalucia godoyi mtDNA (KC353352.1)",
      "z_blind_pass1": 4.34,
      "z_context_pass2": 4.34,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.146,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 86.8,
      "ufboot_2d_dayhoff6": 99.5,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-16",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-0150C3BF2B",
      "extrapolated_biotype_pass1": "Excavate Bioenergetic Complex I-V Supermatrix",
      "true_repository_label_pass2": "Malawimonas jakobiformis mtDNA (NC_002553.1)",
      "z_blind_pass1": 4.26,
      "z_context_pass2": 4.26,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.141,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 87.2,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-17",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-428308679E",
      "extrapolated_biotype_pass1": "Fungal SAM50-SAM35-SAM37 & TOM40-TOM22 Beta-Barrel Assembly",
      "true_repository_label_pass2": "Neurospora crassa SAM/TOM Loci",
      "z_blind_pass1": 4.2,
      "z_context_pass2": 4.2,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.121,
      "rcfv_after_dayhoff6": 0.019,
      "ufboot_1d_raw": 91.8,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-18",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-4938633A05",
      "extrapolated_biotype_pass1": "Mammalian Small Mitoribosomal Subunit (28S SSU + mS22-mS40)",
      "true_repository_label_pass2": "Porcine 55S Mitoribosome SSU (PDB 5AJ3)",
      "z_blind_pass1": 4.23,
      "z_context_pass2": 4.23,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.128,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 90.6,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-19",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-29B390B7E7",
      "extrapolated_biotype_pass1": "Extreme Kinetoplastid Mitoribosome rRNA Compression (610/1150 nt)",
      "true_repository_label_pass2": "Trypanosoma brucei Mitoribosome (PDB 6HIW)",
      "z_blind_pass1": 4.17,
      "z_context_pass2": 4.17,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.139,
      "rcfv_after_dayhoff6": 0.023,
      "ufboot_1d_raw": 88.2,
      "ufboot_2d_dayhoff6": 99.1,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-20",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-7FD7608B8D",
      "extrapolated_biotype_pass1": "Constructive Plant Mitoribosome with Expanded rRNA + PPR Proteins",
      "true_repository_label_pass2": "Arabidopsis thaliana Mitoribosome (PDB 6XYW)",
      "z_blind_pass1": 4.19,
      "z_context_pass2": 4.19,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.125,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 89.9,
      "ufboot_2d_dayhoff6": 99.2,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-21",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-49A8A6703D",
      "extrapolated_biotype_pass1": "Free-Living Aerobic Marine Alphaproteobacteria Sister Lineage",
      "true_repository_label_pass2": "Tistrella mobilis KA081020-065 (NC_017956.1)",
      "z_blind_pass1": 4.29,
      "z_context_pass2": 4.29,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.134,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 85.4,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-22",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-CAE978E1D4",
      "extrapolated_biotype_pass1": "Cardiolipin Synthase (Cls / Crd1) Cristae Curvature Lipid Pathway",
      "true_repository_label_pass2": "Cardiolipin Synthase Ortholog Panel",
      "z_blind_pass1": 4.16,
      "z_context_pass2": 4.16,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.123,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 89.1,
      "ufboot_2d_dayhoff6": 99.1,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "MITO-V25-23",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-512F99D71A",
      "extrapolated_biotype_pass1": "Firmicutes/Clostridia Lateral Gene Transfer of [FeFe]-Hydrogenase HydA",
      "true_repository_label_pass2": "Mislabelled 'Vertical Alphaproteobacterial Proto-Mitochondrial HydA'",
      "z_blind_pass1": 0.88,
      "z_context_pass2": 3.92,
      "discordance_d_ctx": 3.04,
      "rcfv_before_dayhoff6": 0.156,
      "rcfv_after_dayhoff6": 0.025,
      "ufboot_1d_raw": 79.2,
      "ufboot_2d_dayhoff6": 18.4,
      "anomaly_detected": true,
      "anomaly_mechanism": "Pass 1 blind Quartet-MSC & Super-BLAST scan places HydA/PFO inside Firmicutes (Clostridia, gCF = 0.19), refuting vertical alphaproteobacterial inheritance"
    },
    {
      "cohort_id": "MITO-V25-24",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-MITO-44AB60871B",
      "extrapolated_biotype_pass1": "Misbinned Rickettsiales Intracellular Symbiont Contig in Sponge Mitogenome",
      "true_repository_label_pass2": "Mislabelled 'Ancestral Sponge Mitochondrial rpoB Retained Locus'",
      "z_blind_pass1": 0.84,
      "z_context_pass2": 4.08,
      "discordance_d_ctx": 3.24,
      "rcfv_before_dayhoff6": 0.162,
      "rcfv_after_dayhoff6": 0.023,
      "ufboot_1d_raw": 91.4,
      "ufboot_2d_dayhoff6": 19.6,
      "anomaly_detected": true,
      "anomaly_mechanism": "Pass 1 blind tetranucleotide D_KL = 7.2x & Shine-Dalgarno RBS motif prove bacterial endosymbiont contig contamination rather than animal mtDNA"
    }
  ],
  "runtime_ms": 23
}