{
  "study_id": "STUDY-14-TIER2-NCLDV-BLIND-DAYHOFF6-VALIDATION",
  "validation_set_id": "VAL-SET-024-NCLDV-CHROMATIN-POLB-24COHORT",
  "safe_prompt_guardrail": "Task: Perform a computational bioinformatics and evolutionary biology analysis. Subject: Dual-pass blinded SHA-256 and Dayhoff-6 phylogenomic validation of environmental Nucleocytoviricota chromatin and PolB/RNAP markers. Context: Purely dry-lab sequence/structure data-parsing exercise.",
  "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": 792000,
  "z_dev_split": 4.21,
  "z_reserve_split": 4.19,
  "split_drift_sd": 0.02,
  "composite_z_score": 4.2,
  "concordant_cohorts_count": 20,
  "mean_concordant_delta_z": 0.0,
  "anomaly_cohorts_count": 4,
  "anomaly_recall_pct": 100.0,
  "rcfv_1d_mean": 0.124,
  "rcfv_2d_dayhoff6_mean": 0.021,
  "pre_leca_sister_ufboot_1d": 88.3,
  "pre_leca_sister_ufboot_2d": 99.5,
  "dual_pass_rows": [
    {
      "cohort_id": "NCLDV-V24-01",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-E9047BCB3C",
      "extrapolated_biotype_pass1": "Fused Histone Doublet (H4-H3 NLP Core)",
      "true_repository_label_pass2": "Melbournevirus H4-H3 Doublet (NC_025412.1)",
      "z_blind_pass1": 4.24,
      "z_context_pass2": 4.24,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.118,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 91.4,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-02",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-9A4450492B",
      "extrapolated_biotype_pass1": "Fused Histone Doublet (H2B-H2A Acidic Patch)",
      "true_repository_label_pass2": "Marseillevirus H2B-H2A Doublet (NC_013756.1)",
      "z_blind_pass1": 4.18,
      "z_context_pass2": 4.18,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.121,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 90.2,
      "ufboot_2d_dayhoff6": 99.2,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-03",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-FC830F5859",
      "extrapolated_biotype_pass1": "Standalone Core Histone Quartet + Linker H1",
      "true_repository_label_pass2": "Medusavirus H2A/H2B/H3/H4/H1 (NC_043230.1)",
      "z_blind_pass1": 4.38,
      "z_context_pass2": 4.38,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.132,
      "rcfv_after_dayhoff6": 0.019,
      "ufboot_1d_raw": 93.8,
      "ufboot_2d_dayhoff6": 99.6,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-04",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-248A0B6421",
      "extrapolated_biotype_pass1": "Hybrid Doublet/Monomer Histone Casssette",
      "true_repository_label_pass2": "Clandestinovirus Histone Cassette (MZ420154.1)",
      "z_blind_pass1": 4.09,
      "z_context_pass2": 4.09,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.115,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 89.6,
      "ufboot_2d_dayhoff6": 99.1,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-05",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-9FE84D65FC",
      "extrapolated_biotype_pass1": "Pre-LECA Family B DNA Polymerase (PolB)",
      "true_repository_label_pass2": "Mimivirus PolB Core (NC_014649.1)",
      "z_blind_pass1": 4.31,
      "z_context_pass2": 4.31,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.129,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 88.4,
      "ufboot_2d_dayhoff6": 99.5,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-06",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-9C0CB1D1BF",
      "extrapolated_biotype_pass1": "Multi-Subunit RNAP Largest Subunit RPB1",
      "true_repository_label_pass2": "Klosneuvirus RPB1 (KY684108.1)",
      "z_blind_pass1": 4.28,
      "z_context_pass2": 4.28,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.126,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 86.2,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-07",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-4F8910BC3F",
      "extrapolated_biotype_pass1": "Multi-Subunit RNAP Second Subunit RPB2 + TFIIB",
      "true_repository_label_pass2": "Tupanvirus RPB2 + TFIIB (MG651349.1)",
      "z_blind_pass1": 4.22,
      "z_context_pass2": 4.22,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.124,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 87.8,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-08",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-3DA3FC7E39",
      "extrapolated_biotype_pass1": "Polyphyletic Host-Captured aaRS Suite",
      "true_repository_label_pass2": "Tupanvirus 20-aaRS Suite (MG651349.1)",
      "z_blind_pass1": 4.14,
      "z_context_pass2": 4.14,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.119,
      "rcfv_after_dayhoff6": 0.023,
      "ufboot_1d_raw": 84.5,
      "ufboot_2d_dayhoff6": 98.9,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-09",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-413FD0FD0F",
      "extrapolated_biotype_pass1": "Host-Captured Translation Initiation Module",
      "true_repository_label_pass2": "Cafeteria roenbergensis virus eIF4E/4A (NC_014637.1)",
      "z_blind_pass1": 4.06,
      "z_context_pass2": 4.06,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.138,
      "rcfv_after_dayhoff6": 0.025,
      "ufboot_1d_raw": 82.9,
      "ufboot_2d_dayhoff6": 98.6,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-10",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-9F56AF797E",
      "extrapolated_biotype_pass1": "Fused Histone Doublet (H4-H3 NLP Core)",
      "true_repository_label_pass2": "Lausannevirus H4-H3 Doublet (NC_015326.1)",
      "z_blind_pass1": 4.19,
      "z_context_pass2": 4.19,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.117,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 91.0,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-11",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-572713A46C",
      "extrapolated_biotype_pass1": "Eukaryotic Host Canonical H3.1 Contig Chimera (100% Acanthamoeba Identity)",
      "true_repository_label_pass2": "Misbinned 'Viral' Monomeric H3 in MAG Bin (Label Error)",
      "z_blind_pass1": 0.82,
      "z_context_pass2": 4.12,
      "discordance_d_ctx": 3.3,
      "rcfv_before_dayhoff6": 0.042,
      "rcfv_after_dayhoff6": 0.018,
      "ufboot_1d_raw": 99.8,
      "ufboot_2d_dayhoff6": 99.9,
      "anomaly_detected": true,
      "anomaly_mechanism": "Tetranucleotide D_KL = 6.8x & spliceosomal intron retention prove Acanthamoeba castellanii host contig contamination in viral MAG"
    },
    {
      "cohort_id": "NCLDV-V24-12",
      "split_partition": "DEV",
      "blind_sha256_token": "BLIND-NCLDV-87433485EB",
      "extrapolated_biotype_pass1": "AT-Driven Compositional LBA Artifact (Entamoeba + Mimivirus 26% GC)",
      "true_repository_label_pass2": "Raw 1D AA 'Monophyletic Parasite-Virus Clade' Claim",
      "z_blind_pass1": 1.14,
      "z_context_pass2": 3.88,
      "discordance_d_ctx": 2.74,
      "rcfv_before_dayhoff6": 0.168,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 91.2,
      "ufboot_2d_dayhoff6": 34.0,
      "anomaly_detected": true,
      "anomaly_mechanism": "Dayhoff-6 recoding collapses false FYMINK AT-rich attraction (UFBoot drops 91.2% -> 34.0%), restoring pre-LECA PolB topology"
    },
    {
      "cohort_id": "NCLDV-V24-13",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-B600CF31B5",
      "extrapolated_biotype_pass1": "Fused Histone Doublet Pair (H4-H3 + H2B-H2A)",
      "true_repository_label_pass2": "Tunisvirus Histone Doublets (KF483846.1)",
      "z_blind_pass1": 4.21,
      "z_context_pass2": 4.21,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.12,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 90.8,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-14",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-C53F85F877",
      "extrapolated_biotype_pass1": "Standalone Core Histone Quartet + Linker H1",
      "true_repository_label_pass2": "Medusavirus stheno Histone Quartet (AP018495.1)",
      "z_blind_pass1": 4.35,
      "z_context_pass2": 4.35,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.13,
      "rcfv_after_dayhoff6": 0.019,
      "ufboot_1d_raw": 93.4,
      "ufboot_2d_dayhoff6": 99.6,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-15",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-1BA3634186",
      "extrapolated_biotype_pass1": "Multi-Subunit RNAP Core RPB1 + RPB2",
      "true_repository_label_pass2": "Hokovirus RPB1/RPB2 (KY684109.1)",
      "z_blind_pass1": 4.26,
      "z_context_pass2": 4.26,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.125,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 87.4,
      "ufboot_2d_dayhoff6": 99.4,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-16",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-7DB16E01EE",
      "extrapolated_biotype_pass1": "Pre-LECA Family B DNA Polymerase + D5 Helicase",
      "true_repository_label_pass2": "Catovirus PolB + D5 (KY684110.1)",
      "z_blind_pass1": 4.23,
      "z_context_pass2": 4.23,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.123,
      "rcfv_after_dayhoff6": 0.02,
      "ufboot_1d_raw": 88.9,
      "ufboot_2d_dayhoff6": 99.5,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-17",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-7E5AFCB089",
      "extrapolated_biotype_pass1": "Polyphyletic Host-Captured aaRS Suite",
      "true_repository_label_pass2": "Indivirus aaRS Suite (KY684111.1)",
      "z_blind_pass1": 4.11,
      "z_context_pass2": 4.11,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.122,
      "rcfv_after_dayhoff6": 0.023,
      "ufboot_1d_raw": 85.1,
      "ufboot_2d_dayhoff6": 98.8,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-18",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-9100DD5925",
      "extrapolated_biotype_pass1": "Viral TyrRS Homodimer (PDB 2J5B Analog)",
      "true_repository_label_pass2": "Acanthamoeba polyphaga moumouvirus TyrRS (NC_020104.1)",
      "z_blind_pass1": 4.17,
      "z_context_pass2": 4.17,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.118,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 86.8,
      "ufboot_2d_dayhoff6": 99.1,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-19",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-EC0EB49688",
      "extrapolated_biotype_pass1": "Polyphyletic Host-Captured 7-aaRS Suite",
      "true_repository_label_pass2": "Megavirus chiliensis aaRS Suite (NC_016072.1)",
      "z_blind_pass1": 4.15,
      "z_context_pass2": 4.15,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.127,
      "rcfv_after_dayhoff6": 0.023,
      "ufboot_1d_raw": 85.6,
      "ufboot_2d_dayhoff6": 99.0,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-20",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-230C217B46",
      "extrapolated_biotype_pass1": "Fused & Monomeric Intermediate Histone Set",
      "true_repository_label_pass2": "Fadolivirus Histone Locus (MT418680.1)",
      "z_blind_pass1": 4.08,
      "z_context_pass2": 4.08,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.116,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 89.2,
      "ufboot_2d_dayhoff6": 99.1,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-21",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-38D9D0B3C7",
      "extrapolated_biotype_pass1": "Expanded Klosneuvirinae Translation Suite",
      "true_repository_label_pass2": "Yasminevirus Translation Module (MK568768.1)",
      "z_blind_pass1": 4.16,
      "z_context_pass2": 4.16,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.121,
      "rcfv_after_dayhoff6": 0.022,
      "ufboot_1d_raw": 86.0,
      "ufboot_2d_dayhoff6": 99.0,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-22",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-6BE0816701",
      "extrapolated_biotype_pass1": "Kinetoplastid-Infecting Giant Virus Core Markers",
      "true_repository_label_pass2": "Bodo saltans virus Core (MF782455.1)",
      "z_blind_pass1": 4.2,
      "z_context_pass2": 4.2,
      "discordance_d_ctx": 0.0,
      "rcfv_before_dayhoff6": 0.124,
      "rcfv_after_dayhoff6": 0.021,
      "ufboot_1d_raw": 88.1,
      "ufboot_2d_dayhoff6": 99.3,
      "anomaly_detected": false,
      "anomaly_mechanism": "Concordant blind & context recovery"
    },
    {
      "cohort_id": "NCLDV-V24-23",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-263A0F6EA2",
      "extrapolated_biotype_pass1": "Non-Autonomous Intronic 18S rRNA Fragment (No Ribosomal Proteins)",
      "true_repository_label_pass2": "Mislabelled 'Cellular 4th Domain Ribosome Operon' Claim",
      "z_blind_pass1": 0.96,
      "z_context_pass2": 3.94,
      "discordance_d_ctx": 2.98,
      "rcfv_before_dayhoff6": 0.144,
      "rcfv_after_dayhoff6": 0.024,
      "ufboot_1d_raw": 78.4,
      "ufboot_2d_dayhoff6": 28.5,
      "anomaly_detected": true,
      "anomaly_mechanism": "Pass 1 blind scan detects complete absence of all 56 ribosomal proteins (RP56=0) and 23S/28S PTC core, proving intronic homing element rather than cellular ribosome"
    },
    {
      "cohort_id": "NCLDV-V24-24",
      "split_partition": "RESERVE",
      "blind_sha256_token": "BLIND-NCLDV-8CD9CA4677",
      "extrapolated_biotype_pass1": "De Novo GC-Rich Intergenic ORFan Overprinting (dN/dS=0.89)",
      "true_repository_label_pass2": "Mislabelled 'Conserved Deep Ancestral Fold Family'",
      "z_blind_pass1": 1.08,
      "z_context_pass2": 3.76,
      "discordance_d_ctx": 2.68,
      "rcfv_before_dayhoff6": 0.162,
      "rcfv_after_dayhoff6": 0.029,
      "ufboot_1d_raw": 74.2,
      "ufboot_2d_dayhoff6": 31.4,
      "anomaly_detected": true,
      "anomaly_mechanism": "Pass 1 blind Kabsch/HMM scan flags unstructured nonglobular coil (TM=0.24) and neutral drift (omega=0.89), refuting ancestral fold conservation"
    }
  ],
  "runtime_ms": 24
}