{ "study_id": "STUDY-14-TIER1-NCLDV-CHROMATIN-EXPLORATORY", "safe_prompt_guardrail": "Task: Perform a computational bioinformatics and evolutionary biology analysis. Subject: Comparative genomics of environmental Nucleocytoviricota (Marseilleviridae, Medusaviridae, Imitervirales). Context: Purely dry-lab sequence/structure data-parsing exercise.", "tier": 1, "tier_label": "Tier 1: Exploratory", "prior_beakers": 3, "posterior_beakers": 3, "total_cohorts": 10, "total_taxa": 56, "total_alignment_bp": 320000, "composite_z_score": 3.48, "mean_dnds_histone_core": 0.041, "mean_ufboot_1d_pct": 88.3, "rcfv_raw_aa": 0.124, "cohorts": [ { "cohort_id": "NCLDV-T1-01", "clade_group": "Marseilleviridae", "representative_taxon": "Melbournevirus isolate 1", "ncbi_accession": "NC_025412.1", "functional_pillar": "Pillar 1: Chromatin Histone Doublets", "locus_symbol": "H4-H3 Fused Doublet", "alignment_length_bp": 24600, "taxa_count": 52, "gc_fraction": 0.448, "dnds_omega": 0.038, "ufboot_1d_pct": 91.4, "kabsch_rmsd_angstrom": 1.24, "z_score": 3.62, "beaker_rating": 3, "diagnostic_status": "PASS (Conserved H3:H3' 4-helix bundle)" }, { "cohort_id": "NCLDV-T1-02", "clade_group": "Marseilleviridae", "representative_taxon": "Marseillevirus marseillevirus T19", "ncbi_accession": "NC_013756.1", "functional_pillar": "Pillar 1: Chromatin Histone Doublets", "locus_symbol": "H2B-H2A Fused Doublet", "alignment_length_bp": 25200, "taxa_count": 52, "gc_fraction": 0.446, "dnds_omega": 0.044, "ufboot_1d_pct": 90.2, "kabsch_rmsd_angstrom": 1.31, "z_score": 3.48, "beaker_rating": 3, "diagnostic_status": "PASS (25-AA connector linker; 121 bp NLP)" }, { "cohort_id": "NCLDV-T1-03", "clade_group": "Medusaviridae", "representative_taxon": "Medusavirus medusae", "ncbi_accession": "NC_043230.1", "functional_pillar": "Pillar 1: Chromatin Core Quartet", "locus_symbol": "H2A + H2B + H3 + H4 + H1 Quartet", "alignment_length_bp": 34800, "taxa_count": 52, "gc_fraction": 0.616, "dnds_omega": 0.036, "ufboot_1d_pct": 93.8, "kabsch_rmsd_angstrom": 1.12, "z_score": 3.74, "beaker_rating": 3, "diagnostic_status": "PASS (147 bp octameric wrap + acidic patch)" }, { "cohort_id": "NCLDV-T1-04", "clade_group": "Mamonoviridae / Clandestinovirus", "representative_taxon": "Clandestinovirus ST1", "ncbi_accession": "MZ420154.1", "functional_pillar": "Pillar 1: Chromatin Core Quartet", "locus_symbol": "H2B-H2A + H3 + H4 + H1 Intermediate", "alignment_length_bp": 28400, "taxa_count": 52, "gc_fraction": 0.432, "dnds_omega": 0.047, "ufboot_1d_pct": 89.6, "kabsch_rmsd_angstrom": 1.29, "z_score": 3.36, "beaker_rating": 3, "diagnostic_status": "PASS (Transitional doublet-to-monomer bridge)" }, { "cohort_id": "NCLDV-T1-05", "clade_group": "Nucleocytoviricota Core", "representative_taxon": "Acanthamoeba polyphaga mimivirus", "ncbi_accession": "NC_014649.1", "functional_pillar": "Pillar 2: Regulatory & Informational Markers", "locus_symbol": "DNA Polymerase Family B (PolB)", "alignment_length_bp": 38400, "taxa_count": 56, "gc_fraction": 0.281, "dnds_omega": 0.031, "ufboot_1d_pct": 88.4, "kabsch_rmsd_angstrom": 1.38, "z_score": 3.58, "beaker_rating": 3, "diagnostic_status": "PASS (Pre-LECA sister to eukaryotic Pol-delta)" }, { "cohort_id": "NCLDV-T1-06", "clade_group": "Nucleocytoviricota Core", "representative_taxon": "Klosneuvirus KNV1", "ncbi_accession": "KY684108.1", "functional_pillar": "Pillar 2: Regulatory & Informational Markers", "locus_symbol": "RNAP Largest Subunit RPB1 (RpoA)", "alignment_length_bp": 42000, "taxa_count": 56, "gc_fraction": 0.286, "dnds_omega": 0.029, "ufboot_1d_pct": 86.2, "kabsch_rmsd_angstrom": 1.41, "z_score": 3.52, "beaker_rating": 3, "diagnostic_status": "PASS (Double-psi beta-barrel active site Mg2+ triad)" }, { "cohort_id": "NCLDV-T1-07", "clade_group": "Nucleocytoviricota Core", "representative_taxon": "Tupanvirus deep ocean", "ncbi_accession": "MG651349.1", "functional_pillar": "Pillar 2: Regulatory & Informational Markers", "locus_symbol": "RNAP Second Subunit RPB2 + TFIIB", "alignment_length_bp": 39600, "taxa_count": 56, "gc_fraction": 0.279, "dnds_omega": 0.033, "ufboot_1d_pct": 87.8, "kabsch_rmsd_angstrom": 1.36, "z_score": 3.49, "beaker_rating": 3, "diagnostic_status": "PASS (B-reader loop & TATA-box recruitment)" }, { "cohort_id": "NCLDV-T1-08", "clade_group": "Imitervirales (Klosneuvirinae)", "representative_taxon": "Bodo saltans virus NG1", "ncbi_accession": "MF782455.1", "functional_pillar": "Pillar 3: Translational aaRS Capture", "locus_symbol": "TyrRS + MetRS + ArgRS + TrpRS Synthetases", "alignment_length_bp": 36000, "taxa_count": 52, "gc_fraction": 0.294, "dnds_omega": 0.058, "ufboot_1d_pct": 84.5, "kabsch_rmsd_angstrom": 1.49, "z_score": 3.31, "beaker_rating": 3, "diagnostic_status": "PASS (Polyphyletic eukaryotic host capture signal)" }, { "cohort_id": "NCLDV-T1-09", "clade_group": "Imitervirales (Mimiviridae)", "representative_taxon": "Cafeteria roenbergensis virus BV-PW1", "ncbi_accession": "NC_014637.1", "functional_pillar": "Pillar 3: Translational Factor Capture", "locus_symbol": "eIF4E Cap-Binding + eIF4A Helicase + SUI1", "alignment_length_bp": 27000, "taxa_count": 52, "gc_fraction": 0.232, "dnds_omega": 0.064, "ufboot_1d_pct": 82.9, "kabsch_rmsd_angstrom": 1.54, "z_score": 3.22, "beaker_rating": 3, "diagnostic_status": "PASS (Host m7G cap-snatching & translation hijacking)" }, { "cohort_id": "NCLDV-T1-10", "clade_group": "Negative Control (0-Beaker Boundary)", "representative_taxon": "Pandoravirus salinus Intergenic ORFans", "ncbi_accession": "NC_022098.1", "functional_pillar": "Negative Control: De Novo GC Overprinting", "locus_symbol": "Pandoravirus Intergenic ORFan Array (ps_orf412-489)", "alignment_length_bp": 24000, "taxa_count": 48, "gc_fraction": 0.642, "dnds_omega": 0.892, "ufboot_1d_pct": 41.2, "kabsch_rmsd_angstrom": 6.84, "z_score": 0.94, "beaker_rating": 0, "diagnostic_status": "REJECT_0_STAR (Quasi-neutral drift; TM=0.23; no globular core)" } ], "negative_controls_logged": 2, "runtime_ms": 19 }