Untitled ADLA run

Job adla_20260707_070526_d0551175 · ADLA 0.1.7-hardening

Anthropological and educational research use only. ADLA does not diagnose scurvy or vitamin C deficiency; interpret genomic, epigenomic, structural-variant, phasing, workflow-import, microbial/context, and ancient-DNA authentication signals alongside archaeological context, preservation quality, osteological/isotopic evidence, historical diet, contamination controls, damage/authenticity metrics, and biochemical data where available.

Interpretation summary

Overall confidence: insufficient for deficiency call

Sequencing cannot directly measure vitamin C status. In ADLA, genomic and epigenomic findings are anthropological research signals that require archaeological, osteological, isotopic, ecological, historical, and preservation context before interpretation.
Anthropological context mode: modern or unknown research context; corroboration score 20/100.
ADLA imported 1 ancient-DNA authentication/QC report(s). Status: structured authentication evidence imported. These metrics support sample-readiness review, not deficiency diagnosis.
No curated ascorbate-transporter rsID hits were detected in parsed VCF inputs. This is not proof of absence unless target regions were callable.
No mosdepth/coverage target report was parsed. Variant absence and methylation absence should be treated as unknown until target callability is measured.
No target-region modified-base summaries were available. Upload Modkit bedMethyl or run modkit from modBAM through the CLI pipeline.

Priority variants

No priority variants available.

Anthropological context

{
    "sample_age_class": "unknown",
    "sample_material": "unknown",
    "preservation_context": "",
    "anthropological_corroboration_score": 20,
    "score_components": [
        {
            "component": "authentication_report_imported",
            "points": 10,
            "note": "Structured ancient-DNA authentication report(s) were imported."
        },
        {
            "component": "authentication_damage_metric_present",
            "points": 10,
            "note": "Damage/deamination or PMD-style metric was imported."
        },
        {
            "component": "authentication_contamination_metric_present",
            "points": 8,
            "note": "Contamination estimate was imported."
        },
        {
            "component": "unknown_sample_age_penalty",
            "points": -8,
            "note": "Sample age class is unknown, reducing anthropological interpretability."
        }
    ],
    "interpretation_mode": "modern_or_unknown_research_context",
    "methylation_mode": "direct_modbase_exploratory_when_metadata_complete"
}

Authentication aggregate

{
    "report_count": 1,
    "tools_detected": [
        "schmutzi"
    ],
    "status": "structured_authentication_evidence_imported",
    "has_damage_metric": true,
    "has_contamination_metric": true,
    "has_endogenous_fraction": true,
    "has_pmd_metric": true,
    "max_contamination_percent": 2.8,
    "metrics": {
        "contamination_percent": {
            "count": 1,
            "min": 2.4,
            "max": 2.4,
            "mean": 2.4,
            "unit": "percent"
        },
        "mitochondrial_contamination_percent": {
            "count": 1,
            "min": 2.8,
            "max": 2.8,
            "mean": 2.8,
            "unit": "percent"
        },
        "nuclear_contamination_percent": {
            "count": 1,
            "min": 1.9,
            "max": 1.9,
            "mean": 1.9,
            "unit": "percent"
        },
        "endogenous_fraction_percent": {
            "count": 1,
            "min": 47.3,
            "max": 47.3,
            "mean": 47.3,
            "unit": "percent"
        },
        "c_to_t_5prime_percent": {
            "count": 1,
            "min": 14.2,
            "max": 14.2,
            "mean": 14.2,
            "unit": "percent"
        },
        "g_to_a_3prime_percent": {
            "count": 1,
            "min": 11.7,
            "max": 11.7,
            "mean": 11.7,
            "unit": "percent"
        },
        "damage_percent": {
            "count": 1,
            "min": 12.9,
            "max": 12.9,
            "mean": 12.9,
            "unit": "percent"
        },
        "mean_pmd_score": {
            "count": 1,
            "min": 0.87,
            "max": 0.87,
            "mean": 0.87,
            "unit": "score"
        },
        "pmd_positive_percent": {
            "count": 1,
            "min": 68.4,
            "max": 68.4,
            "mean": 68.4,
            "unit": "percent"
        },
        "median_fragment_length_bp": {
            "count": 1,
            "min": 68,
            "max": 68,
            "mean": 68,
            "unit": "bp"
        },
        "mean_fragment_length_bp": {
            "count": 1,
            "min": 79.5,
            "max": 79.5,
            "mean": 79.5,
            "unit": "bp"
        },
        "short_fragment_percent_le100": {
            "count": 1,
            "min": 72.1,
            "max": 72.1,
            "mean": 72.1,
            "unit": "percent"
        }
    },
    "flags": [
        "low_contamination_estimate",
        "damage_metric_present",
        "pmd_metric_present",
        "endogenous_fraction_present"
    ]
}