This is an evidence inventory, not a safety verdict or proof of historical vaccine selection. Native means the unmodified antigen, including any tumor variant. Native coordinate correspondence alone does not establish RNA coverage. Missing assessments are not negative results.
{% for audit in audits %}{% set c = audit.construct %}Product: {{ c.modality }}. Mapping: {{ c.mapping_status }} {{ c.mapping_reason }}
{% if c.native_antigen %}Antigen kind: {{ c.native_antigen.kind }}; gene: {{ c.native_antigen.gene_name }} ({{ c.native_antigen.gene_id }}); transcripts: {{ c.native_antigen.transcript_ids|join(', ') }}; proteins: {{ c.native_antigen.protein_ids|join(', ') }}; species: {{ c.native_antigen.species }}.
{% endif %}Native antigen window [{{ c.native_start }}, {{ c.native_end }}):
{{ c.native_sequence if c.native_sequence is not none else 'Unresolved' }}
Final amino-acid sequence ({{ c.sequence|length }} residues): {{ c.sequence }}
Sequence evidence: {{ c.evidence.source }}; {{ c.evidence.evidence_level }}; {{ c.evidence.provider }} {{ c.evidence.vaccine_version }}. {{ c.evidence.description }}
Record identity: {{ c.cache_identity }}
| Change | Coordinates | Final content | Evidence | Rationale |
|---|---|---|---|---|
| {{ edit.kind }} | Native [{{ edit.start }}, {{ edit.end }}) | {{ edit.replacement }} |
{{ edit.evidence.source }} ({{ edit.evidence.evidence_level }}) | {% if edit.rationale %}{{ edit.rationale.description }} — {{ edit.rationale.source }} ({{ edit.rationale.evidence_level }}){% else %}Unknown{% endif %} |
| Chemical | Final [{{ edit.start }}, {{ edit.end }}) | {{ edit.name }} | {{ edit.evidence.source }} ({{ edit.evidence.evidence_level }}) | {% if edit.rationale %}{{ edit.rationale.description }} — {{ edit.rationale.source }} ({{ edit.rationale.evidence_level }}){% else %}Unknown{% endif %} |
Final residue → native antigen offsets (zero-based; None = no native correspondence):
{{ c.native_residue_offsets|join(', ') }}
Removed or incompletely retained native target intervals: {{ c.removed_target_intervals if c.removed_target_intervals is not none else 'Unresolved' }}.
Retained final targetable intervals: {{ c.targetable_mask.intervals }}. Target-mask overlap is not proof that a previously selected ligand is intact.
MHC: {{ audit.mhc_status }}. {{ audit.reason_codes|join(', ') }} {{ audit.error_message }}
Unassessed processing compartments: {{ audit.unassessed_processing_compartments|join(', ') }}. MHC predictions do not establish cleavage, serum stability, presentation or clinical safety.
{% if audit.mhc_assessment %}Every returned ligand occurrence is retained below. Returned predictions do not establish complete coverage of all patient alleles, lengths or models.
| Ligand | Final interval | Target overlap | Crosses edit boundary | Exact self | Self-source provenance | Prediction evidence |
|---|---|---|---|---|---|---|
{{ ligand.peptide }} |
[{{ ligand.window_start_offset }}, {{ ligand.window_end_offset }}) | {{ ligand.overlaps_targetable }} | {{ ligand.crosses_construct_boundary }} | {{ ligand.occurs_in_self_reference }} |
{% if not ligand.self_reference_match.source_provenance_complete %}Incomplete{% endif %}
{% for source in ligand.self_reference_match.sources %}
{{ source.gene_name }} {{ source.gene_id }} / {{ source.transcript_id }} /
{{ source.protein_id }} / {{ source.species }} {% endfor %} |
{% for p in ligand.predictions %}{{ p.kind }} / {{ p.allele }} /
{{ p.predictor_name }} {{ p.predictor_version }}: score={{ p.score }},
value={{ p.value }}, rank={{ p.percentile_rank }} {% endfor %} |