Input coverage

Counts below describe recorded source identities, deduplicated across inputs. They are not counts of independent biological events, RNA reads, reference ORF models, peptide occurrences or unique products. No supplied evidence recorded means this report cannot establish that a family was assessed or excluded.

{% if not input_coverage.available %}

The source inventory was not recorded for this report. Historical input denominators are unknown.

{% endif %} {% for family in input_coverage.families %} {% for key in ('records', 'admitted', 'ranked', 'represented') %}{% endfor %} {% endfor %}

Source family	Input evidence	Recorded sources	Admitted	Ranked	In products
{{ family.name }}	{{ family.status }}	{{ family[key] if family[key] is not none else 'Unknown' }}

Admission is the recorded construct-admission decision where available. Ranked counts reflect the current configuration. “In products” uses retained source mappings from the actual emitted products; unknown also covers analysis-only reports. Retained predictions do not prove complete inference coverage. Original input denominators are shown separately below.

{% for original in input_coverage.direct %}

Original variant input observation {{ loop.index }}

Input {{ original.input_id | e }}; Vaxrank {{ original.producer_version }}. Unit: {{ original.unit }}. Stage: {{ original.stage }}. Distinct observations of one input are separate histories and must not be added.

{% for key, label in [('loaded', 'Parsed variants loaded'), ('annotatable', 'Variants with annotation results'), ('coding_effect', 'Coding-effect variants'), ('coding_with_rna_protein', 'Coding-effect variants with an RNA-derived protein'), ('with_candidate_windows', 'Variants with candidate windows')] %} {% endfor %}

{{ label }}	{{ original.counts[key] if original.counts[key] is not none else "Not assessed at this stage" }}

{% endfor %} {% if not input_coverage.direct %}

Original VCF/BAM stage counts: unknown (not retained in these inputs). Surviving antigen or prediction rows cannot recover that denominator.

{% endif %} {% if input_coverage.producers %}

Producer observations

{% for producer in input_coverage.producers %}{% endfor %}

Family / sample	Reference models	Resolved coding candidates	Producer state
{{ producer.family }} / {{ producer.sample or 'Unknown' }}	{{ producer.models if producer.models is not none else 'Unknown' }}	{{ producer.candidates }} RNA reconstructions: {{ producer.rna_reconstructions if producer.rna_reconstructions is not none else "Unknown" }}	{{ producer.state or 'Not recorded' }}

{{ producer.family }} event identity: {{ producer.event | tojson | e if producer.event else "Not recorded" }}

{% for producer in input_coverage.producers %}{% if producer.model_outcomes %}

Reference-model outcomes: {{ producer.family }}

{% for model in producer.model_outcomes %}{% endfor %}

Reference model	Compatible RNA reconstructions	Coding candidates	Outcome
{{ model.reference or model.identity }}	{{ model.compatible_rna if model.compatible_rna is not none else 'Unknown' }}	{{ model.candidates if model.candidates is not none else 'Unknown' }}	{{ model.reason or model.state or 'Not recorded' }}

{% endif %}{% endfor %}

One event can produce several reference-model interpretations and many RNA reconstructions. These are separate counting units. See source outcomes for unresolved models and rejected sources.

{% endif %} {% for expression in input_coverage.expression %}

CTA expression input: {{ expression.decisions | length }} measured features; {{ expression.contract.measurement_level }} / {{ expression.contract.expression_unit }}; sample {{ expression.contract.sample_id | e }}; assay {{ expression.contract.assay | e }}.

{% endfor %}

Source outcomes · Original inputs and current report inputs