Source outcomes

Each recorded source is retained here, including sources that never produced a ranked window. Reasons can overlap; they are not disjoint losses. “No ranked window” does not identify a biological absence. Product mappings are listed in the ranking and product sections.

{% for source in input_coverage.sources %}{% endfor %}

Source / gene	Family	Stage / recorded reason	Product outcome
{{ source.identity \| e }}{% if source.gene %} {{ source.gene \| e }}{% endif %}{% if source.context %} {{ source.context \| e }}{% endif %} {{ source.origin \| e }}	{{ source.family }}	{{ source.stage }}{% if source.rank %} (rank {{ source.rank }}){% endif %}{% for reason in source.reasons %} {{ reason \| e }}{% endfor %} {% if source.retained_epitopes is not none %} {{ source.retained_epitopes }} retained epitope records{% endif %}	{{ source.product_outcome \| e }}

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

Unresolved reference models: {{ producer.family }} / {{ producer.sample or 'Unknown' }}

Producer evidence identity: {{ producer.identity | e }}

{{ model.identity | e }} {{ model.context | e }}: {{ model.reason | e }}{% if model.status %} ({{ model.status | e }}){% endif %}

{% endif %}{% endfor %} {% for original in input_coverage.direct %}

Recorded Isovar thresholds: {{ original.isovar_filter_thresholds | tojson | e }}. Failed RNA filters alone do not establish final exclusion when DNA fallback is enabled.

Original variant outcomes: {{ original.input_id | e }}

{% for row in original.variant_outcomes %} {% for key in ('is_coding_nonsynonymous', 'rna_support', 'has_vaccine_peptide') %}{% endfor %}{% endfor %} {% for row in original.annotation_unavailable %}{% endfor %}

Variant	Coding effect	RNA protein	Candidate window	Isovar filter outcomes
{{ row.gene_name \| e }} {{ row.contig }}:{{ row.start }} {{ row.ref }}>{{ row.alt }}	{{ ('Yes' if row[key] else 'No') if row[key] is not none else 'Not assessed at this stage' }}	{% if row.isovar_filter_results %}{% for name, passed in row.isovar_filter_results.items() %}{{ name \| e }}: {{ 'Pass' if passed else 'Fail' }} {% endfor %}{% else %}Not recorded{% endif %}
{{ row.contig }}:{{ row.start }} {{ row.ref }}>{{ row.alt }}	Annotation result unavailable

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

CTA expression admission: {{ expression.identity | e }}

{% for row in expression.decisions %}{% endfor %}

Feature / gene	Expression ({{ expression.contract.expression_unit }})	Recorded decision
{{ row.input_identifier \| e }} {{ row.gene_name \| e }}	{{ row.value if row.value is not none else 'Unknown' }}	{{ row.status \| e }}

{% endfor %}