Cohort Summary Report

Report Date: {{ report_date }}

{% if total_samples is defined and total_samples > 0 and kestrel_counts %}

Cohort Size

Total samples analyzed

Kestrel Positive

{{ "{:.1f}".format((kestrel_counts.positive + kestrel_counts.flagged) / total_samples * 100) }}% positive rate

High Precision Calls

Confidence grade Finding

adVNTR Genotyped

{{ advntr_counts.positive + advntr_counts.flagged + advntr_counts.negative }}

{{ advntr_counts.unestablished }} unestablished

{% if length_tier_kpi %}

{% endif %}

{% endif %} {% if advntr_evidence_provenance %}

adVNTR artifact-evidence provenance

{{ item.sample }}: {{ item.revision }} {% if item.assertion %} — {{ item.assertion }}{% endif %}

{% endif %} {% if decision_profile_groups %}

Decision profile groups

{% if pooled_decision_metrics_suppressed %}

Pooled decision-performance plots are suppressed across decision profile hashes.

{% endif %} {% for group in decision_profile_groups %}

{{ group.profile_id }} — revision {{ group.revision }}

Decision profile SHA-256: {{ group.sha256 }}

Samples: {{ group.samples | join(", ") }}

{% if pooled_decision_metrics_suppressed %}

Profile-specific Kestrel summary

Profile-specific adVNTR summary

{% endif %}

{% endfor %} {% endif %}

Show flagged values

Kestrel Results

{# The pre-rendered table carries the complete molecular-identity quartet; the template performs no inference or client-side completion. #} {% if kestrel_positive and kestrel_positive.strip() %}

{% else %}

No Kestrel variant calls were recorded across this cohort.

{% endif %} {% if not pooled_decision_metrics_suppressed %}

Kestrel Summary Plot

{% if kestrel_counts and total_samples %}

Kestrel Cohort Categorisation

Sample-level verdict distribution across {{ total_samples }} samples

Positive {{ kestrel_counts.positive }} ({{ "{:.1f}".format(kestrel_counts.positive / total_samples * 100) }}%) High precision pathogenic variant

Positive (Flagged) {{ kestrel_counts.flagged }} ({{ "{:.1f}".format(kestrel_counts.flagged / total_samples * 100) }}%) Candidate with quality flag

Negative {{ kestrel_counts.negative }} ({{ "{:.1f}".format(kestrel_counts.negative / total_samples * 100) }}%) No pathogenic candidate

Unestablished {{ kestrel_counts.unestablished }} ({{ "{:.1f}".format(kestrel_counts.unestablished / total_samples * 100) }}%) No result rows contributed

{% endif %}

{% endif %} {% if kestrel_missing %}

{{ kestrel_missing | length }} sample(s) contributed no Kestrel result rows and are counted as Unestablished: {{ kestrel_missing | join(", ") }}.

{% endif %}

adVNTR Results

{# The same server-rendered quartet contract applies here without JavaScript/network. #} {% if advntr_positive and advntr_positive.strip() %}

{% else %}

No adVNTR variant calls were recorded across this cohort.

{% endif %} {% if not pooled_decision_metrics_suppressed %}

adVNTR Summary Plot

{% if advntr_counts and total_samples %}

adVNTR Cohort Categorisation

Sample-level verdict distribution across {{ total_samples }} samples

Positive {{ advntr_counts.positive }} ({{ "{:.1f}".format(advntr_counts.positive / total_samples * 100) }}%) adVNTR called variant

Positive (Flagged) {{ advntr_counts.flagged }} ({{ "{:.1f}".format(advntr_counts.flagged / total_samples * 100) }}%) Candidate with quality flag

Negative {{ advntr_counts.negative }} ({{ "{:.1f}".format(advntr_counts.negative / total_samples * 100) }}%) No variant called

Unestablished {{ advntr_counts.unestablished }} ({{ "{:.1f}".format(advntr_counts.unestablished / total_samples * 100) }}%) adVNTR not run / no rows

{% endif %}

{% endif %} {% if advntr_missing %}

{{ advntr_missing | length }} sample(s) contributed no adVNTR result rows and are counted as Unestablished: {{ advntr_missing | join(", ") }}.

{% endif %} {% if nomenclature_legend %}

Reading key

How to read the coded values in the tables above

{{ entry.term }}{% if entry.label %}{{ entry.label }}{% endif %}: {{ entry.meaning }}

{% if show_kestrel_bam_semantics %}

Kestrel output.bam contains resolved haplotype records, not sequencing reads. Its record counts are haplotype-record support; XD is minimum k-mer depth and does not weight votes or alter names or tiers.

{% endif %}

{% endif %} {% if additional_stats %}

Additional Statistics

{% endif %}

Call frequency

Grouped variant calls across the cohort, sorted ascending by frequency. Calls with frequency at or below the configured threshold are marked in the Below_Cutoff column; no calls are filtered.