{{ report_title }} — {{ basename }}

Detection Result

{% if detection.detected is true %}

{% elif detection.detected is false %}

{% else %} {% if detection.jeffreys_prior_applied %}

ℹ No background reads observed in synthetic controls — noise rate estimated via Jeffreys prior (p_err = {{ noise_rate_str }}).

{% endif %} {% if detection.n_synthetic_controls < 20 %}

⚠ Only {{ detection.n_synthetic_controls }} synthetic controls — p-value reliability is reduced.

{% endif %}

{% if detection.qc_checks %}

QC Checks

{% for check in detection.qc_checks %}

{% if check.passed %}✅{% else %}⚠️{% endif %} {{ check.label }} {{ check.value_str }} threshold: {{ check.threshold_str }}

{% endfor %}

{% endif %}

Assay Metrics

Signature Size

{{ "{:,}".format(detection.signature_size) }}

filtered loci

Mean Coverage

{{ "%.1f"|format(detection.mean_coverage) }}×

at signature loci

Corrected Coverage

{{ "{:,.0f}".format(detection.corrected_coverage) }}

effective depth × loci

Coverage Correction Ratio

corrected / original coverage

Patient vs. Controls

★ Patient: matched patient signature.
● Synthetic control signatures: Signatures drawn from db_control.
Blue violin: Fitted Binomial, according to synthetic control error-rates: Binom(N={{ detection.n_effective }}, p_err={{ noise_rate_str }}).
⎯⎯ Detection threshold (min VAF for Binomial p < {{ "%.0f"|format(detection.alpha * 100) }}%).
·–· Sample-specific LOD = {{ lod_str }} — minimum VAF detectable at {{ "%.0f"|format(detection.lod_recall * 100) }}% recall / {{ "%.0f"|format(detection.lod_fpr * 100) }}% FPR for this patient’s signature size and coverage.
◆ Cohort control signatures.

{% if sbs6_vaf_plots or sbs96_plots %}

Signature Profile & VAF

{% for img in sbs6_vaf_plots %}

{% endfor %} {% if sbs96_plots %} {% for img in sbs96_plots %}

COSMIC-format SBS96 profile from all filtered signature variants. 96 trinucleotide channels grouped by substitution type, normalised to pyrimidine strand.

{% endfor %} {% endif %}

{% endif %} {% if intersection_af_img %}

cfDNA Intersection Allele Fraction

Allele-fraction distribution at signature loci with ≥1 supporting cfDNA read. Red: patient signature loci (signal). Blue: control signature loci (noise).

{% endif %} {% if read_length_img %}

Read Length Distribution

Read length distribution of cfDNA reads at signature loci (after read filter). Red: patient signature loci. Blue: control signature loci. Shorter fragment lengths are enriched in ctDNA due to nucleosomal positioning.

{% endif %} {% if intersection_snvq_img %}

cfDNA Intersection SNVQ Distribution

SNVQ score distribution of cfDNA reads at signature loci (after read filter). Red: patient signature loci. Blue: control signature loci. Higher SNVQ indicates higher confidence in the SNV call.

{% endif %} {% if lq_fraction_hist_img %}

LQ-Reads Fraction per Locus

$LQ-reads fraction histogram$

Per-locus fraction of reads failing the read filter (LQ reads) for matched signature loci. Blue: loci kept (LQ fraction ≤ threshold). Red: loci excluded by the noisy-loci filter. Dashed line: threshold{% if thresh_noise_lq_reads is not none %} ({{ thresh_noise_lq_reads }}){% endif %}.

{% endif %} {% if supporting_reads_hist_img %}

Alt-Supporting Reads per Variant Locus

Distribution of alt-supporting cfDNA read counts per signature locus (after read filter). Red: patient loci — signal. Blue: control loci — noise baseline. Loci with zero supporting reads are not shown; their count is annotated in the plot.

{% endif %} {% if filter_funnel %}

Signature Filter Funnel

{% for row in filter_funnel %} {% endfor %}

Step	Count	% Funnel	% Pass
{{ row.step }} {% if row.desc %} {{ row.desc }} {% endif %}	{{ "{:,}".format(row.count) }}	{{ "%.1f%%"\|format(row.pct_funnel) if row.pct_funnel is not none else "" }}	{{ "%.1f%%"\|format(row.pct_pass) if row.pct_pass is not none else "" }}

{% endif %} {% if read_funnel %}

Read Filter Funnel

{% for row in read_funnel %} {% endfor %}

Step	COUNT (READS)	%FUNNEL (READS)	%PASS (READS)	COUNT (LOCI)	%FUNNEL (LOCI)	%PASS (LOCI)
{{ row.step }} {% if row.desc %} {{ row.desc }} {% endif %}	{{ "{:,}".format(row.count) }}	{{ "%.1f%%"\|format(row.pct_funnel) if row.pct_funnel is not none else "" }}	{{ "%.1f%%"\|format(row.pct_pass) if row.pct_pass is not none else "" }}	{{ "{:,}".format(row.loci_count) if row.loci_count is not none else "" }}	{{ "%.1f%%"\|format(row.pct_funnel_loci) if row.pct_funnel_loci is not none else "" }}	{{ "%.1f%%"\|format(row.pct_pass_loci) if row.pct_pass_loci is not none else "" }}

{% endif %}

For Research Use Only. This report is intended solely for research purposes and has not been validated for clinical diagnostic use. It does not constitute a clinically validated test and should not be used to guide clinical decisions without independent clinical validation. Results may not be accurate for all sample types or conditions.