Date: {{ date }} Modality: {{ modality }} Samples: {{ n_samples }} Total spots/cells: {{ n_spots_total | int }}

Samples passed

Samples failed

Total spots/cells

Median genes (cohort)

Per-Sample QC Metrics

{% if has_mt %}{% endif %} {% for row in table_rows %} {% if has_mt %} {% endif %} {% endfor %}

Sample	Status	n_spots	Median counts	Median genes	Genes detected	Median %MT	%MT > 5%	Fail reasons
{{ row.sample }}	{% if row.qc_pass %}PASS{% else %}FAIL{% endif %}	{{ row.n_spots }}	{{ "%.1f" \| format(row.total_counts_median) if row.total_counts_median is not none else "N/A" }}	{{ "%.1f" \| format(row.n_genes_median) if row.n_genes_median is not none else "N/A" }}	{{ row.n_genes_detected if row.n_genes_detected is not none else "N/A" }}	{{ "%.1f%%" \| format(row.pct_mt_median) if row.pct_mt_median is not none else "N/A" }}	{{ "%.1f%%" \| format(row.pct_mt_gt5 * 100) if row.pct_mt_gt5 is not none else "N/A" }}	{{ row.qc_fail_reasons if row.qc_fail_reasons else "" }}

{% if n_fail > 0 %}

Failed Samples

{{ row.sample }}: {{ row.qc_fail_reasons }}

{% endif %}

QC Plots

Distribution Histograms

{% if plots.qc_2x2_pre %}

{% endif %}

QC 2x2 Pre-filter

{% if plots.qc_2x2_post %}

QC 2x2 Post-filter

{% else %}

Post-filter data not provided

{% endif %}

Violin Distributions

{% if plots.violin_pre %}

{% endif %}

QC Violin Pre-filter

{% if plots.violin_post %}

QC Violin Post-filter

{% else %}

Post-filter data not provided

{% endif %}

Mitochondrial Content

{% if plots.pct_mt %}

{% endif %}

% Mitochondrial per sample

Cross-Sample Comparison (Bar)

{% if plots.comparison_bar %}

{% endif %}

Cross-sample comparison (linear)

{% if plots.comparison_bar_log %} Sample comparison (log10)

{% endif %}

Cross-sample comparison (log10 scale)

Per-Sample Distributions (Violin)

{% if plots.violin_grouped %}

{% endif %}

Per-sample violin (linear)

{% if plots.violin_grouped_log %} Sample violin (log10)

{% endif %}

Per-sample violin (log10 scale)

Sample QC Scatter Matrix

{% if plots.scatter_matrix %}

{% endif %}

Sample QC scatter matrix