{% extends "base-layout.html" %} {% block css %} {{ super() }} {% endblock %} {% macro errors_block() %} {% for error_description, error_content in errors %} {% if error_content %}
{{error_description}}: {{error_content|join(", ")}}
{% endif %} {% endfor %} {% endmacro %} {% macro report_filters() %}

{% endmacro %} {% macro sex_rows_block() %}
{% for sample in sex_rows %} {% endfor %}
Sex metrics from sequencing data
Sample Group Analyzed at Sex according to sequence data Average coverage [x]
Chromosome X Chromosome Y
{{ sample.sample }} {{ sample.case }} {{ sample.analysis_date.date() }} {{sample.predicted_sex}} {{ sample.x_coverage }} {{ sample.y_coverage }}
{% endmacro %} {% macro important_metrics() %}
{% for level_int, level_key in levels.items() %} {% endfor %} {% for sample, stats in completeness_rows %} {% for level_int, level_key in levels.items() %} {% endfor %} {% endfor %}
Average coverage and coverage completeness data
Sample Average coverage[x]Completeness {{ level_int }}x [%]
{{ sample }} {{ stats.mean_coverage|round(2) if stats.mean_coverage is defined }}{{ stats[level_key] if stats[level_key] is defined }}
{% endmacro %} {% macro default_level_metrics() %}
{% for data in default_level_completeness_rows %} {% if data[1] == 100.00 %} {% else %} {% endif %} {% endfor %}
Genes/Transcripts/Exons coverage at default coverage threshold
Sample Fully covered {{ interval_type }} [%] Incompletely covered {{ interval_type }}
{{data[0]}} No incompletely covered intervals. {{ data[1] }} {{ data[2] }}
{% endmacro %} {% macro explanations() %}

General

Chanjo2 was used for coverage analysis based on reads alignment. Chanjo2 computes coverage and coverage completeness using an internal module based on d4tools. The genome has been analyzed at the {{ extras.interval_type }} level, for genes defined at HGNC.

{% if extras.panel_name %}

Final coverage metrics were calculated for genes from the clinical panels. Note that estimations were made regarding coverage and completeness on the level of {{ extras.interval_type }}.

{% endif %}

Average coverage: defined as the mean coverage over a list of genes. Values were calculated as the mean of coverage values over single genes or intervals (transcripts or exons) from single genes e.g. 38.24

Completeness: defined as the ratio of bases sequenced deeper than a specified cutoff. Values were calculated across pooled genes or genes' intervals, according to the sequencing technology used e.g. 10x

Gene/Transcripts/Exons coverage: defined as the ratio of these intervals are fully covered ('i.e. with a completeness of') 100% 'at' {{ extras.default_level }}x.

Gender prediction from data: calculated by comparing relative chromosome coverage (X/Y). Some reads randomly map to the Y chromosome. Therefore, a less than 10 fold difference is used to infer a "male" sample.

{% endmacro %} {% block title %} Coverage report {% endblock %} {% block pdf_export %} {% endblock %} {% block content%} {{ report_filters() }} {% if extras.case_name %}

Case name: {{extras.case_name}}

{% endif %}

Quality report: clinical sequencing

{% if extras.panel_name %}

Based on gene panel: {{ extras.panel_name }}

{% endif %} {{ sex_rows_block() }}

Generally important metrics

{{ important_metrics() }}

Transcript coverage at {{ extras.default_level }}x

{{ default_level_metrics() }}
{{ errors_block() }}

Explanations

{{ explanations() }} {% endblock %} {% block js_code %} {{ super() }} {% endblock %}