{% extends 'report/layouts/base.html' %} {% block body %}

{{ _('Quality report clinical exome sequencing') }}

{% for sample in samples %} {% endfor %}
{{ _('Sample') }} {{ _('Group') }} {{ _('Cutoff') }} [x]
{{ sample.id }} {{ sample.group_id }} {{ sample.cutoff }}

{{ _('Generally important metrics') }} {% if config.CHANJO_PANEL %} {{ _('for') }} {{ config.CHANJO_PANEL_CAPTION }} {% endif %}

{% for sample_id, _, coverage, completeness in key_metrics %} {% endfor %}
{{ _('Sample') }} {{ _('Average coverage') }} [x] {{ _('Average completeness') }} [%]
{{ sample_id }} {{ coverage|round(3) }} {{ (completeness * 100)|round(3) }}

{{ _('Diagnostic yield') }} {% if config.CHANJO_PANEL %} {{ _('for') }} {{ config.CHANJO_PANEL_CAPTION }} {% endif %}

{% for sample_id, _, value in diagnostic_yield %} {% endfor %}
{{ _('Sample') }} {{ _('Diagnostic yield') }} [%]
{{ sample_id }} {{ (value * 100)|round(3) }}

{{ _('Gender confirmation') }}

{% for sample_id, gender, x_coverage, y_coverage in genders %} {% endfor %}
{{ _('Sample') }} {{ _('Gender') }} {{ _('Average coverage') }} [x]
{{ _('Chromosome') }} X {{ _('Chromosome') }} Y
{{ sample_id }} {{ _(gender) }} {{ x_coverage|round(3) }} {{ y_coverage|round(3) }}

{{ _('Explanations') }}

{{ _('General') }}

{{ _('The parts of the genome that has been analyzsed') }} {{ _('is composed of all protein coding, exonic intervals') }} {{ _('referenced in the') }} {{ _('CCDS database') }} . {{ _('Additionally, the data also includes spicing sites') }} ({{ _('donator and acceptor positions') }}, {{ _('two bases on either of each exon') }}.)

{{ _('Coverage') }}: {{ _('An alternative measure of sequence depth') }}. {{ _('It is defined as the ratio of bases') }} {{ _('sequenced deeper than a specified cutoff') }}, {{ _('e.g. 10x') }}. {{ _('The current cutoff is defined per sample') }} {{ _('and is found i the "Cutoff" column (first table)') }}.

{{ _('Completeness') }}: {{ _('gives an overview of the success of sequencing') }}. {{ _("It's defined as the ratio of transcripts") }} {{ _('with a completeness of') }}100%.

{% if config.CHANJO_PANEL %}

{{ _('Generally important metrics') }} {{ _('for') }} {{ config.CHANJO_PANEL_CAPTION }}

{{ _('The measure of coverage was genereated through matching of gene IDs from') }} {{ config.CHANJO_PANEL_CAPTION }}. {{ _('Note that estimations were made regarding coverage and completeness') }} {{ _('on the level of transcripts') }}.

{% endif %}
{% endblock %}