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

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

{% if includes_splice_sites %} {% endif %} {% for sample in samples %} {% if includes_splice_sites %} {% endif %} {% endfor %}
{{ _('Sample') }} {{ _('Group') }} {{ _('Cutoff') }} [x]{{ _('Included splice sites') }}
{{ sample.id }} {{ sample.group_id }} {{ sample.cutoff }}{{ sample.extension }}

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

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

{{ _('Gender prediction from data') }}

{% 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 analyzed') }} {{ _('is composed of all protein coding, exonic intervals') }} {{ _('referenced in the') }} {{ _('CCDS database') }}. {% if includes_splice_sites %} {{ _('Additionally, the data also includes spicing sites') }} ({{ _('donator and acceptor positions') }}, {{ splice_site_interval }} {{ _('bases on either of each exon') }}). {% endif %}

{% if config.CHANJO_PANEL %}

{{ _('Final coverage metrics were calculated for genes from the clinical panels') }}: {{ config.CHANJO_PANEL_NAME }}. {{ _('Note that estimations were made regarding coverage and completeness') }} {{ _('on the level of transcripts') }}.

{% endif %}

{{ _('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%.

{{ _('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') }}.

{% endblock %}