{% extends 'report/layouts/base.html' %} {% block nav %}
  • {{ filters_form(group_id, extras, pdf=True, hidden=True) }}
  • {% endblock %} {% block main %}
    {{ filters_form(group_id, extras) }}

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

    {% if extras.panel_name %}

    {{ _('Based on gene panel') }}: {{ extras.panel_name }}

    {% endif %} {{ overview_table(sex_rows) }}

    {{ _('Generally important metrics') }}

    {{ metrics_table(metrics_rows) }}

    {{ _('Transcript coverage') }} {{ _('at') }}: {{ extras.level }}x

    {{ transcripts_table(tx_rows) }}

    {{ _('Explanations') }}

    {{ explanations(extras.level) }}
    {{ _('End of report') }}
    {% endblock %} {% macro overview_table(sex_rows) %}
    {% for sample in sex_rows %} {% endfor %}
    {{ _('Sample') }} {{ _('Group') }} {{ _('Analyzed at') }} {{ _('Sex') }} {{ _('according to sequence data') }} {{ _('Average coverage') }} [x]
    {{ _('Chromosome') }} X {{ _('Chromosome') }} Y
    {{ sample.sample }} {{ sample.group }} {{ sample.analysis_date.date() }} {{ _(sample.sex) }} {{ sample.x_coverage|round(3) }} {{ sample.y_coverage|round(3) }}
    {% endmacro %} {% macro metrics_table(metrics_rows) %}
    {% for level_int, level_key in levels %} {% endfor %} {% for data in metrics_rows %} {% for level_int, level_key in levels %} {% endfor %} {% endfor %}
    {{ _('Sample') }} {{ _('Average coverage') }} [x]{{ _('Completeness') }} {{ level_int }}x [%]
    {{ data.TranscriptStat.sample.name }} {{ data.mean_coverage|round(2) }}{{ data|attr(level_key)|round(2) if data|attr(level_key) }}
    {% endmacro %} {% macro transcripts_table(transcript_rows) %} {% if extras.show_genes %} {% endif %} {% for data in transcript_rows %} {% if extras.show_genes %} {% endif %} {% else %} {% endfor %}
    {{ _('Sample') }} {{ _('Fully covered transcripts') }} [%] {{ _('Incompletely covered') }} {{ _('transcripts') }}{{ _('Incompletely covered') }} {{ _('genes') }} (max 50)
    {{ data.sample.name }} {{ data.yield|round(3) }} {{ data.missed_count }} / {{ data.total }} {% for tx_stat in data.missed.limit(50) %} {{ tx_stat.transcript.gene_name or tx_stat.transcript.gene_id }} {% else %} - {% endfor %}
    Inga ofullständigt täckta transkript.
    {% endmacro %} {% macro explanations(cutoff) %}

    {{ _('General') }}

    Sambamba {{ _('is used for coverage analysis based on read alignment.') }} {{ _('Duplicates, reads with mapping quality less than 10 as well as bases with a base quality less than 10 are not included in the analysis.') }} {{ _('Bases that overlap between read pairs are only counted once.') }} {{ _('The parts of the genome that has been analyzed') }} {{ _('is composed of all protein coding, exonic intervals') }} {{ _('referenced in the') }} HGNC. {% 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 %}

    {{ _('Completeness') }}: {{ _('defined as the ratio of bases') }} {{ _('sequenced deeper than a specified cutoff') }}, {{ _('e.g. 10x') }}.

    {{ _('Transcript coverage') }}: {{ _('defined as the ratio of transcripts that are fully covered') }}, {{ _('i.e. with a completeness of') }} 100% {{ _('at') }} {{ cutoff }}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 %} {% macro filters_form(group_id, extras, pdf=False, hidden=False) %}
    {% endmacro %}