> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section.md).

# Sample quality section

## Sample quality metrics

The **Sample quality** section in the **Lab tab** gives you a quick view of the reliability of sequencing or array data used in your case.

The metrics displayed in the **Sample quality** section and their underlying calculation vary depending on the case type (see below).

{% columns %}
{% column width="50%" %}

<table><thead><tr><th width="276.72735595703125">NGS case</th></tr></thead><tbody><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sample-quality.md">Sample quality</a> (overall)</td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sex-validation.md">Sex validation</a></td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ploidy.md">Ploidy</a>*</td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/contamination.md">Contamination</a></td></tr><tr><td><p><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/coverage.md">Coverage metrics</a>:</p><ul><li>Average coverage</li><li>% Bases with coverage >10x</li><li>% Bases with coverage >20x</li></ul></td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/percentage-of-mapped-reads.md">% Mapped reads</a></td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/sequencing-error-rate.md">Error rate</a></td></tr></tbody></table>

\*<sub>*Available only for whole genome FASTQ cases.*</sub>
{% endcolumn %}

{% column width="50%" %}

<table><thead><tr><th width="276.72735595703125">Array case</th></tr></thead><tbody><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/array-sample-quality.md">Sample quality</a> (overall)</td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/array-sex-validation.md">Sex validation</a></td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/autosomal-call-rate.md">Autosomal call rate</a></td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/call-rate.md">Call rate</a></td></tr><tr><td><a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/log-r-deviation.md">Log R deviation</a></td></tr></tbody></table>
{% endcolumn %}
{% endcolumns %}

## Overall sample quality status

The overall sample quality status appears next to the Sample quality section title and in the Sample quality card of the Summary dashboard.

The overall sample quality status depends on whether any sample in the case failed a sample quality check.

* <img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-2933d103ce45697a7f27f932a3e2ffc6c16b7ce3%2Fimage%20(174).png?alt=media" alt="" data-size="line"> **Pass:** Every sample quality check passed or was skipped for every sample in the case.
* <img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-184a7241f067453bbaf55f5f3382a9c772a24b29%2Fimage%20(178).png?alt=media" alt="" data-size="line"> **Fail:** At least one sample in the case failed at least one sample quality check.

The overall sample quality status is one of the statuses that determine the [combined quality status](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/combined-quality-status.md).

{% hint style="info" %}
The overall sample quality status is not the same as the [NGS](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sample-quality.md)/[array](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/quality-parameters-38.0+/array-sample-quality.md) sample quality of each sample. The status takes the NGS or array sample quality level into account, but other checks also affect it.
{% endhint %}

## DRAGEN QC

For [eligible cases](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report.md#prerequisites-for-accessing-the-dragen-qc-report), users can also review the results of [DRAGEN QC](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report.md): interactive DRAGEN QC report and DRAGEN QC metric files.

{% hint style="info" %}
DRAGEN QC for array samples is available from version 100.39.0 onwards.
{% endhint %}


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