> 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/ngs-sample-quality-metrics/ngs-sample-quality.md).

# NGS sample quality

The sample quality indicator rates the sequencing reliability of each sample as **High**, **Moderate**, or **Low**. Sample quality is evaluated using different metrics, depending on the sample file type.

## FASTQ sample quality

FASTQ sample quality reflects the confidence level that the sequencing data can support accurate variant calling.

For samples processed from FASTQ files, quality is determined based on the lowest result among these metrics:

* [**Sex validation**](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sex-validation.md)
* [**Average coverage**](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/coverage.md)
* [**Percentage of target bases with coverage greater than or equal to 20×**](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/coverage.md)

### FASTQ sample quality evaluation

{% stepper %}
{% step %}
**Evaluate sex validation**

The system reviews the **sex validation** result for the sample:

* If **sex validation** failed, the system evaluates the FASTQ **sample quality** as low, and no further metrics are considered.
* If **sex validation** passed or is unavailable, the system proceeds to evaluate coverage metrics.
  {% endstep %}

{% step %}
**Evaluate coverage metrics**

The system reviews the results for **average coverage** and the **percentage of target bases with coverage ≥20×** and evaluates them as low, moderate, or high using the thresholds in Table 1.
{% endstep %}

{% step %}
**Assign quality**

The system uses the lower result to assign the FASTQ sample quality.
{% endstep %}
{% endstepper %}

**Table 1. FASTQ sample quality thresholds**

<table><thead><tr><th width="187">Quality</th><th>Sex validation</th><th>Average coverage</th><th>% Target bases with coverage ≥20×</th></tr></thead><tbody><tr><td><strong>Low</strong></td><td>Failed</td><td>≤30×</td><td>&#x3C;70%</td></tr><tr><td><strong>Moderate</strong></td><td>Passed or N/A</td><td>30−45×</td><td>70−80%</td></tr><tr><td><strong>High</strong></td><td>Passed or N/A</td><td>>45×</td><td>>80%</td></tr></tbody></table>

## VCF sample quality

The VCF sample quality reflects the confidence level that the sequencing data can support accurate variant interpretation.

For samples processed from VCF files, quality is determined based on:

* [**Sex validation**](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sex-validation.md)
* [**Error rate**](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/sequencing-error-rate.md)

### VCF sample quality evaluation

{% stepper %}
{% step %}
**Evaluate sex validation**

The system reviews the **sex validation** result for the sample:

* If **sex validation** failed, the system evaluates the VCF **sample quality** as low, and no further metrics are considered.
* If **sex validation** passed or is unavailable, the system proceeds to evaluate **error rate**.
  {% endstep %}

{% step %}
**Evaluate error rate**

The system reviews the results for **error rate** and evaluates them as low, moderate, or high using the thresholds in Table 2.
{% endstep %}

{% step %}
**Assign quality**

The system uses the **error rate** result to assign the VCF sample quality.
{% endstep %}
{% endstepper %}

**Table 2. VCF sample quality thresholds**

<table><thead><tr><th width="187">Quality</th><th width="187.31640625">Sex validation</th><th width="187.29296875">Error rate</th></tr></thead><tbody><tr><td><strong>Low</strong></td><td>Failed</td><td>>45%</td></tr><tr><td><strong>Moderate</strong></td><td>Passed or N/A</td><td>25−45%</td></tr><tr><td><strong>High</strong></td><td>Passed or N/A</td><td>&#x3C;25%</td></tr></tbody></table>


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