> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.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 overall sample quality indicator summarizes sequencing reliability for each sample. Sample quality is evaluated using different metrics, depending on the sample file type.

## Overall FASTQ sample quality

The overall 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 overall 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 overall quality**

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

**Table 1. Overall 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>

## Overall VCF sample quality

The overall 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 overall 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 overall quality**

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

**Table 2. Overall 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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