> 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/contamination.md).

# Contamination

The **Contamination** column reports whether a sample shows signs of DNA contamination, helping ensure data reliability before interpretation.

{% hint style="info" %}
Be mindful that **when contamination is suspected in sequencing data, it could stem from various sources**, including true contamination, sample mix-up, library preparation issues, or technical artifacts.

Always confirm the issue with other quality checks.
{% endhint %}

Contamination is detected using [Peddy](https://pubmed.ncbi.nlm.nih.gov/28190455/) calculations, which estimate the proportion of reads that do not match the expected genotype. This estimate is based on the `idr_baf` score.

`idr_baf` stands for the interdecile range of the B-allele frequency—calculated as the difference between the 90th and 10th percentiles of the distribution of alt / (ref + alt) ratios across all variant sites.

A larger `idr_baf` value indicates greater variability in allele balance, which may suggest sample contamination, particularly from another human DNA sample.

## Results

### No

No contamination detected: `idr_baf` < 0.200.

### Unlikely

Possible contamination, but evidence is weak: 0.200 ≤ `idr_baf` < 0.241.

### Likely

Contamination suspected: 0.241 ≤ `idr_baf` < 0.300.

### Yes

Contamination confirmed: `idr_baf` ≥ 0.300.

### N/A

No data is available:

* v100.41+: The sample contains fewer than 10000 variants. Below this threshold, there are too few variants to validate contamination reliably.
* `idr_baf` = 0.000.
* The case is an older case.

{% hint style="success" %}
Hover over the value to display a tooltip showing the **HET ratio** (proportion of sites that are heterozygous) and the **HET count** (number of heterozygote calls in sampled sites).
{% endhint %}

{% hint style="success" %}
**Tips:**

* Always review contamination results before starting interpretation to rule out technical issues that could explain unexpected variant calls.
* Cross-check contamination results with other QC metrics (e.g., depth, ploidy, sex validation) for a more complete picture of sample quality.
* For family cases, check that no contamination is flagged before relying on inheritance-based filters.
  {% endhint %}

{% hint style="danger" %}
**Warnings:**

* **Panels:**
  * **v100.41+:** Contamination is not performed for samples with fewer than 10000 variants and shows **N/A**.
  * **v100.40 and earlier:** Contamination estimates may be less reliable because fewer variants are available. Cross-check with other QC metrics when interpreting these results.
* **Do not use in isolation**: A "Likely" or "Yes" result should not immediately be considered diagnostic — review case setup, sequencing quality, and sample handling first.
  {% endhint %}


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