> 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/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 be considered in conjunction with a review case setup, sequencing quality, and sample handling first.
  {% endhint %}


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/contamination.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.