> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/general/software-general-faq-list/000007537.md).

# How is zygosity assigned for mitochondrial variant calls with DRAGEN?

DRAGEN processes **chrM** (mitochondrial chromosome) through a **continuous Allele Frequency (AF)** pipeline (similar to the Somatic Variant Calling pipeline). In this case a single ALT allele is considered and the **AF** is estimated, which can be between **0% and 100%**.

A QUAL value is not output in the chrM variant records. Instead, the confidence score is **FORMAT/SQ**, which gives the Phred-scaled confidence that a variant is present at a given locus. The decision to emit a variant or not is decided by comparing the FORMAT/SQ score to a threshold.

* If **FORMAT/SQ < vc-sq-call-threshold**, the variant is not output in the variant call file (VCF), and is banded in a **\<NON\_REF>** region with **FORMAT/GT set to 0/0** (homoplasmic).
* If **FORMAT/SQ > vc-sq-call-threshold**, the variant is output in the VCF.
  * In **DRAGEN v3.x** (prior to v4.0.3), the **FORMAT/GT** is hard coded to **0/1 irrespective** of the **AF** (heteroplasmic).
  * In **DRAGEN v4.0.3**, the **FORMAT/GT** is set to **1/1** if **FORMAT/AF is > 95%** (homoplasmic) and is set to **0/1** if **FORMAT/AF is < 95%** (heteroplasmic).

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                 |
| :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #7537), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007537%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# 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 dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://knowledge.illumina.com/software/general/software-general-faq-list/000007537.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
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.