# 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).

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