# SNV, MNV, and indel quality metrics

The following metrics are calculated for SNVs, MNVs, and indels.

{% hint style="info" %}
The MNV variant type is supported from version 100.39.0.
{% endhint %}

## VCF Filter

* The `FILTER` column value in the VCF, indicating whether a variant passed the caller's quality thresholds or failed specific checks.
* Requires DRAGEN 4.3+.

## Base Quality (BQ)

* Average Phred score for bases supporting the variant.
* High BQ indicates more reliable base calling.

## Depth (DP)

* Total number of reads covering the position.
* It is the count of aligned reads after the removal of duplicate reads and/or reads with `MQ=0`.

## Mapping Quality (MQ)

* Confidence in read placement on the reference genome (Phred-scaled).

## Genotype Quality (GQ)

* Confidence in the zygosity call.
* It is derived from likelihood ratios between genotypes and scaled as Phred.
* This metric is not relevant for mtDNA variants.

## Phasing

* Numeric phase block identifier for TruPath Genome data.
* If a phased genotype is available, the platform appends `_A` for genotype `1|0`, `_B` for genotype `0|1`, or `_AB` for genotype `1|1`.
* Requires DRAGEN 4.5+ and version 100.40.0+.


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