> 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/variant_page/quality_section/quality-metrics-per-variant-type/snv-mnv-and-indel-quality-metrics.md).

# SNV, MNV, and indel quality metrics

The following metrics are calculated for SNV[^1], MNV[^2], and indel[^3] variants.

{% hint style="info" %}
The MNV variant type is supported starting with version 100.39.
{% 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)

* Variant-level quality score shown in Emedgene for SNVs, MNVs, and indels.
* For DRAGEN input, `BQ` is derived from the `QUAL` field in the VCF. DRAGEN VCF files do not include a field named `BQ`.
* For other secondary analysis pipelines, `BQ` may be derived from a different VCF field.
* Higher `BQ` indicates a more confident variant call.

## Depth (DP)

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

## 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+.

[^1]: Single Nucleotide Variant

[^2]: Multi-Nucleotide Variant

[^3]: insertion-deletion


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