# Ploidy

The Ploidy column displays results from the **DRAGEN Ploidy Estimator**, which **detects aneuploidies** and **infers the sex karyotype in whole genome cases**.

Ploidy values are derived from the `*.ploidy_estimation_metrics.csv` DRAGEN output file.

## Ploidy estimation results

<mark style="background-color:$success;">**Pass**</mark>

* **All autosomes fall within the expected ploidy range.** No large‑scale autosomal copy number deviation is detected.

<mark style="background-color:$danger;">**Fail**</mark>

* **At least one autosome has a median ploidy score below 0.9 or above 1.1.**\
  Hover over the result to see which chromosomes are problematic.

**N/A**

* Ploidy metrics are not available.

## Best practices

* **Check ploidy early** in case review to quickly identify potential large‑scale chromosomal abnormalities.
* **Verify sex karyotype** by confirming whether the sex karyotype inferred from ploidy matches the [sex validation](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sex-validation.md) results to rule out sample swaps.
* **A failed ploidy result does not confirm a clinical abnormality**. It indicates aberrant copy number estimation and must be interpreted in the context of other QC metrics and genomic visualization.

## Ploidy availability by workflow

**Ploidy evaluation in the Lab tab is available only for whole genome FASTQ cases.**

In **whole genome FASTQ cases**, ploidy is shown in **both the DRAGEN QC report and the Lab tab.** The DRAGEN pipeline automatically generates the `*.ploidy_estimation_metrics.csv` file, which the platform uses to display ploidy results. Under this workflow, ploidy appears consistently across the interface.

In **whole genome** [**Bring your own DRAGEN (BYOD) VCF cases**](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/prerequisites-for-accessing-the-dragen-qc-report.md#option-2-vcf-case-bring-your-own-dragen-byod), ploidy is shown **only in the DRAGEN QC report, never in the Lab tab.** When a case is created from VCF, the DRAGEN metrics supplied in a `*.metrics.tar.gz` archive are used exclusively to generate the DRAGEN report and are not ingested into the Lab tab. The platform displays **N/A** for Ploidy in the Lab tab.


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