> 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/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ploidy.md).

# Ploidy

The **Ploidy** column shows results from the **DRAGEN Ploidy Estimator**.

The estimator detects aneuploidies and infers sex karyotype in whole genome cases.

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

## Results

### Pass

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

### Fail

At least one autosome has a median ploidy score below `0.9` or above `1.1`.

Hover over the result to identify the affected chromosomes.

### N/A

Ploidy metrics are not displayed in **Sample quality**. This occurs when:

* v100.41+: The sample contains fewer than 10000 variants. Below this threshold, there are too few variants to validate ploidy reliably.
* The case is a whole genome [Bring your own DRAGEN (BYOD) VCF case](/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).
* The case was run with the pipeline older than v32.

## Availability by workflow

Ploidy is available in the **Ploidy** column only for whole genome FASTQ cases.

### Whole genome FASTQ cases

Ploidy appears in the [DRAGEN QC report](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report.md) and the **Ploidy** column.

The DRAGEN pipeline generates `*.ploidy_estimation_metrics.csv`. Its values populate **Sample quality**.

### Whole genome BYOD VCF cases

Ploidy displays **N/A** in the **Ploidy** column.

Metrics in the supplied `*.metrics.tar.gz` archive generate only the DRAGEN QC report. They do not populate **Sample quality**.

Review ploidy in the DRAGEN QC report for these cases.

## Best practices

* Check ploidy early in case review. It can identify potential large-scale chromosomal abnormalities.
* Compare the inferred sex karyotype with [sex validation](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sex-validation.md). This helps identify possible sample swaps.
* A failed result does not confirm an abnormality. Interpret it with other QC metrics and genomic visualizations.


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