Ploidy

The Ploidy column provides results from the DRAGEN Ploidy Estimator, which is designed to detect aneuploidies and determine the sex karyotype in whole genome cases.

Ploidy estimation results:

• Pass All autosomes fall within the expected ploidy range.

• Fail

  At least one autosome shows a median score outside the expected thresholds (below 0.9 or above 1.1).

  • When you hover over a failed result, the system displays which chromosomes are problematic.

• N/A

  Case type is not Whole genome or QC file not available; validation could not be performed.

The ploidy calculation uses values from the *.ploidy_estimation_metrics.csv file.

Tips:

• Use ploidy checks early in case review to spot potential large-scale chromosomal abnormalities.

• Always confirm whether the sex karyotype inferred from ploidy matches the sex validation results to rule out sample swaps.

Failed results do not confirm clinical abnormalities. They only indicate a deviation in copy number estimation and should be reviewed in context of other QC metrics and visualization.