Variant quality summary

Understand the overall quality signal shown for a variant across samples.

The variant quality summary helps you assess the overall reliability of a variant call before reviewing detailed metrics. Overall quality appears at the top of the Quality tab for the proband and in the Pedigree card for all samples, as described below.

Important:

Low quality ≠ irrelevant — in rare cases, important variants may appear low quality due to mapping complexity (e.g., MRJD variants in paralogous regions).

Variants marked low quality may be hidden from your preset filters! Review them in IGV before discarding.

Proband variant quality

At the top of the Quality tab, you can find:

• The overall variant quality in the proband sample, based on caller-specific rules

• A variant caller abbreviation and version

Variant quality for the proband at the top of the Quality tab.

Pedigree card

The Pedigree card is on the left side of the Quality tab. Here, each sample is represented by zygosity and a variant quality grade.

Sample icon in the Pedigree card.

Zygosity

Zygosity appears in the sample icon within the family tree.

Indicates whether the variant is:

• HET: Present in one allele

• HOM: Present in both alleles

• HEMI: Present on the X chromosome in males

• REF: Absent

Variant quality grade

Overall quality based on caller-specific rules.

Shown as a badge next to the sample icon:

• High

• Medium

• Low