Quality tab

The Quality tab gives you a clear, interactive overview of variant quality across all sequenced individuals in a case. It displays zygosity, quality grades, and metrics tailored to each variant type—helping you evaluate data reliability and prepare for accurate interpretation.

Click on a family member’s icon to switch the sample in view.

Tips

Tips:

• Use the Quality tab:

  • Before interpretation — to verify if a variant meets minimum quality thresholds

  • For cross-sample comparisons — to check if the variant is consistently high-quality across proband and relatives

  • To filter analysis — by excluding low-quality calls that may be sequencing artefacts

• Always check the variant type first — quality thresholds vary by variant type and caller.

• For CNVs (DRAGEN 4.4+): Pay attention to the allele-specific copy number display [MCN / (CN-MCN)], which provides richer context for mosaic and allele-level events.

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 and caller

The overall variant quality based on variant caller-specific rules in a proband sample is highlighted on top of the Quality tab, next to the variant caller notation.

Pedigree card

In the pedigree card located on the left of the Quality tab, each sample is represented by zygosity and variant quality grade.

Zygosity

Indicates whether the variant is:

• Present in one allele—HET

• Present in both alleles—HOM

• Present on X-chromosome in males—HEMI

• Absent—REF

Zygosity is displayed in the sample’s icon within the family tree. This is critical for inheritance pattern checks.

Variant quality grade

Overall quality category based on variant caller-specific rules.

Shown as a badge next to the sample’s icon:

• —High

• —Medium

• —Low

Quality metrics per variant type

A variant is assessed using a set of quality metrics tailored to its specific type, which are displayed next to the pedigree card.

SNVs/MNVs/Indels

• VCF Filter (DRAGEN 4.3+) — The FILTER column value in VCF indicating whether a variant passed the caller's quality thresholds or failed some checks.

• Base Quality (BQ) — Average Phred score for bases supporting the variant. High BQ indicates more reliable base calling.

• Depth (DP) — Total number of reads covering the position. It is the count of aligned reads after removal of duplicate reads and/or reads with MQ=0.

• Mapping Quality (MQ) — Confidence in read placement on the reference genome (Phred-scaled).

• Genotype Quality (GQ) — Confidence in zygosity call. It is derived from likelihood ratios between genotypes, scaled as Phred. Not relevant for mtDNA variants.

CNVs called by NGS pipeline

• VCF Filter (DRAGEN 4.3+) — The FILTER column value in VCF indicating whether a variant passed the caller's quality thresholds or failed some checks.

• Norm. depth of cov. (DRAGEN 4.2+, v100.39.0) — Normalized depth of coverage calculated by the Ploidy caller.

• Copy Number — Estimated number of copies in the region.

  • Allele-Specific Copy Number (ASCN) (DRAGEN 4.4+, WGS): In addition to total copy number (CN) based on read depth, the software displays minor and major allele copy numbers identified by the CNV ASCN module in the format [minor/major].

• CNV Quality Score — Phred-scaled confidence score produced by the CNV caller (higher values indicate greater confidence).

• Size — CNV length (bp).

• Bin Count — Number of read-depth bins spanning the CNV.

• NR (DRAGEN Array V1.2+, v37.0+)

• LRD (DRAGEN Array V1.2+, v37.0+)

• Likelihood Ratio (DRAGEN Array V1.3+, v100.39.0+) — Measures confidence in the CNV call — higher values mean stronger evidence.

• Mean LRR (Log R Ratio) (DRAGEN Array V1.3+, v100.39.0+):

  • Calculated as log₂(NR).

  • Shows signal intensity balance across the CNV region.

  • Values close to 0 suggest normal regions; large positive or negative values suggest gains or losses.

• Mosaic Fraction (DRAGEN Array V1.3+, v100.39.0+) — Provides mosaic fraction estimation for mosaic events.

• Likelihood Ratio Score (LRS) (DRAGEN 4.3+, exome/panel) — a log₁₀ ratio of ALT vs REF probability.

CNVs and LOH/ROH called by array pipeline (DRAGEN Array 1.3)

• VCF Filter — Indicates if the variant passed DRAGEN quality checks.

• Likelihood Ratio — Measures confidence in the CNV call — higher values mean stronger evidence.

• Mean LRR (Log R Ratio):

  • Calculated as log₂(NR).

  • Shows signal intensity balance across the CNV region.

  • Values close to 0 suggest normal regions; large positive or negative values suggest gains or losses.

• Mosaic Fraction — Provides mosaic fraction estimation for mosaic events.

• CNV Quality — Shows the caller’s overall confidence in the variant.

• Size — Indicates CNV length in base pairs.

• Bin Count — Shows how many data bins (probe regions) support the CNV. A higher bin count means stronger support for the CNV.

Structural variants (SVs)

SV callers use breakpoint clusters, depth shifts, and split-read evidence to compute QUAL. Large SVs sometimes fail quality thresholds despite real biology being responsible.

• VCF Filter (DRAGEN 4.3+) — The FILTER column value in VCF indicating whether a variant passed the caller's quality thresholds or failed some checks.

• Quality

• Size

• Bin Count

STRs

• VCF Filter (DRAGEN 4.3+) — The FILTER column value in VCF indicating whether a variant passed the caller's quality thresholds or failed some checks.

• Depth — Coverage at repeat locus.

• Repeat Number — Count of repeat units.

• Repeat Length — Base-pair length of repeat tract.

• Confidence Intervals (DRAGEN 4.3+) — For REF and ALT alleles, showing repeat size accuracy.

STR loci in the ARX & HOXA13 genes are always marked Low quality.

Haplotype variants

• Zygosity — Indicates whether the haplotype is present on one chromosome (heterozygous) or both (homozygous), based on the genotype reported in the VCF.

• VCF Filter (DRAGEN 4.3+):

  • Displays the value of the FILTER field from the VCF.

  • This reflects whether the haplotype variant passed DRAGEN’s quality thresholds (PASS) or failed one or more caller checks (e.g., depth, allele balance, phasing constraints).

  • The platform shows the FILTER flag exactly as provided by the caller.

• Min. Genotype Quality:

  • Shows the genotype confidence score assigned by the caller.

  • Higher GQ values indicate greater confidence in the phased genotype underlying the haplotype.

Allele distribution

Allele distribution card provides insight into how sequencing reads support reference and alternate allele for SNVs/MNVs/indels (including mtDNA), and STRs.

SNVs/MNVs/Indels

Allele fractions are shown as pie charts—one per sample—offering an intuitive snapshot of variant distribution across alleles.

For MRJD-called variants, the percent shown as the alternate allele in the graph is from JAF field in the DRAGEN MRJD VCF. JAF reports the allele fraction for alternate alleles across all paralogous regions.

STRs

For STRs, the allele distribution table shows how sequencing reads support an STR variant, helping you evaluate call accuracy. The columns are denoted by REF and ALT – represent reference and alternate allele counts. Rows correspond to three categories:

• In Repeat – Reads aligning within the repeat (higher values improve confidence)

• Flanking – Reads adjacent to the repeat region

• Spanning – Reads covering the entire repeat region