Review how sequencing reads support reference and alternate alleles.
The Allele distribution card of the Quality tab shows how sequencing reads support the reference and alternate allele.
It is available for SNVs, MNVs, indels (both nuclear and mitochondrial), and STRs.
SNVs, MNVs, and indels
The MNV variant type is supported from version 100.39.0.
Allele fractions are shown as pie charts, one per sample. This gives you a quick view of variant distribution across alleles.
For MRJD-called variants, the alternate allele percentage shown in the graph comes from the JAF field in the DRAGEN MRJD VCF. JAF reports the alternate allele fraction across all paralogous regions.
STRs
For STRs, the allele distribution table shows how sequencing reads support an STR variant. This helps you assess call accuracy.
The columns are REF and ALT. They represent reference and alternate allele counts.
Rows are grouped into these 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.
