Starting with Haplogrep 3, the software includes new features for evaluating haplogroups or variants. This includes the possibility to get a visual representation of each top-level haplogroup including the expected variants for each haplogroup (see here) or (b) get frequencies for each selected variant in the samples details page.


We generated 33 top-level clusters according to PhyloTree and gnomAD and (a) group each haplogroup from the phylogeny (b) group each input sample into one of these clusters displayed within the summary dashboard.

Population Frequencies

We also display numerous frequencies for each variant mainly derived from gnomAD. Further annotations are available from the Helix Mitochondrial database and functional predictions from MitImpact.


Haplogrep allows to export annotations. Currently the following annotations are exported.

  • ScorePhastCons100V [MitImpact_db_3.1.0 - PhastCons_100V]
  • ScoreMtoolBox [MitImpact_db_3.1.0 - MtoolBox_DS]
  • ScoreAPOGEE [MitImpact_db_3.1.0 - APOGEE_score]
  • PopFreqGnomeAD [gnomAD v3.1 Frequencies - popFreq]
  • VafGnomADHom [gnomAD v3.1 Annotations - AF_hom]
  • VafGnomADHet [gnomAD v3.1 Annotations - AF_het]
  • Maplocus [Haplogrep Annotation File]
  • AAC [Haplogrep Annotation File]
  • ScoresMutPred [Haplogrep Annotation File]
  • VafHelixHet [Helix Mitochondrial database 20200327 - Helix_vaf_het]
  • VafHelixHom [Helix Mitochondrial database 20200327 - Helix_vaf_hom]

The source file and source column name are added in brackets.