Errors and Warnings

Haplogrep includes different warnings and errors. Please find a list of currently applied measures.


  • The detected haplogroup quality is low. Sample is marked red. Quality <=80%
  • The expected haplogroup is not a super group of the detected haplogroup
  • Common rCRS polymorphism not found! The sample seems not properly aligned to rCRS
  • The sample seems to be aligned to RSRS. Haplogrep only supports rCRS aligned samples
  • The sample misses >2 expected polymorphisms


  • Fasta Alignment check: positions to recheck
  • The detected haplogroup does not match the expected haplogroup but represents a valid sub haplogroup
  • The sample shows ambiguous best results
  • The detected haplogroup quality is moderate. Sample is marked yellow. Quality <= 90% and > 80%
  • The sample contains polymorphimsms that are equal to the reference / The sample contains variants according the rCRS
  • The sample contains >2 global private mutation(s) that are not known by Phylotree
  • The sample contains >=2 local private mutation(s) associated with other Haplogroups
  • Different haplogroup with 2 local private remaining mutation(s) found
  • The sample contains undetermined variants N