What triggers an Error and what is considered a Warning in HaploGrep2? Here’s a short overview of the events:
- 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 ambigous best results
- The sample contains heteroplasmic positions
- 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