When opening the details view of a sample, mutations are displayed in different colours.
In general, each haplogroup is defined by a set of expected mutations. Haplogrep informs users if the expected mutations for the tophit are included in the input sample.
Expected and Included
Mutations displayed in green are mutations that are expected by the tophit and also included in the input sample.
Expected But Not Included
Mutations displayed in red are mutations that are expected by the tophit but not included in the input sample.
Remaining mutations of the input sample are separated by its type.
Hotspots mutations are defined by a high number of occurrences in the used phylogenetic tree.
Local Private Mutations
Local private mutations are mutations that are not associated with the tophit but are included in the phylogenetic tree for other haplogroups.
Global Private Mutations
Global private mutations are not found at all in the phylogenetic tree.