Male haplogroups are determined by a certain kind of marker called single nucleotide polymorphisms (SNPs). However, Family Tree DNA uses short tandem repeats (STR's) to predict a man's haplogroup as follows:
At FTDNA, a Y-DNA haplogroup prediction is calculated using genetic distance. This calculation finds a man's most likely haplogroup. The prediction program compares his Y-DNA STR profile to the results database. The program uses the results of exact and near matches.
The process balances using a reliable number of Y-DNA STR markers and using a database of confirmed haplogroups that is sufficient in size. The program uses 14 Y-DNA STR markers for haplogroup predictions. These are the first 12 STR markers in the Y-DNA test and two additional markers that are tested as check values.
Should someone’s haplotype not be close enough to another for use to confidently predict a haplogroup, FTDNA confirms their backbone haplogroup placement by testing some of their SNPs.