Micro-allele

A micro-allele is an STR with a fractional value, such as 14.2, rather than a whole integer. Micro-alleles are sometimes also referred to as microvariants, fractional markers or partial repeats. Fractional values frequently arise from a deletion, the mutational loss of one or more nucleotides. For example, if the segment being repeated is AGG, one of the triplets can mutate to AG, thus becoming a fractional repeat. Fractional values can also arise from insertions.

The duplicated Y-STR markers DYS385 and DYS464 are particularly prone to partial repeats. If you look at the marker details for DYS385 and DYS464 on the Sorenson Molecular Genealogy Foundation website you will see that there are quite a few results that end in a .1, .2, or a .3. Many STRs have a repeating base pair sequence that is somewhere between 3 to 6 base pairs in length. If the allele value ends in .1 this means that an extra base has been added somewhere in the repeated sequence, possibly at the beginning or at the end of the sequence. If the allele value ends in .2 this means that two extra bases have been added somewhere in the repeated sequence. If the allele value ends in .3 this means that three extra bases have been added somewhere in the repeated sequence.

Micro-alleles have been reported from the outset for all Y-DNA tests processed at Sorenson Genomics. Family Tree DNA has not previously been able to provide support for the reporting of micro-alleles. At some time prior to November 2011 Family Tree DNA displayed the following message on customers' personal pages:

"Important Message From Family Tree DNA!

We are planning an upgrade of all Y-DNA STR (short tandem repeat) related functions. The upgrade will include changes to how STR micro-alleles and palindromic STRs are displayed. It will also change the matching algorithm to utilize an improved calculation for micro-allele and palindromic STR mutations. The result will be more accurate matches and time to a common ancestor calculations. We will provide additional information before the changes are implemented.

For your convenience, we suggest that you download your Y-DNA Results and Y-DNA matches for historical purposes."

The message was subsequently removed, presumably because the implementation of micro-allele reporting was delayed. From around October 2012 project administrators have reported that micro-alleles have been displayed on personal pages for kits transferred from AncestryDNA and for new FTDNA results. It is not yet known when micro-allele reporting will be implemented at FTDNA retrospectively for all previously processed kits. Micro-alleles are not currently displayed on project results pages, and it is not known when or if this reporting will be implemented.

Further reading

• Y-chromosome Short Tandem Repeat Intermediate Variant Alleles DYS392.2, DYS449.2, and DYS385.2 Delineate New Phylogenetic Substructure in Human Y-chromosome Haplogroup Tree by Natalie M. Myres, Kathleen H. Ritchie, Alice A. Lin, Robert H. Hughes, Scott R. Woodward, and Peter A. Underhill. Croatian Medical Journal 2009 June; 50(3): 239–249.
• Allocation of YSTR Microvariant Alleles to Y-Chromosome Binary Haplogroups. Paper presented at the American Society of Human Genetics Annual Meeting, Philadelphia, Pennsylvania, November 2008, by Natalie M. Myres, Kathleen H. Ritchie, Robert Hughes, Alice A. Lin, Scott R. Woodward, Ugo A. Perego and Peter A. Underhill.