The original YCC tree was envisioned to be presented with the branches with the most descendants on the bottom. This means R1 and R2 need to swap positions. With the makeup of direct-to-consumer testing U106 and P312 branches will dominate anything likely to be found under R-M479.
The experimental tree will be moving away from long form haplgroup names in the near future. This will help to reduce the confusion caused by the change.
The HR prefix is simply an abbreviation for haplogroup-r.org. These variants have been placed into the experimental tree without a known name. Since using (chromosome) position [ancestral]->[derived] formats tend to get very long when including long insertion or deletion events, a placeholder name is assigned to all shared variants in the tree. Information about the coordinates can be found by searching the variant index.
When a formal research study or direct-to-consumer lab assigns a name to an HR variant and submits the information to ybrowse.org the HR name is retired. Therefore, it is not recommended to use these names outside discussion of this experimental tree.
Next Generation Sequencing results from the FullGenomes™ catalog are being delivered in GRCh38 coordinates after July 2016. Older tests are being reworked as processing capacity is available.
We also recommend FullGenomes™ for performing Big Y analysis. As part of the service Big Y is converted to the GRCh38 reference. This allows an average of 200,000 bases of coverage with a Big Y returned after August 2015 based on our internal data set. The analysis includes variant calls under FTDNA's ten read threshold, quality assessment, name assignment (if desired), and estimation of over 300 STR values. As a commercial offering this will supply greater quality control than experimentally offered here.
Original vendor VCF/BED files may be used with a coordinate lifting process. A typical Haplgroup R man will lose 200 or more Y chromosome calls due to mapping errors from GRCh19/37.
The ZIP archive containing your lab analysis may be uploaded via the email address in the page footer. We will continue to accept the original BAMs via the Submission Tool. Please allow between four to six weeks for the results to be fully integrated.
The Experimental Tree provides the capability to report several details about a kit. Search for the kit# of interest and click the button. A popup will appear with details on lab IDs, surname, origin, BAM coverage summary, and private mutation details.
The private variants table list details of position, any known names, and scoring information. The GRCh38 Coord is the position recorded in the haplogroup-r.org database. The GRCh37 Coord is the more common location used by testing laboratories. Use this definition when requesting they add new tests. Names represent any existing matches found in ybrowse.org. The Depth column reports the number of reads with the derived allele present. This is systematically limited to having at least four. The Likelihood column is a measure of how certain the genotype caller is the variant exists. The report requires at least 90% (or a 10% chance of being false positive.) The Source column indicates the genotype caller used. Finally, the combBED column indicates if the variant exists in the Big Y target regions. Future updates will report if the variant is contained in the Poznik "Gold Regions" instead.