Smith DNA Project Community Forums

How is a haplogroup from an autosomal test different from Y-DNA tests?

Haplogroups from an autosomal DNA test only provide you with part of the story. While tests like the Big Y-700 and the mtFull Sequence look at your entire Y chromosome or mitochondria, autosomal tests are run on chips in the lab that are comprised of selected SNPs.

FamilyTreeDNA uses a custom Global Screening Array chip from Illumina that looks at about 700,000 SNPs from the autosomes, X chromosome, Y chromosome, and mtDNA. However, because the main purpose of this chip is to determine autosomal results (matching, ancestral populations, etc.), the chips contain minimal Y-DNA and mtDNA SNPs.

This means you’ll only receive a partial haplogroup from an autosomal test. Most customers can expect this haplogroup to have originated in the Metal Age (about 10,000 years ago). Comparatively, a predicted, broad haplogroup from a Y-STR test like the Y-37 or Y-111 will typically have originated in the Stone Age (about 100,000 years ago), and a haplogroup from the Big Y-700 will typically have originated in the Middle Ages or in the Modern Age (about 1,000 to 500 years ago)—within genealogical times.

Microarray chips like the Global Screening Array chip have been updated over time, and the Y-DNA SNP selection on the various chips has also changed and varies from company to company. Haplogroup results may vary from tester to tester, even if they are on the same direct paternal line, depending on which chip their test was processed on and if they have a “no call” or no results for a particular SNP.

While the haplogroup you’ll receive with an autosomal test is better than a broad haplogroup from the Y-37 or Y-111, only a test like the Big Y-700 will provide you with the complete story of your direct paternal line and properly place all testers from the same direct paternal line on the haplotree.

To put this another way, an autosomal tester who is a Smith may not have taken either a YDNA test nor a Big-Y test but may have a haplogroup from the autosomal test. These will not be used for specific matches within a group unless that person has also done YDNA and/or a Big-Y test. If the member is, say, a Brown, has an autosomal test, but Smith is not the paternal line (or doesn't match with other Smiths)  the haplogroup is not relevant in this project. A more defined haplogroup, also, for a Smith will not show up on the Big-Y Time Tree UNLESS that person has done a Big-Y test and has been matched into a group.

Second, keeping up on the YSAPP charts is going to be simply impossible due to the time constraints and work to keep up on what is variably changing numbers for the kits in a group. What was being done was creation of a text file tht included the kit, str markers and some categories for top of the line and location, then run that text file through SAPP. That means that every time a change would be made to a haplogroup, the text file would need to redone. It was a really nice feature that I enjoyed, but the sheer amount of changes now with the autosomal haplogroup make this not feasible for a volunteer project. That led to thinking about another way to show the relationships between matches and back to the custom group chart on smithsworldwide for each matched group that exists. That said, if anyone in one of these groups wants to keep up on the YSAPP, let me know

Third, how to show the new SNPs, in this project,  in a way that makes it easy to see related SNPS in sorted order  EVEN IF the person has not done a Big-Y kit.  For example, the Big-Y Time Tree shows everyone that is matched into a group that has done a Big-Y test (example here but it does not show a person who may, in fact, have a SNP that shows the same terminal SNP as Big-Y but, having not taken the test, is not going to be on the Big-Y Time Tree. Therefore, going to remove the SAPP tree link but CHANGE the custom report on a given group to show the SNP designation in the SNP column. Example here of the GRP-R-M269-16 group. Notice that, on that page, there is a Type of Test column and also a SNP column. If the person has done a big-Y test, the SNP will have a link on it that goes to the BigY Time Tree., otherwise, it will just show the SNP with no link. Don't forget you can always go look at the results of the YDNA testers on the FamilyTreeDNA Y-DNA Chart for the Smith DNA- Official Project all -with explanation here on how to locate your kit or group.

Here is another example from the GRP-R-M269-1 group. (You can click on the picture to see the full group on the custom page). Notice here that most of the yDNA tests have R-M269 as the haplogroup, 4 people have done Big-Y tests and the type of test ALSO says Big-Y in the Type Test column (and links to the Big-Y time tree as well) BUT there is a YDNA test that has R-FT20705 as the haplogroup. This member did not do a Big-Y test so there is no Big-Y descriptor in the type test column, did do an autosomal test and a YDNA test. Matches with this group but WILL NOT SHOW on the Big-Y Time Tree with the other 4 because he did not do a Big-Y test, so the more detailed haplogroup is from his autosomal test.


Clicking on the word "SNP" at the top of that column will sort the SNPS but will not show anyone where the SNP is not yet listed for them on the custom chart. Example here  and again, from GRP-R-M269-1, here is how the custom chart looks with 4 Big-Y tests, sortted.


See, again, how the kits that also did BigY show that in the type test column and have a link to teh Big-Y Time Tree but the ones without Big-Y merely show the SNP (which nonetheless is in order).

It will take a bit of time to go make sure that all the kit SNPs are updated from the YDNA Chart on FamilyTreeDNA for the Smith DNA (Official All) project, so please do not expect the chart to be 100 percent updated with the snap of a finger.

Anyway, this seems like a good solution for the new feature from FTDNA that shows the SNP and also lessens the huge amount of work to keep SAPP files updated.