A Segment-ology TIDBIT

Let’s sort this out. A Chromosome is a long string of DNA – which has the form of the famous double helix. If we flattened out the double helix it would look like a ladder, with two sides connected by lots of rungs. On each end of every rung is a molecule we call a base – called A, C, G or T for short. The two ends of each rung are always paired, with A on one end and T on the other end, or C on one end and G on the other. That’s because in chemistry, the A molecule bonds much more readily with a T; and a C bonds easily with a G. They form what is called a base pair. And if you know one end of each rung, you know the other end. 23 chromosomes make up a genome, and a genome has about 3 billion of these base pairs*.

As we look at one side of the chromosome “ladder” we see one of these molecules at every rung. Important: There is no hard and fast rule about the order of the ACGTs along one side of the ladder.

In our bodies we have two genomes – one set of chromosomes from the father and one set from the mother.

For atDNA testing a laboratory looks at, say, 600,000 specific base pairs called SNPs (pronounced snips). Each of these SNPs is at a specific location on a chromosome, and the lab looks at one side (the “forward” side) and determines if it is an A, C, G, or T. Because we have two of each chromosome, they actually get two values (called alleles), one from the paternal chromosome, and one from the maternal chromosome. Because all these SNPs are floating around in a soup, we don’t know which one is from Mom and which one is from Dad. One convention is to list them alphabetically, resulting in ten possibilities: AA, AC, AG, AT, CC, CG, CT, GG, GT, and TT.  You can see that in these “pairs” the A is not necessarily paired with T. That’s because the DNA from each parent came to you from very different, and usually very distant, paths – they don’t touch or interact with each other. And, the SNP base pairs were chosen for and atDNA test, because they offer variability.

A shared DNA segment between you and a Match consists of a long string of SNPs (usually 1,000 or more) where you have at least one of your two alleles match at least one of your Match’s two alleles. The longer the shared segment, the greater the probability that it had to come from a Common Ancestor.

BOTTOM LINE – As genetic genealogists we are not concerned with the “base pairs” on each end of a rung, we are very much interested in the two SNP alleles we got from our two parents – not called “base pairs.”

*[An experiment you can do at home: at GEDmatch compare your kit to your kit in the one-to-one utility – you’ll match on 22 chromosomes, from start to finish. Add up the “End Locations” and see how close to 3 billion you come – add in about 155 million for Chr X to get a full genome].

[22U] Segment-ology: Confusion about Base Pairs TIDBIT by Jim Bartlett 20180502

A Segment-ology TIDBIT

I’ll try to answer the question: “I just uploaded to GEDmatch, it’s so complex, what do I do now?”

FIRST – take a deep breath, and exhale slowly…….. GEDmatch is a powerful tool, with a lot of features. In many ways it is complex. But it also has some very simple and helpful utilities – I’ll point them out.

SECOND – take a few minutes to look over your GEDmatch homepage – there are several broad areas. The main tools are in the blue box on the right side titled: Analyze Your Data – I’ll come back to that and focus on some of the tools. Other information is in gray boxes – please review the titles before launching into the tools.

On the left side:

–Your Log-in Profile – a box with information about you, and how to change it.

–Learn More – a box with several links to more information about GEDmatch – you might want to click on each one to get a feel for the resources that are there to help you.

–Your DNA Resources – a box with a handy list of your DNA kits at GEDmatch (in the beginning you’ll only have the one you just uploaded, but you can upload more kits whenever you want.)  At the bottom is a link to “EDIT or DELETE” any of your listed DNA Resources – you can open this up to just look.

–Your GEDCOM Resources – a box which lists any GEDCOMs you’ve uploaded, and a link to manage them.

On the right side:

–File Uploads – a box with tools to upload your raw DNA data files and tools to upload GEDCOMs (a GEDCOM is a file of your genealogy, not your DNA)

–Analyze Your Data – a box with tools to utilize your DNA data and a box to utilize GEDCOMS – more below

–Tier 1 Utilities – a box with more tools to utilize your data for folks who pay a subscription (wait to see how much you utilize GEDmatch before you subscribe…)

–Genesis Beta – a box for certain kits (23andMe V5 kits – since July 2017; and LivingDNA kits)

THIRD – So, after this overview, where to start first?

I’d start with the first tool: One-to-many Matches – Click on this link and use the little “down triangle” to see your kit number and select it (or just type in your kit number – the form is like: A123456). Leave everything else alone and click on Display Results. After a second or two, you’ll get a table of your top 2,000 Matches – with their name, email, kit number, and other info. The default is to list the closest Matches first. Please read the information above the table, before we jump into the fun part. It’s important to know this info and that it’s here as a reference (many folks just look immediately at the Matches and then ask questions which are answered in this introductory material).  Next read each of the column titles – some won’t make sense, yet, but note that some folks list Haplogroups; some have linked genealogies [under GED/WikiTree column]; and there is summary data on the Autosomal and X data. The chart is sorted on Total cM, but notice the small blue triangles that let you sort on most columns.

In one sense this is similar to your results at AncestryDNA – a list of Matches with summary DNA info, and sometimes a link to a Tree.

To see the specific DNA segment(s) you share with a Match, click on the A link (under Autosomal Details). This takes you to the “one-to-one” utility, with your kit and the Match’s kit already filled in. Just click on the Submit button to see the DNA segment data. Or, for a more colorful version, go back to the one-to-one page and click on the Graphics and Positions button and then click on Submit. Again, please read the legend at the top first – then scroll down the page to see all 22 chromosomes – a solid blue bar indicates a shared segment. This view puts the shared DNA with a Match into perspective.

Just like with any other DNA site, you still have to work with your Matches and/or their posted Tree to determine a Common Ancestor. The emails at GEDmatch give you a way to do this.

FOURTH

If you know of someone’s GEDmatch kit number, you can click on the “One-to-one compare” utility on your home page and fill in your and your Matches kit numbers to see the shared segment data.

FIFTH

Try the GEDCOM tools. Click on “GEDCOM + DNA Matches” and fill in your kit number to get a list of your DNA Matches with linked GEDCOMs (Trees). Note a Match (under DNA Name) and click on the link under the GEDCOM ID column to get a summary box. Then click on Pedigree, and adjust the number of generations to suit your search.

If you’ve uploaded your own GEDCOM, my favorite utility is “2 GEDCOMs”. Fill in your GEDCOM number (remember it’s listed on the left side of your GEDmatch Homepage, after it’s uploaded) and your Match’s GEDCOM number (from the GEDCOM + DNA Matches list) and hit “Compare”. This amazing utility will list every ancestor who is the same in both GEDCOMs. Finding a Common Ancestor doesn’t get easier than this!

SIXTH

Try the any of the other utilities in the Analyze Your Data box (some are fun, some are helpful):

-Admixture (there are several different utilities from different scientists – noodle around)

–Are your parents related?

–Archaic DNA matches – compare your DNA to DNA from the “Clovis” Man or “Kennewick Man” or “Altai Neanderthal” and other ancient people whose DNA has been extracted. Includes a link to an ancient DNA site. Try the kits in the one-to-one utility.

You cannot “hurt” anything here – so click on anything that interests you and noodle around.

SUMMARY

GEDmatch lets you compare with folks who have tested at other companies –to find close relatives who tested, but not at the same company you used. Find new relatives – particularly close ones.

A main feature is the ability to “see” the shared segments with your Matches – including between different companies. This feature is essential for Triangulation and/or Chromosome Mapping.

Note: I often find Matches who tested at one of the companies, but for some reason don’t show up as a Match at that company.  I’ve tested at all the companies, and still find many new Matches at GEDmatch.

The 2 GEDCOMs utility gets you straight to Common Ancestors (you have to have uploaded your GEDCOM too).

In the end, it’s still up to you to find to work with your Matches (and their info) to find Common Ancestors. GEDmatch provides some good tools to help.

[22T] Segment-ology: First Time at GEDmatch TIDBIT by Jim Bartlett 20180501