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