Question about DNA and genetic inheritance (details inside)

That kind of testing has a certain level of speculation. The algorithm that comes up with those percentages is not perfect. It’s like when you see a temperature reading carried out to six decimal places but the equipment making the measurement is only good to one.
Genetic testing is just not refined enough yet to give that kind of resolution yet it is often reported as such. The one I used allows you to adjust out some of this speculation on your reports.

Then there is another alternative that could be rather uncomfortable….

I’m not afraid to discuss uncomfortable alternatives…

There is always the possibility, however slight, that who he thinks are his parents – and in particular, of course, the father that he believes to be his parent (and who may believe it himself) – are not his parents.

If the boy’s birth mother had been impregnated by the father’s brother, for example (and who knows the parentage of the uncle?), then that could affect the results.

However, in the case where the parents are as certain and reliable as they can be, then I would tend to agree with @ARE_you_kidding_me on this. “Capability” of the results algorithm has to be taken into account. In addition to the perfect sterility of the test equipment and testing lab, that is.

I have considered getting sequenced by another company that also supplied raw data and running a script to compare the results. I think those results are quite good. Where I think the speculation errors happen mostly is in the algorithms they use against the gene sequence to determine your ethnic heritage. I have zero faith that I’m 10.2% irish or .1% pacific islander but “speculative” report shows it.
Also there are different generations of sequencing chips, some test for more genes and that greatly influences how ethnicity is calculated. Have to compare apples to apples

Unless things have changed dramatically in the last couple of years, those percentages are typically going to be “best guesses” based on some number of locally varying gene “flags”. It’s definitely not meant to be used like this.

I’m not even sure using it to deduce your parents would be possible, based just on that. For example let’s say we’re only talking about two areas, just to simplify things. To make it even simpler, we’ll say your parents are found to be

Mom – 40% Region A, 60% Region B
Dad – 60% Region A, 40% Region B

What would your results be? Not 50%/50%... maybe 70/30 or even 70/25/5 if there are genes both your parents are heterozygous for. Your genes aren’t an average of your parents. This can be displayed in any genetic trait, your skin tone, eye color, hair color, height, etc wouldn’t be an average of your parents and you may have a large difference to both without any outside influence as is being inferred here.

So what they ARE saying with those percentages is they have certain genes that show up in certain populations with regularity. Some, well studied populations probably have hundreds of “flags” that can indicate a connection, some lesser studied probably only have a handful. They may even be using reference populations to give you a best guess where you fit.

It could be one flag that shows a 3% difference in an area. It could be one missing from a parent to make the same difference. It could be they weight certain flags for a region and surrounding regions using some kind of overlaying vectors.

In his shoes I would track down what flags are being used and how based on the company doing the testing, but I certainly wouldn’t be shocked by a couple percentage points here and there.

ETA: here’s 23andme’s explanation of how they get similar results it’s a lot of good science that ends up with a good guesstimate.

Also, testing site/personnel can affect an outcome. If protocol is loose, a sample can show data from an additional source, from hair, or a sneeze.