Overlapping matches on the X chromosome for two males at 23andMe

Question

I've come across some Detailed segment data from 23andMe that I've never seen before that I don't understand. Detailed segment data in 23andMe is available under the "Family & Friends" menu item when you select "Advanced DNA Comparison".

These are two males being compared. They are closely related and have 31 segment matches on chromosomes 1 to 22. The problem is with the X chromosome.

The image shows what 23andMe displays for the four X matches in its Detailed segment data.

Note that the first two matches overlap each other, and the 3rd and 4th matches overlap each other. The first and third matches are listed as having Identity "Complete" and the 2nd and 4th have identify "Half".

23andMe explains that "completely identical" is when both copies of the chromosome are identical between two people.

However, with both of these people being male, they each have only one X chromosome.

Why is 23andMe listing overlapping matches on the X chromosome in this case for two males? What does this mean?

Answer 1

This is 23andMe's response to a query about this issue:

We have reviewed what you have reported with our product scientists. They have concluded that the shared segments you are seeing with Christopher is a normal result for what a grandfather would share with their grandson on their X chromosome.

It should be noted as well that the DNA Comparison is showing you two segments of your X chromosome rather than four. Because the X chromosome is haploid in males, 23andMe's IBD inference algorithm reports both half identical and completely identical when comparing the X chromosome between two male customers. As a result, identical segments are reported as both half and completely identical.

I hope this explanation is helpful, and I apologize for any confusion this may have caused. Please let me know if you have any additional questions.