The Pseudoautosomal Region (or PAR) is a region on the tips of both X and Y allosomes that behaves like the autosomes during meiosis replication. As a result, most tools report the region separately from either chromosome X or Y}} and always as a diploid value. ((DNA test techniques cannot usually distinguish which chromosome sourced the DNA read. The region is large enough to have genes and undergo recombination in biological males with both X and Y}}. Often, the best analysis models to align ((NGS results too have the PAR region masked out on the Y chromosome. Forcing all read fragments from the region to be aligned on the X chromosome.

The reference models specifically defined the PAR areas of each allosome to be the same length. Although the coordinate start point in each allosome may be different. This to further emphasize the near identical regions that exist in each. When these regions are vastly different, meiosis may fail or lead to generating an Y chromosome that makes the individual sterile.

Note that in some rare cases, the SRY gene from the Y chromosome, that exists near the PAR, gets copied into the X chromosome in a seemingly biological female with two X's. Thus causing more alignment of read segments from NGS testing onto the Y chromosome than expected. Also causing some ambiguity in the individual depending on how the gene is activated.

Special Note on the T2T v2.0 Reference Model

As you will notice, in the table above, the T2T v2.0 reference model has differing lengths for the PAR regions in the X and Y. Which caused them to release a variant analysis model with the Y PAR masked out. The explanation is simple. The X in the T2T v2.0 reference came from the CHM13 reference with the rest of the autosomes. But as that sample has no Y, they took the Y only from the HG002 model that had just also had a T2T model developed of its X and Y by the HPP. So there was no attempt to make the two chromosomes coordinate-similar in the PAR. As a result, we had early on promoted the use of the HPP HG002 model, which pre-existed the T2T v2.0 by 6 months, and had the CHM13 autosomes and HG002 allosomes. Thus making the PAR similar and usable for alignment and variant determination. But even that model had not masked the PAR of Y out. And worse yet, the HG002 model used in T2T v2.0 was HG002 v0.7. It was nowhere near complete and quality checked. In the intervening two years, due to the Q100 project, the HG002 model is now up to v1.1 and has attained a quality measurement of Q78. And is a complete (all chromosomes) model of HG002 with no use of CHM13.

External References

• Mangs, A. Helena, et al, "The Human Pseudoautosomal Region (PAR): Origin, Function and Future"
• Wikipedia Pseudoautosomal Region overview
• HG002 Q100 Project
• SRY Gene Overview