What Does Chr "Par" Stand For In The Latest 1000Genomes Vcf File?

Question

[Biomed]

I found entries for chr "PAR" in the latest 1000genomes vcf file. Does anyone know what that stands for? Thanks

Answer 1

[Pierre Lindenbaum]

PAR = Pseudo-Autosomal Regions

see also this question: Coordinates Of Par Regions On Ensembl Y Chromosome

[Biomed]

Thanks Pierre, you are to the point, as always.

Answer 2

[Shigeta]

It wouldn't hurt here to explain Pseudo-Autosomal Regions. Autosomal (Chromosomes 1-22 in humans) always show up in pairs.

Since they can appear as single copies in males Y and the X chromosomes are not autosomal chromosomes. BTW they still don't behave as autosomal chromosomes in females where there appear in pairs.

The PAR regions are the 2 spans which are still very similar, remnants of the time when the X and Y diverged from a single autosomal chromosome. Especially for applications which want to know the number of copies of a chromosome or segment, its useful to keep track of the PARs.