During the metaphase, all chromosomes look like an `X` to the exception of the chromosome `Y`. See below

[![enter image description here][1]][1]

Why `Y` then? Well, according to [wikipedia][2]:

> Stevens named the chromosome "Y" simply to follow on from Henking's "X" alphabetically.

Note that many species don't have sexual chromosomes and note that in many species, the `Y`-looking chromosome is present in the female but not in the male. In such case we call this `Y`-looking chromosome `W` and we call the `X`-looking chromosome `Z`. Very likely [this post will interest you][3].


  [1]: https://i.sstatic.net/tJUeB.jpg
  [2]: https://en.m.wikipedia.org/wiki/Y_chromosome
  [3]: http://biology.stackexchange.com/questions/27511/do-males-of-all-sexual-species-have-y-chromosomes