I think this gives you the answer
'For example, the image on the right shows indices for hg38 version of the human genome. You can see that there are actually three choices: (1) hg38, (2) hg38 canonical and (3) hg38 canonical female. The hg38 contains all chromosomes as well as all unplaced contigs. The hg38 canonical does not contain unplaced sequences and only consists of chromosomes 1 through 22, X, Y, and mitochondria. The hg38 canonical female contains everything from the canonical set with the exception of chromosome Y.'
This is copied from https://wiki.galaxyproject.org/Learn/GalaxyNGS101