The chromosome Y sequence has the Pseudo Autosomal Regions (PAR) hard masked. This practice is consistent with the 1000 Genome Consortium's decision to hard mask these regions inchromosomeY in order to prevent mis-mapping of reads and issues in variant calling on the gender chromosomes.

The masked Y pseudoautosomal regions are chrY:10001-2649520 and chrY:59034050-59363566. (A related file can be downloaded from ftp://ftp.ensembl.org/pub/release-56/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.56.dna.chromosome.Y.fa.gz)

The following background information is from the UCSC site http://genome.ucsc.edu/cgi-bin/hgGateway?org=human&db=hg19

"The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) that were taken from the corresponding regions in the X chromosome and are exact duplicates:

chrY:10001-2649520 and chrY:59034050-59363566 chrX:60001-2699520 and chrX:154931044-155260560"