hg19 reference

The Human Genome version 19 (hg19) reference is a human genome reference that is based on the Genome Reference Consortium's human genome assembly version 37 with patch 5 (GRCh37.p5), and its equivalent UCSC hg19 reference. For more information, see the Genome Reference Consortium's website: ncbi.nlm.nih.gov/grc/human/data. Several notable differences exist between the hg19 reference in Torrent Suite™ Software and the GRCh37.p5/UCSC hg19 reference sequences:

• The Y chromosome PAR regions in the hg19 reference are hard masked with 'N', while the GRCh37.p5 reference Y chromosome PAR regions are unmasked.

• Three nucleotide positions that are masked with 'N' in the GRCh37/UCSC hg19 reference have IUPAC ambiguity codes in hg19 reference sequence.

• The hg19 reference in Torrent Suite™ Software uses the Revised Cambridge Reference Sequence (rCRS) for chromosome M, while UCSC hg19 uses the original chromosome M sequence.

For more information, see genome.ucsc.edu/cgi-bin/hgGateway?org=human&db=hg19. To download sequence and annotation data, go to the Genome Browser FTP server at hgdownload.soe.ucsc.edu/goldenPath/hg19 or the Downloads screen at hgdownload.soe.ucsc.edu/downloads.html#human.