This directory contains the two sequences that 
should be used to align ENCODE sequence data to GRCh37/hg19 reference genomes.  
There is one sequence for female DNA, and the other for male DNA.  
The only difference between the sequences is that the male sequence 
includes chrY data with the PAR regions hard-masked (with N's).

These sequences are composed of all the autosomes plus the 
X chromosome from GRCh37. The male sequence also
includes the chrY sequence from GRCh37.  
None of the random chromosomes, chrUn chromosomes, 
or haplotype chromosomes are included in either reference sequence.
The mitochondrial genome included in both references is the chrM 
sequence currently in use on the UCSC hg19 browser (NC_001807).  
This sequence is NOT considered to be the most representative of human.

See this site for a discussion on what has changed between 
the old reference mitochondrial eequence and the new reference 
mitochondrial sequences.
http://mitomap.org/bin/view/MITOMAP/HumanMitoSeq

This directory also contains the ENCODE pilot regions lifted to hg19.