# Reference specification for hg19 see http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=184117983&chromInfoPage=
version	1

# Unless otherwise specified, assume diploid linear. Well-formed chromosomes should be explicitly listed 
# separately so this applies primarily to unplaced contigs and decoy sequences
either	def	diploid	linear

# List the autosomal chromosomes explicitly. These are used to help determine "normal" coverage levels
# during mapping and variant calling
either	seq	chr1	diploid	linear
either	seq	chr2	diploid	linear
either	seq	chr3	diploid	linear
either	seq	chr4	diploid	linear
either	seq	chr5	diploid	linear
either	seq	chr6	diploid	linear
either	seq	chr7	diploid	linear
either	seq	chr8	diploid	linear
either	seq	chr9	diploid	linear
either	seq	chr10	diploid	linear
either	seq	chr11	diploid	linear
either	seq	chr12	diploid	linear
either	seq	chr13	diploid	linear
either	seq	chr14	diploid	linear
either	seq	chr15	diploid	linear
either	seq	chr16	diploid	linear
either	seq	chr17	diploid	linear
either	seq	chr18	diploid	linear
either	seq	chr19	diploid	linear
either	seq	chr20	diploid	linear
either	seq	chr21	diploid	linear
either	seq	chr22	diploid	linear

# Define how the male and female get the X and Y chromosomes 
male	seq	chrX	haploid	linear	chrY
male	seq	chrY	haploid	linear	chrX
female	seq	chrX	diploid	linear
female	seq	chrY	none	linear
#PAR1 pseudoautosomal region
male	dup	chrX:60001-2699520	chrY:10001-2649520
#PAR2 pseudoautosomal region
male	dup	chrX:154931044-155260560	chrY:59034050-59363566

# And the mitochondria
either	seq	chrM	polyploid	circular