# Reference specification for ARS-UCD1.2_Btau5.0.1Y
# Chromosome Definitions: http://genome.ucsc.edu/cgi-bin/hgTracks?chromInfoPage=&hgsid=2284666482_HQnhMuYc3A1tqcYRPIq19THoKj5U
# PAR Definition: https://doi.org/10.3168/jds.2018-15638
version 1
# Default Sequence Settings ----
# Unless otherwise specified, assume diploid linear. Well-formed
# chromosomes should be explicitly listed separately so this
# applies primarily to unplaced contigs and decoy sequences
# sex    line-type    ploidy    shape
either    def    diploid    linear
# Specific Sequencing Settings ----
# List the autosomal chromosomes explicitly. These are used to help
# determine "normal" coverage levels during mapping and variant calling
# sex    line-type    chr-name    ploidy    shape
either    seq    1    diploid    linear
either    seq    2    diploid    linear
either    seq    3    diploid    linear
either    seq    4    diploid    linear
either    seq    5    diploid    linear
either    seq    6    diploid    linear
either    seq    7    diploid    linear
either    seq    8    diploid    linear
either    seq    9    diploid    linear
either    seq    10    diploid    linear
either    seq    11    diploid    linear
either    seq    12    diploid    linear
either    seq    13    diploid    linear
either    seq    14    diploid    linear
either    seq    15    diploid    linear
either    seq    16    diploid    linear
either    seq    17    diploid    linear
either    seq    18    diploid    linear
either    seq    19    diploid    linear
either    seq    20    diploid    linear
either    seq    21    diploid    linear
either    seq    22    diploid    linear
either    seq    23    diploid    linear
either    seq    24    diploid    linear
either    seq    25    diploid    linear
either    seq    26    diploid    linear
either    seq    27    diploid    linear
either    seq    28    diploid    linear
either    seq    29    diploid    linear
# Define how the male and female get the X and Y chromosomes
# sex    line-type    chr-name    ploidy    shape    allosome
male    seq    X    haploid    linear    X
male    seq    Y    haploid    linear    Y
female    seq    X    diploid    linear
female    seq    Y    none    linear
# PAR pseudo-autosomal region
male	dup	X:133300518-139009144	Y:25001-43300181
# And the mitochondria
either	seq	MT	polyploid	circular
