Last updated 2019-02-19

This directory contains recombination maps and recombination hotspots 
for the Arabian horse split by chromosome.

Files named *_map.txt include the recombination map for that particular
chromosome. They are split into three columns. The first column ('bp') refers
to the basepair position. The second column ('cM') refers to the cumulative
centimorgans up to this position. The third column ('cM/Mb') refers to the
recombination rate in centimorgans per megabase between this position and
the next position.

Files named *_hotspots.txt include positions of predicted recombination
hotspots for that particular chromosome. They are split into five columns.
The first ('hotStart') and second ('hotEnd')  columns refer to the starting
and ending  positions in basepairs, respectively. The third column refers to
the p-value for significance of that hotspot based on up to 1,000 coalescent
simulations. P-values equal to zero reflect hotspots for which none of the
1,000 simulations detected a false hotspot under a constant rate model (see
Methods section). The fourth column ('cM_across_hotspots') refers to the total
map distance incentimorgans across the predicted hotspot. The fifth column
('peak_rate') refers to the highest recombination rate in centimorgans
detected within the hotspot.

The file titled Arab_unique_hotspots.txt contains the list of hotspots
predicted in the Arabian horse that were not predicted in any other breed
included in this study. This file is identical in format to the *_hotspots.txt
file with the exception of an additional column to identify the chromosome
on which the hotspot was predicted.

The file titled Arab_unique_coldspots.txt contains the list of unique coldspots
for the Arabian horse. These are regions of the genome in which a hotspot
was predicted in all breeds except the Arabian and where the recombination
rate for the Arabian is below the chromosomal average. This file contains four
columns. The first three columns identify the chromosome and start and end
positions in basepairs. The fourth column refers to the average recombination
rate across the coldspot.
