This directory contains the fasta file of the chromosomes sequences, generated with a quick script. Most scaffolds could not be oriented, so there are a lot of sequences that are in the wrong orientation. The chromosomes_defs file contains information on how each scaffold scored and was oriented.

chromosome_defs_sorted.txt

this file contains scaffolds mapped to the genetic map.

Columns:
scaffold name
chromosome
cM position
marker count
forward score
reverse score
orientation (R/F/?)