Simplest format for the Map file:

1. Each marker should be represented in this file, in order of their physical location. 
   The first entry for each marker is the chromosome number.

2. The second entry should be the genetic distance in cM relative to the starting marker 
   (0.0 for the marker on the furthest end).

3. The third position should contain the number of alleles at that marker, 
   which should be no more than 99.

4. Finally, the numeric name of each allele should be followed by its frequency.

For example, markers on the same chromosome:

1 0.0 3 1 0.18 2 0.55 3 0.27
1 5.0 4 1 0.01 2 0.07 3 0.86 4 0.06
1 7.0 3 301 0.32 302 0.61 303 0.07
1 13.0 5 401 0.14 402 0.02 403 0.79 404 0.01 405 0.04

For example, markers on different chromosomes (/unlinked markers):

1 0 3 1 0.18 2 0.55 3 0.27
2 0 4 1 0.01 2 0.07 3 0.86 4 0.06
3 0 3 301 0.32 302 0.61 303 0.07
4 0 5 401 0.14 402 0.02 403 0.79 404 0.01 405 0.04