Map file contains information about markers: chromosome, location, order and name of the marker. File format described here is used by Mega2 converter program.
Map file is general ASCII-text file (created with notepad or some other text editor) and it contains header line and three columns.
Header line
Chromosome Haldane Name
Second column in header line specifies map function (haldane or kosambi) used in conversion from cM to recombination fraction. But AUTOGSCAN assumes Haldane cM map! Columns after header line:
Column 1: Chromosome number Column 2: Location (continuous cM-map) Column 3: Name of the marker
Example of chromosome 7 with 6 markers:>
Chromosome Haldane Name 7 0 D7S2233 7 2 ATA100 7 6 D7S9339 7 11 WATR567 7 11.9 D7S1122 7 15 D7S5566
Markers distances are in cM (centi-morgans) and map is continuous. Map does not have to start from 0 cM. Markers have to be in same order in pedigree file.
Last line of the file must be empty line!
Map files have to be separated by chromosome and name files according to chromosme as map1.dat, map2.dat, ..., map22.dat