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This data file contains the locus map, i.e., the order of the loci and the recombination frequencies between them. One may provide sex-average or sex specific values. All analysis is performed using only those loci in both the map and locus data files. If there is a trait locus to be analyzed, then it must be the first locus listed in both the map and locus data files.
Fortran uses the following format codes, also called descriptors, to describe data: (A) is used for character data, (I) for integer data, (F) for numbers with decimals, and (X) for blank spaces. For example, (A8) specifies a word of length eight characters, (I2) specifies an integer occupying two spaces, (F8.5) specifies that the following eight spaces contain a number with a decimal part and (1X) specifies a single blank space.
The map file has a very simple format. There are two types of lines.
The first type of line contains the name of a locus in the first eight columns, i.e.,
read using the format specification (A8). Between each two of these locus lines is
a line listing the recombination frequency between those flanking loci. If there
is only one recombination frequency on this line, it is the sex-average value and
read using the specification (8X, F8.5). If there are two values, then the first
is the female recombination frequency and the second is the male; these are read
using the specification (8X, F8.5, F8.5).
It is important to realize that the analysis will be performed using only those loci in both the map and locus data files (see the description of the locus data file format). So, maintaining a set of locus and pedigree data files with a large collection of loci and then editing only the map file is an easy method to change which loci an analysis is performed on.
Another important consideration is that if there is a trait locus
to be analyzed, then it must be the first locus in both the map and locus data files.
The recombination frequency specified between the trait locus and the first marker
locus is not currently used.
An example map file:
_______________________________<top of file>___________________
____________________________<bottom of file>___________________
Another example MAP.DAT file is available with annotations.