# 123456789 bychromosome -filetype map.inp ^ ^ ^ ^ space space space spaceThe spaces are necessary, because the input is token based. The program will read the second token in the file as a long integer and use it as an identifier for the file. Thus, each file should have a unique identifier following the pound symbol.
The -filetype map.inp tells the QTL Cartographer programs that this is a map.inp formatted file. The bychromosome word is a vestige of an idea that simply needs to hang around.