"Mapped reads" are interpreted as the alignments of the reads.  "Pre-RSEM" alignments are in Bowtie "concise" format, where each line is of the form:

[read_num][orientation]:<[contig_num,start_position,num_mismatches]>

read_num is the 0-based index of the read and contig_num is the 0-based index of the contig (according to the orders of the contigs and reads in their respective files).