Percentage of informative reads for different sequencing read lengths and types. Reads or read pairs, respectively, can only contribute to mapping-by-sequencing if their alignments overlap with at least one marker or mutations (informative reads). The number of informative reads from single-end and paired-end sequencing are shown in purple and blue, respectively. The lower graphs refer to a mutation density, which is typical for backcross populations (here, 1,400 mutations per mutant genome). The upper graphs refer to the number of marker in outcross populations (281,668 and 291,973 for single-end and paired-end sequencing).