Overlapping paired reads
Depending on the sequencing protocol paired reads may overlap. If the mates of an overlapping pair disagree on one or more positions (e.g. due to sequencing errors) the viewer will represent this as a paired read with an IUPAC code. Where there is a gap in one of the reads, an N will be inserted. This reflects the way the Workbench variant detection tools would treat disagreements - if two overlapping reads do not agree about the variant base, they are both ignored. If you wish to inspect the mates of overlapping pairs you can check the side panel option 'Show strands of paired reads'. An example is shown in figure 28.24.
Figure 28.24: Discrepancies in the overlapping region of overlapping paired reads are indicated using Ns and IUPAC codes (top). When the individual reads of each pair are displayed by checking the box "Show strands of paired reads" in the Side Panel, the bases of each member of the pairs are displayed (bottom).