Per base N content

If a sequencer is unable to make a base call with sufficient confidence, it will write an N instead of a conventional base call. This plot displays the percentage of base calls at each position or bin for which an N was called.

Figure

It’s not unusual to see a very high proportion of Ns appearing in a sequence, especially near the end of a sequence But this curve should never rises noticeably above zero. If it does this indicates a problem occurred during the sequencing run.