The Contig Editor is used for viewing and editing de novo and reference assembly contigs in Assembler and as the main editor in Align to Reference. However, the Editor's interface does change depending on which function it is being used for. This page deals with the Contig Editor as used in Assembler for de novo assemblies. Please see Contig Editor for Reference Assemblies or Contig Editor - Align to Reference to see how this is used for editing alignments produce by Align To Reference.
Note that a current limitation means that only single read based contigs can be edited. All file based contigs cannot be edited. This means all reference contigs.
Whenever you edit a sample sequence, that residue is given the quality value 99 (except gaps, which are given the value 0). The value 99 overrides all other considerations in the consensus calculation, so editing a single residue will cause the consensus to become that residue. If you edit sequences so that there is a conflict, the consensus will be given the IUPAC value representing the conflict.
Reads are represented by a different symbol in the Map View depending on whether the read is from a 454, SOLiD, Illumina or a Sanger sequencer. This is useful for hybrid assembly as you can easily visualize the provenance of the reads. NOTE that for performance reasons individual reads are NOT shown in reference assemblies.