Displaying a Conflicts Graph

The Conflicts graphic in the Strategy View displays how well the constituent sequences agree with the consensus by plotting a conflict score.

 

The conflict score is calculated by first evaluating all of the bases and gaps within a column and assigning each a score:

 

      Bases that do not match the consensus = 1

 

      Gaps = 0.25

 

      N’s and X’s = 0.5

 

The sum of all of the scores in the column is divided by the total number of bases in the column, and then multiplied by 100.

 

This calculation is repeated for each column in the specified Conflict Count Window, as defined under Strategy Viewing & Coverage parameters. Finally, an average is calculated for all of the scores within the Conflict Count Window, and that average value is the conflict score that is plotted on the Conflicts graph.

 

Note that the presence of conflicts does not necessarily indicate the consensus sequence is wrong. The conflicts summary is rather intended to alert you to potential problem areas. Use of Trace Evidence consensus calling usually resolves conflicts without the need for manual editing.

 

Click the box next to the word Conflicts to display the Conflicts graph.

 

 

The scale along the left side of the Conflicts graph indicates the conflict score at each position in the contig.

 

Note that if the Conflicts graph is displayed while edits are made to the alignment in the Alignment View, the Conflict graph is updated automatically.