The Contig match table
The Contig match table has a row representing one or more matches of a contig from the BLAST search. When a reference sequence is used, each row represents the match of a contig (or part of a contig) to the reference sequence. Consecutive matches are linked to make the view cleaner. One contig can result in several matches in the table. Double-clicking the match will open a view where the reference is shown at the top, and all matches are shown below. The match that was double-clicked is high-lighted as shown in figure 2.5.
Figure 2.5: The contigs aligned to a reference sequence. Note that the Compactness in the Side Panel is set to Low which makes it possible to see the names of the contigs.
When no reference sequence is available, the contigs will be aligned against each other as shown in figure 2.6.
Figure 2.6: The contigs aligned to themselves. In this example, the top match is the contig itself with a perfect alignment. There is a big overlap with contig 78, which seems to share a region with contig 50. The bottom match from contig 35 is faded which mean that contig 35 does not match contig 50 in the region shown but there is a match somewhere else.
The contig match table contains the following columns:
| Reference | The name of the reference sequence |
| Contig | The name of the contig |
| Reference start | Start position of the match in the reference sequence |
| Reference end | End position of the match in the reference sequence |
| Contig start | Start position of the match in the contig sequence |
| Contig end | End position of the match in the contig sequence |
| Contig span length | Span size in the underlying contig for the match including regions |
| between linked matches | |
| Match count | Number of linked sub-matches contained in this match |
| Aligned nucleotides | The number of aligned nucleotides in the match (excluding regions |
| between linked matches) | |
| Contig percentage | Percentage of the contig nucleotides covered by the match |
| Identity | Percentage of matching nucleotides in the match |
The Contig match table describes the mapping of the contigs relative to the selected reference. Two functions are available in the Contig match table:
- Show Contig Matches. Shows a visulization of the matches.
- Refresh Contig Matches. Updates the contig matches after manual editing of the contigs.
Note! After manual editing of the contigs you must manually refresh the contig matches, otherwise the match table and the match view will not be up to date.