To view the Contigs and Scaffolds section, click on the Explorer panel expand bar entitled Contigs and Scaffolds. If you can’t see the Explorer panel, choose View > Explorer to make it visible.

This section consists of a table showing all of the contigs, their lengths, constituent sequences and positions. Below these are the names of sequences that were not placed in any contigs. If scaffolds exist, they are also included in the table.The table’s data columns are described in the table below.

  • To sort contigs, click once or twice on any of the column headers to sort by that value in ascending/descending order. If scaffolds are present, clicking on any column header will first sort by the position of the scaffold, and then sort the contigs within each scaffold. |
  • To edit the Name or Position fields, hold the mouse cursor down on the field for one second, then release. Then overwrite or append to the existing name.
Column header Description
Name The name of the contig. Some contigs may have coordinates displayed in parentheses next to the name. These are always based on the original, ungapped reference sequence. The purpose of the coordinates is to show the relative positioning of the contig with respect to the original template. When two contigs are joined, the new contig retains the name and original coordinates of the 5’ contig. When a contig is split using the Contig > Split at Insertion command, the new 5’ contig keeps the original name and coordinates. The new 3’ contig is given the identical name appended with “[2]”.
Length The length of the individual contig, including gaps and/or edits. Note that subtracting one Name coordinate from the other may yield a result that does not match the number shown in the Length column. This is because the Name coordinates are based on the ungapped and unedited reference sequence, while the Length value includes gaps and edits.
Sequences The number of sequences in the contig.
Position The position of each ordered contig or “scaffold. A “0” indicates that contigs or scaffolds have not been ordered.

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