Per-Template Report is one of several Project Report views and is only available when certain .assembly projects are open in SeqMan Ultra. This report displays the contents of a file written by SeqMan NGen’s XNG assembler called perTemplateResults.txt. The report’s table can be customized to display a wide variety of data columns in any desired order.
To access the view, choose View > Project Report > Per-Template Report.
To select which columns to display in this table, or to rename or reorder the columns, click the Change options in this view () tool. The Choose Columns dialog appears.
Available columns are on the left, while currently-applied columns are on the right.
- To add a column to the display, select its name on the left and press the right arrow key to move it to the right.
- To remove a column from the display, select its name on the right and press the left arrow key to move it to the left.
- To change the order of displayed columns, select the column name you wish to move on the right, then use the up/down arrows to place it in the desired order.
- To create a custom header for a displayed column, select its name on the right, then choose the Configure column tool (). In the popup dialog, type in the desired name and press OK.
Descriptions of each column appear below in alphabetical order.
Column Name | Description |
---|---|
0 Coverage Cnt | The number of bases in the reference sequence with zero coverage in the alignment. |
Consistent Pair Seq Count | For paired end sequencing (i.e. Illumina), the number of aligned read pairs that are correctly oriented and within the specified minimum and maximum distances. |
Group ID | Experiment Name assigned by the user when setting up the assembly in SeqMan NGen. |
Inconsistent Pair Seq Count | For paired end sequencing (i.e. Illumina), the number of aligned read pairs that are incorrectly oriented and/or outside the specified minimum and/or maximum distances. |
Median Coverage | The median depth of coverage across the individual contig. |
PairDist Median | The median distance between paired reads in the data set. |
RootName | The file name and complete file path of the template file without the .bam extension. |
SNP Count | The number of potential SNPs that were identified. |
Seq Count | The number of sequences in the template file. |
Seqfile | The file name and complete file path of the template file, including the .bam extension. |
Template | The file name and complete file path of the template file-of-files, including the .template.fof extension. |
Template Coverage % | The percentage of bases in the template covered by aligned sequence reads. |
Template ID | Internal identifier of the template used by DNASTAR for trouble-shooting. |
Template Length | The length of the template in base pairs. |
Template Spec | File pathway to the reference sequence. |
Template Title | The complete field of the reference sequence. |
Template Title Full | (DNASTAR internal use only) |
Total Seq Count | The total number of sequences in the layout for that template. Includes assembled and unassembled reads. Both halves of a split read are counted whether they aligned or not. |
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