Tracks are graphical data displays that run along the length of your sequences in the Strategy and Alignment views. To learn how to apply, show or hide tracks, or to edit track options, see Work with Data Tracks. The following table shows all the tracks that can be displayed within the Strategy view.
|Tracks panel category & track name||Image|
|Strategy header > Contig|| Applying this track only has an effect if you are displaying the Strategy view for a contig scaffold. If a scaffold Strategy view is open, the track shows bars denoting the placement and name of each contig.
|Strategy header > Coverage|| This histogram represents the depth of sequences throughout the assembly. The numbers to the left of the histogram indicate the actual number of sequences represented. Hover over any part of the histogram to display information about that location.
Based on the Strategy Viewing and Coverage parameters, the histogram will appear:
|Strategy header > Pair Consistency||The Pair Consistency histogram displays a summary of either split reads (for non-paired data) or good versus bad paired end sequence data content (for paired reads). Hover over any part of the histogram to display information about that location.
The deeper the Pair Consistency histogram , the more recognized pair of reads there are. Note that SeqMan Ultra cannot distinguish whether inconsistent pairs are due to naming errors or assembly errors.
|Strategy header > Reference > Features|
|Strategy header > Ruler|| A gap-aware sequence ruler.
|Strategy header > Split reads|
|(Sequences)|| The lower half of the Strategy view displays arrows representing the individual sequences in the contig, including color-coded information about paired-end data.
, hover over the first member for a tooltip with coordinates of its mate pair.
, right-click on the first member and select Show Mate Pair.
The point of the arrowhead represents the 3’ end and the tail represents the 5’ end. Solid arrows pointing right represent sequences assigned to the top strand of the consensus sequence. Dash-lined arrows pointing left represent sequences assigned to the bottom (complementary) strand of the consensus sequence. The arrows use the color coding shown in the table below.
Paired end sequence data are forward and reverse sequence reads originating at opposite ends of the same fragment. Even though such a pair of reads may not overlap by sequence similarity, they belong in the same contig. If the reads are assembled into different contigs, the knowledge they are linked may help in joining two contigs together though it may instead indicate that the reads are misassembled or misnamed. Paired end data can also be used for within-contig assembly evaluation. If the two reads for a given pair are not in opposite orientations, for instance, an assembly problem may be indicated. Finally, if the distance between the two reads is known, this information can also be used to confirm whether or not the assembly is correct. When using paired end sequence data to evaluate assemblies, be sure to allow for the possibility that there may be errors in some of the sequence names.
Certain actions may affect the current classification (coloring) of the sequences in the Strategy view. For example, deleting a contig or scaffold in the Explorer panel may remove one of a paired end pair. The coloring of its pair sequence would then be updated to black. Other actions that affect coloring include: adding or deleting sequences from your project or reverse complementing, aligning, force joining, splitting, or ordering contigs.
|Black||Represents reads for which no paired data information is available or recognized.|
|Green||Represents paired reads in the same contig whose assembly locations are consistent with the pair specifier parameters.|
|Dark Blue||Represents paired reads in different contigs in the scaffold whose assembly locations are consistent with pair specifier parameters.|
|Pale Blue||Represents paired reads in different contigs (in the same or different scaffolds) whose assembly locations could be consistent with pair specifier parameters if the contigs were rescaffolded or reordered. The number appearing next to the pale blue arrows indicates which contig the other member of the pair is in.|
|Orange||Represents paired reads in different contigs whose assembly locations or orientations are inconsistent with pair specifier parameters, even if the contigs were rescaffolded or reordered.|
|Red||Represents paired reads in the same contig whose locations or orientation are inconsistent with pair specifier parameters.|
|Pink||Represents split reads in the same contig whose locations or orientation are inconsistent with pair specifier parameters.|
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