The Pair Consistency track can be displayed in the Strategy view header, if desired. To display the Pair Consistency track, you must check its box in the Tracks panel and also click the associated plus sign (if any) in the Strategy view header.
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.
- Green above the baseline indicates the presence of pairs that are consistent with the current assembly.
- Red below the baseline indicates the presence of pairs that are inconsistent with the current assembly due to relative orientation, distance apart, or both.
- Gold below baseline spans regions corresponding to paired reads in different contigs whose assembly locations or orientations are inconsistent with pair specifier parameters, even if the contigs were rescaffolded or reordered.
- Pink below the baseline represents split reads in the same contig whose locations or orientation are inconsistent with pair specifier parameters.
Note that SeqMan Ultra cannot distinguish whether inconsistent pairs are due to naming errors or assembly errors.
Currently, the Pair Consistency track does not have editable options. However, you can add white space above and/or below the track using sliders in the Layout section.
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