Hello Hannah, The annotation of gaps is described in detail on the track's description page. To view this, open the Assembly browser, click on the track name, and scroll down into the Methods. The section of interest is titled "Gap Annotation" for the Conservation track. The Chain/Net pair-wise tracks also have descriptions of gap annotation in the "Display Conventions" sections.
To address you question briefly, if there is a double-line, then there is a gap/unaligned bases within a contiguous region (data is part of the same "block"). If there are no lines, then that indicates that the regions surrounding the area are distinct aligned regions (data is part of two distinct "blocks"). If after examining the documentation you still have questions, please let us know. Perhaps include a specific set of coordinates, assembly, track, and any other details so that we can examine the same data together for the explanation. Thank you, Jennifer Jackson UCSC Genome Bioinformatics Group Hannah Watkins wrote: > Hello, > > I am using comparative analysis and am confused about the gap > annotation. What is the difference between getting double lines > across the screen, and getting no lines at all? I realize that the > double lines have one or more unalignable bases in the region, but > what does no line mean? Is having a double line basically equivalent > to having no line? > > Thanks, > Hannah Watkins > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
