Description

This track shows the current Repeat Browser consensus being visualized as well as information on the consensus sequence.

Click directly on the track in the genome browser window to see information for the current repeat. You should see a big table above description if you did that.

Repeat Browser Name: is the name of the repeat in Repeat Browser nomenclature.

DFAM Record: is the closest DFAM record to the repeat name. This is usually the same as the Repeat Browser name. Notable exceptions are for many LINEs (where Dfam has no full length consensus), where we typically link to the 3' end. Note also that many ERVs are labeled ERV-int in RepeatMasker but are simply ERV in Dfam/Repeat Browser nomenclature ("int-strip"). A few ERV-ints in RepeatMasker nomenclature correspond to a single ERV in Dfam. Searching for any of these Repeat Masker names will take you to the same consensus (see the MLT ERV family as an example).

DFAM Type: The type of repeat

DFAM Class: The class of repeat

DFAM Organism: Organism/lineage for which the annotation is expected to be found.

DFAM Comment: Comments about the element.

RepeatMasker Names: Name in RepeatMasker output.

Number of copies in genome, total: Number of copies in hg38 output that match the Repeat Browser name.

Copies in genome, per RepeatMasker Name: Count in the hg38 output that match the RepeatMasker name.

Liftable copies: Number of copies that are lifted to the consensus via the chain file.

Sequence Source(s): exact = exactly the same as Dfam, cons = built by Repeat Browser, int-strip = Dfam and RepeatMasker equivalent (after stripping int from RepeatMasker name), add = manual addition

Length of 99% percentile in genome: Length of element in the 99% in length distribution histogram.

Maximum length in genome: Longest element of this type in hg38.

Length of top50 alignment: Length of the 50 elements used to make the alignment (for Sequence source = cons)

Number of Ns in top50 consensus: Number of Ns in the alignment.

Ratio of alignment length to top50 length: A metric to assess how representative the consensus is compared to the population of instances (close to 1 is good).

Display Conventions and Configuration

The long black bar spans the entire length of the repeat.

Links to length distributions for the repeat type can be found at the top of the page.

Methods

This table was ouput from the build_tracks steps of Repeat Browser construction. You can view the raw file as summary.tsv.

Email: jferna10@ucsc.edu or mhaeussl@ucsc.edu