f8f3947eb9f2a6827713dd266a49d7a4659285c1 jnavarr5 Wed May 22 09:45:10 2019 -0700 Updating http to https for fr1, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/fugu/gap.html src/hg/makeDb/trackDb/fugu/gap.html index 3872a7e..8119bd7 100644 --- src/hg/makeDb/trackDb/fugu/gap.html +++ src/hg/makeDb/trackDb/fugu/gap.html @@ -1,28 +1,28 @@

Description

This track depicts gaps in the assembly of chrUn, the "unordered chromosome" for this browser. Gaps are represented as black boxes. If the relative order and orientation of the contigs on either side of the gap is known, it is a bridged gap. In this case, a white line is drawn through the black box representing the gap and the gap is labeled "yes".

This assembly contains the following types of gaps:

Fragment - gaps within a scaffold.
Contig - gaps between scaffolds. These gaps, represented by 1000 Ns, are placeholders between scaffolds that were added as part of the construction of chrUn. Because the order and orientation between the scaffolds is unknown, contig gaps are considered to be unbridged.

For a discussion of gaps and the JAZZ assembler see the supplemental material for:

Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A et al. - + Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002 Aug 23;297(5585):1301-10. PMID: 12142439