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  Schema for Gap - Gap Locations
  Database: bosTau4    Primary Table: gap    Row Count: 75,654
Format description: Gaps in golden path
fieldexampleSQL type info description
bin 585smallint range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3267int unsigned range start position in chromosome
chromEnd 3767int unsigned range end position in chromosome
ix 2int range ix of this fragment (useless)
n Nchar(1) values always 'N'
size 500int unsigned range size of gap
type fragmentvarchar(255) values contig, clone, fragment, etc.
bridge yesvarchar(255) values yes, no, mrna, bacEndPair, etc.

  Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

  Gap (gap) Track Description


This track depicts gaps in the assembly. Many of these gaps — with the exception of intractable heterochromatic gaps — may be closed during the finishing process.

Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is supported by read pair data, it is a bridged gap and a white line is drawn through the black box representing the gap.

This assembly contains the following principal types of gaps:

  • Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. (In this context, a contig is a set of overlapping sequence reads. A supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads.) These are represented by varying numbers of Ns in the assembly. Fragment gap sizes are usually taken from read pair data.
  • Clone - gaps between supercontigs linked by the fingerprint map. In general, these are represented by 5,000 Ns in the assembly.