Schema for Gap - Gap Locations
  Database: susScr3    Primary Table: gap    Row Count: 183,621   Data last updated: 2012-04-13
Format description: Gaps in golden path
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(6) range Indexing field to speed chromosome range queries.
chrom GL892247-1varchar(255) values Reference sequence chromosome or scaffold
chromStart 1163int(10) unsigned range start position in chromosome
chromEnd 1263int(10) unsigned range end position in chromosome
ix 2int(11) range index count of this fragment (obsolete/useless)
n Uchar(1) values 'N' for gaps of known size, 'U' for gaps of unknown size
size 100int(10) unsigned range size of gap
type fragmentvarchar(255) values scaffold, contig, clone, fragment, etc.
bridge novarchar(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 shows the gaps in the Aug. 2011 pig genome assembly.

Genome assembly procedures are covered in the NCBI assembly documentation.
NCBI also provides specific information about this assembly.

The definition of the gaps in this assembly is from the AGP file delivered with the sequence. The NCBI document AGP Specification describes the format of the AGP file.

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:

  • clone - gaps between clones in scaffolds (count: 5,323; all of size 50,000 bases)
  • other - gaps added at UCSC to annotate strings of Ns that were not marked in the AGP file (count: 14,502; size range: 1 - 109 bases)
  • fragment - gaps between whole genome shotgun contigs (count: 163,796; all of size 100 bases)