Schema for Gap - Gap Locations
  Database: hg19    Primary Table: gap    Row Count: 497   Data last updated: 2020-02-20
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 chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned range start position in chromosome
chromEnd 10000int(10) unsigned range end position in chromosome
ix 1int(11) range index count of this fragment (obsolete/useless)
n Nchar(1) values 'N' for gaps of known size, 'U' for gaps of unknown size
size 10000int(10) unsigned range size of gap
type telomerevarchar(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 depicts gaps in the assembly. These gaps — with the exception of intractable heterochromatic gaps — will 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 known, 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 the same map contig. These may be bridged or not.
  • Contig — non-bridged gaps between map contigs.
  • Centromere — non-bridged gaps from centromeres.
  • Telomere — non-bridged gaps from telomeres.
  • Heterochromatin — non-bridged gaps from large blocks of heterochromatin.
  • Short Arm — non-bridged long gaps on the short arm of the chromosome.

See also

NCBI discussion of genome assembly procedures.


The Feb. 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium.