Schema for Gap - Gap Locations
  Database: hg38    Primary Table: gap    Row Count: 829   Data last updated: 2022-10-19
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 shows the gaps in the GRCh38 (hg38) genome assembly defined in the AGP file delivered with the sequence. These gaps are being closed during the finishing process on the human genome. For information on the AGP file format, see the NCBI AGP Specification. The NCBI website also provides an overview of genome assembly procedures, as well as specific information about the hg38 assembly.

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:

  • short_arm - short arm gaps (count: 5; size range: 5,000,000 - 16,990,000 bases)
  • heterochromatin - heterochromatin gaps (count: 11; size range: 20,000 - 30,000,000 bases)
  • telomere - telomere gaps (count: 48; all of size 10,000 bases)
  • contig - gaps between contigs in scaffolds (count: 285; size range: 100 - 400,000 bases)
  • scaffold - gaps between scaffolds in chromosome assemblies (count: 470; size range: 10 - 624,000 bases)