Schema for Gap - Gap Locations
  Database: mm39    Primary Table: gap    Row Count: 324   Data last updated: 2020-07-27
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 100000int(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 100000int(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 Jun. 2020 mouse 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:

  • centromere - gaps for centromeres are included when they can be reasonably localized (count: 20; all of size 2,890,000 bases)
  • short_arm - a gap inserted at the start of an acrocentric chromosome (count: 21; all of size 10,000 bases)
  • telomere - telomere gaps (count: 42; all of size 100,000 bases)
  • contig - gaps between contigs in scaffolds (count: 60; size range: 8,000 - 500,000 bases)
  • scaffold - gaps between scaffolds in chromosome assemblies (count: 181; size range: 27 - 522,000 bases)