Schema for Gap - Gap Locations
  Database: canFam3    Primary Table: gap    Row Count: 23,876   Data last updated: 2012-01-06
Format description: Gaps in golden path
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 100int(10) unsigned range end position in chromosome
ix 1int(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 short_armvarchar(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 draft assembly (Sep. 2011, Broad CanFam3.1 (GCA_000002285.2)) of the dog genome.

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 - 100 bases of Ns marked at the beginning of each chromosome
  • Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. These are represented by varying numbers of Ns in the assembly. In this context, a contig is a set of overlapping sequence reads and a supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads. Fragment gap sizes are usually taken from read pair data.
  • Clone - gaps between supercontigs linked by the physical map. In general, these are represented by 1,000 Ns in the assembly.
  • Other - sequences of Ns in the assembly that were not annotated in the AGP file as gap. Added by UCSC.