Schema for Gap - Gap Locations
  Database: galGal6    Primary Table: gap    Row Count: 942   Data last updated: 2018-10-11
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 13096int(10) unsigned range start position in chromosome
chromEnd 13196int(10) unsigned range end position in chromosome
ix 2int(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 100int(10) unsigned range size of gap
type scaffoldvarchar(255) values scaffold, contig, clone, fragment, etc.
bridge yesvarchar(255) values yes, no, mrna, bacEndPair, etc.

Sample Rows
 
binchromchromStartchromEndixnsizetypebridge
585chr113096131962N100scaffoldyes
586chr11597541598544N100scaffoldyes
586chr11786431787436N100scaffoldyes
587chr126308926318910N100scaffoldyes
590chr172746372756312N100scaffoldyes
590chr175744375754314N100scaffoldyes
591chr180593380603316N100scaffoldyes
591chr184035084045018N100scaffoldyes
591chr186332386342320N100scaffoldyes
591chr188183988193922N100scaffoldyes

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Gap (gap) Track Description
 

Description

This track shows the gaps in the Mar. 2018 chicken 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: 18; all of size 500,000 bases)
  • contig - gaps between contigs in scaffolds (count: 50; size range: 10 - 50,000 bases)
  • scaffold - gaps between scaffolds in chromosome assemblies (count: 874; size range: 10 - 74,650 bases)