Schema for Gap - Gap Locations
  Database: bosTau6    Primary Table: gap    Row Count: 74,465   Data last updated: 2011-05-10
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 16543int(10) unsigned range start position in chromosome
chromEnd 16643int(10) unsigned range end position in chromosome
ix 2int(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 fragmentvarchar(255) values scaffold, contig, clone, fragment, etc.
bridge yesvarchar(255) values yes, no, mrna, bacEndPair, etc.

Sample Rows
 
binchromchromStartchromEndixnsizetypebridge
585chr116543166432U100fragmentyes
585chr124602247024U100fragmentyes
585chr138959390516N92fragmentyes
585chr154732548328U100contigno
585chr1626506275010U100contigno
585chr1732367333612U100contigno
585chr1746697476914U100fragmentyes
585chr1762407634016U100fragmentyes
585chr1782127831218U100fragmentyes
586chr120103420143220N398fragmentyes

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

Gap (gap) Track Description
 

Description

This track depicts gaps in the draft assembly (Nov. 2009, UMD_3.1 (NCBI project 10708, accession GCA_000003055.3)) of the cow genome. Many of these gaps — with the exception of intractable heterochromatic gaps — may 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 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:

  • fragment - Gap between sequence contigs.
  • contig - Gap between clone contigs. These are represented by 5,000 Ns in the assembly.
  • other - Unknown bases marked 'N' in the sequence that were not in the assembly AGP file definition of gaps.
See also: AGP specification