Schema for Gap - Gap Locations
  Database: ailMel1    Primary Table: gap    Row Count: 119,126   Data last updated: 2010-02-03
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 GL192338.1varchar(255) values Reference sequence chromosome or scaffold
chromStart 375int(10) unsigned range start position in chromosome
chromEnd 433int(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 58int(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

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 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 types of gaps:

  • Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. (In this context, a contig is a set of overlapping sequence reads. A supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads.) These are represented by varying numbers of Ns in the assembly. Fragment gap sizes are usually taken from read pair data.

There are 119,126 fragment gaps in this draft assembly with a combined total of 54,196,184 bases of Ns. All these gaps are bridged gaps.