Schema for Gap - Gap Locations
  Database: mm10    Primary Table: gap    Row Count: 734   Data last updated: 2021-04-08
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 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
 
binchromchromStartchromEndixnsizetypebridge
585chr101000001N100000telomereno
585chr11000001100002N10000short_armno
9chr111000030000003N2890000centromereno
756chr122433268224665105N33242contigno
144chr175055556751215567N66000contigno
1236chr185347103854471039N100000contigno
1776chr115611874315616874311N50000contigno
1981chr118299167918303809013N46411contigno
30chr118345393118350393115N50000contigno
256chr119200177619205177617N50000contigno

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 assembly (Dec. 2011, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) of the mouse genome. These gaps - with the exception of intractable centromere gaps - will 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 known, 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:

    (In this context, a contig is a set of overlapping sequence reads.)
  • Clone - gaps between clones (114 gaps).
  • Contig - gaps between map contigs, various sizes (104 gaps).
  • Telomere - 42 gaps for telomeres (100,000 Ns)
  • Centromere - 20 gaps for centromeres (size: 2,890,000 Ns)
  • Short_arm - 21 gaps for the short arm (10,000 Ns) at base positions 100,001-110,000 of each chromosome.
  • other - sequence of Ns in the assembly that were not marked as gaps in the AGP assembly definition file, various sizes (384 gaps).
  • Fragment - a single gap of 31 bases in chrX_GL456233_random.