Schema for Gap - Gap Locations
  Database: hg19    Primary Table: gap    Row Count: 457
fieldexampleSQL type info
bin 585smallint(6) range
chrom chr1varchar(255) values
chromStart 0int(10) unsigned range
chromEnd 10000int(10) unsigned range
ix 1int(11) range
n Nchar(1) values
size 10000int(10) unsigned range
type telomerevarchar(255) values
bridge novarchar(255) values

Sample Rows
 
binchromchromStartchromEndixnsizetypebridge
585chr10100001N10000telomereno
586chr11774172274174N50000cloneyes
587chr12677193177196N50000contigno
588chr14713685213688N50000contigno
605chr12634220268422032N50000cloneyes
76chr13845268399526847N150000contigno
684chr11305299813102998151N50000cloneyes
85chr11321991213319912154N100000contigno
688chr11355716213607162157N50000cloneyes
89chr11712565817175658196N50000cloneyes

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. These gaps - with the exception of intractable heterochromatic 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:

  • Clone - gaps between clones in the same map contig. These may be bridged or not.
  • Contig - non-bridged gaps between map contigs.
  • Centromere - non-bridged gaps from centromeres.
  • Telomere - non-bridged gaps from telomeres.
  • Heterochromatin - non-bridged gaps from large blocks of heterochromatin.
  • Short Arm - non-bridged long gaps on the short arm of the chromosome.

See also

NCBI discussion of genome assembly procedures.

Credits

The Feb. 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium.