Schema for Gap - Gap Locations
  Database: dm6    Primary Table: gap    Row Count: 572
fieldexampleSQL type info
bin 748smallint(6) range
chrom chr2Lvarchar(255) values
chromStart 21485538int(10) unsigned range
chromEnd 21485638int(10) unsigned range
ix 1int(11) range
n Nchar(1) values
size 100int(10) unsigned range
type clonevarchar(255) values
bridge yesvarchar(255) values

Sample Rows
 
binchromchromStartchromEndixnsizetypebridge
748chr2L21485538214856381N100cloneyes
756chr2L22420241224203412N100cloneyes
585chr2R436844683N100cloneyes
585chr2R24426245264N100cloneyes
588chr2R4168844228845N6000cloneyes
590chr2R7489317490316N100cloneyes
596chr2R147235014724507N100cloneyes
598chr2R182618318262838N100cloneyes
613chr2R375956737596679N100cloneyes
743chr2R207807072078080710N100cloneyes

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 Aug. 2014 D. melanogaster 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:

  • other - gaps added at UCSC to annotate strings of Ns that were not marked in the AGP file (count: 572; size range: 10 - 53,860 bases)