Schema for Assembly - Assembly from Fragments
  Database: dm6    Primary Table: gold    Row Count: 1,870
fieldexampleSQL type info
bin 1smallint(6) range
chrom chr2Lvarchar(255) values
chromStart 0int(10) unsigned range
chromEnd 23513712int(10) unsigned range
ix 1int(11) range
type Ochar(1) values
frag AE014134.6varchar(255) values
fragStart 0int(10) unsigned range
fragEnd 23513712int(10) unsigned range
strand +char(1) values

Sample Rows
 
binchromchromStartchromEndixtypefragfragStartfragEndstrand
1chr2L0235137121OAE014134.6023513712+
1chr2R0252869361OAE013599.5025286936+
1chr3L0281102271OAE014296.5028110227+
1chr3R0320793311OAE014297.3032079331+
9chr4013481311OAE014135.401348131+
585chrM0195241OKJ947872.2019524+
585chrUn_CP007071v10199561WCP007071.1019956+
585chrUn_CP007072v10444111WCP007072.1044411+
585chrUn_CP007073v10131571WCP007073.1013157+
585chrUn_CP007074v10762241WCP007074.1076224+

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

Assembly (gold) Track Description
 

Description

This track shows the sequences used 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 this assembly is from the AGP file delivered with the sequence. The NCBI document AGP Specification describes the format of the AGP file.

In dense mode, this track depicts the contigs that make up the currently viewed scaffold. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within a scaffold is always known; therefore, a line is drawn in the graphical display to bridge the blocks.

Component types found in this track (with counts of that type in parentheses):

  • W - whole genome shotgun (1,862)
  • O - other sequence (8)