Schema for Assembly - Assembly from Fragments
  Database: galVar1    Primary Table: gold    Row Count: 511,878   Data last updated: 2016-03-02
Format description: How to get through chromosome based on fragments
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(6) Indexing field to speed chromosome range queries.
chrom NW_007726111v1varchar(255) Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned start position in chromosome
chromEnd 1953int(10) unsigned end position in chromosome
ix 1int(11) ix of this fragment (useless)
type Wchar(1) (W)GS contig, (P)redraft, (D)raft, (F)inished or (O)ther
frag JMZW01000001.1varchar(255) which fragment
fragStart 0int(10) unsigned start position in frag
fragEnd 1953int(10) unsigned end position in frag
strand +char(1) + or - (orientation of fragment)

Sample Rows

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

Assembly (gold) Track Description


This track shows the sequences used in the Jun. 2014 malayan flying lemur 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 (511,877)
  • O - one other sequence (chrM/NC_004031.1)