Schema for Assembly - Assembly from Fragments
  Database: canFam3    Primary Table: gold    Row Count: 7,633   Data last updated: 2012-01-05
Format description: How to get through chromosome based on fragments
fieldexampleSQL type info description
bin 0smallint(6) range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 100int(10) unsigned range start position in chromosome
chromEnd 69553753int(10) unsigned range end position in chromosome
ix 2int(11) range ix of this fragment (useless)
type Wchar(1) values (W)GS contig, (P)redraft, (D)raft, (F)inished or (O)ther
frag JH373152.1varchar(255) values which fragment
fragStart 0int(10) unsigned range start position in frag
fragEnd 69553653int(10) unsigned range end position in frag
strand +char(1) values + 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 draft assembly (Sep. 2011, Broad CanFam3.1 (GCA_000002285.2)) of the dog genome. See also NCBI Assembly information: NCBI assembly/GCF_000002285.3 (Broad CanFam3.1) Whole-genome shotgun reads were assembled into contigs. When possible, contigs were grouped into scaffolds (also known as "supercontigs"). The order, orientation and gap sizes between contigs within a scaffold are based on paired-end read evidence.

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.

All components within this track are of fragment type "W": Whole Genome Shotgun contig. The mitochondrial sequence "chrM" is type "F" - finished.