Schema for Assembly - Assembly from Fragments
  Database: macEug2    Primary Table: gold    Row Count: 1,211,418   Data last updated: 2010-11-04
Format description: How to get through chromosome based on fragments
fieldexampleSQL type description
bin 585smallint(6) Indexing field to speed chromosome range queries.
chrom ABQO010000034varchar(255) Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned start position in chromosome
chromEnd 1085int(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 ABQO010000034.1varchar(255) which fragment
fragStart 0int(10) unsigned start position in frag
fragEnd 1085int(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 Sep. 2009 Macropus eugenii (Tammar Wallaby) draft assembly (NCBI project 12587 GCA_000004035.1) produced by the Tammar Wallaby Genome Sequencing Consortium. 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).