Schema for Assembly - Assembly from Fragments
  Database: mm9    Primary Table: gold (chr1_gold)    Row Count: 1,486   Data last updated: 2007-07-19
Format description: How to get through chromosome based on fragments
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 9smallint(6) range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3000000int(10) unsigned range start position in chromosome
chromEnd 3223464int(10) unsigned range end position in chromosome
ix 2int(11) range ix of this fragment (useless)
type Fchar(1) values (W)GS contig, (P)redraft, (D)raft, (F)inished or (O)ther
frag AC157543.8varchar(255) values which fragment
fragStart 0int(10) unsigned range start position in frag
fragEnd 223464int(10) unsigned range end position in frag
strand -char(1) values + or - (orientation of fragment)

Sample Rows
 
binchromchromStartchromEndixtypefragfragStartfragEndstrand
9chr1300000032234642FAC157543.80223464-
76chr1322346433746453FAC157545.1246186197367+
76chr1337464535863164FAC157542.116211677+
76chr1358631637764725FAC102110.823576213732+
76chr1377647238683076FAC174931.2091835-
76chr1386830739906057FAC102154.90122298-
76chr1399060541232618FAC132914.70132656-
9chr1412326142679799FAC111099.1551261195979+
77chr14267979440065710FAC113280.120132678-
77chr14400657453860211FAC129937.838490176435+

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 draft assembly of the mouse genome. 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.

Clone Type Key:

  • W - Whole Genome Shotgun contig
  • F - Finished
  • A - In Active Finishing
  • D - Draft