Schema for Assembly - Assembly from Fragments
  Database: mm10    Primary Table: gold    Row Count: 1,015   Data last updated: 2021-04-08
Format description: How to get through chromosome based on fragments
fieldexampleSQL type info description
bin 1smallint(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 22433268int(10) unsigned range end position in chromosome
ix 4int(11) range ix of this fragment (useless)
type Fchar(1) values (W)GS contig, (P)redraft, (D)raft, (F)inished or (O)ther
frag GL456083.2varchar(255) values which fragment
fragStart 0int(10) unsigned range start position in frag
fragEnd 19433268int(10) unsigned range end position in frag
strand +char(1) values + or - (orientation of fragment)

Sample Rows
 
binchromchromStartchromEndixtypefragfragStartfragEndstrand
1chr13000000224332684FGL456083.2019433268+
0chr122466510750555566FGL456084.2052589046+
2chr175121556853471038FGL456085.2010225547+
0chr18544710315611874310FGL456086.2070671640+
3chr115616874318299167912FGL456087.2026822936+
247chr118303809018345393114FGL456209.20415841+
3chr118350393119200177616FGL456088.208497845+
3chr119205177619537197118FGL456089.203320195+
9chr10310000075018765FGL456154.204401876+
1chr107576744578628077FGL456155.2050286063+

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 assembly (Dec. 2011, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) of the mouse genome. Whole-genome shotgun reads were assembled into contigs. When possible, contigs were assembled into chromosomes. The order, orientation and gap sizes between contigs within a chromosome are based on paired-end read evidence.

In dense mode, this track depicts the contigs that make up the currently viewed chromosome. 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. When the relative order and orientation of the contigs within a chromosome is known, a line is drawn in the graphical display to bridge the blocks.

Clone Type Key:

  • W - Whole Genome Shotgun contig
  • F - Finished
  • O - Other sequence (mitochondrial)