Schema for Assembly - Assembly from Fragments
  Database: hg19    Primary Table: gold    Row Count: 28,665   Data last updated: 2020-02-20
Format description: How to get through chromosome based on fragments
fieldexampleSQL type info description
bin 585smallint(6) range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 10000int(10) unsigned range start position in chromosome
chromEnd 10615int(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 AP006221.1varchar(255) values which fragment
fragStart 36116int(10) unsigned range start position in frag
fragEnd 36731int(10) unsigned range end position in frag
strand -char(1) values + or - (orientation of fragment)

Connected Tables and Joining Fields
        hg19.fishClones.accNames (via gold.frag)
      hg19.hg19ContigDiff.name (via gold.frag)
      hg19.hg38ContigDiff.name (via gold.frag)
      hg19.seq.acc (via gold.frag)

Sample Rows
 
binchromchromStartchromEndixtypefragfragStartfragEndstrand
585chr110000106152FAP006221.13611636731-
73chr1106151774173FAL627309.15102166904+
73chr12274172677195FAP006222.1040302+
73chr13177194713687FAL732372.150153649+
73chr15213686329179FAC114498.20111549+
73chr163291781248410FAL669831.130179567+
73chr181248499828911FAL645608.30954186759+
9chr1998289112726812FAL390719.472000130979+
74chr11127268123742713FAL162741.442000112159+
74chr11237427131987214FAL139287.24200084445+

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 finished assembly of the human genome. This assembly merges contigs from overlapping drafts and finished clones into longer sequence contigs. The sequence contigs are ordered and oriented when possible by mRNA, EST, paired plasmid reads (from the SNP Consortium) and BAC end sequence pairs.

In dense mode, this track depicts the path through the draft and finished clones (aka the golden path) used to create the assembled sequence. Clone boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist in the path, spaces are shown between the gold and brown blocks. If the relative order and orientation of the contigs between the two blocks is known, a line is drawn to bridge the blocks.

Clone Type Key:

  • F - Finished (HTGS phase 3)
  • O - Other sequence (typically means no HTG keyword)
  • P - Pre draft
  • W - WGS contig

See also

NCBI discussion of genome assembly procedures.

Credits

The Feb. 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium.