Schema for Hg18 Diff - Contigs New to GRCh37/(hg19), Not Carried Forward from NCBI Build 36(hg18)
  Database: hg19    Primary Table: hg19ContigDiff    Row Count: 1,124   Data last updated: 2010-09-07
Format description: Browser extensible data
fieldexampleSQL type info description
bin 585smallint(5) unsigned 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
name AP006221.1varchar(255) values Name of item
score 500int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 10000int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 10615int(10) unsigned range End of where display should be thick (stop codon)
itemRgb 10715653int(10) unsigned range Used as itemRgb as of 2004-11-22

Connected Tables and Joining Fields
        hg19.gold.frag (via hg19ContigDiff.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
585chr11000010615AP006221.1500-1000010615163,130,5
73chr110615177417AL627309.15500+10615177417163,130,5
74chr115165501621653AL691432.541000+1516550162165328,206,40
74chr116216531730263AL031282.1500+16216531730263163,130,5
9chr120744862252409AL590822.371000+2074486225240928,206,40
75chr123802492532985AL139246.211000+2380249253298528,206,40
626chr154353605464633CR812477.100+54353605464633216,30,5
78chr154646335536678BX284671.5500+54646335536678163,130,5
86chr11381195413931542AL354712.191000+138119541393154228,206,40
86chr11393154214040428AL359771.27500+1393154214040428163,130,5

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Hg18 Diff (hg19ContigDiff) Track Description
 

Description

This track shows the differences between the GRCh37 (hg19) and previous NCBI Build 36 (hg18) human genome assemblies, indicating contigs (or portions of contigs) that are new to the hg19 assembly.

The following color/score key is used:

colorscorechange from hg18 to hg19
 0New contig added to hg19 to update sequence or fill gaps present in hg18
 500Different portions of this same contig used in the construction of hg19 and hg18 assemblies
 1000Updated version of an hg18 contig in which sequence errors have been corrected

Use the score filter to select which categories to show in the display.

Methods

The contig coordinates were extracted from the AGP files for both assemblies. Contigs that matched the same name, same version, and the same specific portion of sequence in both assemblies were considered identical between the two assemblies and were excluded from this data set. The remaining contigs are shown in this track.

Credits

The data and presentation of this track were prepared by Hiram Clawson, UCSC Genome Browser engineering.