Schema for Hg38 Diff - Contigs Dropped or Changed from GRCh37(hg19) to GRCh38(hg38)
  Database: hg19    Primary Table: hg38ContigDiff    Row Count: 6,097   Data last updated: 2014-02-13
Format description: Browser extensible data
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 317719int(10) unsigned range Start position in chromosome
chromEnd 471368int(10) unsigned range End position in chromosome
name AL732372.15varchar(255) values Name of item
score 500int(10) unsigned range Optional score, nominal range 0-1000
strand +char(1) values + or -
thickStart 317719int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 471368int(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 hg38ContigDiff.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
73chr1317719471368AL732372.15500+317719471368163,130,5
73chr1632917812484AL669831.13500+632917812484163,130,5
74chr111272681237427AL162741.44500+11272681237427163,130,5
74chr112374271319872AL139287.24500+12374271319872163,130,5
595chr113265281392451AL391244.11500-13265281392451163,130,5
74chr115165501621653AL691432.54500+15165501621653163,130,5
74chr117302631893454AL109917.22500+17302631893454163,130,5
75chr126842202804248AL592464.24500+26842202804248163,130,5
75chr128042482909351AL589702.8500+28042482909351163,130,5
76chr132266603365232AL354743.33500+32266603365232163,130,5

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

Hg38 Diff (hg38ContigDiff) Track Description
 

Description

This track shows the differences between the GRCh37 (hg19) and GRCh38 (hg38) human genome assemblies, indicating hg19 contigs (or portions of contigs) that were not carried forward to the newer assembly.

The following color/score key is used:

item
color
item
score
type of change from hg19 to hg38
 0hg19 contig dropped in the construction of the hg38 assembly
 500Different portions of this same contig used in the construction of hg38 and hg19 assemblies
 1000Contig updated in hg38 to correct sequence errors present in hg19 version

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.