Schema for Hg19 Diff - Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19)
  Database: hg38    Primary Table: hg38ContigDiff    Row Count: 23,632   Data last updated: 2014-01-01
Format description: Browser extensible data
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 177417int(10) unsigned range Start position in chromosome
chromEnd 207666int(10) unsigned range End position in chromosome
name FO538757.3varchar(255) values Name of item
score 0int(10) unsigned range Optional score, nominal range 0-1000
strand +char(1) values + or -
thickStart 177417int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 207666int(10) unsigned range End of where display should be thick (stop codon)
itemRgb 14163461int(10) unsigned range Used as itemRgb as of 2004-11-22

Connected Tables and Joining Fields
        hg38.gold.frag (via hg38ContigDiff.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
586chr1177417207666FO538757.30+177417207666216,30,5
73chr1347968501617AL732372.15500-347968501617163,130,5
73chr1501617535988FO681485.20-501617535988216,30,5
73chr1697537835050AL669831.13500+697537835050163,130,5
591chr1835050835333KF495845.10-835050835333216,30,5
591chr1835333871977AL669831.13500+835333871977163,130,5
591chr1871977872551KF454898.10+871977872551216,30,5
591chr1872551877104AL669831.13500+872551877104163,130,5
594chr111918881261208AL162741.44500+11918881261208163,130,5
594chr112612081261666KF495840.10-12612081261666216,30,5

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

Hg19 Diff (hg38ContigDiff) Track Description
 

Description

This track shows the differences between the GRCh38 (hg38) and previous GRCh37 (hg19) human genome assemblies, indicating contigs (or portions of contigs) that are new to the hg38 assembly.

The following color/score key is used:

colorscorechange from hg19 to hg38
 0New contig added to hg38 to update sequence or fill gaps present in hg19
 500Different portions of this same contig used in the construction of hg38 and hg19 assemblies
 1000Updated version of an hg19 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.