Schema for liftOver & ReMap - UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg38
  Database: hg19    Primary Table: chainHg38ReMapAxtChain    Row Count: 2,141   Data last updated: 2020-02-11
Format description: Summary info about a chain of alignments
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 0smallint(5) unsigned range Indexing field to speed chromosome range queries.
score 20790952225double range score of chain
tName chr1varchar(255) values Target sequence name
tSize 249250621int(10) unsigned range Target sequence size
tStart 10000int(10) unsigned range Alignment start position in target
tEnd 249240621int(10) unsigned range Alignment end position in target
qName chr1varchar(255) values Query sequence name
qSize 248956422int(10) unsigned range Query sequence size
qStrand +char(1) values Query strand
qStart 10000int(10) unsigned range Alignment start position in query
qEnd 248946422int(10) unsigned range Alignment end position in query
id 2int(10) unsigned range chain id

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
020790952225chr124925062110000249240621chr1248956422+100002489464222
5852510528chr12492506211029737148chr1248956422+180832207666958
5861444789chr1249250621139218154500chr9138394717-1164951317361125
7314571217chr1249250621317719471368chr1248956422-248454805248608454479
5871515440chr1249250621326096342202chr9138394717+1382782221382943301111
5881173745chr1249250621449273461786chrUn_KI270748v193321+80848933211188
589320976chr1249250621543121547935chrUn_KI270748v193321-22771269111531
591810846chr1249250621814800825076chr2064444167-35082013350922971284
591817498chr1249250621814800825076chr2064444167-34644391346546441282
59769256chr124925062116490941650080chr1248956422+165134516523391864

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

liftOver & ReMap (liftHg38) Track Description
 

Description

This track shows alignments from the hg19 to the hg38 genome assembly, used by the UCSC liftOver tool and NCBI's ReMap service, respectively.

Display Conventions and Configuration

The track has three subtracks, one for UCSC and two for NCBI alignments.

The alignments are shown as "chains" of alignable regions. The display is similar to the other chain tracks, see our chain display documentation for more information.

Data access

UCSC liftOver chain files for hg19 to hg38 can be obtained from a dedicated directory on our Download server. The NCBI chain file can be obtained from the MySQL tables directory on our download server, the filename is 'chainHg38ReMap.txt.gz'.

Both tables can also be explored interactively with the Table Browser or the Data Integrator.

Methods

ReMap 2.2 alignments were downloaded from the NCBI FTP site and converted with the UCSC kent command line tools. Like all data processing for the genome browser, the procedure is documented in our hg19 makeDoc file.

Credits

Thanks to NCBI for making the ReMap data available and to Angie Hinrichs for the file conversion.