Schema for liftOver & ReMap - UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg38
  Database: hg19    Primary Table: liftOverHg38    Row Count: 1,278   Data last updated: 2019-12-16
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 20851231461double 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
020851231461chr124925062110000249240621chr1248956422+100002489464222
5862512chr1249250621177376177417chr1958617616+2428232428641031
7314571217chr1249250621317719471368chr1248956422-248454805248608454495
59750767chr124925062115828611584456chr1248956422+171465517162461032141
68213696chr12492506211282216212822307chr1248956422+12762227127623725498870
102527822chr12492506211300139213684890chr1248956422-235696198236176247240
68415264chr12492506211302799413037141chr1_KI270766v1_alt256271+10979201191953
8523706chr12492506211303063613330101chr1_KI270766v1_alt256271-81803236181392
6844819chr12492506211304612413049666chr1248956422-2356249082356310993340
6847217chr12492506211310299813103076chr1248956422+1293283812932916883954

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.