Schema for LiftOver & ReMap - UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg19
  Database: hg38    Primary Table: chainHg19ReMap    Row Count: 5,315   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 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
score 15882668double range score of chain
tName chr1varchar(255) values Target sequence name
tSize 248956422int(10) unsigned range Target sequence size
tStart 10000int(10) unsigned range Alignment start position in target
tEnd 177417int(10) unsigned range Alignment end position in target
qName chr1varchar(255) values Query sequence name
qSize 249250621int(10) unsigned range Query sequence size
qStrand +char(1) values Query strand
qStart 10000int(10) unsigned range Alignment start position in query
qEnd 177417int(10) unsigned range Alignment end position in query
id 1int(10) unsigned range chain id

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
7315882668chr124895642210000177417chr1249250621+100001774171
586316143chr1248956422177417180832chr1690354753-1632681666922
5862510506chr1248956422180832207666chr1249250621+10297371483
733809466chr1248956422257666297968chr1249250621+2274172677194
7314571217chr1248956422347968501617chr1249250621-2487792532489329025
588189818chr1248956422432812434869chrUn_gl000227128374+13866159156
733244617chr1248956422501617535988chr1690354753-1289101632527
9102031194chr12489564225859881649185chr1249250621+52136815845518
59769256chr124895642216513451652339chr1249250621+164909416500809
9100879246chr124895642216531052702781chr1249250621+1584551263422010

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

LiftOver & ReMap (liftHg19) Track Description
 

Description

This track shows alignments from the hg38 to the hg19 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 'chainHg19ReMap.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. The UCSC tool chainSwap was used to swap target and query genome to show the mappings on the hg38 genome. 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.