Schema for LiftOver & ReMap - UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg19
  Database: hg38    Primary Table: chainHg19ReMapAxtChain    Row Count: 2,115   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 248956422int(10) unsigned range Target sequence size
tStart 10000int(10) unsigned range Alignment start position in target
tEnd 248946422int(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 249240621int(10) unsigned range Alignment end position in query
id 2int(10) unsigned range chain id

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
020790952225chr124895642210000248946422chr1249250621+100002492406212
586316143chr1248956422177417180832chr1690354753-1632681666921517
5862510528chr1248956422180832207666chr1249250621+1029737148961
7314571217chr1248956422347968501617chr1249250621-248779253248932902478
588189818chr1248956422432812434869chrUn_gl000227128374+13866159151624
733244617chr1248956422501617535988chr1690354753-128910163252892
59769256chr124895642216513451652339chr1249250621+164909416500801838
75274678chr124895642227520412765339chr1249250621+261759126320871542
6142200194chr124895642239070193929978chr1_jh806574_fix22982+022959999
684666523chr12489564221300438413011666chr1249250621-2357746922357819621352

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.