Schema for LiftOver & ReMap - UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg19
  Database: hg38    Primary Table: liftOverHg19    Row Count: 25,374   Data last updated: 2020-01-03
Format description: Summary info about a chain of alignments
fieldexampleSQL type info description
bin 0smallint(5) unsigned range Indexing field to speed chromosome range queries.
score 20849626768double 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
020849626768chr124895642210000248946422chr1249250621+100002492406212
586296831chr1248956422177417180753chr1690354753-163268166613816
5863443chr1248956422180186180225chr11135006516+175914175959977
586167820chr1248956422180754196196chr15102531392-10099259012410
5864714chr1248956422180805180868chr7159138663+100411018823749811
5861166chr1248956422180868180894chr5180915260+11537115637666873
58636081chr1248956422180894187018chr1249250621+10231164962576
5864230chr1248956422181595181657chrY59373566-11914119764545
5862140909chr1248956422181797207666chr2243199373-1288396371288654931926
5862599chr1248956422186590186625chr1690354753+65754657894470

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.