UCSC liftOver mm39 Track Settings
UCSC liftOver alignments to mm39   (All Mapping and Sequencing tracks)

Display mode:      Duplicate track

Color track based on chromosome:  on off

Filter by chromosome (e.g. chr10):

Display data as a density graph:

Display data as a rearrangement graph:
Data schema/format description and download
Data last updated at UCSC: 2023-03-07


This track shows the 'lift over' calculated alignments from the mm39/mouse to the mm10/mouse genome assembly, used by the UCSC liftOver tool.

Display Conventions and Configuration

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 mm39 to mm10 can be obtained from a dedicated directory on our download server mm10/liftOver directory. Specifically, the mm10ToMm39.over.chain.gz file.

The table can also be explored interactively with the Table Browser or the Data Integrator.


The lift over chain file is constructed with the doSameSpeciesLiftOver processing using the blat genome alignment program.