Alt Haplotypes Track Settings
Reference Assembly Alternate Haplotype Sequence Alignments   (All Mapping and Sequencing tracks)

Display mode:      Duplicate track

Color track by bases: Help on base coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion

Display data as a density graph:

Display data as a rearrangement graph:
Data schema/format description and download
Assembly: Mouse Dec. 2011 (GRCm38/mm10)
Data last updated at UCSC: 2021-05-12

p14 Note: Includes annotations on GRCh38.p14 patch sequences


This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. Mismatching bases are highlighted in red. Several types of alignment gap may also be colored; for more information, see Alignment Insertion/Deletion Display Options.


The alignments were provided by NCBI as GFF files and translated into the PSL representation for browser display by UCSC.