Description

These tracks show the two types of patch sequences from the Genome Reference Consortium (GRC) patch releases:

Fix Patches

This track shows alignments of fix patch sequences to main chromosome sequences in the reference genome assembly. When errors are corrected in the reference genome assembly, the Genome Reference Consortium (GRC) adds fix patch sequences containing the corrected regions. This strikes a balance between providing the most complete and correct genome sequence, while maintaining stable chromosome coordinates for the original assembly sequences.

Fix patches are often associated with incident reports displayed in the GRC Incidents track.

Alt Haplotypes

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

Both tracks follow 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.

By default, the tracks are only visible when there are items in the view window. This can be disabled by the checkbox Hide empty subtracks.

Credits

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