Alt Map Super-track Settings
GRCh38 Haplotype to Reference Sequence Mapping Correspondence Tracks   (All Mapping and Sequencing tracks)

Display mode:   

Alt Map  GRCh38 Alignments to the Alternate Sequences/Haplotypes
Haplotypes  GRCh38 Haplotype to Reference Sequence Mapping Correspondence


This track shows the locations of the alternate sequences and haplotypes defined by the Genome Reference Consortium (GRC) on the GRCh38 (hg38) reference sequence. The GRC generates multiple representations (haplotypes/alternate loci) for regions that are too complex to be represented by a single path.

Alt Map

The Alt Map track shows a PSL alignment of the data in the NCBI alternate sequence/haplotype mapping files to the reference sequence, allowing a side-by-side comparison of the two. Alignments are displayed in black and indicate gaps and insertions in the query and target sequences, depending on the track configuration settings. For information on interpreting the alignment display, see the reference pages on display conventions for PSL alignment tracks and alignment insertion/deletion display options.


Items in the Haplotype track, displayed in blue, show locations on the reference genome that correspond to the alternate sequence/haplotype regions. Click on an item to display a link to the corresponding position in the alternate sequence/haplotype (from the reference sequence) or to the corresponding reference sequence location (from the alternate sequence/haplotype).


The locations of the alternate sequence/haplotypes, which have been established by NCBI, are specified in the ALT_REF_LOCI_*/alt_scaffolds/alignments/*.gff files in the GRCh38 GenBank directory. The GRC used the NCBI Genomic Aligner (NG Aligner) to align the alternate loci specifically to the primary chromosomes on which their anchor sequence is found.

The NCBI GFF/cigar annotation files were converted to PSL format with the kent command line program, gff3ToPsl.


For general information about the genome assembly process, see the overview of genome assembly procedures on the NCBI website. NCBI also provides specific information about the hg38 assembly.