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.
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
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,
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.