Description
Patch release 11 is the eleventh patch release for the GRCh38 assembly.
Patch release 11 includes all contents that were in patch release 10.
This is a minor release of GRCh38 that does not disrupt the coordinate
system in the reference sequence GRCh38.
Total patch scaffolds in this patch release: 123
Patch scaffolds of type FIX: 64
Patch scaffolds of type NOVEL: 59
Haplotypes
Items in the Haplotype track show sequence variation present in the
population for certain sections of the genome. Items in this track were either
designated as alternate loci or novel patches by the GRC. To view the alternate
sequence, click on the "Fetch alternate sequence" link that appears on the sequence
details pages. Data points in this track are always displayed in
blue.
Patches
Items in the Patch track indicate areas of the sequence that have
been corrected by the GRC and will be updated to new sequence in the next full
human assembly release. To view the new, corrected sequence, click on the
"Fetch alternate sequence" link that appears on the sequence
details pages. Data points in this track are always displayed in
red.
Alignment
The Alignment track is the PSL representation of the Chain
track. This PSL representation allows the side-by-side alignment to be
viewed. It was created from the Chain track data using
the chainToPsl kent source utility. This track follows the display
conventions for
PSL alignment tracks. Alignments are displayed in black and,
depending on the track configuration settings, may be interspersed with
vertical orange lines.
Chain Track
The chain track shows the alignment of human genome alternate sequence to the
human Dec. 2013 (GRCh38/hg38) genome sequence using a gap scoring system that allows
longer gaps than traditional affine gap scoring systems. It can also
tolerate gaps in both human and the alternate sequence simultaneously.
Net Track
The net track shows the best human/alternate chain for every part of the alternate
sequence. It is useful for finding orthologous regions and for studying genome
rearrangement. The human sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) assembly.
In full display mode, the top-level (level 1) chains are the largest, highest-scoring
chains that span this region. In many cases, gaps exist in the top-level chain. When
possible, these are filled in by other chains that are displayed at level 2. The gaps in
level 2 chains may be filled by level 3 chains and so forth.
In the graphical display, the boxes represent ungapped alignments; the lines represent
gaps. Click on a box to view detailed information about the chain as a whole; click on a
line to display information about the gap. The detailed information is useful in determining
the cause of the gap or, for lower level chains, the genomic rearrangement.
Individual items in the display are categorized as one of four types (other than gap):
- Top - The best, longest match. Displayed on level 1.
- Syn - Line-ups on the same chromosome as the gap in the level above it.
- Inv - A line-up on the same chromosome as the gap above it, but in the opposite orientation.
- NonSyn - A match to a chromosome different from the gap in the level above.
Data points in this track are displayed according to the chromosome color key
that appears just below the Browser display (e.g., data points on
chromosome 21 appear in pink).
The chain track displays boxes joined together by either single or
double lines. The boxes represent aligning regions.
Single lines indicate gaps that are largely due to a deletion in the
human assembly or an insertion in the alternate sequence.
Double lines represent more complex gaps that involve substantial
sequence in both sequences.
Definitions
- Genome Patch: A sequence contig/scaffold that corrects sequence
in a major release of the genome, or adds sequence to it.
- FIX patch: A patch that corrects sequence or reduces an assembly gap
in a given major release. FIX patch sequences are meant to be
incorporated into the primary or existing alt-loci assembly units at
the next major release, and their accessions will then be
deprecated.
- NOVEL patch: A patch that adds sequence to a major release. Typically,
NOVEL patch sequences are meant to be incorporated into the assembly
as new alternate loci at the next major release, and their
accessions will not be deprecated (UCSC term: "new haplotype sequence").
Patch release 11 summary table
References
Data obtained from the
Genome Reference Consortium (GRC). For more information, please see the
GRC Introduction to Patches page, details for GRCh38.p11, and the
GRC p.11 FTP site for downloads.
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