Description

Patch release 9 is the ninth patch release for the GRCh38 assembly. Patch release 9 includes all contents that were in patch release 8. 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: 96
Patch scaffolds of type FIX: 48
Patch scaffolds of type NOVEL: 48

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 9 summary table

References

Data obtained from the Genome Reference Consortium:   FTP.