Schema for Mouse Chain/Net - Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments
  Database: rheMac10    Primary Table: chainMm39    Row Count: 3,043,888   Data last updated: 2020-10-21
Format description: Summary info about a chain of alignments
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
score 118949double score of chain
tName chr1varchar(255) Target sequence name
tSize 223616942int(10) unsigned Target sequence size
tStart 8538int(10) unsigned Alignment start position in target
tEnd 26585int(10) unsigned Alignment end position in target
qName chr11varchar(255) Query sequence name
qSize 121973369int(10) unsigned Query sequence size
qStrand +char(1) Query strand
qStart 58120862int(10) unsigned Alignment start position in query
qEnd 58130511int(10) unsigned Alignment end position in query
id 4545int(10) unsigned chain id

Connected Tables and Joining Fields
        rheMac10.chainMm39Link.chainId (via chainMm39.id)
      rheMac10.netMm39.chainId (via chainMm39.id)

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
585118949chr1223616942853826585chr11121973369+58120862581305114545
5855204chr122361694291209209chr1195154279-970678397068722451973
58540256chr1223616942919110519chr13120883175+2160629121607601115151
58531420chr12236169424538446823chr11121973369+5813810158139409195102
5854796chr12236169425194352149chr3159745316-1525695181525697232562076
73896394chr122361694269946279655chr11121973369+5819661958357951343
5853534chr12236169427688276947chr1890720763+576137557614402924818
5853545chr12236169427688276946chr2181755017-1368660641368661282922235
5857314chr12236169428001080463chr1961420004-48671503486722501952778
5859931chr12236169428003180468chr9124359700-1023923051023926751492858

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Mouse Chain/Net (chainNetMm39) Track Description
 

Description

This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns.

Chain Track

The chain track shows alignments of mouse (Jun. 2020 (GRCm39/mm39)) to the rhesus genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and rhesus simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

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 mouse assembly or an insertion in the rhesus assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the rhesus genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.

In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.

Net Track

The net track shows the best mouse/rhesus chain for every part of the rhesus genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The mouse sequence used in this annotation is from the Jun. 2020 (GRCm39/mm39) assembly.

Display Conventions and Configuration

Chain Track

By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.

To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.

Net Track

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.

Methods

Chain track

Transposons that have been inserted since the mouse/rhesus split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single rhesus chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:

 ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain:
-linearGap=medium

tableSize    11
smallSize   111
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300

Net track

Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Credits

Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program.

The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.

The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent.

The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.

References

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961