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  Schema for Mouse Net - Mouse (July 2007/mm9) Alignment Net
  Database: bosTau4    Primary Table: netMm9    Row Count: 3,388,723
Format description: Database representation of a net of alignments.
fieldexampleSQL type description
bin 585smallint unsigned Indexing field to speed chromosome range queries.
level 1int unsigned Level of alignment
tName chr1varchar(255) Target chromosome
tStart 1716int unsigned Start on target
tEnd 2405int unsigned End on target
strand +char(1) Orientation of query. + or -
qName chr14varchar(255) Query chromosome
qStart 86551890int unsigned Start on query
qEnd 86552555int unsigned End on query
chainId 495396int unsigned Associated chain Id with alignment details
ali 656int unsigned Bases in gap-free alignments
score 18382double Score - a number proportional to 100x matching bases
qOver -1int Overlap with parent gap on query side. -1 for undefined
qFar -1int Distance from parent gap on query side. -1 for undefined
qDup 665int Bases with two or more copies in query. -1 for undefined
type topvarchar(255) Syntenic type: gap/top/syn/nonsyn/inv
tN 0int Unsequenced bases on target. -1 for undefined
qN 0int Unsequenced bases on query. -1 for undefined
tR 62int RepeatMasker bases on target. -1 for undefined
qR 21int RepeatMasker bases on query. -1 for undefined
tNewR -1int Lineage specific repeats on target. -1 for undefined
qNewR -1int Lineage specific repeats on query. -1 for undefined
tOldR -1int Bases of ancient repeats on target. -1 for undefined
qOldR -1int Bases of ancient repeats on query. -1 for undefined
tTrf 31int Bases of tandem repeats on target. -1 for undefined
qTrf 0int Bases of tandem repeats on query. -1 for undefined

  Connected Tables and Joining Fields
        bosTau4.chainMm9.id (via netMm9.chainId)
      bosTau4.chainMm9Link.chainId (via netMm9.chainId)

  Sample Rows

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

  Mouse Net (netMm9) Track Description


This track shows the best mouse/cow chain for every part of the cow genome. It is useful for finding orthologous regions and for studying genome rearrangement. The mouse sequence used in this annotation is from the July 2007 (mm9) assembly.

Display Conventions and Configuration

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.


Chains were derived from blastz 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.


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

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 program RepeatMasker.

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


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.

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.