Schema for D. erecta (DereRS2) Net - D. erecta (Oct. 2018 (The University of Chicago/DereRS2)) Alignment Net
  Database: DereCAF1    Primary Table: netDereRS2    Row Count: 6,678   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
level 1int(10) unsigned range
tName scaffold_5035varchar(255) values
tStart 0int(10) unsigned range
tEnd 338int(10) unsigned range
strand -char(1) values
qName QMER02000005varchar(255) values
qStart 3776325int(10) unsigned range
qEnd 3776663int(10) unsigned range
chainId 293159int(10) unsigned range
ali 338int(10) unsigned range
score 29642double range
qOver -1int(11) range
qFar -1int(11) range
qDup 338int(11) range
type topvarchar(255) values
tN 0int(11) range
qN 0int(11) range
tR 0int(11) range
qR 0int(11) range
tNewR -1int(11) range
qNewR -1int(11) range
tOldR -1int(11) range
qOldR -1int(11) range
tTrf 0int(11) range
qTrf 175int(11) range

Sample Rows
 
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851scaffold_50350338-QMER020000053776325377666329315933829642-1-1338top0000-1-1-1-10175
5851scaffold_2645582-QMER020000163131887313246516114357754029-1-1578top00384422-1-1-1-100
5851scaffold_9500707+QMER020000017889887789059412791170766749-1-1707top0000-1-1-1-100
5851scaffold_49580718+QMER020000072188603218932112528471867966-1-1718top0097107-1-1-1-101
5851scaffold_49560728+QMER020000074146095414682212590172767685-1-1727top00413408-1-1-1-1411408
5851scaffold_5032353728+QMER020000053633005363338334786437523784-1-1378top0000-1-1-1-100
5851scaffold_48520753-QMER02000042523945314512448275168326-1-10top00309602-1-1-1-100
5851scaffold_49320770+QMER020000052118132211890212032877070342-1-1770top0000-1-1-1-1770770
5851scaffold_3020188+QMER02000001192520111925219748535618614586-1-1186top00680-1-1-1-140
5851scaffold_5610852-QMER0200002872610372695510176685280763-1-1852top00283732-1-1-1-100

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

D. erecta (DereRS2) Net (netDereRS2) Track Description
 

Description

This track shows the best D. erecta/D. erecta chain for every part of the D. erecta genome. It is useful for finding orthologous regions and for studying genome rearrangement. The D. erecta sequence used in this annotation is from the Oct. 2018 (The University of Chicago/DereRS2) (DereRS2) 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.

Methods

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.

Credits

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.

References

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-Mouse Alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).