Schema for D. grimshawi Net - D. grimshawi (Apr. 2014 (GEP/DgriImproved)) Alignment Net

Database: dm3 Primary Table: netDgriImproved Row Count: 105,704

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	11215	`int(10) unsigned`	range
`tEnd`	152877	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	scaffold_15252	`varchar(255)`	values
`qStart`	17002063	`int(10) unsigned`	range
`qEnd`	17160374	`int(10) unsigned`	range
`chainId`	247	`int(10) unsigned`	range
`ali`	17520	`int(10) unsigned`	range
`score`	768052	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	0	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	8441	`int(11)`	range
`qR`	7852	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	460	`int(11)`	range
`qTrf`	1544	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
73	1	chr2L	11215	152877	-	scaffold_15252	17002063	17160374	247	17520	768052	-1	-1	0	top	8441	7852	-1	-1	-1	-1	460	1544
585	2	chr2L	11521	11770	-	scaffold_15252	17159716	17160066	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11923	12077	-	scaffold_15252	17159406	17159563	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13517	-	scaffold_15252	17158492	17158542	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	14098	14127	-	scaffold_15252	17157880	17157912	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	14883	14935	-	scaffold_15252	17157083	17157130	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15718	17050	-	scaffold_15252	17154147	17156300	0	0	0	-1	-1	-1	gap	90	0	-1	-1	-1	-1	0	0
585	2	chr2L	17141	104471	-	scaffold_15252	17058926	17154056	0	0	0	-1	-1	-1	gap	7560	3785	-1	-1	-1	-1	394	867
585	3	chr2L	22122	24965	+	scaffold_15203	11318992	11321751	1453	2234	91697	-1	-1	0	nonSyn	249	98	-1	-1	-1	-1	0	0
585	4	chr2L	22689	22737	+	scaffold_15203	11319562	11319628	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0

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

D. grimshawi Net (netDgriImproved) Track Description


	Description This track shows the best D. grimshawi/D. melanogaster chain for every part of the D. melanogaster genome. It is useful for finding orthologous regions and for studying genome rearrangement. The D. grimshawi sequence used in this annotation is from the Apr. 2014 (GEP/DgriImproved) (DgriImproved) 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).

Description

Display Conventions and Configuration

Methods

Credits

References