Schema for ReAS Repeats - RepeatMasker using ReAS Repeat Library

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Schema for ReAS Repeats - RepeatMasker using ReAS Repeat Library

Database: DmojImproved Primary Table: ReAS Row Count: 97,844

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	779	`int(10) unsigned`	range
`name`	DmojImproved_ReAS_327	`varchar(255)`	values
`score`	3707	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	0	`int(10) unsigned`	range
`thickEnd`	779	`int(10) unsigned`	range
`itemRgb`	15095053	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	779	`longblob`
`chromStarts`	0	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	improved_6498	0	779	DmojImproved_ReAS_327	3707	-	0	779	230,85,13	1	779	0
585	improved_6498	768	4561	DmojImproved_ReAS_45	16667	+	768	4561	230,85,13	2	441,3327	0,466
585	improved_6498	4538	4605	DmojImproved_ReAS_197	330	-	4538	4605	230,85,13	1	67	0
585	improved_6498	4608	9317	DmojImproved_ReAS_45	22731	+	4608	9317	230,85,13	1	4709	0
585	improved_6498	9306	10333	DmojImproved_ReAS_327	3653	-	9306	10333	230,85,13	1	1027	0
585	improved_6498	10322	14861	DmojImproved_ReAS_45	18232	+	10322	14861	230,85,13	2	2914,1580	0,2959
585	improved_6498	14225	15084	DmojImproved_ReAS_42	2623	-	14225	15084	230,85,13	1	859	0
585	improved_6498	15073	17517	DmojImproved_ReAS_45	21835	+	15073	17517	230,85,13	1	2444	0
585	improved_6498	47814	48960	DmojImproved_ReAS_95	4599	+	47814	48960	230,85,13	1	1146	0
585	improved_6498	49762	50508	DmojImproved_ReAS_505	4588	-	49762	50508	0,0,200	1	746	0

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

ReAS Repeats (ReAS) Track Description


	Description This track shows the transposon fragments identified by RepeatMasker using the ReAS library produced by the Drosophila 12 Genomes Consortium. References Li R, et al. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol. 2005 Sep;1(4):e43. Epub 2005 Sep 23. The species-specific ReAS transposon libraries (v2) are available for download at the FlyBase FTP site Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.