Schema for RepeatModeler Classified - RepeatMasker using Classified RepeatModeler Repeat Library

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Schema for RepeatModeler Classified - RepeatMasker using Classified RepeatModeler Repeat Library

Database: DmojImproved Primary Table: RepeatModeler Row Count: 130,557

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	768	`int(10) unsigned`	range
`name`	DmojImproved_RpM_5_family-880	`varchar(255)`	values
`score`	4220	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	0	`int(10) unsigned`	range
`thickEnd`	768	`int(10) unsigned`	range
`itemRgb`	15095053	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	768	`longblob`
`chromStarts`	0	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	improved_6498	0	768	DmojImproved_RpM_5_family-880	4220	-	0	768	230,85,13	1	768	0
585	improved_6498	768	1209	DmojImproved_RpM_1_family-49	3862	+	768	1209	0,0,200	1	441	0
585	improved_6498	1234	4603	DmojImproved_RpM_1_family-33	30505	+	1234	4603	0,0,200	1	3369	0
585	improved_6498	4608	5704	DmojImproved_RpM_1_family-49	7167	+	4608	5704	0,0,200	1	1096	0
585	improved_6498	5700	8324	DmojImproved_RpM_1_family-33	23097	+	5700	8324	0,0,200	1	2624	0
585	improved_6498	8136	9317	DmojImproved_RpM_5_family-1774	9691	+	8136	9317	230,85,13	1	1181	0
585	improved_6498	9299	10322	DmojImproved_RpM_4_family-721	4419	-	9299	10322	230,85,13	1	1023	0
585	improved_6498	10463	13236	DmojImproved_RpM_1_family-33	24490	+	10463	13236	0,0,200	1	2773	0
585	improved_6498	13281	14660	DmojImproved_RpM_5_family-1774	9246	+	13281	14660	230,85,13	1	1379	0
585	improved_6498	14246	15073	DmojImproved_RpM_5_family-880	4530	-	14246	15073	230,85,13	1	827	0

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

RepeatModeler Classified (RepeatModeler) Track Description


	Description This track shows the transposon fragments identified by RepeatMasker using the species-specific RepeatModeler library constructed by the GEP. The consensus sequences produced by RepeatModeler were reclassified using the protocol described in the supplemental methods section. References Smit, AFA, Hubley, R. RepeatModeler Open-1.0. http://www.repeatmasker.org. 2008-2010. Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.