Schema for Combined Library - Repeats Identified by the Combined Repeat Library

Database: dm6 Primary Table: centroids Data last updated: 2015-12-14
Big Bed File: /gbdb/dm6/bbi/dm6_centroids.bb
Item Count: 67,519
Format description: Browser extensible data, with extended fields for detail page

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15683782	Start position in chromosome
`chromEnd`	15684440	End position in chromosome
`name`	QUASIMODO_LTR	Short Name of item
`score`	999	Score from 0-1000
`strand`	+	+ or -
`thickStart`	15683782	Start of where display should be thick (start codon)
`thickEnd`	15684440	End of where display should be thick (stop codon)
`reserved`	0,0,200	Used as itemRgb as of 2004-11-22
`repClass`	LTR	Repeat class
`swScore`	5661	SW score

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	repClass	swScore
chr2L	15683782	15684440	QUASIMODO_LTR	999	+	15683782	15684440	0,0,200	LTR	5661
chr2L	15684440	15686758	QUASIMODO_I-int	999	+	15684440	15686758	0,0,200	LTR	19652
chr2L	15686758	15687262	HOBO	999	-	15686758	15687262	128,0,0	DNA	4353
chr2L	15687260	15688164	HOBO	999	-	15687260	15688164	128,0,0	DNA	7959
chr2L	15690714	15690793	Helitron-1N1_DVir	981	-	15690714	15690793	230,85,13	RC	408
chr2L	15696342	15696423	DNAREP1_DM	979	+	15696342	15696423	230,85,13	RC	388
chr2L	15702714	15702767	Gypsy-22_DY-LTR	983	-	15702714	15702767	0,0,200	LTR	238
chr2L	15718779	15719437	QUASIMODO_LTR	999	+	15718779	15719437	0,0,200	LTR	5661
chr2L	15719437	15721755	QUASIMODO_I-int	999	+	15719437	15721755	0,0,200	LTR	19652
chr2L	15721755	15722259	HOBO	999	-	15721755	15722259	128,0,0	DNA	4353

Combined Library (centroids) Track Description


	Description This track shows the repeats identified by RepeatMasker using a combined Drosophila repeat library. The sequences in the combined repeat library were obtained from the following sources: Helentrons and HINE elements from Thomas J et al., 2014 Species-specific ReAS repeat library from the Drosophila 12 Genomes Consortium Drosophila transposons in the RepBase library Species-specific LTRharvest repeat library Species-specific RepeatModeler repeat library Species-specific dnaPipeTE repeat library Species-specific Tedna repeat library References Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (8 November 2007) Thomas J, Vadnagara K, Pritham EJ. DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons). Mob DNA. 2014 Jun 4;5:18. Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0. 2013-2015.

Description

References