Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DrhoGB2 Primary Table: RepeatModeler_LINE Data last updated: 2014-11-20
Big Bed File: /gbdb/DrhoGB2/bbi/DrhoGB2_LINE.bb
Item Count: 20,367
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFPP02000086	Genomic sequence name
`chromStart`	564	Start in genomic sequence
`chromEnd`	610	End in genomic sequence
`name`	rnd-5_family-11972	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	305	Smith Waterman alignment score
`milliDiv`	4.3	Base mismatches in parts per thousand
`milliDel`	0.0	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-406	-#bases after match in genomic sequence
`repClass`	LINE	Class of repeat
`repFamily`	Jockey	Family of repeat
`repStart`	-928	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	80	End in repeat sequence
`repLeft`	35	-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	swScore	milliDiv	milliDel	milliIns	genoLeft	repClass	repFamily	repStart	repEnd	repLeft
AFPP02000086	564	610	rnd-5_family-11972	0	-	305	4.3	0.0	0.0	-406	LINE	Jockey	-928	80	35

RepeatModeler (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.

Description

References