Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DkikGB2 Primary Table: RepeatModeler_RC Data last updated: 2014-11-20
Big Bed File: /gbdb/DkikGB2/bbi/DkikGB2_RC.bb
Item Count: 14,295
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFH02000021	Genomic sequence name
`chromStart`	437	Start in genomic sequence
`chromEnd`	524	End in genomic sequence
`name`	rnd-1_family-144	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	601	Smith Waterman alignment score
`milliDiv`	10.3	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`	-481	-#bases after match in genomic sequence
`repClass`	RC	Class of repeat
`repFamily`	Helitron	Family of repeat
`repStart`	-504	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	89	End in repeat sequence
`repLeft`	3	-#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
AFFH02000021	437	524	rnd-1_family-144	0	-	601	10.3	0.0	0.0	-481	RC	Helitron	-504	89	3

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