Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DsuzGB1 Primary Table: RepeatModeler_Retroelements Data last updated: 2014-11-20
Big Bed File: /gbdb/DsuzGB1/bbi/DsuzGB1_Retroelement.bb
Item Count: 1
Format description: RepeatMasker .out record

field	example	description
`chrom`	KI419312	Genomic sequence name
`chromStart`	82399	Start in genomic sequence
`chromEnd`	82494	End in genomic sequence
`name`	rnd-1_family-575	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	661	Smith Waterman alignment score
`milliDiv`	11.6	Base mismatches in parts per thousand
`milliDel`	1.1	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-150891	-#bases after match in genomic sequence
`repClass`	Retroelement	Class of repeat
`repFamily`	Retroelement	Family of repeat
`repStart`	1	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	96	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
KI419312	82399	82494	rnd-1_family-575	0	+	661	11.6	1.1	0.0	-150891	Retroelement	Retroelement	1	96	-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