Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DbipGB2 Primary Table: RepeatModeler_Retroelements Data last updated: 2014-11-20
Big Bed File: /gbdb/DbipGB2/bbi/DbipGB2_Retroelement.bb
Item Count: 4,458
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFE02000023	Genomic sequence name
`chromStart`	5834	Start in genomic sequence
`chromEnd`	5869	End in genomic sequence
`name`	rnd-4_family-27	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	251	Smith Waterman alignment score
`milliDiv`	9.8	Base mismatches in parts per thousand
`milliDel`	4.9	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-8334	-#bases after match in genomic sequence
`repClass`	Retroelement	Class of repeat
`repFamily`	Retroelement	Family of repeat
`repStart`	305	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	341	End in repeat sequence
`repLeft`	-814	-#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
AFFE02000023	5834	5869	rnd-4_family-27	0	+	251	9.8	4.9	0.0	-8334	Retroelement	Retroelement	305	341	-814

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