Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DkikGB2 Primary Table: RepeatModeler_LINE Data last updated: 2014-11-20
Big Bed File: /gbdb/DkikGB2/bbi/DkikGB2_LINE.bb
Item Count: 16,352
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFH02000021	Genomic sequence name
`chromStart`	506	Start in genomic sequence
`chromEnd`	568	End in genomic sequence
`name`	rnd-5_family-536	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	398	Smith Waterman alignment score
`milliDiv`	5.1	Base mismatches in parts per thousand
`milliDel`	0.0	Bases deleted in parts per thousand
`milliIns`	5.1	Bases inserted in parts per thousand
`genoLeft`	-437	-#bases after match in genomic sequence
`repClass`	LINE	Class of repeat
`repFamily`	Jockey	Family of repeat
`repStart`	-50	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	335	End in repeat sequence
`repLeft`	277	-#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	506	568	rnd-5_family-536	0	-	398	5.1	0.0	5.1	-437	LINE	Jockey	-50	335	277
AFFH02000021	565	861	rnd-1_family-175	0	+	2450	6.1	0.0	0.3	-144	LINE	Jockey	480	774	-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