Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DkikGB2 Primary Table: RepeatModeler_DNA Data last updated: 2014-11-20
Big Bed File: /gbdb/DkikGB2/bbi/DkikGB2_DNA.bb
Item Count: 15,494
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFH02000003	Genomic sequence name
`chromStart`	0	Start in genomic sequence
`chromEnd`	357	End in genomic sequence
`name`	rnd-5_family-1471	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	2980	Smith Waterman alignment score
`milliDiv`	4.8	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`	-741	-#bases after match in genomic sequence
`repClass`	DNA	Class of repeat
`repFamily`	hAT	Family of repeat
`repStart`	283	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	639	End in repeat sequence
`repLeft`	0	-#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
AFFH02000003	0	357	rnd-5_family-1471	0	+	2980	4.8	0.0	0.0	-741	DNA	hAT	283	639	0
AFFH02000003	357	1079	rnd-5_family-1473	0	-	1947	25.4	6.2	4.8	-19	DNA	DNA	-58	1865	1134

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