Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DbiaGB2 Primary Table: RepeatModeler_DNA Data last updated: 2014-11-20
Big Bed File: /gbdb/DbiaGB2/bbi/DbiaGB2_DNA.bb
Item Count: 19,829
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFD02000007	Genomic sequence name
`chromStart`	17	Start in genomic sequence
`chromEnd`	140	End in genomic sequence
`name`	rnd-2_family-48	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	407	Smith Waterman alignment score
`milliDiv`	21.7	Base mismatches in parts per thousand
`milliDel`	4.1	Bases deleted in parts per thousand
`milliIns`	2.4	Bases inserted in parts per thousand
`genoLeft`	-2247	-#bases after match in genomic sequence
`repClass`	DNA	Class of repeat
`repFamily`	DNA	Family of repeat
`repStart`	-394	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	429	End in repeat sequence
`repLeft`	305	-#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
AFFD02000007	17	140	rnd-2_family-48	0	-	407	21.7	4.1	2.4	-2247	DNA	DNA	-394	429	305
AFFD02000007	1924	2196	rnd-2_family-48	0	-	670	26.2	4.0	4.4	-191	DNA	DNA	0	823	553

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