Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DrhoGB2 Primary Table: RepeatModeler_DNA Data last updated: 2014-11-20
Big Bed File: /gbdb/DrhoGB2/bbi/DrhoGB2_DNA.bb
Item Count: 16,656
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFPP02000091	Genomic sequence name
`chromStart`	595	Start in genomic sequence
`chromEnd`	1011	End in genomic sequence
`name`	rnd-2_family-83	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	3529	Smith Waterman alignment score
`milliDiv`	3.4	Base mismatches in parts per thousand
`milliDel`	1.9	Bases deleted in parts per thousand
`milliIns`	0.2	Bases inserted in parts per thousand
`genoLeft`	0	-#bases after match in genomic sequence
`repClass`	DNA	Class of repeat
`repFamily`	DNA	Family of repeat
`repStart`	1	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	423	End in repeat sequence
`repLeft`	-103	-#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
AFPP02000091	595	1011	rnd-2_family-83	0	+	3529	3.4	1.9	0.2	0	DNA	DNA	1	423	-103

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