Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DkikGB2 Primary Table: RepeatModeler_Unknown Data last updated: 2014-11-20
Big Bed File: /gbdb/DkikGB2/bbi/DkikGB2_Unknown.bb
Item Count: 40,175
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFH02000009	Genomic sequence name
`chromStart`	0	Start in genomic sequence
`chromEnd`	78	End in genomic sequence
`name`	rnd-1_family-135	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	417	Smith Waterman alignment score
`milliDiv`	14.5	Base mismatches in parts per thousand
`milliDel`	2.6	Bases deleted in parts per thousand
`milliIns`	2.6	Bases inserted in parts per thousand
`genoLeft`	-1005	-#bases after match in genomic sequence
`repClass`	Unknown	Class of repeat
`repFamily`	Unknown	Family of repeat
`repStart`	1	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	78	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
AFFH02000009	0	78	rnd-1_family-135	0	+	417	14.5	2.6	2.6	-1005	Unknown	Unknown	1	78	0
AFFH02000009	983	1083	rnd-1_family-477	0	+	722	11.0	0.0	0.0	0	Unknown	Unknown	1	100	-59

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