Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DbipGB2 Primary Table: RepeatModeler_DNA Data last updated: 2014-11-20
Big Bed File: /gbdb/DbipGB2/bbi/DbipGB2_DNA.bb
Item Count: 25,155
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFE02000023	Genomic sequence name
`chromStart`	142	Start in genomic sequence
`chromEnd`	450	End in genomic sequence
`name`	rnd-5_family-7590	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	1863	Smith Waterman alignment score
`milliDiv`	12.3	Base mismatches in parts per thousand
`milliDel`	1.0	Bases deleted in parts per thousand
`milliIns`	0.8	Bases inserted in parts per thousand
`genoLeft`	-13753	-#bases after match in genomic sequence
`repClass`	DNA	Class of repeat
`repFamily`	DNA	Family of repeat
`repStart`	-290	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	1355	End in repeat sequence
`repLeft`	977	-#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
AFFE02000023	142	450	rnd-5_family-7590	0	-	1863	12.3	1.0	0.8	-13753	DNA	DNA	-290	1355	977
AFFE02000023	4345	5029	rnd-5_family-7590	0	-	4853	6.7	4.5	2.1	-9174	DNA	DNA	-930	715	16

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