Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DbipGB2 Primary Table: RepeatModeler_Unknown Data last updated: 2014-11-20
Big Bed File: /gbdb/DbipGB2/bbi/DbipGB2_Unknown.bb
Item Count: 44,626
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFE02000007	Genomic sequence name
`chromStart`	0	Start in genomic sequence
`chromEnd`	310	End in genomic sequence
`name`	rnd-1_family-561	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	2458	Smith Waterman alignment score
`milliDiv`	2.6	Base mismatches in parts per thousand
`milliDel`	0.0	Bases deleted in parts per thousand
`milliIns`	0.7	Bases inserted in parts per thousand
`genoLeft`	-757	-#bases after match in genomic sequence
`repClass`	Unknown	Class of repeat
`repFamily`	Unknown	Family of repeat
`repStart`	49	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	356	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	strand	swScore	milliDiv	milliDel	milliIns	genoLeft	repClass	repFamily	repStart	repEnd	repLeft
AFFE02000007	0	310	rnd-1_family-561	+	2458	2.6	0.0	0.7	-757	Unknown	Unknown	49	356	0
AFFE02000007	313	952	rnd-5_family-817	-	2845	1.9	9.2	0.6	-115	Unknown	Unknown	0	694	1
AFFE02000007	953	1067	rnd-1_family-608	+	889	6.1	0.0	0.0	0	Unknown	Unknown	1	114	-179

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