Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DtakGB2 Primary Table: RepeatModeler_LINE Data last updated: 2014-11-20
Big Bed File: /gbdb/DtakGB2/bbi/DtakGB2_LINE.bb
Item Count: 11,846
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFI02000001	Genomic sequence name
`chromStart`	11	Start in genomic sequence
`chromEnd`	1194	End in genomic sequence
`name`	rnd-5_family-3761	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	1289	Smith Waterman alignment score
`milliDiv`	29.0	Base mismatches in parts per thousand
`milliDel`	5.2	Bases deleted in parts per thousand
`milliIns`	6.7	Bases inserted in parts per thousand
`genoLeft`	-18624	-#bases after match in genomic sequence
`repClass`	LINE	Class of repeat
`repFamily`	LINE	Family of repeat
`repStart`	-191	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	1971	End in repeat sequence
`repLeft`	1	-#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
AFFI02000001	11	1194	rnd-5_family-3761	-	1289	29.0	5.2	6.7	-18624	LINE	LINE	-191	1971	1
AFFI02000001	1194	2079	rnd-5_family-1088	-	7443	4.1	0.3	1.8	-17739	LINE	LINE	0	1408	537
AFFI02000001	3275	3644	rnd-5_family-1088	-	3353	1.1	0.0	0.0	-16174	LINE	LINE	-871	537	169
AFFI02000001	4137	4279	rnd-5_family-1088	-	1155	1.3	13.3	0.0	-15539	LINE	LINE	-1246	162	1
AFFI02000001	11669	11743	rnd-5_family-1438	-	252	29.7	0.0	0.0	-8075	LINE	LINE	-77	276	203

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