Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DbipGB2 Primary Table: RepeatModeler_LINE Data last updated: 2014-11-20
Big Bed File: /gbdb/DbipGB2/bbi/DbipGB2_LINE.bb
Item Count: 26,176
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFE02000023	Genomic sequence name
`chromStart`	0	Start in genomic sequence
`chromEnd`	176	End in genomic sequence
`name`	rnd-1_family-12	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	1450	Smith Waterman alignment score
`milliDiv`	2.9	Base mismatches in parts per thousand
`milliDel`	1.1	Bases deleted in parts per thousand
`milliIns`	0.6	Bases inserted in parts per thousand
`genoLeft`	-14027	-#bases after match in genomic sequence
`repClass`	LINE	Class of repeat
`repFamily`	LINE	Family of repeat
`repStart`	-1724	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	177	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
AFFE02000023	0	176	rnd-1_family-12	-	1450	2.9	1.1	0.6	-14027	LINE	LINE	-1724	177	1
AFFE02000023	482	1708	rnd-5_family-49	+	8909	8.1	4.5	0.9	-12495	LINE	Jockey	40	1309	0
AFFE02000023	1763	2236	rnd-1_family-22	+	4163	1.5	2.3	0.0	-11967	LINE	Jockey	1396	1879	-200
AFFE02000023	2235	2558	rnd-1_family-13	-	2981	0.9	0.0	0.0	-11645	LINE	Jockey	-219	2508	2186
AFFE02000023	2569	4344	rnd-1_family-13	-	8304	4.9	8.5	0.3	-9859	LINE	Jockey	-742	1985	66
AFFE02000023	6537	8224	rnd-1_family-94	+	14209	2.9	2.3	0.3	-5979	LINE	Jockey	1	1721	-866
AFFE02000023	8205	9290	rnd-1_family-34	+	8780	3.4	5.4	1.0	-4913	LINE	Jockey	489	1621	-527
AFFE02000023	9275	10376	rnd-1_family-33	+	9062	4.7	2.8	0.3	-3827	LINE	Jockey	22	1134	0

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