Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DeugGB2 Primary Table: RepeatModeler_LTR Data last updated: 2014-11-20
Big Bed File: /gbdb/DeugGB2/bbi/DeugGB2_LTR.bb
Item Count: 28,580
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFPQ02000031	Genomic sequence name
`chromStart`	37585	Start in genomic sequence
`chromEnd`	37655	End in genomic sequence
`name`	rnd-1_family-379	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	422	Smith Waterman alignment score
`milliDiv`	12.9	Base mismatches in parts per thousand
`milliDel`	4.3	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-8854	-#bases after match in genomic sequence
`repClass`	LTR	Class of repeat
`repFamily`	Pao	Family of repeat
`repStart`	1	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	73	End in repeat sequence
`repLeft`	-133	-#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
AFPQ02000031	37585	37655	rnd-1_family-379	+	422	12.9	4.3	0.0	-8854	LTR	Pao	1	73	-133
AFPQ02000031	37707	37829	rnd-5_family-34	-	251	25.2	9.0	2.3	-8680	LTR	Pao	-1551	156	27
AFPQ02000031	37920	37955	rnd-1_family-379	+	233	5.7	5.7	0.0	-8554	LTR	Pao	69	105	-101
AFPQ02000031	37950	38169	rnd-1_family-322	-	1258	12.3	18.7	0.0	-8340	LTR	Pao	-78	260	1
AFPQ02000031	38151	38200	rnd-1_family-532	+	306	14.3	0.0	0.0	-8309	LTR	Pao	4	52	-29
AFPQ02000031	38193	38376	rnd-1_family-329	-	1099	12.1	13.1	1.0	-8133	LTR	Pao	-134	248	44
AFPQ02000031	38684	38773	rnd-1_family-485	+	487	14.6	14.6	0.0	-7736	LTR	Pao	131	232	0
AFPQ02000031	38773	38803	rnd-1_family-350	-	564	15.1	8.6	0.0	-7706	LTR	Pao	-83	181	144
AFPQ02000031	38829	38928	rnd-1_family-405	-	613	18.2	0.0	0.0	-7581	LTR	Pao	-1	210	112
AFPQ02000031	38937	39384	rnd-1_family-135	+	2942	9.7	9.6	0.6	-7125	LTR	Pao	2	488	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