Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DtakGB2 Primary Table: RepeatModeler_Unknown Data last updated: 2014-11-20
Big Bed File: /gbdb/DtakGB2/bbi/DtakGB2_Unknown.bb
Item Count: 88,632
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFI02000001	Genomic sequence name
`chromStart`	9622	Start in genomic sequence
`chromEnd`	10475	End in genomic sequence
`name`	rnd-1_family-199	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	6987	Smith Waterman alignment score
`milliDiv`	5.2	Base mismatches in parts per thousand
`milliDel`	0.3	Bases deleted in parts per thousand
`milliIns`	0.2	Bases inserted in parts per thousand
`genoLeft`	-9343	-#bases after match in genomic sequence
`repClass`	Unknown	Class of repeat
`repFamily`	Unknown	Family of repeat
`repStart`	0	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	841	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	9622	10475	rnd-1_family-199	-	6987	5.2	0.3	0.2	-9343	Unknown	Unknown	0	841	1
AFFI02000001	11353	11550	rnd-1_family-199	-	1342	8.6	16.8	0.0	-8268	Unknown	Unknown	0	841	612
AFFI02000001	11552	11690	rnd-5_family-2359	-	817	5.9	13.8	1.9	-8128	Unknown	Unknown	0	154	1
AFFI02000001	13481	13937	rnd-1_family-211	-	2538	14.6	5.5	0.6	-5881	Unknown	Unknown	-351	478	1
AFFI02000001	13934	14069	rnd-5_family-1817	+	1122	4.4	0.0	0.0	-5749	Unknown	Unknown	955	1089	0
AFFI02000001	14075	14546	rnd-3_family-31	-	2539	9.5	2.1	1.7	-5272	Unknown	Unknown	-1021	473	1
AFFI02000001	14543	14697	rnd-1_family-89	-	1114	9.7	0.7	0.0	-5121	Unknown	Unknown	-42	391	237
AFFI02000001	14694	15347	rnd-1_family-36	-	4093	10.3	0.8	0.0	-4471	Unknown	Unknown	-822	575	1
AFFI02000001	15321	15619	rnd-1_family-271	+	1625	11.5	7.0	6.7	-4199	Unknown	Unknown	221	519	-296
AFFI02000001	15617	15810	rnd-1_family-355	+	1241	10.5	0.0	1.1	-4008	Unknown	Unknown	157	347	-144

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