Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DeugGB2 Primary Table: RepeatModeler_RC Data last updated: 2014-11-20
Big Bed File: /gbdb/DeugGB2/bbi/DeugGB2_RC.bb
Item Count: 7,255
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFPQ02000031	Genomic sequence name
`chromStart`	9066	Start in genomic sequence
`chromEnd`	9128	End in genomic sequence
`name`	rnd-3_family-30	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	395	Smith Waterman alignment score
`milliDiv`	16.1	Base mismatches in parts per thousand
`milliDel`	0.0	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-37381	-#bases after match in genomic sequence
`repClass`	RC	Class of repeat
`repFamily`	Helitron	Family of repeat
`repStart`	681	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	742	End in repeat sequence
`repLeft`	-416	-#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	9066	9128	rnd-3_family-30	+	395	16.1	0.0	0.0	-37381	RC	Helitron	681	742	-416
AFPQ02000031	15721	16792	rnd-3_family-30	-	8427	5.1	0.0	4.3	-29717	RC	Helitron	0	1158	132
AFPQ02000031	19968	20081	rnd-2_family-9	-	405	23.9	0.9	3.6	-26428	RC	Helitron	-238	628	519
AFPQ02000031	20380	20461	rnd-5_family-1652	+	283	20.8	1.2	5.1	-26048	RC	Helitron	783	860	-1074
AFPQ02000031	20545	21148	rnd-3_family-30	+	3109	16.4	1.7	3.7	-25361	RC	Helitron	192	782	-376
AFPQ02000031	22574	22659	rnd-1_family-27	+	284	24.7	4.7	0.0	-23850	RC	Helitron	27	115	-5
AFPQ02000031	22673	22957	rnd-3_family-30	-	899	21.4	4.3	5.9	-23552	RC	Helitron	-146	1012	818
AFPQ02000031	24225	24592	rnd-3_family-30	+	2650	18.9	6.2	1.4	-21917	RC	Helitron	148	819	-339
AFPQ02000031	24877	24915	rnd-3_family-30	+	2650	18.9	6.2	1.4	-21594	RC	Helitron	820	892	-266
AFPQ02000031	25246	25528	rnd-3_family-30	-	1409	13.6	21.3	0.9	-20981	RC	Helitron	-304	854	516

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