Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DsuzGB1 Primary Table: RepeatModeler_RC Data last updated: 2014-11-20
Big Bed File: /gbdb/DsuzGB1/bbi/DsuzGB1_RC.bb
Item Count: 27,237
Format description: RepeatMasker .out record

field	example	description
`chrom`	AWUT01012676	Genomic sequence name
`chromStart`	60542	Start in genomic sequence
`chromEnd`	60866	End in genomic sequence
`name`	rnd-1_family-0	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	1806	Smith Waterman alignment score
`milliDiv`	6.9	Base mismatches in parts per thousand
`milliDel`	7.0	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-33729	-#bases after match in genomic sequence
`repClass`	RC	Class of repeat
`repFamily`	Helitron	Family of repeat
`repStart`	-448	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	2857	End in repeat sequence
`repLeft`	2572	-#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
AWUT01012676	60542	60866	rnd-1_family-0	-	1806	6.9	7.0	0.0	-33729	RC	Helitron	-448	2857	2572
AWUT01012676	60611	60911	rnd-5_family-1004	+	1556	14.5	8.7	0.9	-33684	RC	Helitron	43	365	-518
AWUT01012676	60884	60943	rnd-6_family-168	-	426	8.5	0.0	0.0	-33652	RC	Helitron	-519	591	533
AWUT01012676	60972	61124	rnd-3_family-79	+	455	12.7	9.2	7.1	-33471	RC	Helitron	281	435	-420
AWUT01012676	60999	61383	rnd-5_family-1233	-	1603	13.8	6.4	1.1	-33212	RC	Helitron	-1153	1074	485
AWUT01012676	71769	71962	rnd-1_family-0	-	1456	6.2	0.0	0.0	-22633	RC	Helitron	-457	2848	2656
AWUT01012676	73336	73499	rnd-1_family-0	-	853	8.1	0.3	1.2	-21096	RC	Helitron	-450	2855	2734
AWUT01012676	73384	73612	rnd-6_family-976	+	721	21.7	18.4	1.1	-20983	RC	Helitron	53	319	-158
AWUT01012676	73494	73726	rnd-4_family-53	-	1762	3.5	9.5	0.0	-20869	RC	Helitron	-314	462	209
AWUT01012676	75858	75929	rnd-5_family-1233	-	397	14.1	2.8	0.0	-18666	RC	Helitron	-1348	879	807

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