Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DbipGB2 Primary Table: RepeatModeler_RC Data last updated: 2014-11-20
Big Bed File: /gbdb/DbipGB2/bbi/DbipGB2_RC.bb
Item Count: 6,481
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFE02000026	Genomic sequence name
`chromStart`	1796	Start in genomic sequence
`chromEnd`	2166	End in genomic sequence
`name`	rnd-5_family-3336	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	3056	Smith Waterman alignment score
`milliDiv`	5.3	Base mismatches in parts per thousand
`milliDel`	1.9	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-5959	-#bases after match in genomic sequence
`repClass`	RC	Class of repeat
`repFamily`	Helitron	Family of repeat
`repStart`	815	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	1191	End in repeat sequence
`repLeft`	0	-#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
AFFE02000026	1796	2166	rnd-5_family-3336	+	3056	5.3	1.9	0.0	-5959	RC	Helitron	815	1191	0
AFFE02000026	2139	2785	rnd-1_family-274	+	1497	17.5	0.0	0.1	-5340	RC	Helitron	1	223	0
AFFE02000026	2836	2961	rnd-5_family-2214	+	777	8.0	9.6	0.0	-5164	RC	Helitron	1	137	-309
AFFE02000026	2967	3018	rnd-1_family-594	+	445	2.0	0.0	0.0	-5107	RC	Helitron	1	51	-753
AFFE02000026	3036	3919	rnd-1_family-611	+	5145	4.0	2.5	0.2	-4206	RC	Helitron	1	804	0
AFFE02000026	3877	3986	rnd-1_family-648	-	849	6.4	0.9	0.0	-4139	RC	Helitron	0	404	295
AFFE02000026	3984	4075	rnd-1_family-648	-	652	6.6	1.1	0.0	-4050	RC	Helitron	-241	163	72
AFFE02000026	4559	4966	rnd-1_family-591	-	3227	3.7	10.1	0.0	-3159	RC	Helitron	-10	448	1
AFFE02000026	4989	5586	rnd-4_family-1406	-	4554	6.2	6.2	0.0	-2539	RC	Helitron	0	634	1
AFFE02000026	5587	5712	rnd-1_family-550	-	1004	6.3	0.8	0.0	-2413	RC	Helitron	-33	652	527

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