Schema for DGRP TE Insertions (ngs_te_mapper) (R5) - Transposon Insertions in DGRP Lines Identified by ngs_te

Schema for DGRP TE Insertions (ngs_te_mapper) (R5) - Transposon Insertions in DGRP Lines Identified by ngs_te_mapper (R5)

Database: dm6 Primary Table: dgrp_ngs_te_mapper Row Count: 8,024 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	9069	`int(10) unsigned`	range
`chromEnd`	9074	`int(10) unsigned`	range
`name`	Max-element_LTR_Pao	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	9069	`int(10) unsigned`	range
`thickEnd`	9074	`int(10) unsigned`	range
`itemRgb`	200	`int(10) unsigned`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb
585	chr2L	9069	9074	Max-element_LTR_Pao	1	+	9069	9074	0,0,200
585	chr2L	10294	10298	412_LTR_Gypsy	1	+	10294	10298	0,0,200
585	chr2L	16072	16079	1360_TIR_P	1	-	16072	16079	128,0,0
585	chr2L	16909	16911	pogo_TIR_Pogo	1	-	16909	16911	128,0,0
585	chr2L	46576	46581	roo_LTR_Pao	1	-	46576	46581	0,0,200
585	chr2L	61533	61537	mdg1_LTR_Gypsy	1	+	61533	61537	0,0,200
585	chr2L	91261	91265	opus_LTR_Gypsy	1	+	91261	91265	0,0,200
585	chr2L	115250	115254	gypsy_LTR_Gypsy	1	+	115250	115254	0,0,200
585	chr2L	126788	126790	pogo_TIR_Pogo	1	-	126788	126790	128,0,0
586	chr2L	219312	219314	pogo_TIR_Pogo	1	-	219312	219314	128,0,0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

DGRP TE Insertions (ngs_te_mapper) (R5) (dgrp_ngs_te_mapper) Track Description

Description

This track shows the locations of LTR retrotransposon and TIR DNA transposon insertions in 166 of the Drosophila melanogaster Genetic Reference Panel (DGRP) lines. The dataset corresponds to a modified version of Supplemental File S4 from the manuscript by Linheiro RS and Bergman CM, 2012. The file was obtained from the figshare web site. The coordinates of the insertion sites were lifted from the D. melanogaster release 5 assembly to the release 6 assembly.

The score field corresponds to the number of DGRP lines which have the transposon insertion. The color of the feature corresponds to its repeat class:

Repeat Class	Description	Color
TIR	Terminal Inverted Repeats (DNA Transposons)
LTR	Long Terminal Repeats (Retrotransposons)

References

Linheiro RS, Bergman CM. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS One. 2012;7(2):e30008.

Manee MM, Jackson J, Bergman CM. Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila. Genome Biol Evol. 2018 Jun 1;10(6):1533-1545.