Schema for LTRharvest - LTR Fragments Identified by LTRharvest

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Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DmojImproved Primary Table: ltrharvest_target_site_duplication Row Count: 4,067

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	543	`int(10) unsigned`	range
`chromEnd`	15519	`int(10) unsigned`	range
`name`	repeat_region1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	543	`int(10) unsigned`	range
`thickEnd`	15519	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	4,4	`longblob`
`chromStarts`	0,14972	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
585	improved_6498	543	15519	repeat_region1	1000	+	543	15519	0	2	4,4	0,14972
585	improved_6498	55754	59765	repeat_region2	1000	+	55754	59765	0	2	4,4	0,4007
585	improved_6498	74777	87479	repeat_region3	1000	+	74777	87479	0	2	4,4	0,12698
585	improved_6498	88504	99927	repeat_region4	1000	+	88504	99927	0	2	4,4	0,11419
585	improved_6498	101063	110695	repeat_region5	1000	+	101063	110695	0	2	5,5	0,9627
585	improved_6498	121038	123724	repeat_region6	1000	+	121038	123724	0	2	4,4	0,2682
586	improved_6498	138772	144834	repeat_region7	1000	+	138772	144834	0	2	4,4	0,6058
586	improved_6498	156886	171312	repeat_region8	1000	+	156886	171312	0	2	4,4	0,14422
586	improved_6498	176542	182382	repeat_region9	1000	+	176542	182382	0	2	5,5	0,5835
586	improved_6498	186672	191746	repeat_region10	1000	+	186672	191746	0	2	4,4	0,5070

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

LTRharvest (ltr_harvest) Track Description


	Description LTRharvest is used to identify putative long terminal repeats (LTR) retrotransposons in the D. mojavensis genome using the following parameters: -mintsd 4 -maxtsd 20 -minlenltr 100 -maxlenltr 1000 -mindistltr 1000 -maxdistltr 15000 Additional features within the LTR retrotransposons are annotated using LTRdigest. References D. Ellinghaus, S. Kurtz, and U. Willhoeft. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9:18, 2008. S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Research, 37(21):7002-7013 (2009).