Schema for LTR_Finder - LTR Fragments Identified by LTR

Schema for LTR_Finder - LTR Fragments Identified by LTR_Finder

Database: DmojImproved Primary Table: ltr_finder_ltr Row Count: 12,627

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	1237	`int(10) unsigned`	range
`chromEnd`	17504	`int(10) unsigned`	range
`name`	LTRfinder_ltr_1	`varchar(255)`	values
`score`	6	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	1237	`int(10) unsigned`	range
`thickEnd`	17504	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	1705,1677	`longblob`
`chromStarts`	0,14590	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	improved_6498	1237	17504	LTRfinder_ltr_1	6	-	1237	17504	2	1705,1677	0,14590
585	improved_6498	1237	13226	LTRfinder_ltr_0	6	+	1237	13226	2	2172,2150	0,9839
585	improved_6498	5392	15938	LTRfinder_ltr_3	6	-	5392	15938	2	806,851	0,9695
585	improved_6498	5392	13226	LTRfinder_ltr_2	6	+	5392	13226	2	2848,2890	0,4944
585	improved_6498	5709	13226	LTRfinder_ltr_4	6	+	5709	13226	2	2531,2528	0,4989
585	improved_6498	116222	124351	LTRfinder_ltr_5	6	-	116222	124351	2	443,443	0,7686
586	improved_6498	178775	191347	LTRfinder_ltr_6	6	-	178775	191347	2	129,129	0,12443
586	improved_6498	180010	188421	LTRfinder_ltr_7	7	-	180010	188421	2	962,962	0,7449
586	improved_6498	184851	204321	LTRfinder_ltr_8	6	-	184851	204321	2	389,389	0,19081
586	improved_6498	186326	191347	LTRfinder_ltr_9	6	-	186326	191347	2	129,129	0,4892

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

LTR_Finder (ltr_finder) Track Description


	Description LTR_Finder is used to identify putative LTR retrotransposons in the D. mojavensis genome. References Zhao Xu, Hao Wang LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research. 2007 July; 35(Web Server issue): W265-W268.

Description