Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust

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Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust

Database: DkikGB2 Primary Table: windowmaskerSdust Row Count: 1,051,516

field	example	SQL type
`bin`	585	`smallint(5) unsigned`
`chrom`	AFFH02000003	`varchar(255)`
`chromStart`	23	`int(10) unsigned`
`chromEnd`	57	`int(10) unsigned`

Sample Rows

bin	chrom	chromStart	chromEnd
585	AFFH02000003	23	57
585	AFFH02000003	285	305
585	AFFH02000003	426	450
585	AFFH02000003	453	496
585	AFFH02000003	589	612
585	AFFH02000003	649	667
585	AFFH02000003	740	757
585	AFFH02000003	825	852
585	AFFH02000003	934	953
585	AFFH02000003	1020	1051

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

WM + SDust (windowmaskerSdust) Track Description


	Description This track depicts masked sequence as determined by WindowMasker. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site. Methods To create this track, WindowMasker was run with the following parameters: windowmasker -mk_counts true -input DkikGB2.fa -output wm_counts windowmasker -ustat wm_counts -sdust true -input DkikGB2.fa -output repeats.bed The repeats.bed (BED3) file was loaded into the "windowmaskerSdust" table for this track. References Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941