Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust
  Database: DgriCAF1    Primary Table: windowmaskerSdust    Row Count: 1,173,070   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom scaffold_0varchar(255)
chromStart 28int(10) unsigned
chromEnd 53int(10) unsigned

Sample Rows
 
binchromchromStartchromEnd
585scaffold_02853
585scaffold_017441770
585scaffold_019731994
585scaffold_020082029
585scaffold_021262146
585scaffold_022672347
585scaffold_023712389
585scaffold_024962515
585scaffold_025612582
585scaffold_026192641

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 DgriCAF1.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input DgriCAF1.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