Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust
  Database: DserGB1    Primary Table: windowmaskerSdust    Row Count: 1,113,448   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom MTTC01000001varchar(255)
chromStart 444int(10) unsigned
chromEnd 465int(10) unsigned

Sample Rows
 
binchromchromStartchromEnd
585MTTC01000001444465
585MTTC0100000129232930
585MTTC0100000171237130
585MTTC0100000176887710
585MTTC010000011022210242
585MTTC010000011026310293
585MTTC010000011328813307
585MTTC010000011353013548
585MTTC010000011397514056
585MTTC010000011406614121

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 DserGB1.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input DserGB1.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