Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust
  Database: wuhCor1    Primary Table: windowmaskerSdust    Row Count: 33   Data last updated: 2020-01-29
Format description: Browser extensible data
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom NC_045512v2varchar(255) values Reference sequence chromosome or scaffold
chromStart 1268int(10) unsigned range Start position in chromosome
chromEnd 1279int(10) unsigned range End position in chromosome
name NC_045512v2.1varchar(255) values Name of item

Sample Rows
 
binchromchromStartchromEndname
585NC_045512v212681279NC_045512v2.1
585NC_045512v213551367NC_045512v2.2
585NC_045512v217651777NC_045512v2.3
585NC_045512v222032215NC_045512v2.4
585NC_045512v230543065NC_045512v2.5
585NC_045512v230723084NC_045512v2.6
585NC_045512v236273638NC_045512v2.7
585NC_045512v253005311NC_045512v2.8
585NC_045512v262126225NC_045512v2.9
585NC_045512v262436254NC_045512v2.10

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 wuhCor1.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input wuhCor1.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