Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust
  Database: hs1    Primary Table: hub_567047_windowMasker Data last updated: 2022-02-06
Big Bed File Download: /gbdb/hs1/bbi/windowMasker.bb
Item Count: 16,163,340
The data is stored in the binary BigBed format.

Format description: Browser Extensible Data
fieldexampledescription
chromCP068254.1Reference sequence chromosome or scaffold
chromStart6715Start position in chromosome
chromEnd6739End position in chromosome

Sample Rows
 
chromchromStartchromEnd
CP068254.167156739
CP068254.168516888
CP068254.176527672
CP068254.178607883
CP068254.179067938
CP068254.180398059
CP068254.181718190
CP068254.189008907
CP068254.195299550
CP068254.198999920

WM + SDust (hub_567047_windowMasker) Track Description
 

Description

This track depicts masked sequence as determined by WindowMasker on the the 24 Jan 2022 Homo sapiens/GCA_009914755.4_T2T-CHM13v2.0/GCA_009914755.4 genome assembly. 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 GCA_009914755.4_T2T-CHM13v2.0.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCA_009914755.4_T2T-CHM13v2.0.unmasked.fa -output windowmasker.intervals
The windowmasker.sdust.bed included masking for areas of the assembly that are gap. The file was 'cleaned' to remove those areas of masking in gaps, leaving only the sequence masking. The final result covers 1,297,712,987 bases in the assembly size 3,117,292,070 for a percent coverage of % 41.63.

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