This track depicts masked sequence as determined by WindowMasker on the the 26 Nov 2019 Sciurus vulgaris/GCA_902686455.1_mSciVul1.1/GCA_902686455.1 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.


To create this track, WindowMasker was run with the following parameters:

windowmasker -mk_counts true -input GCA_902686455.1_mSciVul1.1.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCA_902686455.1_mSciVul1.1.unmasked.fa -output windowmasker.intervals
perl -wpe 'if (s/^>lcl\|(.*)\n$//) { $chr = $1; } \
   if (/^(\d+) - (\d+)/) { \
   $s=$1; $e=$2+1; s/(\d+) - (\d+)/$chr\t$s\t$e/; 
   }' windowmasker.intervals > windowmasker.sdust.bed
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 906,609,938 bases in the assembly size 2,878,591,032 for a percent coverage of % 31.49.


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