This track depicts masked sequence as determined by WindowMasker on the the 02 Jun 2014 Mycobacterium avium subsp. hominissuis A5/GCF_000696715.1_Maq_reference_guided_assembly/GCF_000696715.1 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 GCF_000696715.1_Maq_reference_guided_assembly.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCF_000696715.1_Maq_reference_guided_assembly.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 1,331,515 bases in the assembly size 4,870,506 for
a percent coverage of % 27.34.
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