Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust
  Database: hub_32_GCA_013030995.1    Primary Table: hub_32_windowMasker Data last updated: 2022-02-22
Big Bed File: https://hgdownload.soe.ucsc.edu/hubs/GCA/013/030/995/GCA_013030995.1/bbi/GCA_013030995.1_ASM1303099v1.windowMasker.bb
Item Count: 6,776,820
Format description: Browser Extensible Data
fieldexampledescription
chromWTSS01000001.1Reference sequence chromosome or scaffold
chromStart28591Start position in chromosome
chromEnd28624End position in chromosome

Sample Rows
 
chromchromStartchromEnd
WTSS01000001.12859128624
WTSS01000001.12868028712
WTSS01000001.12889228913
WTSS01000001.12896429022
WTSS01000001.12912729151
WTSS01000001.12931229330
WTSS01000001.12935229373
WTSS01000001.12938429418
WTSS01000001.12946829493
WTSS01000001.12960229695

WM + SDust (hub_32_windowMasker) Track Description
 

Description

This track depicts masked sequence as determined by WindowMasker on the the 11 May 2020 Anser cygnoides/GCA_013030995.1_ASM1303099v1/GCA_013030995.1 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.

Methods

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

windowmasker -mk_counts true -input GCA_013030995.1_ASM1303099v1.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCA_013030995.1_ASM1303099v1.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 236,080,587 bases in the assembly size 1,113,895,350 for a percent coverage of % 21.19.

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