1 November 2021
Jeffrey M. Kidd
University of Michigan

This directory contains a callable genome mask file calculated from 1,987 samples 
processed by the Dog10K Consortium.


Regions of the genome that are accessible by short read sequencing were identified from
the alignment of 1,987 samples. Positions that are ‘N’ in the genome reference, positions
where >=10% of aligned reads have a mapping quality (MQ) of 0, and regions where the total
coverage was more than 50% away from the median coverage were identified as failing the 
callability mask.  Cutoffs were determined separately for the autosomes and X-PAR region 
and the non-PAR segment of the X chromosome.

Cutoffs:
Region			Median	Low	High
Autosomes+X PAR	36634  		18317	54951
non-PAR X		27621		13810.5	41431.5
 
Regions that pass these criteria, and thus are amendable to analysis using short-read 
data, are reported in the file PASS.bed.  A total of 2,259,749,455 positions pass the 
above criteria.