Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts

I am getting different counts for the number of bases on reference covered by aligned reads using samtools depth/mpileup and BEDTools genomeCoverageBed commands. I am using samtools-0.1.19 and bedtools-2.17.0

samtools mpileup -ABQ0 -d10000000 -f ref.fas qry.bam > qry.mpileup
samtools depth -q0 -Q0 qry.bam > qry.depth

genomeCoverageBed -ibam qry.bam -g ref.genome -dz > qry.dz
wc -l qry.[dm]*
  1026779 qry.depth
  1027173 qry.dz
  1026779 qry.mpileup

Any ideas? Thanks