Snp prediction accuracy is low in all difficult mapping areas

[oranges7]

Hi,
I use v3.1 stratification BED files,HG003 GUPPY3.6.0 data for testing, why the accuracy of snp and indel is not high，The results show that only 55%. I queried the results of Truth Challenge V2 and found that the accuracy of snp is more than 98%. What is the reason?
The default parameters I use

[oranges7]

Is this normal? I use bed files with high confidence regions, and the results are normal.
Looking forward to your reply