Q: Haplotype genomes have no peak

[bigshark12345]

I got a plant genome, and I call peak with nine mixed chromosomes and two haplotype assembled chromosomes(x1x2),
But the x1x2 barely got a peak.
What I gave to the company was 10 mixed genomes, and when I compared the same data to the 10 mixed chromosomes, every chromosome had basically normal peaks
I wonder why? (Because of x1x2?)