Q: Why peak region didn't appear with lower q-value than cut-off

[khsjh]

Use case
I run macs2 with below command per q-value cut-off 0.05, 0.1 and 0.5
macs2 callpeak -f BAMPE -g hs -n sample_ID -t sample_remove_duplicate_mito.bam --outdir ./peak --min-length 100 --q 0.1

Describe the problem
A clear and concise description of what happend.
When I visualize macs2 results (narrowPeak), some region is differ with q-value 0.05 and q-value 0.1 or 0.5.
Of course It is possible that some peaks couldn't be filtered strict cut-off 0.05. But in my case, that region was demonstrated that the q-value is lower that 0.0005 in narrowPeak file which was generated with q-value 0.1 and q-value 0.5.
Why this region didn't appeared with q-value 0.05 (default) option?

Describe the solution you tried
A clear and concise description of any solutions you've tried.
I use several options such as --nomodel, -B, --nolambda
But the specific region didn't appeared with q-value 0.05

Additional context
Add any other context or screenshots about your use case here.
The region that has problem is below
q-value 0.1
chr15 58203995 58204158 mHeart_RT1_DNA_peak_954 52 . 6.79179 10.0781 5.2493 42

q-value 0.5
chr15 58203994 58204167 mHeart_RT1_DNA_peak_7137 52 . 6.79179 10.0781 5.2493 43

q-value 0.05
The region didn't exist

The IGV screenshot that located in specific region is here.
There are bam coverage and bam file fragment information.

[martindemko]

Hi, I'm experiencing the same thing. Moreover, when I use some relaxed cutoff (let say 1 to get all peaks) to filter peaks down by myself, I'm getting a very different number of peaks compared to the using of the same cutoff directly in macs callpeak command. It scares me. Why is this happening, is there some logical explanation, please? Thanks