# Why does Nucmer Genome alignment produce faulty Dot plot?

I am using Mummer v.3.23 to make a dot plot between two genomes of the same species. One genome was assembled using PacBio and one from Dovetail. None of them is chromosome-level assembly. One has 3578 contigs (Reference) and the other has ~12000 contigs (Query). I used nucmer option to make the genome alignment. The code was:

nucmer --mumreference -p Genome_alignment Ref.fasta Query.fasta


Then, I filtered the output delta file using the following command:

delta-filter -q -r Genome_alignment.delta > Delta.filter


Then, I used generated a weird-looking dot plot using the following command:

mummerplot --png Delta.filter -R Ref.fasta -Q Query.fasta --prefix=output


But the plot does not have any diagonal line and it looks very messy.

Can you please suggest how can I make a better dot plot with a diagonal line? What am I doing wrong here? Thank you.