Weird translocation results

[aminakur]

I ran MUM&Co to detect SV between two varieties of the same species. I observed multiple large translocations in the output (in addition to other smaller SVs). For example:

ref_chr query_chr       ref_start       ref_stop        size    SV_type query_start     query_stop      info
chr01   CM020633.1      1000    13862942        13861942        transloc        367     14309343        [chr08:5094415[
chr01   CM020633.1      1000    13862942        13861942        transloc        367     14309343        ]chr11:24521807]
chr01   CM020633.1	13875813        23593880        9718067 transloc        14309338        24284010        [chr08:7002249[
chr01   CM020633.1	13875813        23593880        9718067 transloc        14309338        24284010        ]chr10:20453007]
chr01   CM020633.1	23606808        35271472        11664664        transloc        24284030        35962660        [chr10:20468470[
chr01   CM020633.1	23606808        35271472        11664664        transloc        24284030        35962660        ]chr08:14766499]

The sizes of the translocations are 10-13 Mb. The chromosome sizes in this species are 31-43 Mb. I have visualized the nucmer alignment results as a dotplot and the chromosomes look collinear:

How would you interpret these results?

[SAMtoBAM]

Hi there
Could you share an SVG of the whole genome alignment?
What is within these regions
Just a simple guess, most likely these regions across the different chromosomes contain shared repeats and therefore MUM&Co is finding alignments that bridge these chromosomes and interpreting it as a translocation. Have you tried increasing the -minlen?