Duplicate Mutations at the Same Chromosomal Position in VCF Outputs

[Prothama Manna]

Hello,

I am simulating a population bottleneck and have configured my code to output VCF files every ten generations. However, at several generations (for example, 193 and 203), I observe two distinct mutations occurring at the exact same chromosomal position—and this issue also appears in other generations. As I understand it, having two independent mutations at the same site in a haploid genome should not be possible.

Has anyone encountered this before or have any ideas about why it might be happening?

Thank you for your help.

Have a great rest of your day,

Best,

Pro

[Ben Haller]

Hi Prothama,

You can certainly have mutation A arise in one individual at position P, and mutation B arise in a different individual at position P, and have both alleles segregating in the population simultaneously.  Even within a single individual, mutation A could arise at position P and mutation B could arise later on the background of A (in the same individual, or in a descendant of it) and be stacked on top of it, unless mutation stacking is disabled in your model (which does not appear to be the case).  The screenshot you took of the VCF output doesn't let me see the calls for the mutations, so I can't say for sure which of those things might have happened in your simulation; probably both can happen.  The MULTIALLELIC tag emitted by SLiM is the indication that there is more than one mutation segregating at the same posiion; you can filter those sites out, if they cause trouble in your analysis.  Search the manual for "MULTIALLELIC" for more information, in several different sections.  Happy modeling!

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


Prothama Manna wrote on 6/3/25 10:28 AM:

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SLiM forward genetic simulation: http://messerlab.org/slim/
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