Added marker mutations are MULTIALLELIC and introgressed mutations have different MID

[Aubrey Baolong Pham]

Hi Ben,

I am trying to simulate Human and Archaic introgression, and using neutral marker mutations to detect the archaic introgression. The intention here is to be able to find what part of the human genome came from archaic ancestry and what came from human ancestry. 

I noticed in the SLiM output, that the mutations I'm manually added are 'MULTIALLELIC' and have different MID's. I'm not sure if this is the expected behavior or if there is a way to prevent this? I want to be able to add neutral mutations that are not 'MULTIALLEIC.'

Another strange behavior I have encountered is the marker mutations that introgressed into the Human population have different MID's compared to the Archaic individual I sampled from my population. For example, a marker mutation I added has MID 949383459 and 973788339 in my Archaic individual and 915586701 in my human file. I was wondering what could be causing the MID's to not match?

Below are screenshots of the code I'm using to add neutral mutations and an example of what I'm talking about. Also let me know if further details are needed.

Thanks,

Aubrey