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#General Comments:
I was able to clone your repository.
It seems that your code is written outside the R code chunks. So I was not able to run it first. But I just copied the code into the chunk at it ran so perfectly. So I suggest to add your code to the chunk.

#Maize and Teosinte
The output files for this section are generated correctly. so you did well in the inspection and processing sections.

#Plots
Your plots are generated perfectly. But here is a suggestion: you can add unknown and multiple columns in your SNP Counts per Chromosome plot.