How do you find the number of SNPs per gene given a genotype and a map file?

Question

[eternalshadowrose]

Given one file: genotype.csv which has the nucleotides of SNPs (just assuming its the less represented nucleotide at this point) at different positions of a chromosome and another file which provides the range of nucleotides for the gene, how do you count the number of SNPs within all genes? The X6114, etc being the sample number.

I'm assuming that I will need to create a loop to find the major allele first for every row, and then make sure its above the starting position and below the ending position of a given gene.

Example files

[zx8754]

See this post:

• Assigning SNPs to gene names based on genomic coordinates