# Mutations in known DNA sequence: which test to use?

I am analysing a double knockout (mouse), and trying to see whether restoring one or another of the genes it's missing affects specific positions preferentially in a third gene.

The data* looks like this: /non-DNA simplification below for the non-biologists/

Position    DoubleKO    DoubleKO+1    DoubleKO+2
Base:       A     G     A     G       A     G

1           1     2     3     4       5     6
2           7     8     9     10      11    12
...
N=~500      1     2     3     4       5     6


* counted on a per-position basis from multiple runs of Sanger sequencing - so not NGS, and the numbers are low

So the task is to find the position, or positions, (which ranges from 1 to 500) in which the ratio of G:A (bases, I'm only considering two, not all four in the DNA) is different in a statistically significant manner for

[(DoubleKO+1) vs (DoubleKO)] and [(DoubleKO+2) vs (DoubleKO)]


Note the following contrast is not of interest:

[(DoubleKO+1) + (DoubleKO+2)] vs (DoubleKO)


Questions:

1. Which statistical test or tests should I use?

2. How should I correct for multiple testing in this experiment?

1. Yes, NGS is more informative. This isn't technically feasible at the moment.
2. I can have a count for each of the bases (ATGC) + uncalled (N) at each point as well, and this encapsulates the universe of possibilities that "base" can be. So if we need to have this information, we do - but the main interest is these two bases - since they are chemically converted into each other, and can't become C or T in this context.
3. I have read the following other questions/links, and can't see quite how they should be applied to my problem:

FamilyStructure   JustMumAndDad           Mum+Dad+KidA         Mum+Dad+KidB