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1. Copy the entire data from the homoplasmy_only tab (from Merged_QC.csv file) and paste it into a new excel file. Next, follow the steps described below.
2. First, name the 1^st tab as homoplasmic_variants. The first tab contains the total number of variants (number of rows). Take a side note of the total number of variants you have.
3. Create a 2^nd tab and call it as unique_homoplasmic_variants. Copy and paste the entire data from the 1st sheet 1^st tab into the 2nd 2^nd and exclude all the duplicate variants, this way you are going to keep only unique/bi-allelic variants. Take a side note of the number of unique variants you have at this step. 
4. Create a new column in the unique_homoplasmic_variants tab called Type_of_mutation. The Type_of_mutation column will show a number that indicates the type of substitution mutation which 1 will refer to a transition type and 2 to a transversion type. In transition, one purine is substituted for another purine or one pyrimidine is substituted for another pyrimidine (Transitions are: A>G, G>A, C>T or T>C). In transversion, a purine base is substituted for a pyrimidine base or vice versa (Transversions are: A>C, C>A, G>T, T>G, G>C or C>G). In figure 3, you can double-check the different types of substitution mutations.

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Figure 3 - Type of mutation 

1. Check out the columns Ref and Variant (columns D and E) and add the number 1 into the column Type every time that you identify a transition Next, take a side note of the total number of transitions you have into the column Type.
2. Check out the columns Ref and Variant (columns D and E) and add the number 2 into the column Type every time that you identify a transversion Next, take a side note of the total number of transversions you have into the column Type.
3. Calculate the percentage (%) of both transitions and transversions in comparison to the total of unique variants.
4. Calculate transition/transversion rate by dividing the percentage (%) of transitions by the percentage (%) of transversions.

#NOTE: Check out at the end of this section an example of how the excel file was organized in different sheets based on the QC steps (Figure 2).

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