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#NOTE: Save the excel file as Merged_QC.csv.
Homoplasmy
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– transition and transversion
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ratio.
VERY IMPORTANT STEP! It is highly recommended to have at least two people doing together the steps described in this section.
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- 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 value 1 (when you identify a transition) or add the value 2 (when you identify a transversion) type to the column Type_of_mutation.
- Next, take a side note of the total number of transitions and transversions you have into the column Type_of_mutation.
- 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.
- Calculate the percentage (%) of Calculate the percentage (%) of both transitions and transversions in comparison to the total of unique variants.
- Calculate transition/transversion rate ratio by dividing the percentage (%) of transitions by the percentage (%) of transversions.
Example:
Total number of homoplasmic variants: 1211
Total number of unique/bi-allelic variants: 335
Number of transitions in comparison to the total number of unique/bi-allelic variants: 325 (97,01%)
Number of transversions in comparison to the total number of unique/bi-allelic variants: 10 (2,99%)
Transitions/transversions ratio Ti/Tv: 32.44:1.
NOTE: The reference ratio of Ti/Tv for homoplasmic variants goes from 20:1 to 38:1.
Heteroplasmy - transition and transversion ratio.
- Copy the entire data from the heteroplasmy _only tab (from Merged_QC.csv file) and paste it into a new excel file. Next, follow all the steps described above for the "Homoplasmy - transition and tranversion ratio" analysis.
#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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