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K. Maclaine 06_04_2021
The mtDNA mutation spectrum in the PolG mutator mouse reveals germline and somatic selection; Maclaine, Kendra D, Stebbings, Kevin A, Havird, Justin C

Readme file for the output files from “KM_2021_BCFtoCSV”:
Additional Files 3-6
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"old_animal": old name for animal in Maclaine et. al 2020. 
"Animal": new animal name, a-n. 
"tissue": Brain or Liver
"sample_name": Animal+Tissue ex "AL" animal A, Liver 
"ref_num": number in reference genome 
"ref": reference base 
"mut_freq": mutation frequeny as given by the bcf file 
"ref_allele_count": reference allele count as given by the bcf file from mutect output
"mut_allele_count": mutation allele count as given by the bcf file from mutect output
"mutated_base": what base the reference was mutated to 
"som_germ":"somatic" or "germline", germline if the mutation was found in both tissues, else somatic.
"gene": particular CDS gene/rRNA/tRNA/D-loop that the mutation was in, else given NA 
"coding_non": CDS/rRNA/tRNA/D-loop
"surrounding": gives the bases that surround the mutation
"mut_freq_div_gene_len": mutation frequency divided by the gene length 
"mut_freq_div_len": mutation frequency divided by the length of the CDS/tRNA/rRNA/D-loop region
"count_div_gene_len": mutation count divided by the gene length 
"count_div_len": mutation count divided by the length of the CDS/tRNA/rRNA/D-loop region
"amino_start": for CDS regions, gives the starting amino acid 
"amino_start_group": for CDS regions, gives the starting amino acid group
"amino_mut": for CDS regions, gives the amino acid the reference was mutated to
"amino_mut_group":for CDS regions, gives amino acid group of amino_mut
"mut_type":silent/missense/nonsense 
"conserve_non":conservative (mutation did not change group) or radical (mutation changed group)

The column names for the indel mutation excel are as follows: 
"old_animal": old name for animal in Maclaine et. al 2020. 
"Animal": new animal name, a-n. 
"tissue": Brain or Liver
"sample_name": Animal+Tissue ex "AL" animal A, Liver 
"ref_num": number in reference genome 
"ref": reference base(s)
"mut_freq": mutation frequeny as given by the bcf file 
"ref_allele_count": reference allele count as given by the bcf file from mutect output
"mut_allele_count": mutation allele count as given by the bcf file from mutect output
"mutated_base": what base(s) the reference was mutated to 
"som_germ": "somatic" or "germline" 
"i_d": insertion or deletion 
"frame":frameshift or not 
"gene": particular CDS gene/rRNA/tRNA/D-loop that the mutation was in, else given NA 
"coding_non": CDS/rRNA/tRNA/D-loop
"mut_freq_div_gene_len": mutation frequency divided by the gene length 
"mut_freq_div_len": mutation frequency divided by the length of the CDS/tRNA/rRNA/D-loop region
"count_div_gene_len": mutation count divided by the gene length 
"count_div_len": mutation count divided by the length of the CDS/tRNA/rRNA/D-loop region
"Change": number of bases the indel added or deleted