I propose to have three separate files with the following columns (plus additional columns inherent to pysamstats):
alt_count_acgt
geno_count_acgt
noise_percent_acgt
contributing_sites_acgt
alt_count_inc_deletions
geno_count_inc_deletions
noise_percent_inc_deletions
contributing_sites_inc_deletions
alt_count_inc_n
geno_count_inc_n
noise_percent_inc_n
contributing_sites_inc_n
C>A - geno_count, alt_count, noise, contributing_sites
C>G - geno_count, alt_count, noise, contributing_sites
C>T - geno_count, alt_count, noise, contributing_sites
T>A - geno_count, alt_count, noise, contributing_sites
T>C - geno_count, alt_count, noise, contributing_sites
T>G - geno_count, alt_count, noise, contributing_sites