Flow Space Alternate Allele Calculation (FAO) calculation
Flow Space Alternate Allele Calculation (FAO) is calculated with the following formula.
AF: Allele frequency
AO: Alternate allele depth at position
RO: Reference allele depth at position
DP: Total depth at position
FAO: Flow space alternate allele depth at position
FRO: Flow space reference allele depth at position
FDP: Flow total depth at position
FAO is usually equal to AO; however, due to complex alleles and/or downsampling*, FAO may differ from AO.
AF = FAO / (FAO + FRO) and not FAO / FDP. This is because FDP may include reads that do not fit the flow space profile of any hypothesis; in such cases, FDP ≥ FAO + FRO and this is not used in allele frequency calculation.
*FAO along with all the F tags are subject to downsampling but AO/DP/RO/SAF/SAR/SRF/SRR are not. So when total coverage is higher than the downsampling cutoff, FAO tends to be smaller than AO.