For hotspot positions, sometimes an allele with zero coverage is reported in the Allele Coverage and Allele Ratio columns of the Analysis Results table.
This is by design and occurs only with hotspot positions. For hotspot positions, the Analysis Results table reports all alleles that have any evidence in either basespace or in flowspace. Alleles with zero coverage appear in the Analysis Results table for a hotspot position if the second alternate allele has nonzero reads reported in basespace (even though zero reads are reported in flowspace).
