Relevant VarScan2 output fields are below (all other columns can be N/A): Reference allele (col 3) Variant IUPAC format (col 4) Variant Read Depth (cols 5,6) Allele frequency (expressed as percent) (col 7) P-value (col 12) Variant Read 1 +/- strand counts (cols 15,16) Variant Read 2 +/- strand counts (cols 17,18) Variant allele (col 19)