Understanding the output of pileup2snp

Question

[e.rempel]

Hi,

I have a question regarding the output of the tool varscan pileup2snp. The input is the pileup file generated by samtools mpileup without reference. One particular line from the input is

1   16259813    N   80  G$g$aaGAGAaggaAGGaaGaGAgaAGaAgAAGGaAAAAAGAAaaGAaGgGgAGaGAGAgGggGAAAAgAAGgggAGGGAA^]G    BBCDigfDIHEHDgBJGDHDlkHcBJEJ]J/H?JiJmJIjJJFkJG^F?<JlFIJmJDJACJIEeJCJEJCDCHHHH>F@

So there are 80 reads covering this position, there is an N, since we don't have a reference. As I understand it, there are basically two nucleotides (G and A) found in this position. In the output there are these corresponding two lines

Chrom   Position    ... VarAllele
1       16259813    ...      A
1       16259813    ...      A

This is confusing to me, since I expect a G instead of the second A. Can anybody help me understand this issue? Thx.

The output file was generated by

varscan pileup2snp pileup.tsv --min-coverage 10 --min-base-qual 30 --output-vcf 1 > output.txt