Are coordinates 0-based?

[avershinina]

Hi,

I have a question about base coordinates and how they are used. On the example picture, a base with coordinate 554320 is G on a reference, C is alt allele. I would assume the program would show 554320-554321 coordinate for it. However, in the program output, this G has coordinate 554319 - 554320. Are these coordinates 0-based? Or am I missing something?

thanks in advance,
Alisa

[avershinina]

Answering to myself: they are. Looked up in the alignment. Nucleotide at coordinate 4 (according to samtools tview) has a coordinate 3-4 in piledriver output.