I know of at least two coordinate systems in use for describing genomic positions. Does anyone know which system is used by Biomart (specifically, the biomaRt R package) when it returns genomic coordinates?
BioMart, whether web-based or via biomaRt is essentially an interface to Ensembl. Ensembl uses "1-based" coordinates. From their tutorial (scroll down to "Coordinates"):
Ensembl, and many other bioinformatics applications, use inclusive coordinates which start at 1. The first nucleotide of a DNA sequence is 1 and the first amino acid of a protein sequence is also 1. The length of a sequence is defined as end - start + 1.