The presence of nucleotide substitution bias in Nimblegen resequencing arrays has been previously described (15) . However, this knowledge has so far been used only to improve probe design. In this article, we propose a novel method that makes use of nucleotide substitution bias in the array to improve base-calling accuracy and call rate. The key idea is to build a likelihood model of the substitution bias among the probes of non-ambiguous calls on the array; then use this to call bases with ambiguous signals.