Fast and accurate detection of genomic polymorphism is increasingly under demand, fuelled by many large genome projects. The software package ssahaSNP detects homozygous SNPs and insertion/deletion events on a eukaryotic genome scale from millions of shotgun reads. Matching seeds of a few kmer words are found to locate the position of the read on the genome. Full sequence alignment is then performed to detect base variations. Quality values of both variation bases and neighbouring bases are checked to exclude possible sequence base errors. To increase the accuracy of detection in some cases, it requires that the same mutation event is mapped by two or more shotgun reads.