Fig. 2.

Representing a reference sequence and a reference space for genomic alignment. (A) A hash table consists of an offset file of possible 12mers and a position file containing a sorted list of genomic positions for each 12mer. (B) SNPs in a genomic 12mer are represented by duplicating the position in the lists for all combinations of major and minor alleles within the 12mer. (C) Major alleles are represented in one compressed genome, while minor alleles are represented in another compressed genome.