Fig. 1

Top left: A multiple alignment for a collection of alternate haplotypes (H1–H9), and a reference sequence (R). Marked bases are in bold and alternate alleles are colored. Middle left: The text T, formed by concatenating rows of the multiple alignment (eliding gaps). Bottom left: The edit table E, with alternate-allele coloring. Right: A partial illustration of the marker array in relation to \(\mathrm{\textsf{SA}}\), the relevant suffixes themselves (truncated to fit), and the \(\mathrm{\textsf{BWT}}\). Colors and bolding highlight where marked bases and alternate alleles end up in the suffixes