Two false-positive SNPs in Y. pestis map to imperfect repeat regions. (Top row) CO92 reference and (bottom row) non-reference genome, with CO92 coordinates indicated below. Repeat units are colored in alternating blue and orange text. (Top panel) An 18 bp tandem repeat in Y. pestis La Paz; (bottom panel) 16 bp tandem repeat in Y. pestis 90A-4021. Bases that differ from the consensus sequence are underlined.