Percentage PMEN1 reference coding sequences identified identically within 104 pneumococcal genomes. Points represent independent pneumococcal isolates. Isolates representing CCs for which n ≥ 3 are labeled by CC. Isolates representing CCs for which n < 3 are labeled as 'Miscellaneous CCs'. Black line represents mean percentage identical coding sequences ± 2 standard deviations (gray lines). Isolates of interest are labeled: (1) CGSP14; (2) USA18; (3) CDC2088-04; (4) PMEN3; (5) CDC3059-06; and (6) 23F/4 (also see Additional file 4).