Synteny plot of H. pylori strain B8 (top) vs. strain HPAG1 (bottom). The plot is based on pairwise blastn hits (blast version 2.2.21) with the following parameters: E-value: 10, minimum sequence identity: 80%, minimum bit score: 80. Red indicates homologous regions. Blue indicates inverted homologous regions. White indicates regions without homology in the other genome. The yellow arrow marks the PZ of strain B8. The graph was created by the Artemis Comparison tool. The synteny plots of strain B8 versus strains J99 and P12 can be found in Additional file 1, Figures S3 and Figure S4.