Examples of probable assembly errors in RefSeq bacterial genomes. (A) Salmonella enterica subsp. enerica (CP009768.1). (B) Desulfitobacterium hafniense Y51 (NC_007907.1). The diagrams show the GC skew (gray) and cumulative GC skew (green line) of the original (left) and the modified (right) versions of the genomes (all calculated with window size of 1000 bp, and slide size of 10 bp). The location and direction of repeat sequences leading to the abnormal GC skew are indicated by red arrows. After flipping the repeat-bounded sequences, the genomes show the pattern expected for genomes that undergo bidirectional replication (right). For more examples, see Supplemental Figures S6 and S7.