Comparison of SNPs, insertions, and deletions called across sequencing technologies. (A) List of published sequences for the four previously sequenced isolates (N16961, O395, H1, and H2) examined in this study. (B) Comparison of new Illumina sequences to GenBank references. The number of differences identified in the new sequence relative to the GenBank reference is shown in the table, with the number of differences confirmed by alignment to additional strains shown in parentheses. (C) Comparison of Illumina-based and PacBio-based SNP, insertion, and deletion calls relative to the Sanger-sequenced N16961 reference [GenBank:AE003852, GenBank:AE003853]. The number of variants called in PacBio sequencing only (red circle), in Illumina sequencing only (blue circle), or in both (intersection) are shown. For the N16961 sequences, the number of differences confirmed by alignment to additional strains is shown in parentheses. For H1 and H2, only variants that do not correspond to likely errors in the N16961 reference sequence are counted.