Figure 1

Fiftyfold coverage suffices for whole-genome assembly and detection of most sequence varients. (A) The N50 of the assembly, shown over a range of coverage depths (5x-250x), rapidly increases up to 50x coverage, and then plateaus. The median N50 of assemblies of five disjoint sets of reads at each depth of coverage is shown. (B) The number of SNPs detected increases rapidly up to 50x coverage, and gradually thereafter. (C) The number of insertions and deletions detected increases rapidly up to 20x coverage, and plateaus after 50x coverage. SNPs, insertions, and deletions in all isolates except for O395* are called relative to the N16961 genome [GenBank:AE003852, GenBank:AE003853]. For the O395* sample, due to the large number of differences (>20,000 SNPs) from the N16961 reference, SNPs, insertions, and deletions were identified instead against the Sanger-sequenced O395 reference [GenBank:CP000626, GenBank:CP000627].