Correction for variants detected by self-alignment (Steps A and C).
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aSNVs detected by Mauve whole-genome alignment of the reference Rd and 86-028NP genomes.bAlleles shared between Rd-RR and NP-NN, due to introduction of MAP7 antibiotic resistance alleles.cAlleles shared between Rd-RR and NP-NN that are variant only in the Rd reference.dAlleles shared that were originally non-ACGT bases in the Rd reference.eAlleles found only in NP-NN.fAlleles in NP-NN that are MAP7-specific.gAlleles found only in Rd-RR.hFinal set of SNVs used for cross-validation (Table 5).
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2015-12-02



