Variant sequences detected in the first experiment with pilE from N. gonorrhoeae MS11.

aThe average k-mer depth of the variant portion of the assembly divided by the average k-mer depth of same-sized regions immediately on either side of the variant sequence.bThe frequency in the presence of RecA divided by the frequency in the absence of RecA.cNot all silent loci in strain MS11 have been sequenced and annotated. The donor sequence could be one of these “missing” silent copies. Alternatively this allele may represent a mosaic sequence derived from multiple recombination events.