Fig. 6.

Distribution of Corynebacterium non-reference allele abundances across ISS samples, at detected loci in each ISS sample. Sequence reads were mapped to the C. ihumii GD7 reference. All alleles meeting depth thresholds at variant positions were identified in each sample. The number of variants at each non-reference allele fraction bin is visualized as stacked histograms where color indicates the number of alleles present in the sample at that position; however, all variants in the largest fraction bin (0.9 < non-reference allele fraction ≤ 1.0) were mono-allelic and no variant had more than two present alleles within the sample. The histograms are analogous to non-reference allele frequency spectrums, where allele frequencies are estimated directly from read counts of present alleles