130 Chapter 7 indicate position −42 (4470140) and −32 (4470150) are the lowest scoring positions on the consistency index concerning the promoter and attenuator region, respectively, 0.05882353 and 0.07142857 (see also Fig. S1). To access how extreme these values are, we calculated the consistency index for all SNP positions in the chromosome (see Fig. S2). All consistency indexes <1.0 are plotted in the outer ring (ring A) of Fig. 4. Results show that only 9640 out of 5056572 positions (0.19%) had a consistency index ≤0.07142857 (see Fig. 4, ring a, cut-off is indicated by a black circle). This clearly indicates that positions with low consistency indexes are rare, but not unique. Although these 9640 positions have a low consistency index, we do not yet know their relation to CTX resistance. Figure 3. WebLogo sequence logo with both bits and probability score for the promoter and the attenuator region. Consistency index and the minimum number of changes on the tree per position are represented in the bar charts below the sequence logos. Orange bars are positions containing SNPs that are tested for homoplasy. Blue bars are positions containing insertions that are tested for homoplasy.
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