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Ninety-eight mycobacterial isolates were grouped into 19 clusters with an overall clustering percentage of 58.3%.
The 123 strains showed great genetic diversity and a low clustering percentage.
Ninety-eight isolates were clustered into 19 strain groups with clustering percentage of 58.3%.
Missing data as a result of incomplete matching may have contributed to a slight underestimate of the observed clustering percentage and of the number of secondary cases per source case (18, 19).
Because no reliable estimates exist of the incidence and prevalence of MDR TB in Shandong Province, we do not know the percentage of MDR TB case-patients who were hospitalized in the study hospital and thus cannot estimate the extent to which we underestimated the clustering percentage.
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The contrasting diploid-like clustering percentages for di-allelic SNPs versus the SNP-SNPs clearly indicates that the intended ploidy reduction effect was achieved by the haploSNP strategy.
This value is much smaller than clustering percentages obtained for gene expression in T. reesei under other conditions such as conidiation [ 24].
Other clustering definitions that use geopolitical boundaries had higher average clustering percentages when the same 3-year window periods were used (national-level, 77.3%; state-level, 57.1%; county-level, 38.7%).
The within-cluster percentage error (calculated as one standard deviation from cluster mean thickness) decreases with distance from source when 5 and 10 clusters are used showing that over similar scales, proximal deposits are more variable than distal deposits.
Based on these analyses a cluster percentage of 95% was used for the analysis given below because it allowed up to 3 nucleotide differences with the seed sequence per OTU.
Figure 3 shows a plot of the number of reads in an OTU having <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0015406.e013.PNG" class= inline-graphic"/> mismatches compared to the most frequent read in the OTU at a cluster percentage of 92%.
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