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[…] esser confidence sites. Paired sites corresponding to mapping of both 5′ and 3′ ends in all isolates on which it occurred were classified as high confidence sites. Paired insertion sites for which both ends were mapped in at least 50% of the isolates on which they were found to occur were considered of medium confidence. Insertion sites in which only one end of the IS6110 was mapped were considered of lesser confidence. Furthermore, insertion site hits mapped to M. tuberculosis H37Rv were excluded to avoid repetitive mapping., The genomic data of publicly available M. tuberculosis strains (format FASTA) were included in the analysis through conversion to FASTQ format reads using the program dwgsim v.0.1.10, and mapped and analyzed as described above. When necessary, DNA sequence alignment was performed using the CLC Sequence Viewer v7.6.1 (CLC bio®, Aarhus N, Denmark) and visualized in BioEdit v7.1.3.0 (T. Hall)., A MIRU-VNTR-based dendrogram was constructed in the public MIRU-VNTRplus database using the Dsw measure of genetic distance for tandem repeat loci [] and the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) clustering method. Spoligotyping profile was inferred from raw read data using the SpolPred software followed by comparison to the SITVIT WEB database [, ]. A phylogenetic tree based on SNPs was constructed using Seaview 4.3.5 [] using the Maximum Likelihood method. The analysis involved 76 nucleotide sequences with a total of 11271 sites in the final dataset. Tree topology was tested using the most recent approximate Likelihood Ratio Test (aLRT) as an alternative to bootstrap., Putative impact of selected compensatory mutations on protein function was assessed through the use of SIFT scores (available at http://sift.jcvi.org/) [] computed from the query alignment against UniRef90 database hits (with less than 90% identity, with a median sequence conservation equal to 3.00)., Any statistical analysis was conducted using the SPSS software., All sequencing data have been submitted to the European Nucle […]

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