Simplified overview of scanning process and preparation. “Testsuites” are python source files that define the SNPs of interest (or in this case a 3 base pair long region) as well as other relevant genetic information (in this case the katG gene in which mutations can confer isoniazid resistance). This information is used to extract a “target sequence” from a reference MTBC genome: on both sides, additional bases (“flanks”) are concatenated to avoid border effects within the sequence of interest. During the scanning process, every read is trimmed depending on its PHRED score (in this case, a quality cutoff of Q = 13 was defined which corresponds to the ASCII character “/”). After the scanning, the part of the reads that matched the target sequence and exceeded the minimum quality score (represented with gray bars) are assembled to a “coverage” that indicates the overall coverage depth as well as all detected mutations (green). In a further step, additional information is generated from this coverage (such as the resulting amino acid sequence) and finally a short “result” string is generated that summarizes the result of the scanning process.