Fig. 1

The work flow and output of RD-Analyzer. a A schematic representation of the processes in RD-Analyzer. RD-Analyzer accepts sequence reads in FASTQ format. The input sequence reads are mapped to reference RD sequences, after which read depths along the reference sequences would be calculated. Normally, an RD is identified as ‘present’ in the MTC isolate if the median ratio of read depth along the reference sequence is above a specified threshold (default of 0.09 for all RDs, except 2.97 for RD12^can). The default setting of using the median ratio (ratio at the 50^th percentile) can be changed to other percentiles subject to user’s preference. Small RDs are detected from CIGAR strings of mapped reads spanning the potential deletion region. The default RD-Analyzer uses the LUSs of 31 RDs and performs lineage prediction using rules elaborated in Additional file 2: Table S2. The extended version of RD-Analyzer allows for user-defined reference RD sequences without strain prediction. b An example output file of default RD-Analyzer. c An example output file of extended RD-Analyzer