Identifying MIRU CNV utilizing RD and mate pair. (a) Mean normalized RD values at MIRU locus 802 (+/− 100 bp). Mean RD values represented by dashed blue line while two standard deviations above and below the mean RD values corresponds to red and green dotted lines, respectively. Strain H-3, containing a MIRU insertion relative to the inoculum strain, is represented by the black line. Shaded area corresponds to the MIRU coordinates. (b) Mean normalized mate pair distance values at MIRU locus 802 (+/− 100 bp). The color scheme is identical to plotted read depth values. Strain shown is again H-3.