Fig. 2

Alignment of MinION long reads to pWCP. a The alignment of long reads that cover >50% of the pWCP genome (only 12 of 13 total long reads are shown; we omitted 1 from this display solely due to space considerations). Each rectangular figure shows high scoring pairs (HSPs) and their alignments between pWCP and long reads. The broken HSPs that are parallel to each other are due to low-quality regions in long read sequences, and they are shown in different shades. Concentric circles around pWCP demonstrate the alignment of each long read and their start and stop positions. b The alignment of long reads that cover <50% of the pWCP genome (only 5 of 6 are shown). Every long read shown in the figure has a hit to the IS110 TE