Table 5. List of large structural variations in the isolates of Patient 1.

Using isolate P1Bm2009 as a reference, we mapped the long Nanopore reads of the subsequent isolates from Patient 1 to reveal large structural variations that escape SNP analysis. All structural variations are found in C1 and are fixed after their appearance in agreement with the SNP analysis (Fig 8). Isolates P1Bm2011a and P1Bm2012b, which originated from the same sputum sample as P1Bm2011b and P1Bm2012a, respectively, appear to come from separate lineages.

Strains	Chr	Type	Function
P1Bm2013-2015	1	Insertion	Intergenic, IS3 in the rRNA cluster (5S, 16S, 23S)
P1Bm2011b-2015	1	Breakend	Glycosyltransferase
P1Bm2011b-2015	1	Breakend	Intergenic, next to IS256
P1Bm2011a-2015	1	Deletion	Phosphoribosyltransferase
P1Bm2012b	1	Deletion	Glycosyltransferase
P1Bm2015	1	Deletion	SDR family NAD-p-dependent oxidoreductase