Table 2. Large structural variations in the isolates of Patient 2–4.
By setting the isolate P1Bm2009 as a reference, we mapped the long Nanopore reads of the isolates from patients 2 to 4 to identify large structural variations that escape SNPs analysis. We omitted from this list indels found in intergenic regions (11) and hypothetical proteins (8). The full list of structural variations can be found in Tables G and H in S1 Tables.
| Strains | Chr | Position | Function |
|---|---|---|---|
| P2Bm2011b | 1 | 17536 | Insertion of IS3 into type IV secretion system tip protein VgrG |
| P2Bm2011b, P2Bm2018 | 1 | 59006 | Insertion of IS5 into intergenic promoter of type II secretion system secretin GspD |
| P2Bm2018 | 1 | 482440 | Deletion in long-chain fatty acid—CoA ligase |
| P4Bm2019 | 1 | 762540 | Deletion EamA family transporter, hypothetical prot, RES family NAD+ phosphorylase |
| P4Bm2019 | 1 | 825939 | Deletion glutamine—fructose-6-phosphate transaminase (isomerizing) |
| P2Bm2011b, P2Bm2018 | 1 | 860357 | Large deletion including regulator proteins |
| P2Bm2011b, P2Bm2018 | 1 | 1084705 | Deletion IS3 family transposase |
| P2Bm2011b | 1 | 1126373 | Insertion of IS3 into GlxA family transcriptional regulator |
| P2Bm2011b, P2Bm2018, P4Bm2019 | 1 | 1250973 | Deletion IS256 family transposase |
| P2Bm2011b | 1 | 1383320 | Insertion of IS5 into ornithine acetyltransferase |
| P2Bm2011a, P2Bm2018 | 1 | 2112493 | Prophage deletion |
| P2Bm2011a, P2Bm2018 | 1 | 2882469 | Insertion of IS5 into PTS sugar transporter/HPr kinase/phosphorylase |
| P2Bm2011a,b, P2Bm2018 | 2 | 199631 | Deletion in polyketide cyclase |
| P2Bm2011b, P2Bm2018 | 2 | 234973 | Insertion of IS5 into peroxidase-related enzyme |
| P2Bm2011b | 2 | 297796 | Insertion of IS5 into transposase |
| all | 2 | 386097 | Deletion IS3 family transposase |
| P2Bm2011b | 2 | 851128 | Insertion of IS5 into type IV secretion system baseplate subunit TssF |
| P2Bm2011b | 2 | 865794 | Insertion of IS3 into DUF3304 domain-containing protein |
| P2Bm2018 | 2 | 906456 | Insertion of IS5 into DEAD/DEAH box helicase |
| P2Bm2011b | 2 | 921221 | Insertion of IS5 into multidrug transporter subunit MdtN |
| P2Bm2011b | 2 | 1052623 | Insertion of IS5 into twin-arginine translocation pathway signal |
| P2Bm2011b, P2Bm2018 | 2 | 1770117 | Insertion of IS5 into Tat pathway signal protein |
| P2Bm2011b | 2 | 1892870 | Prophage deletion |
| P2Bm2011b | 2 | 2294168 | Insertion of IS5 into aldo/keto reductase |
| P2Bm2011a,b, P2Bm2018 | 3 | 128274 | Prophage deletion |
| P2Bm2011a,b | 3 | 599926 | Insertion of IS5 into PLP-dependent aminotransferase family protein |