New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 287112	NA (NA)	32 (1.760)	19/168	0.1	91.4%	intergenic (‑55/‑99)	BW25113_RS01405/BW25113_RS01410	IS1‑like element IS1B family transposase/hypothetical protein
	?	NZ_CP009273	= 481508	3 (0.170)					coding (292/648 nt)	acrR	multidrug efflux transporter transcriptional repressor AcrR

AGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAA  >  NZ_CP009273/287030‑287195                                                                                   |                                                                                    aggGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAAtttt                                                                              <  2:54645/90‑1 (MQ=37)    gACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAg                                                                           >  2:452369/1‑90 (MQ=40)                  aCAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCAc                                                             <  2:530229/90‑1 (MQ=255)                     gAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTa                                                          >  1:195163/1‑90 (MQ=255)                     gAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTa                                                          >  2:422294/1‑90 (MQ=255)                         ccACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTa                                                      <  1:108728/90‑1 (MQ=255)                         ccACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTa                                                      <  1:155093/90‑1 (MQ=255)                               gAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGa                                                <  1:393514/90‑1 (MQ=255)                                    ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATc                                           >  1:104503/1‑90 (MQ=255)                                     cTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCCCGTCCCTATGTCGAATATCt                                          <  2:359786/90‑1 (MQ=255)                                              acCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATaa                                 <  1:422294/90‑1 (MQ=255)                                                 atcatACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGt                              >  2:242869/1‑90 (MQ=255)                                                 atcatACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGt                              >  1:90217/1‑90 (MQ=255)                                                       cacTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGa                        >  1:96831/1‑90 (MQ=255)                                                           aaaTCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCga                    >  1:66160/1‑90 (MQ=255)                                                           aaaTCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCga                    >  1:343325/1‑90 (MQ=255)                                                              tCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGagaa                 <  1:263924/90‑1 (MQ=255)                                                                 gTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAagag              >  1:482914/1‑90 (MQ=255)                                                                     gTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTgg                                        <  2:295289/60‑1 (MQ=255)                                                                     gTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTgg                                        >  1:295289/1‑60 (MQ=255)                                                                      ttGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGc         <  2:104503/90‑1 (MQ=255)                                                                           agcaTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAgg    <  1:421206/90‑1 (MQ=255)                                                                           agcaTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAgg    >  1:339900/1‑90 (MQ=255)                                                                           agcaTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAgg    >  2:71867/1‑90 (MQ=255)                                                                             caTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGaa  <  2:28649/90‑1 (MQ=255)                                                                              aTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATa                                  >  2:254804/1‑57 (MQ=255)                                                                              aTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATa                                  <  1:254804/57‑1 (MQ=255)                                                                                   |                                                                                    AGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAA  >  NZ_CP009273/287030‑287195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.