New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 270859	NA (NA)	16 (0.740)	14/162	0.4	69.8%	intergenic (‑67/‑177)	BW25113_RS01325/mmuP	IS5‑like element IS5 family transposase/S‑methylmethionine permease
	?	NZ_CP009273	= 481485	7 (0.320)					coding (269/648 nt)	acrR	multidrug efflux transporter transcriptional repressor AcrR

AAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTG  >  NZ_CP009273/270773‑270941                                                                                       |                                                                                   aaGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCgg                                                                                 <  1:441044/90‑1 (MQ=32)   tgTAAGTTGATGCCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTGGTTCGCACCTTCCGGAg                                                                               <  2:499891/89‑1 (MQ=255)    gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAgg                                                                              <  1:213338/90‑1 (MQ=37)    gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAgg                                                                              <  1:372435/90‑1 (MQ=37)           gatgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATg                                                                       >  2:471446/1‑90 (MQ=255)                  cATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTggc                                                                >  1:75629/1‑90 (MQ=255)                      atgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGcc                                                            <  1:471090/90‑1 (MQ=255)                       tgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGccc                                                           <  1:319942/90‑1 (MQ=255)                          aCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCttt                                                        >  2:506339/1‑90 (MQ=255)                                 tCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATc                                                 <  1:274507/90‑1 (MQ=255)                                       gCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCgg                                                                                 >  2:429516/1‑52 (MQ=33)                                       gCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCgg                                                                                 <  1:429516/52‑1 (MQ=33)                                       gCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGatta                                           >  2:293774/1‑90 (MQ=255)                                         tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGattatt                                         >  2:214918/1‑90 (MQ=255)                                         tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGattatt                                         >  2:199081/1‑90 (MQ=255)                                                    aaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCAccc                              <  2:75629/90‑1 (MQ=255)                                                     aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCg                             <  1:316158/90‑1 (MQ=255)                                                          aTCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTAtt                        >  2:203668/1‑90 (MQ=255)                                                               atatCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAgcg                   >  2:219535/1‑90 (MQ=255)                                                               atatCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAgcg                   >  2:133028/1‑90 (MQ=255)                                                               atatCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAgcg                   >  1:535613/1‑90 (MQ=255)                                                                tatCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAgcgc                  >  1:278544/1‑90 (MQ=255)                                                                     gggACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGgc             >  1:285704/1‑90 (MQ=255)                                                                     gggACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGgc             >  2:573440/1‑90 (MQ=255)                                                                      ggACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGgcg            <  1:293774/90‑1 (MQ=255)                                                                        aCTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTGTCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGcgcg          >  2:500296/1‑90 (MQ=255)                                                                           tGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGc       >  1:39704/1‑90 (MQ=255)                                                                                gCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTg  <  2:278544/90‑1 (MQ=255)                                                                                gCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTg  <  1:292550/90‑1 (MQ=255)                                                                                     ttCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCAcc                               <  1:599902/56‑1 (MQ=255)                                                                                     ttCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCAcc                               >  2:599902/1‑56 (MQ=255)                                                                                       |                                                                                   AAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTG  >  NZ_CP009273/270773‑270941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ 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.