New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	269666 =	NA (NA)	19 (0.930)	8/166	0.8	100%	intergenic (+2/+146)	ykfC/BW25113_RS01325	reverse transcriptase domain‑containing protein/IS5‑like element IS5 family transposase
	?	NZ_CP009273	= 481436	0 (0.000)					coding (220/648 nt)	acrR	multidrug efflux transporter transcriptional repressor AcrR

CAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT  >  NZ_CP009273/269580‑269753                                                                                       |                                                                                        cAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGaa                                                                                      <  1:478628/90‑1 (MQ=255)   gTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAgg                                                                                    <  1:381001/90‑1 (MQ=255)   gTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAgg                                                                                    <  1:345323/90‑1 (MQ=255)          tGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAAt                                                                             <  1:29460/90‑1 (MQ=255)               agaTGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCg                                                                        >  2:218263/1‑90 (MQ=255)                gaTGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCgg                                                                       >  2:99180/1‑90 (MQ=255)                gaTGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCgg                                                                       >  2:601494/1‑90 (MQ=255)                      aGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAt                                                                 <  1:242096/90‑1 (MQ=255)                      aGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAt                                                                 <  1:328235/90‑1 (MQ=255)                         ggTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAttct                                                              >  1:243704/1‑90 (MQ=255)                           tctcAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAttcttc                                                            <  1:464179/90‑1 (MQ=255)                           tctcAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAttcttc                                                            >  2:150571/1‑90 (MQ=255)                                aCGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGc                                                       <  2:36189/90‑1 (MQ=255)                                   aTCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGa                                                    >  2:156396/1‑90 (MQ=255)                                   aTCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGa                                                    >  2:285700/1‑90 (MQ=255)                                    tCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAc                                                   >  1:513118/1‑90 (MQ=255)                                    tCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAc                                                   >  2:333732/1‑90 (MQ=255)                                     cccGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACt                                                  <  2:6303/90‑1 (MQ=255)                                        gCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAgg                                                                                    >  1:157298/1‑53 (MQ=255)                                        gCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAgg                                                                                    <  2:157298/53‑1 (MQ=255)                                             agaAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatt                                          <  2:108919/90‑1 (MQ=255)                                              gaAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcattt                                         >  2:354620/1‑90 (MQ=255)                                                            tCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGtt                           >  1:387236/1‑90 (MQ=255)                                                                             gCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTtctc          >  1:576119/1‑90 (MQ=39)                                                                              cACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTcc         >  2:69794/1‑90 (MQ=38)                                                                                cTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCg       >  2:509848/1‑90 (MQ=35)                                                                                   ttATGGAGGGTATGAATAACGGGGGAAATTCTTCTCGGCCGACTCACACATTTCATTTCTTCATGTTTTAGGCGATTTTCTCTGCCGTaa    <  1:287601/90‑1 (MQ=2)                                                                                   ttATGGAAGGGGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTaa    >  1:286240/1‑90 (MQ=18)                                                                                     aTGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAt  <  2:61781/90‑1 (MQ=32)                                                                                       |                                                                                        CAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT  >  NZ_CP009273/269580‑269753

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ 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.