New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	269666 =	NA (NA)	17 (0.810)	9/166	0.7	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                                                                                      <  2:402719/90‑1 (MQ=255)                   gCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGa                                                                    <  1:371564/90‑1 (MQ=255)                   gCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGa                                                                    <  1:388824/90‑1 (MQ=255)                     gAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGaaa                                                                  >  1:110862/1‑90 (MQ=255)                         ggTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAttct                                                              >  1:158684/1‑90 (MQ=255)                                   ttgccGCAGGAGAAAGCCAGAAAGTTGGTGGCATCGCTGACATAACTGTTATGGAAGGTTGGAAGAAATGGGTAAATTCTTCTGGGCTgg                                                    >  1:91295/4‑89 (MQ=255)                                   aTCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGa                                                    >  2:485250/1‑90 (MQ=255)                                    tCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATtcttct                                                           <  2:74061/82‑1 (MQ=255)                                    tCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATtcttct                                                           >  1:74061/1‑82 (MQ=255)                                      ccGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTc                                                 <  2:213427/90‑1 (MQ=255)                                       cGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCa                                                <  1:45624/90‑1 (MQ=255)                                            gagaAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcat                                           <  1:555554/90‑1 (MQ=255)                                            gagaAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcat                                           >  2:331966/1‑90 (MQ=255)                                                            tCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGtt                           >  2:601850/1‑90 (MQ=255)                                                                                cTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCg       >  2:421000/1‑90 (MQ=35)                                                                                   ttATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTaa    <  1:220655/90‑1 (MQ=33)                                                                                     aTGGAAGGTGCGAATAAGCGGCGACATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAt  <  1:335115/90‑1 (MQ=12)                                                                                       |                                                                                        CAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT  >  NZ_CP009273/269580‑269753

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ 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.