New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1391494	NA (NA)	5 (0.380)	4/166	1.0	100%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
	?	NZ_CP009273	1972747 =	0 (0.000)					intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC

TGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGA  >  NZ_CP009273/1972661‑1972834                                                                                       |                                                                                        tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTa                                                                                      >  1:357943‑M2/87‑90 (MQ=255)     cTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgga                                                                                  <  1:166006‑M1/90‑4 (MQ=255)              acacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACGCAATTACTTAAggaaggtgcgaa                                                                         >  1:349615‑M1/1‑78 (MQ=255)                   cacaTACAAGGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggggcgaacaagt                                                                    >  1:321545‑M1/1‑73 (MQ=255)                      aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc                                                                 <  2:195838‑M1/90‑21 (MQ=255)                                ggggggCTGCGATTTTCAATAATGCGTGATGCAGATTACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgaga                                                       <  2:379330‑M1/90‑31 (MQ=255)                                   gggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtcccggatatgagatca                                                    >  1:168229‑M1/1‑57 (MQ=255)                                    atgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGgtg                                                   <  1:2592‑M2/39‑1 (MQ=255)                                        gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgttt                                               >  1:281275‑M1/1‑52 (MQ=255)                                           gactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACtttt                                                             <  1:223848‑M2/29‑1 (MQ=255)                                           gactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACtttt                                                             >  2:223848‑M2/45‑73 (MQ=255)                                                            aTGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaac                           <  1:133442‑M1/90‑59 (MQ=255)                                                                               cTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcat        >  1:93416‑M1/1‑13 (MQ=255)                                                                                    ttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATg   <  1:263744‑M2/87‑1 (MQ=255)                                                                                     tACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaactt  <  2:203939‑M1/90‑84 (MQ=255)                                                                                       |                                                                                        TGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGA  >  NZ_CP009273/1972661‑1972834

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 34 ≤ 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.