New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	1972747 =	0 (0.000)	5 (0.410)	5/160	0.7	100%	intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
	?	NZ_CP009273	2282399 =	NA (NA)					pseudogene (2/2532 nt)	yejO	autotransporter YejO

AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTA  >  NZ_CP009273/1972658‑1972815                                                                                          |                                                                     gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                      >  1:117405‑M1/90‑90 (MQ=255) gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                      >  2:29631‑M1/90‑90 (MQ=255)  catttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcct                                                                     >  2:201992‑M1/89‑90 (MQ=255)   atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcctt                                                                    >  2:40202‑M1/88‑90 (MQ=255)   atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcctt                                                                    >  1:192460‑M1/88‑90 (MQ=255)   atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcctt                                                                    >  1:348089‑M1/88‑90 (MQ=255)    tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTa                                                                   <  1:337464‑M1/4‑1 (MQ=255)          ggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATaa                                                             >  1:252093‑M1/81‑90 (MQ=255)           gagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATaaa                                                            >  2:337876‑M1/80‑90 (MQ=255)            tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt                                                           >  2:22797‑M1/1‑83 (MQ=255)                       gctcgaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                >  2:198264‑M1/68‑90 (MQ=255)                           aaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACtt                                            >  1:268086‑M1/64‑90 (MQ=255)                              aCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata                                         >  1:359665‑M1/1‑65 (MQ=255)                                ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatg                                       >  1:161472‑M1/1‑63 (MQ=255)                                      aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                      >  2:86062‑M1/53‑53 (MQ=255)                                      aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                      >  2:361392‑M1/53‑53 (MQ=255)                                      aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                      <  1:86062‑M1/1‑1 (MQ=255)                                      aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                      <  1:361392‑M1/1‑1 (MQ=255)                                           gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgttt                            >  1:103475‑M1/1‑52 (MQ=255)                                                                    gATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggt   >  2:266991‑M1/1‑27 (MQ=255)                                                                     tccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgcta  <  1:190595‑M1/69‑1 (MQ=255)                                                                                          |                                                                     AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTA  >  NZ_CP009273/1972658‑1972815

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ 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.