New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1391494	NA (NA)	6 (0.670)	5/164	0.5	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

AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATG  >  NZ_CP009273/1972658‑1972833                                                                                          |                                                                                       gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                                        <  2:64364‑M2/1‑1 (MQ=255) gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                                        <  2:224037‑M2/1‑1 (MQ=255)      tacgggagaaaaaatcggctcaaacatgaagaaatgagatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAAc                                                                                   <  1:22997‑M2/6‑1 (MQ=255)            tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt                                                                             >  1:214484‑M1/1‑83 (MQ=255)                      cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt                                                                   >  1:101019‑M1/1‑73 (MQ=255)                       gctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                                  <  2:2428‑M2/23‑1 (MQ=255)                       gctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                                  <  2:176726‑M2/23‑1 (MQ=255)                                      aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGgt                                                   >  1:111945‑M2/53‑90 (MQ=255)                                                     ataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgga                                    <  2:214484‑M1/90‑49 (MQ=255)                                                        gccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACttttgttttg                                                      <  1:154378‑M2/35‑1 (MQ=255)                                                        gccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACttttgttttg                                                      >  2:154378‑M2/35‑69 (MQ=255)                                                        atGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagcc                                 >  1:170975‑M1/1‑39 (MQ=255)                                                             tGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccataga                            >  2:107189‑M1/1‑34 (MQ=255)                                                                  cAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagg                       <  1:107189‑M1/90‑62 (MQ=255)                                                                  cAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcacgtttgtcatctggagccatagaacagg                       >  2:55870‑M1/1‑29 (MQ=255)                                                                                   tCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatc      <  2:170975‑M1/90‑79 (MQ=255)                                                                                       ttACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaact  >  2:109474‑M1/1‑8 (MQ=255)                                                                                          |                                                                                       AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATG  >  NZ_CP009273/1972658‑1972833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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.