New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1391494	NA (NA)	3 (0.180)	3/166	1.4	37.8%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
	?	NZ_CP009273	1972747 =	5 (0.290)					intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC

AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCT  >  NZ_CP009273/1972658‑1972819                                                                                          |                                                                         gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                          <  2:157907‑M2/1‑1 (MQ=255) gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                          <  2:221167‑M2/1‑1 (MQ=255)      tACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAc                                                                     <  2:487342/90‑1 (MQ=255)         tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATa                                                                  <  1:481543/90‑1 (MQ=255)                                ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACttttgtt                                           >  1:86641/1‑90 (MQ=255)                                 gaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                    >  1:356715‑M2/58‑80 (MQ=255)                                 gaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                    <  2:356715‑M2/23‑1 (MQ=255)                                       atgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGgtg                                    <  2:39897‑M2/39‑1 (MQ=255)                                                                   aGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgc        <  2:59164/90‑1 (MQ=255)                                                                         cacaAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgct  >  2:138714/1‑90 (MQ=255)                                                                                          |                                                                         AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCT  >  NZ_CP009273/1972658‑1972819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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.