New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1391494	NA (NA)	17 (0.490)	10/166	1.3	94.5%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
	?	NZ_CP009273	1972747 =	1 (0.030)					intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC

AGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTT  >  NZ_CP009273/1391417‑1391579                                                                              |                                                                                      agaAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCa                                                                           >  2:559440/1‑90 (MQ=38)   aaaaaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAAt                                                                         <  1:259916/90‑1 (MQ=40)   aaaaaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAAt                                                                         <  1:694098/90‑1 (MQ=40)   aaaaaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAAt                                                                         <  1:979961/90‑1 (MQ=40)       aaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGt                                                                     <  1:150310/90‑1 (MQ=255)         tCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTg                                                                   <  1:222961/90‑1 (MQ=255)                 aaCATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTaaa                                                           <  2:1006169/90‑1 (MQ=255)                         gaaatgaaatGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTa                                                   <  2:421936/90‑1 (MQ=255)                         gaaatgaaatGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTa                                                   <  2:311244/90‑1 (MQ=255)                         gaaatgaaatGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTa                                                   <  2:1131409/90‑1 (MQ=255)                           aatgaaatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATACGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAag                                                 <  2:590688/90‑1 (MQ=255)                              gaaatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAgagg                                              <  2:490256/90‑1 (MQ=255)                                aatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAgaggtg                                            >  2:506599/1‑90 (MQ=255)                                   gaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAgaggtgagg                                         <  1:506599/90‑1 (MQ=255)                                            aGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAAt                                                                             <  2:103653/45‑1 (MQ=40)                                            aGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAAt                                                                             >  1:103653/1‑45 (MQ=40)                                               cGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAg                             <  2:696765/90‑1 (MQ=255)                                                   aagaaTTTCCCCGCTTATCCGCCCCTTACCTAACCAATCAACCCGTTGCTTGTAAATCCCGCCAAGAGGTGAGGTTTTcagaccagaccc                         <  1:945169/90‑3 (MQ=25)                                                    agaaTTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAAc                        <  2:872452/90‑1 (MQ=255)                                                         ttCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGa                   <  1:90029/90‑1 (MQ=255)                                                                 ttATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCAt           <  2:315082/90‑1 (MQ=255)                                                                 ttATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCAt           <  1:715125/90‑1 (MQ=255)                                                                      cGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTAt      <  2:261290/90‑1 (MQ=255)                                                                      cGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTAt      <  2:985679/90‑1 (MQ=255)                                                                          ccTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGtt  <  1:682951/90‑1 (MQ=255)                                                                          ccTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGtt  <  1:282007/90‑1 (MQ=255)                                                                              |                                                                                      AGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTT  >  NZ_CP009273/1391417‑1391579

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ 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.