New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2282398 =	NA (NA)	9 (0.450)	6/170	1.1	81.8%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
	?	NZ_CP009273	3512437 =	2 (0.100)					intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ

AGCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGT  >  NZ_CP009273/3512349‑3512522                                                                                         |                                                                                      atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCt                                                                                      >  1:223303‑M2/89‑90 (MQ=255)  tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTa                                                                                     >  2:401937‑M2/88‑90 (MQ=255)  gCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGtactac                                                                                       >  1:145653/1‑88 (MQ=255)  gCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGtactac                                                                                       <  2:145653/88‑1 (MQ=255)   ttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTaa                                                                                    <  2:116768‑M2/4‑1 (MQ=255)    tAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAG                                                                                   <  2:9979‑M2/90‑1 (MQ=255)      cgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAGAc                                                                                 <  1:66317‑M2/7‑1 (MQ=255)       cTGGCGACCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaa                                                                                >  2:255649‑M2/1‑87 (MQ=255)               aaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAGACTATTCGTTa                                                                        <  1:469771‑M2/16‑1 (MQ=255)                         ttttCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctg                                                              <  2:327620‑M2/90‑22 (MQ=255)                         ttttCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctg                                                              <  2:293251‑M2/90‑22 (MQ=255)                                  aCCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagat                                                     >  2:486606‑M2/1‑60 (MQ=255)                                   cccATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatc                                                    >  2:302346‑M2/1‑59 (MQ=255)                                             cAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtca                                          <  1:32487‑M2/90‑42 (MQ=255)                                             cAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtca                                          <  1:54838‑M2/90‑42 (MQ=255)                                                   gAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgga                                    >  1:351312‑M2/1‑43 (MQ=255)                                                   gAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgga                                    >  2:107808‑M2/1‑43 (MQ=255)                                                      gccgagaagaatttccccgcttattcgcaccttccCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACAt                                 >  1:472053‑M2/36‑90 (MQ=255)                                                          atTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatag                             <  2:371693‑M2/90‑55 (MQ=255)                                                              gaatttccccgcttattcgcaccttccCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGaa                         <  2:472053‑M2/63‑1 (MQ=255)                                                              cGTTTCTCTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaaca                         >  1:545900‑M2/1‑32 (MQ=255)                                                                  tctcTGCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggt                     >  1:540979‑M2/1‑28 (MQ=255)                                                                   tccccgcttattcgcaccttccCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTc                    >  1:331877‑M2/23‑90 (MQ=255)                                                                       gCCATTTTTTCGGTACTACTAAGgaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatc                >  2:32487‑M2/1‑23 (MQ=255)                                                                                     ttccCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGt  >  1:450850‑M2/5‑90 (MQ=255)                                                                                         |                                                                                      AGCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGT  >  NZ_CP009273/3512349‑3512522

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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.