New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2282398 =	NA (NA)	17 (0.860)	10/166	0.6	94.4%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
	?	NZ_CP009273	3512437 =	1 (0.050)					intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ

GGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCC  >  NZ_CP009273/2282334‑2282479                                                                 |                                                                                  ggACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAAtt                                                          >  2:113443/1‑90 (MQ=255)                   tctcACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGt                                        >  1:87064/1‑90 (MQ=255)                           tACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcat                                >  1:119282/1‑90 (MQ=255)                            aCTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAAt                                                           >  1:175836/1‑62 (MQ=255)                            aCTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAAt                                                           <  2:175836/62‑1 (MQ=255)                            aCTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcatt                               >  1:466918/1‑90 (MQ=255)                                 aCAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATttcttc                          >  1:579579/1‑90 (MQ=255)                                    gTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATg                       >  2:577039/1‑90 (MQ=255)                                         tGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGa                  >  2:127635/1‑90 (MQ=255)                                          gCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAg                 <  2:87064/90‑1 (MQ=255)                                              aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAAt                                                           >  1:291248/1‑44 (MQ=255)                                              aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAAt                                                           <  2:291248/44‑1 (MQ=255)                                              aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa             >  1:422084/1‑90 (MQ=255)                                              aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa             <  1:382283/90‑1 (MQ=255)                                              aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa             >  1:195076/1‑90 (MQ=255)                                              aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa             >  2:79799/1‑90 (MQ=255)                                              aTGCTATGGGTGAATATAAGGAAGGGGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa             >  2:382283/1‑90 (MQ=255)                                                      ggTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGc                                                 <  2:124943/46‑1 (MQ=255)                                                      ggTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGc                                                 >  1:124943/1‑46 (MQ=255)                                                         gAATATAAGGAAGGTGGGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTccc  >  2:442621/1‑90 (MQ=255)                                                                 |                                                                                  GGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCC  >  NZ_CP009273/2282334‑2282479

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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.