New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2282398 =	NA (NA)	27 (1.100)	13/166	0.5	77.1%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
	?	NZ_CP009273	3512437 =	8 (0.330)					intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ

ACCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTT  >  NZ_CP009273/2282312‑2282473                                                                                       |                                                                            aCCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATaaggaa                                                                          <  1:713736/90‑1 (MQ=255)   cAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATaaggaagg                                                                        <  2:308633/90‑1 (MQ=255)                       ggACAACACCATCAACTGTCTCACCATACTCAACAGTTTATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAAtt                                                    >  2:252379/1‑90 (MQ=255)                            acacCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATtcttct                                               >  1:704686/1‑90 (MQ=255)                                        gTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAg                                   >  1:525253/1‑90 (MQ=255)                                          ctcACCATACTCAACAGTTTATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtc                                 <  1:252379/90‑1 (MQ=255)                                             aCCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatt                              <  2:312744/90‑1 (MQ=255)                                                  aCTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcatt                         >  1:391322/1‑90 (MQ=255)                                                  aCTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcatt                         <  2:391322/90‑1 (MQ=255)                                                               tGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGa            >  2:212158/1‑90 (MQ=255)                                                                         aTGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAttttt  >  1:536789/1‑90 (MQ=255)                                                                                       |                                                                            ACCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTT  >  NZ_CP009273/2282312‑2282473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.