New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2282398 =	NA (NA)	19 (1.180)	12/168	0.3	100%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
	?	NZ_CP009273	3512437 =	0 (0.000)					intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ

AACCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAA  >  NZ_CP009273/2282311‑2282483                                                                                        |                                                                                      aaCCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATaagga                                                                                     <  1:269176/90‑1 (MQ=255)      gCTGGATATCTTTTTCCAGGACAACACCATCCACTGTCTCACCCTACACAACCGTTCATGCCAATGCGATCCGTGACATTaaggaacgcg                                                                                >  2:357961/1‑86 (MQ=255)      gCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTg                                                                                >  2:78422/1‑90 (MQ=255)                             acacCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATtcttct                                                         >  2:86848/1‑90 (MQ=255)                                   tCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTg                                                   <  1:369538/90‑1 (MQ=255)                                                   aCTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcatt                                   >  2:328785/1‑90 (MQ=255)                                                           gTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGGATAAGCGGGGAAATTCTTCTCGTCTGACTCAGTCATTTCATTTCTTCATg                           >  1:423352/1‑90 (MQ=255)                                                             tGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGtt                         >  1:167352/1‑90 (MQ=255)                                                             tGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGtt                         >  1:427321/1‑90 (MQ=255)                                                                     aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa                 >  1:203767/1‑90 (MQ=255)                                                                     aTGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa                 >  2:52552/1‑90 (MQ=255)                                                                         tATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAtttt             >  2:260787/1‑90 (MQ=255)                                                                                gAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTccc      >  1:320661/1‑90 (MQ=37)                                                                                gAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTccc      >  2:438400/1‑90 (MQ=37)                                                                                gAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCGGATTCAGTCATTTCATTTCTTCCTGTTTGTGCCGATTTTTTCTccc      >  2:274971/1‑90 (MQ=11)                                                                                    ataAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTaa  >  2:343693/1‑90 (MQ=31)                                                                                        |                                                                                      AACCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAA  >  NZ_CP009273/2282311‑2282483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ 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.