New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	3 (0.090)	10 (0.350)	7/148	1.4	84.5%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	1 (0.040)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

TCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4532416‑4532507 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCT  <  NZ_CP009273/4532803‑4532729                                                                                                                                                                         TCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGC                                                                               <  2:493429/90‑1                                 TGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGAC                                               <  2:341632/90‑1                                   ATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAA                                             <  1:144847/90‑1                                                            AAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTT                    <  2:378172/90‑1                                                              AAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAA                  <  2:213416/90‑1                                                              AAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAA                  <  2:663140/90‑1                                                                              AGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCT  >  1:243699/1‑90                                                                              AGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAA                                             >  1:531617/1‑47                                                                              AGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAA                                             <  2:531617/47‑1                                                                                   ATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTT                         <  1:248226/62‑1                                                                                   ATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTT                         >  2:248226/1‑62                                                                                                                                                                         TCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4532416‑4532507 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCT  <  NZ_CP009273/4532803‑4532729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ 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.