New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	12 (0.340)	6 (0.190)	5/150	1.9	26.2%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	23 (0.740)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

CATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4532417‑4532507 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAGATGT  <  NZ_CP009273/4532803‑4532715                                                                                                                                                                                      CATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCC                                                                                            >  1:685248/1‑90                                                     AAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACT                                                                                   >  1:233799/1‑47                                                     AAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACT                                                                                   <  2:233799/47‑1                                                            AAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTA                                 <  1:354021/90‑1                                                             AAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAA                                <  2:715451/90‑1                                                                                  ATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATT           >  2:617743/1‑90                                                                                  ATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATT           >  2:727245/1‑90                                                                                   TTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTT          >  2:236612/1‑90                                                                                     GGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTAT        <  2:868750/90‑1                                                                                       GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG      <  1:140992/90‑1                                                                                       GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG      <  1:402008/90‑1                                                                                       GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG      <  2:570371/90‑1                                                                                       GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG      <  2:991714/90‑1                                                                                           ATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAGATGT  >  1:843645/1‑90                                                                                                                                                                                      CATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4532417‑4532507 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAGATGT  <  NZ_CP009273/4532803‑4532715

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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.