New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	11 (0.770)	6 (0.470)	5/152	0.7	44.7%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	5 (0.390)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

TTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4532447‑4532507 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG  <  NZ_CP009273/4532803‑4532719                                                                                                                                                    TTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGA                                                          >  2:185829/1‑90                       AAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGT                                    >  2:349978/1‑90                             AAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTT                              <  1:326853/90‑1                             AAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTT                              <  2:326394/90‑1                                               AGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCT            >  1:240040/1‑90                                                    ATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATT       >  1:332945/1‑90                                                         GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG  <  1:185829/90‑1                                                         GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG  >  1:254642/1‑90                                                         GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG  <  1:272256/90‑1                                                         GGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG  <  1:349978/90‑1                                                                                                                                                    TTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4532447‑4532507 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAG  <  NZ_CP009273/4532803‑4532719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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.