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

GAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGAT  >  NZ_CP009273/4532439‑4532592                                                                     |                                                                                      gaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaataa                                                                  >  2:157021/1‑90 (MQ=255)         ttGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcgga                                                          >  2:185829‑M1/1‑61 (MQ=255)                aaCTTATTGATAATAAAGTT‑AAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCa                                                                              <  2:345268/62‑1 (MQ=255)                aaCTTATTGATAATAAAGTT‑AAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCa                                                                              >  1:345268/1‑62 (MQ=255)                   ttATAGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                                                <  2:37739/90‑1 (MQ=255)                               aaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgt                                    >  2:349978‑M1/1‑39 (MQ=255)                                     aaaaaaCAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggctt                              <  2:326394‑M1/90‑58 (MQ=255)                                     aaaaaaCAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggctt                              <  1:326853‑M1/90‑58 (MQ=255)                                                       aGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatct            >  1:240040‑M1/1‑15 (MQ=255)                                                       aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTa            >  1:49024/1‑90 (MQ=255)                                                        gACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTaa           <  1:157021/90‑1 (MQ=255)                                                         aCAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATACTAAAAAACGACAAAAAGCATCTAAc          <  2:270390/90‑1 (MQ=255)                                                          catttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCCCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt         <  1:109589/87‑1 (MQ=255)                                                            aTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatt       >  1:332945‑M1/1‑10 (MQ=255)                                                               ggggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTg    <  2:184810/90‑1 (MQ=255)                                                               ggggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTg    <  2:69881/90‑1 (MQ=255)                                                                gggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa   <  2:13751/90‑1 (MQ=255)                                                                 ggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatag  <  1:349978‑M1/90‑86 (MQ=255)                                                                 ggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatag  <  1:272256‑M1/90‑86 (MQ=255)                                                                 ggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatag  >  1:254642‑M1/1‑5 (MQ=255)                                                                 ggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatag  <  1:185829‑M1/90‑86 (MQ=255)                                                                     |                                                                                      GAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGAT  >  NZ_CP009273/4532439‑4532592

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.