New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4532499 =	5 (0.300)	8 (0.540)	6/148	0.7	60.5%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	6 (0.410)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

TAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTT  >  NZ_CP009273/4532411‑4532588                                                                                         |                                                                                          taatCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATT                                                                                          <  2:42827‑M1/90‑1 (MQ=255)           cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                                >  1:237481‑M1/79‑90 (MQ=255)                  tctgtacactttgttttgtaaacgagtttgactgccaacactgcccagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCat                                                                         >  2:482185‑M1/72‑90 (MQ=255)                    ttAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCatat                                                                       <  2:52130/90‑1 (MQ=255)                          ctttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTcc                                                                           <  1:415289‑M1/17‑1 (MQ=255)                          ctttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTcc                                                                           >  2:415289‑M1/64‑80 (MQ=255)                          ctttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCataaa                                                                 <  1:245443‑M1/27‑1 (MQ=255)                                               gactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                                            >  2:136361‑M1/43‑90 (MQ=255)                                                tATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttc                                           <  1:65907‑M1/90‑41 (MQ=255)                                                        ataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATc                                                                      >  1:409285/1‑55 (MQ=255)                                                        ataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATc                                                                      <  2:409285/55‑1 (MQ=255)                                                           aaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgt                                <  1:302250‑M1/90‑52 (MQ=255)                                                            aGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgtt                               <  2:13806‑M1/90‑53 (MQ=255)                                                                           aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa                >  1:12302‑M1/15‑90 (MQ=255)                                                                           aaaagatgaaacatTTGGGGCCAAACTGTCCATATCACAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa                >  2:245443‑M1/15‑90 (MQ=255)                                                                                   aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTa        >  2:270826/1‑90 (MQ=255)                                                                                        aTTGGGGCCAttttgactcatagaggaaagcatcgcggac                                                     <  1:484448‑M1/40‑31 (MQ=255)                                                                                        aTTGGGGCCAttttgactcatagaggaaagcatcgcggac                                                     >  2:484448‑M1/1‑10 (MQ=255)                                                                                        aTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGt   >  2:360914/1‑90 (MQ=255)                                                                                         ttGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttattt  >  1:360914‑M1/1‑9 (MQ=255)                                                                                         |                                                                                          TAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTT  >  NZ_CP009273/4532411‑4532588

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ 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.