New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4532499 =	2 (0.110)	7 (0.420)	7/150	0.7	61.5%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	7 (0.420)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

TAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACT  >  NZ_CP009273/4532411‑4532585                                                                                         |                                                                                       tcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacattt                                                                                       >  2:84357‑M1/89‑90 (MQ=255)           cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                             >  2:20909‑M1/79‑90 (MQ=255)                       acactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCat                                                                 <  1:416003‑M1/24‑1 (MQ=255)                            ttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATc                                                                   <  1:77112‑M1/22‑1 (MQ=255)                            ttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATc                                                                   >  2:77112‑M1/62‑83 (MQ=255)                                  tgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTAc                                                      >  2:254265‑M1/56‑90 (MQ=255)                                                actgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCaa                                        >  1:249742‑M1/42‑90 (MQ=255)                                                 aTTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaagttgttca                                       >  1:445978‑M1/1‑49 (MQ=255)                                                 aTTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttca                                       <  2:449005‑M1/90‑42 (MQ=255)                                                 aTTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAg                                       >  1:225921/1‑90 (MQ=255)                                                                           aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa             <  1:279526‑M1/76‑1 (MQ=255)                                                                                aCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgtta        <  1:374794‑M1/90‑73 (MQ=255)                                                                                   aGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatct     >  1:279512‑M1/1‑15 (MQ=255)                                                                                      cAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt  <  2:438644/90‑1 (MQ=255)                                                                                        aTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaa                     <  1:516905‑M1/69‑60 (MQ=255)                                                                                        aTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaa                     >  2:516905‑M1/1‑10 (MQ=255)                                                                                         |                                                                                       TAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACT  >  NZ_CP009273/4532411‑4532585

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ 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.