New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4532499 =	3 (0.110)	13 (0.530)	7/150	1.1	56.9%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	17 (0.700)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

AACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAA  >  NZ_CP009273/4532421‑4532574                                                                               |                                                                            cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                  >  1:340140‑M1/79‑90 (MQ=255) cagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                  >  2:737140‑M1/79‑90 (MQ=255)       ttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCa                                                            >  1:419307‑M1/73‑90 (MQ=255)       ttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCa                                                            >  2:65879‑M1/73‑90 (MQ=255)                ctttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                  <  1:722803‑M1/12‑1 (MQ=255)                ctttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAAc                                                                  >  2:722803‑M1/64‑75 (MQ=255)                ctttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCataaa                                                   <  2:259238‑M1/27‑1 (MQ=255)                  ttgttttgtaaacgagtttgactgccaacactgcacagtttccccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCataaata                                                 <  2:529378‑M1/29‑1 (MQ=255)                     agagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGt                                              <  2:513863/90‑1 (MQ=255)                                    cTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                               <  2:478354/90‑1 (MQ=255)                                     gactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                              >  2:150167‑M1/43‑90 (MQ=255)                                       aTTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAg                            >  2:561643/1‑90 (MQ=255)                                                 tgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAata                  <  2:760983‑M1/60‑1 (MQ=255)                                                                 aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTttttcaca                              <  1:764493‑M1/48‑4 (MQ=255)                                                                 aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                              >  2:764493‑M1/15‑62 (MQ=255)                                                                 aaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaa  >  1:259238‑M1/15‑90 (MQ=255)                                                                               |                                                                            AACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAA  >  NZ_CP009273/4532421‑4532574

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.