New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	1 (0.090)	9 (0.900)	8/150	0.3	82.2%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	3 (0.300)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

CATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACG  >  NZ_CP009273/4532716‑4532886                                                                                        |                                                                                    cATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtg                                                                                   >  1:297410‑M2/1‑88 (MQ=255)    cTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggcc                                                                                <  1:256918‑M2/90‑6 (MQ=255)    cTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggcc                                                                                <  2:120640‑M2/90‑6 (MQ=255)                aTAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttg                                                                    <  1:311967‑M2/90‑18 (MQ=255)                              ttAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttt                                                      <  1:110253‑M2/90‑32 (MQ=255)                              ttAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttt                                                      <  2:317345‑M2/90‑32 (MQ=255)                                aaGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAAc                                                    <  1:179398/90‑1 (MQ=255)                                  gCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaat                                                                           <  1:114187‑M2/65‑11 (MQ=255)                                  gCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaat                                                                           >  2:114187‑M2/1‑55 (MQ=255)                                     aacaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaact                                               <  2:63530‑M2/90‑39 (MQ=255)                                     aacaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGc                                               <  2:256918/90‑1 (MQ=255)                                              aCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGc                                      <  1:50235/90‑1 (MQ=255)                                                                      tttCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctc              >  2:128794‑M2/1‑19 (MQ=255)                                                                            ctATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctcttttta        <  2:134724‑M2/90‑78 (MQ=255)                                                                                  gTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaattttt  <  1:58748‑M2/90‑84 (MQ=255)                                                                                        |                                                                                    CATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACG  >  NZ_CP009273/4532716‑4532886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ 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.