New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 4532507	4 (0.090)	3 (0.070)	3/284	NT	15.9%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	CP009273	= 4532803	28 (0.680)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

TGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGAT  >  CP009273/4532234‑4532732                                                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                  cctgcatcaactgcgccagcggcgttaagaacttcccctttaaagtgaacggtcccaccattaaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacangggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaaaatTTGGGGCCaa                                                                                                                                                                                                                                  <  1:614183‑M1/10‑1 (MQ=255)  ctgcatcaactgcgcaagcggcgttaacaacttcccctttaaagtgaacggtcccaccattaaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCaaa                                                                                                                                                                                                                                 >  1:247890‑M1/265‑275 (MQ=255)         gacacagacacagnngttaacgacttaccctttcaaggcaaccgcaccaccattaaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagatttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCa                                                                                                                                                                                                                          >  2:614178‑M1/258‑275 (MQ=255)                                                               aaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacggttgccagagttttaattttcatgctgctttcctttccaaaaactatttctaaatcgaaatgtgcagtcgttaggtacactttgttttgtaaacgagtttgactgccaacactgccccgtgttcccacaaccgacgaaacatTTGGGGCCCAACTGCCCATACCATAACTCAGACACGTATTTTTTCACAAGCCTCCAAACaataaaaacca                                                                                                                                                                      <  2:105362‑M1/70‑4 (MQ=255)                                                               aaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTg                                                                                                                                                                                                                              <  2:206691‑M1/14‑1 (MQ=255)                                                                   gtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCa                                                                                                                                                                                                                          >  1:206694‑M1/200‑217 (MQ=255)                                                                         gcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgcggctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttggaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTGGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                                                                                                                                                                                             >  1:55159‑M1/194‑240 (MQ=255)                                                                                              ttATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttata                                                                                                                                     <  1:361793‑M1/275‑95 (MQ=255)                                                                                                    agggacagagccgacagaacaacgatggccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGCGCCAAACTGTCCNTATCATAANTAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAAc                                                                                                                                                      <  1:550940‑M1/86‑1 (MQ=255)                                                                                                      ggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgcaaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTCACGTAATTTTTCTAAAGCAAAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTATATCtgttnattatagaca                                                                                                                              <  2:63854‑M1/110‑6 (MQ=255)                                                                                                          agagccgacagaacaacgcttgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt                                                                                                                                                         >  1:63854‑M1/161‑243 (MQ=255)                                                                                                                    cGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggag                                                                                                               >  1:17515‑M1/1‑159 (MQ=255)                                                                                                                      acaacgattgccagagttttaattctcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAttttt                                                                                                                                                                                                 <  1:579576‑M1/43‑1 (MQ=255)                                                                                                                          cgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                                                                                                                                                                                             >  2:579571‑M1/145‑191 (MQ=255)                                                                                                                          aCTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGGTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTAAGGCCAAACTGNCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAAATCAATAATAAATAAATTTCacaaca                                                                                                         >  1:761029/1‑275 (MQ=255)                                                                                                                                          ccAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAACTTACTTTCACATCACCTCCGCTatat                                                                                             >  1:54890/1‑271 (MQ=255)                                                                                                                                                                   tttaTGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGATAATAGGTTTTATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagagaagaatgaggaagatgcgtcgagccacagaaacgttagctttaca                                                                <  2:17515‑M1/274‑164 (MQ=255)                                                                                                                                                                      actatttctagatcgtcatgggcagttgttatgtacacttgggtttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgagtcatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTGTTTCTCAAGCAGAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCAt                                                              >  1:105362‑M1/101‑274 (MQ=255)                                                                                                                                                                                        tggttagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacaattttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTcc                                           >  1:648991‑M1/83‑275 (MQ=255)                                                                                                                                                                                               tcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTTTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGATTCTGTGGCTCGACGCATCGTCATCATTCCGCCCTcgaaaaaac                                    <  2:648984‑M1/200‑3 (MQ=255)                                                                                                                                                                                                     aaaaaaaaaaaaGAGTTTTAATTTAACTTATTTATAATAAAGTTAAAAAAACAAATAAATACAATACAATTGGCAAAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAATAATATTAAAAAACGACAAAAAGCATCTAACTTTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAACGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCa                              <  2:761020/273‑1 (MQ=255)                                                                                                                                                                                                        atacttttttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATg                            >  1:390453‑M1/67‑274 (MQ=255)                                                                                                                                                                                                                  ttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCaaa                                                                                                                                                                                                                                 >  2:695061‑M1/57‑67 (MQ=255)                                                                                                                                                                                                                               tgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGACCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt                                                                                                                                                         <  2:455791‑M1/83‑1 (MQ=255)                                                                                                                                                                                                                                 tATTTATAATTTGGTTAAAAAAACACAAAAATACAAGACAATTGGGGCCAAACTTTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCAGGCAATATAAACATCTATAAATAAAGAt  <  2:54890/275‑1 (MQ=255)                                                                                                                                                                                                                                   tgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt                                                                                                                                                     >  1:455796‑M1/40‑126 (MQ=255)                                                                                                                                                                                                                                             gcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGc                                                                                                                                                                                         <  1:752491‑M1/51‑1 (MQ=255)                                                                                                                                                                                                                                               acagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGa                                                                                                                                                                     <  1:521847‑M1/71‑1 (MQ=255)                                                                                                                                                                                                                                                 agttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaa                                                                                                                                                                                     >  2:752482‑M1/26‑80 (MQ=255)                                                                                                                                                                                                                                                   ttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaa                                                                                                                                                                 >  2:521842‑M1/24‑98 (MQ=255)                                                                                                                                                                                                                                                                     gACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttgg                                                                                                                                                                             >  1:306546‑M1/1‑14 (MQ=255)                                                                                                                                                                                                                                                                         aTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggctta                                                                                                                                                                         <  2:306542‑M1/68‑59 (MQ=255)                                                                                                                                                                                                                                                                          ttGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctatt                                                                                                                                                               >  1:616036‑M1/1‑9 (MQ=255)                                                                                                                                                                                                                                                                              ggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgtta                                                                                                                                                           <  2:616031‑M1/77‑73 (MQ=255)                                                                                                                                                                                                                                                                                  attttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatt                                                                                                                                                   >  2:419559‑M1/1‑1 (MQ=255)                                                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                  TGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGAT  >  CP009273/4532234‑4532732

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.