New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	21 (0.430)	13 (0.280)	12/476	1.9	38.7%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	21 (0.450)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

TTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAA  >  NC_000913/4542742‑4543236                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                           ttAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACCTCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGccc                                                                                                                                                                                                                                                      >  2:343677/1‑251 (MQ=255)             aaaaaGCATCTAACAGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCGATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCAt                                                                                                                                                                                                                                          <  2:26051/251‑1 (MQ=255)                           tGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTATTCTCTCCAAAAACCACCTCATGCACTATAAACATCTATAAATAAAGATAAAAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGACCGCGATGCTTTCCTCTATAACTAAAAATGGACCAAAATGTTTCATCTTTTTGGGGaaa                                                                                                                                                                                                                             >  2:103355/1‑250 (MQ=255)                                       aaaTTATTTCTATTGTAAATTAATTTCCCATCACCTCCGCTATATGTAAAGCTAACGTTTATGTGGATCGAAGCATCTTCCTCCTTCTTCTATCAAAAAACAACCTCATGCAATATAAACATCTATAAATAACGATAAAAATAAAATATTAATCAAACAAATAAAATGAAAAAGATTGTCCGCGATGCTTTCCTCTATGAGTCTAAATGGCACACAATGTTTCATCTTTTGGGGGAAAACTGTACAGTGtt                                                                                                                                                                                                                >  2:466101/1‑251 (MQ=255)                                        aaTTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCGCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTAGGAGTCAAAATGGCCCGAAATGGTTCATCTTTTGTGGGAAAACTGTGCAGTGTTg                                                                                                                                                                                                               <  2:356422/251‑1 (MQ=255)                                              ttCTATTGTAAATTAATTTCACATAACCTCCGCTATATGTAAAGGTAACGTGTCTGTGGCGCGACGCATCTTCCGCATTCTTCTCTCCAAAAACCACCTCATTCAATATAAACATCGAGAAATAAAGATAACAATAGAATATTAAGCCAACCTATAAACTGAAAAAGTTGGTCCGCGATGCTTTCCTCGAGGAGTCAATATGGCCCCAAATGTTTCATTTTGTTGGGGAAAACTAGGCAGTGTTGGCAGt                                                                                                                                                                                                          <  2:214151/250‑1 (MQ=255)                                                                 cacaTCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttct                                                                                                                                                                                      <  1:279323‑M2/251‑71 (MQ=255)                                                                 cacaTCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacacaaca                                                                                                                                                                                       <  2:2694/250‑1 (MQ=255)                                                                                atatGTACAGATAACGTTTCTGTGGCTCGCCGCATCTTCCTCATTCTTCTCACCAAAACCCCCCTCATGCAATATAAACCTCTATCAATACAGCTAACAATAGAATATTAAGCAAACAAATAAACTGAAAAAGATTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttcttatcaataagttaaatctaacctcttctctttttaatttttct                                                                                                                                                                       <  2:208331‑M2/251‑86 (MQ=255)                                                                                atatGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAATTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaattttt                                                                                                                                                                         >  2:88555‑M2/1‑166 (MQ=255)                                                                                      aaaGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatg                                                                                                                                                                 <  1:423849‑M2/251‑92 (MQ=255)                                                                                              cGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGAAAACCATAGAATATTAAGCCAACAAATAAACTAAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCCAATGTTTCATCTTTTGGGGGAAAACTGTGCCGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGTACGACTGCCCCTGGCGAtt                                                                                                                                                         >  2:43539/1‑251 (MQ=255)                                                                                               atatttgtggagcgacgaATCTTCCTCATTATTCCCACCAAAAACCACCTCATGCAATATAAACAACTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAGTGCCCCAAATGTTTCTTCTTTTTGGGGAAAACTGTTCATTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACTTTACGACTGCCCATCTCGAttt                                                                                                                                                        <  2:296813/239‑1 (MQ=255)                                                                                                 ttCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGGGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTa                                                                                                                                                       <  1:244998/250‑1 (MQ=255)                                                                                                            gACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATTCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTTAAAAAGTTTGTCCGCGATGCGTTCCTCTATGAGTCAAAAttgccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatc                                                                                                                                           >  2:397090‑M2/1‑138 (MQ=255)                                                                                                                                          accaccTCATGCAATATAAACATCTATAAATAAAGCTAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAAct                                                                                                             >  1:135485/1‑251 (MQ=255)                                                                                                                                               cccATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAATCCAACAAATAAACTGAAAAAGTTTGTCCGCGATTCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAActcttgc                                                                                                        <  2:411974/249‑4 (MQ=255)                                                                                                                                                     cAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgt                                                                                                  >  1:258230/1‑251 (MQ=255)                                                                                                                                                         ataAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattacttgcggtataacgcacagtatgg                                                                                               >  2:501233‑M2/1‑93 (MQ=255)                                                                                                                                                          taAACATCTATAAATAAAAATAACACTAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTACTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaaagcgcagcattactggcggtataacgcaaagtaagg                                                                                               <  2:470516‑M2/249‑158 (MQ=255)                                                                                                                                                              cATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTc                                                                                         <  1:343677/251‑1 (MQ=255)                                                                                                                                                                        taaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTcc                                                                               >  2:154474/1‑251 (MQ=255)                                                                                                                                                                         aaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttcacttttgaatttttcgtttatgagatgatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatgtcgaatagttcgatgcca                                                                              >  2:99851‑M2/1‑77 (MQ=255)                                                                                                                                                                                   aTAGAATATTAAGCCAACACATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcc                                                                    <  1:421778‑M2/251‑185 (MQ=255)                                                                                                                                                                                            tAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcctgaattaa                                                            <  1:11656‑M2/250‑193 (MQ=255)                                                                                                                                                                                             aaGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTg                                                          >  1:284411/1‑251 (MQ=255)                                                                                                                                                                                                      aaTAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcctgaattaaacgagtatctg                                                 >  1:334417‑M2/1‑48 (MQ=255)                                                                                                                                                                                                                aaaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCCAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTCCAAAACACAGTGTACAGACCGACTGCCCATGTCGCTTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGtt                                        >  1:215467/1‑250 (MQ=255)                                                                                                                                                                                                                    gTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCCTGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAAtgg                                   >  2:219044/1‑251 (MQ=255)                                                                                                                                                                                                                         tCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcctgaattaaacgagtatctgcaccccgccccgccaattc                              <  1:251682‑M2/251‑223 (MQ=255)                                                                                                                                                                                                                          ccGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAACTAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACACCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGAc                             >  1:68240/1‑251 (MQ=255)                                                                                                                                                                                                                                    ttCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcctgaattaaacgagtatctgcaccacgctccgccaattcataaccgca                     >  2:87517‑M2/1‑18 (MQ=255)                                                                                                                                                                                                                                                  aaaaTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGGCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTaa                                      <  1:482274/218‑1 (MQ=255)                                                                                                                                                                                                                                                  aaaaTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGAAGTCAAAATCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCCGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTaa                                      >  2:482274/1‑218 (MQ=255)                                                                                                                                                                                                                                                     aTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACGGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGGTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTaa  <  2:135485/251‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                           TTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAA  >  NC_000913/4542742‑4543236

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ 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.