New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	0 (0.000)	4 (0.320)	4/246	NT	33.3%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	16 (1.270)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

GCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACA  >  NC_000913/4542818‑4543171                                                                                                                                                                          |                                                                                                                                                                                          gCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                                                                                                                                 >  2:207831/1‑211 (MQ=255)    atatGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAAAAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTGGGGGGAAAACTGTGCAGTGTTg                                                                                                                                              <  1:207832/211‑1 (MQ=255)             gCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggcc                                                                                                                                                                                      <  2:263387‑M2/162‑6 (MQ=255)                aaCGTTTCGGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggcccca                                                                                                                                                                                   >  1:263388‑M2/1‑154 (MQ=255)                  cGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGACCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCAt                                                                                                                                                                         >  1:125882/1‑170 (MQ=255)                     ttCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGACCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCtt                                                                                                                                                                      <  2:125881/170‑1 (MQ=255)                                   gCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACt                                                                                                                                                         >  2:6764/1‑169 (MQ=255)                                      tCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgtg                                                                                                                                                      <  1:6764/169‑1 (MQ=255)                                            taaaaaaacatcccaaaaacccacctCATGCAATTTAAACATCTATAAAAAAAAGTAACAATAGAATATTAAGCCAAAAAATAAACTTAAAAAGTTTGTCCGCGAATCTTTCCTCTATGAGGCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataac                                         >  2:248232‑M2/13‑127 (MQ=255)                                                         cAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACt                                                                                                                                                         >  2:140942/1‑147 (MQ=255)                                                            aaaCC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgtg                                                                                                                                                      <  1:140943/147‑1 (MQ=255)                                                                   ccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTCTGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaattcaaacctcttctctttttaatttttcgtttataagattatttctttcccatattccgccaaaacgagaagcattactggcggtataacgcaaagaatggccagtctcttat                  <  1:248233‑M2/273‑170 (MQ=255)                                                                         gCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGa                                                                                                           >  2:256229/1‑178 (MQ=255)                                                                            atatAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACg                                                                                                        <  1:256230/178‑1 (MQ=255)                                                                               taAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgg                                                                                                                                                                  >  2:220804/1‑117 (MQ=255)                                                                                  aCATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTggggg                                                                                                                                                               <  1:220805/117‑1 (MQ=255)                                                                                                                                               ccGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattat                                                                                         <  1:124487‑M2/126‑99 (MQ=255)                                                                                                                                                  cgATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttc                                                                                      >  2:124486‑M2/1‑25 (MQ=255)                                                                                                                                                                aTGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCt     >  2:264199/1‑193 (MQ=255)                                                                                                                                                                  gAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGt                >  2:158104/1‑180 (MQ=255)                                                                                                                                                                   aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACa  <  1:264200/193‑1 (MQ=255)                                                                                                                                                                     tCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTccc             <  1:158105/180‑1 (MQ=255)                                                                                                                                                                          |                                                                                                                                                                                          GCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACC‑ACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACA  >  NC_000913/4542818‑4543171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ 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.