New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	33 (0.580)	18 (0.340)	13/256	2.6	38.8%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	26 (0.490)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

GCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATG  >  NC_000913/4542553‑4542825                                                                                                                                           |                                                                                                                                        gCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCaaa                                                                                                                                       <  1:291660/140‑1 (MQ=255)   cAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGAATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAAc                                                                                                                                      <  2:769939/140‑1 (MQ=255)      tAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgac                                                                                                                                  <  2:34663‑M1/140‑8 (MQ=255)      tAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgac                                                                                                                                  <  2:753406‑M1/140‑8 (MQ=255)      tAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgac                                                                                                                                  <  1:713997‑M1/140‑8 (MQ=255)         tgctgcTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactca                                                                                                                               <  2:495982‑M1/140‑11 (MQ=255)           ctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCatat                                                                                                                             <  2:315881/140‑1 (MQ=255)             gctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCa                                                                                                                                <  1:116626/135‑1 (MQ=255)             gctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCa                                                                                                                                >  2:116626/1‑135 (MQ=255)              ctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCat                                                                                                                          >  1:734640/1‑140 (MQ=255)               tCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCa                                                                                                                           >  2:689915/1‑138 (MQ=255)               tCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCa                                                                                                                           <  1:689915/138‑1 (MQ=255)                                gggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaat                                                                                                                      >  1:219436/1‑126 (MQ=255)                                gggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaat                                                                                                                      <  2:219436/126‑1 (MQ=255)                                    aagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtct                                                                                                    >  2:902204/1‑140 (MQ=255)                                     agaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAATAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                                                                                                   >  2:670759/1‑140 (MQ=255)                                     agaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                                                                                                   >  2:282569/1‑140 (MQ=255)                                     agaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                                                                                                   <  1:902204/140‑1 (MQ=255)                                                 aTAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttg                                                                                       >  1:386891‑M1/1‑90 (MQ=255)                                                  tAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgt                                                                                      <  1:885889‑M1/140‑52 (MQ=255)                                                       gAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggct                                                                                 <  1:308878‑M1/140‑57 (MQ=255)                                                                   agagaagagGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaaa                                                                     <  1:229273/140‑1 (MQ=255)                                                                          agGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatct                                                              <  1:548241‑M1/140‑76 (MQ=255)                                                                            gTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAAc                                                            >  2:246799/1‑140 (MQ=255)                                                                             tttGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt                                                           <  1:61797/140‑1 (MQ=255)                                                                             tttGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt                                                           <  1:796754/140‑1 (MQ=255)                                                                               tGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGt                                                         >  2:374476/1‑140 (MQ=255)                                                                                gATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGtt                                                        <  1:374476/140‑1 (MQ=255)                                                                                 aTTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttattta                                                       >  2:81061‑M1/1‑58 (MQ=255)                                                                                   ttAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttata                                                     <  2:386891‑M1/140‑85 (MQ=255)                                                                                   ttAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttata                                                     <  1:645558‑M1/140‑85 (MQ=255)                                                                                   ttAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttata                                                     <  2:368425‑M1/140‑85 (MQ=255)                                                                                    tAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatag                                                    <  1:358080‑M1/140‑86 (MQ=255)                                                                                     aaCTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata                                                   >  1:519/1‑140 (MQ=255)                                                                                                 aataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattatt                                        >  2:927373/1‑140 (MQ=255)                                                                                                 aataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattatt                                        >  2:166053/1‑140 (MQ=255)                                                                                                  ataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                       <  2:533020/140‑1 (MQ=255)                                                                                                   taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgca                                      >  1:772659‑M1/1‑41 (MQ=255)                                                                                                                aCAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggttttt                         <  2:772659‑M1/140‑113 (MQ=255)                                                                                                                aCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaattaa                         >  2:770331/1‑140 (MQ=255)                                                                                                                      aaataCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagag                   <  2:208286‑M1/140‑119 (MQ=255)                                                                                                                        ataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACAt                 <  1:246799/140‑1 (MQ=255)                                                                                                                          aCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagag                   <  1:848355‑M1/136‑119 (MQ=255)                                                                                                                          aCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagag                   >  2:848355‑M1/1‑18 (MQ=255)                                                                                                                           cAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc              <  1:282569/140‑1 (MQ=255)                                                                                                                           cAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc              >  2:4434/1‑140 (MQ=255)                                                                                                                             aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCt            <  1:927373/140‑1 (MQ=255)                                                                                                                                cAATTGGGGCCAAACTGTCCATATCATAAATAAGTGACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCg         <  2:663832/140‑1 (MQ=255)                                                                                                                                 aaTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGc        <  1:770331/140‑1 (MQ=255)                                                                                                                                   ttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCta      <  2:519/140‑1 (MQ=255)                                                                                                                                   ttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCta      >  2:161842/1‑140 (MQ=255)                                                                                                                                       ggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagagaagaatgaggaagatgc  >  1:598226‑M1/1‑5 (MQ=255)                                                                                                                                           |                                                                                                                                        GCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTG‑ATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATG  >  NC_000913/4542553‑4542825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.