New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	41 (0.950)	16 (0.400)	14/224	2.0	30.5%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	35 (0.880)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

TATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  NC_000913/4542547‑4542838                                                                                                                                                |                                                                                                                                                     cgttctgccagtaATTCTGCTCGTTTTGGCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAtttt                                                                                                                                                  <  1:32165‑M1/142‑5 (MQ=255)   taCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgac                                                                                                                                               <  3:101358‑M1/149‑8 (MQ=255)   taCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTc                                                                                                                                               <  2:16217/149‑1 (MQ=255)       gCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcat                                                                                                                                           <  5:56953‑M1/149‑12 (MQ=255)        ccAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTAATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAAGTTATTGATAATAAATTTAAAAAAACAAATAAAAAAAATACAATTGGGGCCAtttt                                                                                                                                                  >  2:32165‑M1/1‑137 (MQ=255)          aGTAATGCTGCTCGTTTTGCCGGTTTATTTGAATGAAATAATCTCATAAACGAAAATTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGTGCCaa                                                                                                                                                     <  2:171713/136‑1 (MQ=255)          aGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCaa                                                                                                                                                     >  1:171713/1‑136 (MQ=255)          aGTAATGCTGCGCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCa                                                                                                                                        <  2:202591/149‑1 (MQ=255)              aTGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataa                                                                                                                                     <  3:195644/148‑1 (MQ=255)               tgctgcTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgac                                                                                                                                               >  1:97097‑M1/1‑130 (MQ=255)               tgctgcTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgac                                                                                                                                               <  2:97097‑M1/137‑8 (MQ=255)                                       ggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaacttttt                                                                                                               >  3:119243‑M1/1‑106 (MQ=255)                                       ggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaacttttt                                                                                                               <  4:119243‑M1/145‑40 (MQ=255)                                        gaaagataTAATCGCATAAACGAAAAATTAAAAAGAGAAGCGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAAGACAAGACAATTGGGGCCAAACTGTCCAGATCATAAATAAGGTACGTATTTTTTCTCAAGCa                                                                                                           >  4:180811/1‑148 (MQ=255)                                        gaaagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtc                                                                                                                  >  1:38130/1‑141 (MQ=255)                                        gaaagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtc                                                                                                                  <  2:38130/141‑1 (MQ=255)                                               ataatCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAata                                                                                                   >  6:166960/1‑149 (MQ=255)                                                    ctcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggct                                                                                              >  1:145191‑M1/1‑93 (MQ=255)                                                     tcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaa                                                                                              >  5:170816/1‑148 (MQ=255)                                                          aaCGAAAAATTAAAAAGAGAAGATGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGa                                                                                        <  3:132167/149‑1 (MQ=255)                                                           aCGAAAAATTAAAAGGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAtttt                                                                                                                                                  >  1:98186‑M1/1‑86 (MQ=255)                                                           aCGAAAAATTAAAACGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAtttt                                                                                                                                                  <  2:98186‑M1/90‑5 (MQ=255)                                                           aCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatatt                                                                                       <  2:145191‑M1/149‑64 (MQ=255)                                                             gAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttttt                                                                                                                   >  2:180375/1‑119 (MQ=255)                                                                   ttAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCaa                                                                                                              <  6:10832/118‑1 (MQ=255)                                                                   ttAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGc                                                                                >  8:90798/1‑148 (MQ=255)                                                                      aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatc                                                                            >  1:43381‑M1/1‑75 (MQ=255)                                                                      aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATc                                                                             <  7:90798/148‑1 (MQ=255)                                                                          gagaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt                                                                        <  6:170816/149‑1 (MQ=255)                                                                             aagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGtt                                                                     >  3:14343/1‑149 (MQ=255)                                                                              agagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt                                                                    <  5:166960/149‑1 (MQ=255)                                                                                  gTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata                                                                <  8:2156/149‑1 (MQ=255)                                                                                            aCTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattat                                                      >  1:121661/1‑149 (MQ=255)                                                                                              ttATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGTGGCCAAACTGTCCATATCATAAATAATTTACGTATTTTTTCTCAAGCATAAAAATAtt                                                                                                 <  5:182145/104‑1 (MQ=255)                                                                                                   gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaa                                                                                             >  8:181948/1‑103 (MQ=255)                                                                                                   gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaa                                                                                             <  7:181948/103‑1 (MQ=255)                                                                                                   gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTa                                                 <  4:8093/147‑1 (MQ=255)                                                                                                   gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAta                                               >  3:8093/1‑148 (MQ=255)                                                                                                      aataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGCCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt                                                                        >  2:200346/1‑121 (MQ=255)                                                                                                      aataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGCCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt                                                                        <  1:200346/121‑1 (MQ=255)                                                                                                        taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                               >  1:230451/1‑128 (MQ=255)                                                                                                        taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                               <  2:230451/128‑1 (MQ=255)                                                                                                          aaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggttt                                        <  2:43381‑M1/149‑111 (MQ=255)                                                                                                                aaaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                  <  2:121661/149‑1 (MQ=255)                                                                                                                aaaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGACCATATAATAAATAAGTTACGTATTTTTTCTCAATCCTAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                  <  3:180811/149‑1 (MQ=255)                                                                                                                     aCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATc                             <  4:14343/149‑1 (MQ=255)                                                                                                                               aCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                                    <  4:124052/116‑1 (MQ=255)                                                                                                                               aCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                                    >  3:124052/1‑116 (MQ=255)                                                                                                                                 gaaaCATTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCtata                 >  5:33145/4‑149 (MQ=255)                                                                                                                                 aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattat                                                      <  5:44617/112‑1 (MQ=255)                                                                                                                                 aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattat                                                      >  6:44617/1‑112 (MQ=255)                                                                                                                                      aaTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttg                                     >  7:25723‑M1/1‑11 (MQ=255)                                                                                                                                      aaTTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttg                                     <  8:25723‑M1/124‑114 (MQ=255)                                                                                                                                        ttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAtt                                               <  7:71073/112‑1 (MQ=255)                                                                                                                                        ttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAtt                                               >  8:71073/1‑112 (MQ=255)                                                                                                                                           gggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAGAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCt        >  5:50417/1‑148 (MQ=255)                                                                                                                                                attttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgt                                                                                <  7:144716‑M1/71‑71 (MQ=255)                                                                                                                                                attttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgt                                                                                >  8:144716‑M1/1‑1 (MQ=255)                                                                                                                                                aaaCTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGtt  >  7:16988/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                     TATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  NC_000913/4542547‑4542838

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ 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.