New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 4532507	24 (0.560)	11 (0.280)	11/278	2.8	31.2%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	CP009273	= 4532803	26 (0.650)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

TGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGG  >  CP009273/4532658‑4532950                                                                                                                                                  |                                                                                                                                                    tgtgGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtgg                                                                                                                                                  >  1:626011‑M2/1‑146 (MQ=255)  gtgGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCACCAAATAAACTGACATAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggc                                                                                                                                                 >  2:358692‑M2/1‑145 (MQ=255)     gCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggcccc                                                                                                                                              >  2:638907‑M2/1‑142 (MQ=255)                           ttctCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTATGTCCGCGATGCTTTCCTCTATGAGTCCAAAtagccccaattgtcttgtatttatttgtt                                                                                                                        >  2:494712‑M2/1‑120 (MQ=255)                                 ccAAAAACCACCTCATGCAATATAAACATCTATAAATCAAGATAACAACAGAATATTAATCCAACAAATAAACTGAAAAAGTTTGTACGAGATGGTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTCTCGGGGAAAAcgg                                                                                                                  >  2:259194/1‑147 (MQ=255)                                 ccAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTCTGAGTCAAAATGGCCCCAAATGTTTCATCTTTCGCGGGAAAACtg                                                                                                                  >  1:223587/1‑149 (MQ=255)                                  cAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAAgtgt                                                                                                                 >  2:60083/1‑149 (MQ=255)                                         caccCCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttatt                                                                                                          >  1:187820‑M2/1‑106 (MQ=255)                                           ccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattat                                                                                                        <  1:124206‑M2/149‑46 (MQ=255)                                             taatgCAATATAAACATCCATAAATAAAGATACCAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGACGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatca                                                                                                      >  2:388590‑M2/3‑102 (MQ=255)                                               aTGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCACAATGCTTCACCTTTTGGGGGAAAACTGTGCAGTGTTGGcgg                                                                                                    >  2:555081/1‑147 (MQ=255)                                               aTGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCATCTATGAGTCAAAAtggccacaattgtcttgtatttatttgtttttttaactttattatcaat                                                                                                    <  2:263627‑M2/149‑50 (MQ=255)                                                      ataAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaa                                                                                             >  2:1813‑M2/1‑93 (MQ=255)                                                          aCATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCGGTCAAACTCGtt                                                                                         >  2:278366/1‑149 (MQ=255)                                                                 taaataaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaa                                                                                  <  1:612445/149‑1 (MQ=255)                                                                   aataaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCAGAGATGCTTTCTAATAAGATGCAAAATGGCCCCAAATGTTTCAACTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaacc                                                                                >  2:251511/1‑148 (MQ=255)                                                                      aaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAg                                                                             >  2:338522/1‑149 (MQ=255)                                                                               aaTAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGaa                                                                    <  1:567180/149‑1 (MQ=255)                                                                                  aGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGa                                                                 >  1:582914/1‑149 (MQ=255)                                                                                  aGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGa                                                                 >  2:177894/1‑149 (MQ=255)                                                                                      tatTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgttt                                                             <  2:45598‑M2/149‑89 (MQ=255)                                                                                          aaGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCAt                                                         >  1:426099/1‑149 (MQ=255)                                                                                             ccAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTc                                                      <  1:672683/149‑1 (MQ=255)                                                                                             ccAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTc                                                      >  1:333995/1‑149 (MQ=255)                                                                                                        aCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcc                                           >  1:396915‑M2/1‑43 (MQ=255)                                                                                                           gAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccgt                                        <  2:560653‑M2/149‑110 (MQ=255)                                                                                                           gAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGt                                        >  1:550200/1‑149 (MQ=255)                                                                                                               aaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGttttt                                    <  2:592875/149‑1 (MQ=255)                                                                                                                   ttGTCCTCGATGCTTTCCTCTATGAGTCAACATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaa                                <  2:580193/149‑1 (MQ=255)                                                                                                                   tcgTCCTCGATGCTTTCCTCTATGAGTCAAAATGTCCCCAAATGTTTCATCTTTTGGTGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaa                                <  2:85267/147‑1 (MQ=255)                                                                                                                    tgcccGCGATTCTTTCCTCTAAGAGTCAAAATGGCCCCAAATGTTTCATCATTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAACCTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaa                               <  2:215101/146‑1 (MQ=255)                                                                                                                        cgcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaaggaa                           >  1:564926/1‑149 (MQ=255)                                                                                                                        cgcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGCACAAAACGACTGCCCATGACGATTTAGAAATAGTTTTTTgaaaggaa                           >  1:53653/1‑149 (MQ=255)                                                                                                                                 ttCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcat                  >  1:212038‑M2/1‑18 (MQ=255)                                                                                                                                      ctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGCAGGCAGCATGAAAAt             >  2:109036/1‑149 (MQ=255)                                                                                                                                         cgAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTaa          <  1:259194/148‑1 (MQ=255)                                                                                                                                          gAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTaaa         <  1:177894/149‑1 (MQ=255)                                                                                                                                          gAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGATTTTTGAAAGGAAAGCAGCATGAAAATTaaa         >  1:554621/1‑149 (MQ=255)                                                                                                                                             tCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctcttttttttttttcttttatgagattatttctttcccataatccgccaaacctagcagcattcctggtgttcc      <  2:588465‑M2/149‑144 (MQ=255)                                                                                                                                                 aaTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTgg  <  2:550200/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                    TGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGG  >  CP009273/4532658‑4532950

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.