New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	0 (0.000)	22 (0.300)	21/526	NT	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

CCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAAG  >  NC_000913/1978202‑1978766                                                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                         cccaccgaGAATAACCAACATGATATTGAAGCGGATTCATCACACCCCGTGAAGTCGCGGGGAAGACCCGGTAAAGAATAAGTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAGCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGAGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATg                                                                                                                                                                                                                                                                          <  1:530727/301‑1 (MQ=255)         gAATAACCAACTTTATGTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATCCACCGGAGGGGGGCTGCGATTTTCAATAATGCTTGATGCATATCACACAAAACACTCAATTACTTAACATAAATGtatactt                                                                                                                                                                                                                                                                   >  2:651607‑M1/1‑293 (MQ=255)         aaagaaCCAACTTTATTTGTATGCAGTTTCACATCACGCCGGGATGTCTCCGGCAAGCACCGGTAAAAAAGAAGTAGTATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTAAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATgtataagtc                                                                                                                                                                                                                                                                  <  1:728823/297‑9 (MQ=255)                   cTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCCCATCCAACGGATCGGGGCTGCGATTTTCAATAATGCGTGCTGCAGATCACACAACACCCTCAATTACTTAACATAAATGtataagtctacctttttt                                                                                                                                                                                                                                                        >  1:376963‑M1/1‑283 (MQ=255)                                     ttaccGCACCCCGTGATGTCTCCGGGAAACCCCTGTAAAAAATAAGTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATTGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATTAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                                                                                                                                                                                      <  1:685832‑M1/299‑37 (MQ=255)                                                                               taatTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaac                                                                                                                                                                                            <  1:148246‑M1/301‑79 (MQ=255)                                                                                                             gCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtaatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaattgggatgttgcgatca                                                                                                                                                              >  1:628212‑M1/1‑193 (MQ=255)                                                                                                                     cAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAAGGTGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgagtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgctcacagtcaaaaa                                                                                                                                                      >  2:246495‑M1/1‑185 (MQ=255)                                                                                                                     aagAACCAACTTTTTGGTTTAATATGGCATTACAAATAGAAATGGGTCTGTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGTGCTGCGATTTTCAATAATGCGTGATTCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaat                                                                                                                                                      <  2:187023‑M1/300‑117 (MQ=255)                                                                                                                        accctccttgttGGTTTAAAATTGCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTTTACTCGTCACTACACGCACATCCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatctaaatgggatgttgcgcacagtcaaaata                                                                                                                                                     <  1:254420‑M1/294‑118 (MQ=255)                                                                                                                        aaCCACCTTTTTGGTTTAATATGTCCTTACAAAGAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACAGACAACGGAGGTGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataac                                                                                                                                                   <  1:159372‑M1/301‑120 (MQ=255)                                                                                                                        aaCCAACTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataac                                                                                                                                                   <  1:460015‑M1/301‑120 (MQ=255)                                                                                                                                                            aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgc                                                                                                                                                                 >  1:477715‑M1/1‑146 (MQ=255)                                                                                                                                                            aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgc                                                                                                                                                                 <  2:477701‑M1/251‑106 (MQ=255)                                                                                                                                                                  ttcTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTAATAGTCACTACACGCACATACAACGGATGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACATAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgc                                                                                                         <  2:524726‑M1/300‑162 (MQ=255)                                                                                                                                                                  gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttccatctgttaaaagttttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataataatctgctatcaatgatcactttcatg                                                                                                          >  1:512488‑M1/1‑140 (MQ=255)                                                                                                                                                                  gTCTTTACAATTATCTAAGATTTTTCCTAAATCGACGCAAATGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaat                                                                                                                       <  2:315942‑M1/287‑148 (MQ=255)                                                                                                                                                                             tATATAAGATTTTTCCTAAAGCGACGCAAATGTAATCGTAACTACACGGACATACAACGGAGGGGGGCTGAGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTAAATTACTTAACATAAATGtataagtcatacttttgttgtgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagata                                                                                              <  2:512465‑M1/301‑173 (MQ=255)                                                                                                                                                                                                       caaattgaacgtgaaatacacgaacagacaactGAGGGGGCCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAGTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccg                                                                    <  1:246501‑M1/285‑199 (MQ=255)                                                                                                                                                                                                       cAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaatacc                                                                                                   >  2:641086‑M1/1‑103 (MQ=255)                                                                                                                                                                                                                             caaaaaaaacggagggGGGGTGCGATTTTAAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAAGGtataagtcatacttttggtttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatac                                               <  2:628187‑M1/293‑220 (MQ=255)                                                                                                                                                                                                                                                     aTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactaaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaaagccaacaatcaacttaaa                      >  2:318332‑M1/1‑57 (MQ=255)                                                                                                                                                                                                                                                                         aagAACACACAAAACACTAAATTAATTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaaaggcaacaatcaacttaatgttaatgaaatgttttacat  <  1:318338‑M1/300‑265 (MQ=255)                                                                                                                                                                                                                                                                          aGATCACACAAAACACTAAATTACTTAACATAAATG                                                                                                                                                                                                                                                                          >  2:497229‑M1/1‑36 (MQ=255)                                                                                                                                                                                                                                                                                           cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaactaatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttac                                                                      >  1:744561‑M1/1‑19 (MQ=255)                                                                                                                                                                                                                                                                                           cAATTACTGAAAATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttac                                                                      <  2:744534‑M1/215‑197 (MQ=255)                                                                                                                                                                                                                                                                                                        tAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaatacc                                                                                                   >  2:174926‑M1/1‑6 (MQ=255)                                                                                                                                                                                                                                                                                                        tAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaatacc                                                                                                   <  1:174933‑M1/173‑168 (MQ=255)                                                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                         CCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAAG  >  NC_000913/1978202‑1978766

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ 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.