New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4957603 =	40 (1.420)	4 (0.160)	4/216	NT	10.2%	intergenic (‑41/+122)	fliH/fliG	flagellar assembly protein FliH/flagellar motor switch protein
	?	NC_002947	4957693 =	35 (1.420)					intergenic (‑131/+32)	fliH/fliG	flagellar assembly protein FliH/flagellar motor switch protein

CCGGTTCGGGCTCCGGTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCG  >  NC_002947/4957454‑4957752                                                                                                                                                      |                                                                                                                                                      ccggtacgggtcagcgacgtggaaaccgcgcagaaagaaatcctcaccattgcccggcgcatggccgaggccggcgagatcgtgctcggcggcaagggcgccgaggaaatgatctaaggtattcgcgatcccatagccgacgccgccttt                                                                                                                                                       <  1:183774‑M1/1‑1 (MQ=255)  cGGTTCGGGCTCCGGTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCtt                                                                                                                                                      <  1:240758/150‑1 (MQ=255)     ttCGGGCTCCGGTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTa                                                                                                                                                   >  2:119468/1‑150 (MQ=255)        gggCTCCGGTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCTAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGa                                                                                                                                                <  2:384626/150‑1 (MQ=255)         ggtcagcgacgtggaaaccgcgcagaaagaaatcctcaccattgcccggcgcatggccgaggccggcgagatcgtgctcggcggcaagggcgccgaggaaatgatctaaggtattcgcgatcccatagccgacgccgccttTTGTAGGAg                                                                                                                                               <  1:699103‑M1/9‑1 (MQ=255)           cTCCGGTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCg                                                                                                                                             >  1:141169/1‑150 (MQ=255)            tCCGGTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCgg                                                                                                                                            <  2:135380/150‑1 (MQ=255)               ggTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGtt                                                                                                                                         >  2:388194/1‑150 (MQ=255)               cgacgtggaaaccgcgcagaaagaaatcctcaccattgcccggcgcatggccgaggccggcgagatcgtgctcggcggcaagggcgccgaggaaaggatctaaggtattcgcgatcccatagccgacgccgccttTTGTAGGAGCGGGtt                                                                                                                                         >  2:183774‑M1/136‑150 (MQ=255)                      gaaaccgcgcagaaagaaatcctcaccattgcccggcgcatggccgaggccggcgagatcgtgctcggcggcaagggcgccgaggaaatgatctaaggtattcgcgatcccatagccgacgccgccttTTGTAg                                                                                                                                                  >  1:216783‑M1/129‑134 (MQ=255)                      gaaaccgcgcagaaagaaatcctcaccattgcccggcgcatggccgaggccggcgagatcgtgctcggcggcaagggcgccgaggaaatgatctaaggtattcgcgatcccatagccgacgccgccttTTGTAg                                                                                                                                                  <  2:216783‑M1/6‑1 (MQ=255)                            aGCTTGGCAGCGTCGACACGTCCACGTCCTCGAGGTCGCGGGCACGGATCAGGTCGCTCGGGTGGTGCCGGTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGc                                                                                                                            <  1:13288/150‑1 (MQ=255)                              cTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGAGAGTTCCCCagcgttcgcct                                                                                                                          <  2:575146/150‑8 (MQ=255)                               ttGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTc                                                                                                                         <  1:255484/150‑1 (MQ=255)                                            cacaTCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAAcc                                                                                                            >  2:293685/1‑150 (MQ=255)                                                  cACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGAtt                                                                                                      <  2:97270/150‑1 (MQ=255)                                                  cACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGAtt                                                                                                      >  2:265426/1‑150 (MQ=255)                                                      cccTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCa                                                                                                  >  1:319339/1‑150 (MQ=255)                                                       ccTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGATAACCTCGATTGCCAg                                                                                                 >  2:547712/1‑150 (MQ=255)                                                           gAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGAcc                                                                                             <  1:631201/150‑1 (MQ=255)                                                              tggccgaggccggcgagatcgtgctcggcggcaagggcgccgaggaaatgatctaatgtattcgcgatcccatagccgacgccgccttTTGTAGGAGAGGGTTTACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGAc                                                                                          >  1:324259‑M1/89‑150 (MQ=255)                                                                   gggCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTc                                                                                                          <  2:657184/129‑1 (MQ=255)                                                                   gggCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTc                                                                                                          >  1:657184/1‑129 (MQ=255)                                                                    aggccggcgagatcgtgctcggcggcaagggcgccgaggaaatgatctaaggtattcgcgatcccatagccgacgccgccttTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTc                                                                                    >  1:692001‑M1/83‑150 (MQ=255)                                                                        cGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCgg                                                                                <  1:265426/150‑1 (MQ=255)                                                                           aTCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTa                                                                                                                                                   <  1:42772/80‑1 (MQ=255)                                                                           aTCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTa                                                                                                                                                   >  2:42772/1‑80 (MQ=255)                                                                           aTCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCa                                                                                                  >  1:146596/1‑129 (MQ=255)                                                                           aTCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCa                                                                                                  <  2:146596/129‑1 (MQ=255)                                                                              aGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAAc                                                                          <  1:344047/150‑1 (MQ=255)                                                                              aGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAAc                                                                          <  1:119468/150‑1 (MQ=255)                                                                                            gtgtTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTCCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACaaaa                                                            <  1:40263/150‑1 (MQ=255)                                                                                             tgtTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAg                                                           >  2:217064/1‑150 (MQ=255)                                                                                                tCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAggcg                                                        <  1:217064/150‑1 (MQ=255)                                                                                                tCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAggcg                                                        <  2:522256/150‑1 (MQ=255)                                                                                                 cTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAggcgg                                                       >  1:3046/1‑150 (MQ=255)                                                                                                           cATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCtt                                                                                                                                                      >  1:254617/1‑45 (MQ=255)                                                                                                           cATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCtt                                                                                                                                                      <  2:254617/45‑1 (MQ=255)                                                                                                            aTGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATg                                            <  1:744233/150‑1 (MQ=255)                                                                                                                   cATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATcgc                                     <  1:388194/150‑1 (MQ=255)                                                                                                                    aTGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTGTGGGATcgcg                                    >  1:12384/1‑150 (MQ=255)                                                                                                                      gTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTc                                                                                                                         <  1:176921/63‑1 (MQ=255)                                                                                                                      gTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTc                                                                                                                         >  2:176921/1‑63 (MQ=255)                                                                                                                      gTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGaa                                  <  2:464493/150‑1 (MQ=255)                                                                                                                      gTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGaa                                  <  2:319339/150‑1 (MQ=255)                                                                                                                          ttcgcgatcccatagccgacgccgccttTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCgg                                                                                <  2:214389‑M1/72‑1 (MQ=255)                                                                                                                          ttcgcgatcccatagccgacgccgccttTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCgg                                                                                >  1:214389‑M1/29‑100 (MQ=255)                                                                                                                          tcAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGAc                                                                                              <  1:39189/86‑1 (MQ=255)                                                                                                                          tcAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGAc                                                                                              >  2:39189/1‑86 (MQ=255)                                                                                                                              aCCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAg                          <  1:293685/150‑1 (MQ=255)                                                                                                                                cATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAggcggc                                                      >  1:221524/1‑120 (MQ=255)                                                                                                                                cATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAggcggc                                                      <  2:221524/120‑1 (MQ=255)                                                                                                                                   gTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCAt                     >  1:213835/1‑150 (MQ=255)                                                                                                                                    ttCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCAtt                    <  2:213835/150‑1 (MQ=255)                                                                                                                                          cGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCg              >  1:451788/1‑150 (MQ=255)                                                                                                                                                    ccTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACaaaa                                                            <  1:705570/94‑1 (MQ=255)                                                                                                                                                    ccTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACaaaa                                                            >  2:705570/1‑94 (MQ=255)                                                                                                                                                    ccTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAAGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTgc    >  1:656813/1‑150 (MQ=255)                                                                                                                                                      TTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTgccg  <  1:30929‑M1/150‑1 (MQ=255)                                                                                                                                                      TTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTgccg  <  1:441690‑M1/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                      CCGGTTCGGGCTCCGGTTCCGGGTCGAAGCTTGGCAGCGTCCACACATCCACGCCCTCGAGGTCGCGGGCACGGATCAGGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCG  >  NC_002947/4957454‑4957752

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.