New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4977437 =	43 (0.950)	4 (0.090)	4/238	NT	8.6%	coding (500/1110 nt)	flgI	flagellar P‑ring protein
	?	NC_002947	4977484 =	44 (1.020)					coding (453/1110 nt)	flgI	flagellar P‑ring protein

GAAGTCGGGGCGATTGAGGTTCAGGGTCAGGGTATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACGGTGATGTCCACCACCTGGCCCGGCTT  >  NC_002947/4977340‑4977633                                                                                                                                                 |                                                                                                                                                      gAAGTCGGGGCGATTGAGGTTCAGGGTCAGGGTATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCTGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCaaa                                                                                                                                                  <  1:819334/150‑1 (MQ=255)  ctgcgcggcggcagcctgttgatgaccccgctcaagggtatcgacggcaacgtttacgccattgcccagggcaacctggtcgtgggtggctttgacGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAg                                                                                                                                                 >  2:33394‑M1/97‑150 (MQ=255)            gATTGAGGTTCAGGGTCAGGGTATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGa                                                                                                                                       >  2:324926/1‑150 (MQ=255)                   gTTCAGGGTCAGGGTATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGtt                                                                                                                                <  1:500453/150‑1 (MQ=255)                      cagggtccgggtATTCCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCCCCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGcc                                                                                                                             <  1:758345/150‑1 (MQ=255)                       agggtcagggtATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGccc                                                                                                                            <  2:929479/150‑1 (MQ=255)                           tcagggtATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTggg                                                                                                                        <  1:602565/150‑1 (MQ=255)                             agggtATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTgg                                                                                                                         >  2:946212/1‑147 (MQ=255)                             agggtATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTgg                                                                                                                         <  1:946212/147‑1 (MQ=255)                                gtATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATg                                                                                                                   <  1:324926/150‑1 (MQ=255)                                 tATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACAGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATgg                                                                                                                  >  1:315374/1‑150 (MQ=255)                                      cccTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTaa                                                                                                             >  2:759067/1‑150 (MQ=255)                                      cccTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTaa                                                                                                             >  1:1191721/1‑150 (MQ=255)                                          ggTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGt                                                                                                         >  1:1163620/1‑150 (MQ=255)                                                  ccGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCg                                                                                                 >  1:997276/1‑150 (MQ=255)                                                        ggTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATAccc                                                                                           >  2:514082/1‑150 (MQ=255)                                                          tACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAg                                                                                                                                   >  2:1053960/1‑108 (MQ=255)                                                          tACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAg                                                                                                                                   <  1:1053960/108‑1 (MQ=255)                                                          tACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCtt                                                                                         <  2:997276/150‑1 (MQ=255)                                                              gCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTg                                                                                                       >  1:650645/1‑132 (MQ=255)                                                              gCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTg                                                                                                       <  2:650645/132‑1 (MQ=255)                                                                aCGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCg                                                                                                 <  1:238545/136‑1 (MQ=255)                                                                aCGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCg                                                                                                 >  2:238545/1‑136 (MQ=255)                                                                 cGCTCGACACTGGCACCACCCGCGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCGCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCggg                                                                                  <  1:756320/150‑1 (MQ=255)                                                                  gCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCgggg                                                                                 >  1:405049/1‑150 (MQ=255)                                                                   cccGACACTGGCACCCCCCGCGACACCGCCAGCCGCCGGCACTTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGCGCTCAAAGCCACCCACTCCCAAGTTGCCCTGGGCAATGGCGTAAACGTCTCCGTCGATACCCTTGAGCGGGGt                                                                                <  2:315374/148‑1 (MQ=255)                                                                   cTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGt                                                                                >  2:3716/1‑150 (MQ=255)                                                                       acacTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGtcatc                                                                            <  1:3716/150‑1 (MQ=255)                                                                       acacTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTCGCCGTCGa                                                                                                <  1:709428/130‑1 (MQ=255)                                                                       acacTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTAGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGa                                                                                                >  2:709428/1‑130 (MQ=255)                                                                           acctggtcgtgggtggctttgacGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCaaa                                                                                                                                                  >  1:906935‑M1/24‑76 (MQ=255)                                                                           acctggtcgtgggtggctttgacGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCaaa                                                                                                                                                  <  2:906935‑M1/53‑1 (MQ=255)                                                                                    ccGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTTGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGc                                                                                                                 >  1:781475/1‑100 (MQ=255)                                                                                    ccGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTTGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGc                                                                                                                 <  2:781475/100‑1 (MQ=255)                                                                                    ccGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTgccgc                                                               >  1:284901/1‑150 (MQ=255)                                                                                    ccGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTgccgc                                                               >  2:492884/1‑150 (MQ=255)                                                                                           ctttgacgccgagggccgtgacggctcgaagatcactgtcaacgtgccgtcggcGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAg                                                        >  2:33394‑M2/55‑150 (MQ=255)                                                                                            tttgacgccgagggccgtgacggctcgaagatcactgtcaacgtgccgtcggcGTCAAAGCCACCCACGACCAGGt                                                                                                                                 <  2:906935‑M2/23‑1 (MQ=255)                                                                                            tttgacgccgagggccgtgacggctcgaagatcactgtcaacgtgccgtcggcGTCAAAGCCACCCACGACCAGGt                                                                                                                                 >  1:906935‑M2/54‑76 (MQ=255)                                                                                             ggCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGc                                                      >  1:1142385/1‑150 (MQ=255)                                                                                              gCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGct                                                     >  2:693402/1‑150 (MQ=255)                                                                                                cAGCCGACGGCACGTTGACAGTGATCTTCGAGCCATCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGctct                                                   >  1:1001439/1‑150 (MQ=255)                                                                                                 aGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCtt                                                  >  1:546303/1‑150 (MQ=255)                                                                                                    CGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGa                                               >  1:492884‑M1/1‑150 (MQ=255)                                                                                                              gacggctcgaagatcactgtcaacgtgccgtcggcGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATc                                     <  1:33394‑M2/115‑1 (MQ=255)                                                                                                                 aCAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATcgac                                  <  1:514082/150‑1 (MQ=255)                                                                                                                 aCAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATcgac                                  >  1:560181/1‑150 (MQ=255)                                                                                                                        tCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACgg                           >  2:1067921/1‑150 (MQ=255)                                                                                                                             gAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACGGTGATg                      >  2:543106/1‑150 (MQ=255)                                                                                                                               gCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACGGTGATGTc                    <  2:546303/150‑1 (MQ=255)                                                                                                                               gCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACGGTGATGTc                    <  2:405049/150‑1 (MQ=255)                                                                                                                                 cGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACGGTGATGTcca                  <  2:619158/150‑1 (MQ=255)                                                                                                                                       ggCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCggg                                                                                  >  2:900577/1‑80 (MQ=255)                                                                                                                                       ggCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCggg                                                                                  <  1:900577/80‑1 (MQ=255)                                                                                                                                                 gTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGCAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACGGTGATGTCCACCACCTGGCCCGGCtt  >  1:1152033/1‑150 (MQ=255)                                                                                                                                                 |                                                                                                                                                      GAAGTCGGGGCGATTGAGGTTCAGGGTCAGGGTATTGCCCTGGTTGAAGCCGCTCGGTACCGCACGCTCGACACTGGCACCACCCGGGATACGGCCAGCCGACGGCACGTTGACAGTGATCTTCGAGCCGTCACGGCCCTCGGCGTCAAAGCCACCCACGACCAGGTTGCCCTGGGCAATGGCGTAAACGTTGCCGTCGATACCCTTGAGCGGGGTCATCAACAGGCTGCCGCCGCGCAGGCTCTTCGAGTTACCGATCGACGACACGGTGATGTCCACCACCTGGCCCGGCTT  >  NC_002947/4977340‑4977633

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