New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	3776206 =	46 (0.940)	3 (0.060)	3/238	NT	6.6%	coding (208/363 nt)	PP_3338	cytochrome bd‑type quinol oxidase
	?	NC_002947	3776224 =	41 (0.880)					coding (226/363 nt)	PP_3338	cytochrome bd‑type quinol oxidase

GTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTCGCTTGGCTGATCCGACTGTTCA  >  NC_002947/3776085‑3776373                                                                                                                                             |                                                                                                                                                      gTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCt                                                                                                                                             <  1:812443/150‑1 (MQ=255)  ttCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCtt                                                                                                                                            <  2:1050546/150‑1 (MQ=255)  ttCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCtt                                                                                                                                            >  2:784290/1‑150 (MQ=255)  tgcAGCATGCACAACCTGCTCTAGTTCATGGCGGTGCCGATCCTGGGGCTGGTGACGTGCTACGGGCTGCTACGGGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCtt                                                                                                                                            <  1:925652/148‑1 (MQ=255)      gCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCa                                                                                                                                        >  2:300198/1‑150 (MQ=255)       cATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCAt                                                                                                                                       >  2:598459/1‑150 (MQ=255)          gCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTGGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAg                                                                                                                                    >  1:78073/1‑150 (MQ=255)            acaACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGcc                                                                                                                                  >  2:717029/1‑150 (MQ=255)            acaACCTGCTCTGGTTCATGCCGGTGCCGACCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGcc                                                                                                                                  >  2:631284/1‑150 (MQ=255)               aCCTGCTCTGGTTCATGCCGGTGCCGAGCCTGGTGCTGGTGACGGGCGACGGGCTGCTACGGGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCATGGAGCAT‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCtgt                                                                                                                               <  1:1260399/150‑1 (MQ=25)                 tgcctaccagcatgaagccgtggctctggcgcggcgctgcggcttcccagatgctgatcgacggcgggatgatgtttgtccacaggctgatgccaaggccgctgtagcccagattttcctgggcTACAGCGGCCTTGGCATCAGCCtgtg                                                                                                                              <  1:185449‑M2/26‑1 (MQ=255)                 cTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTgg                                                                                                                             <  1:717029/150‑1 (MQ=255)                    ctctGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCa                                                                                                                          >  1:586796/1‑150 (MQ=255)                         gTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAAcat                                                                                                                     <  1:300198/150‑1 (MQ=255)                             aTGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACatcatc                                                                                                                 <  2:798028/150‑1 (MQ=255)                             aTGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACatcatc                                                                                                                 <  2:251116/150‑1 (MQ=255)                                          ctggggcggcgctgcggcttcccagatgctgatcgacggcgggatgatgtttggccacaggctgatgccaaggccgctgtagcccagattttcctgggcTACAGCGGCCtt                                                                                                                                            <  1:1059728‑M2/12‑1 (MQ=255)                                          ctggggcggcgctgcggcttcccagatgctgatcgacggcgggatgatgtttggccacaggctgatgccaaggccgctgtagcccagattttcctgggcTACAGCGGCCtt                                                                                                                                            >  2:1059728‑M2/100‑111 (MQ=255)                                             tggtgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGc                                                                                                                                         >  2:276931/1‑110 (MQ=255)                                             tggtgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGc                                                                                                                                         <  1:276931/110‑1 (MQ=255)                                                tgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATccc                                                                                                               <  2:868184/133‑1 (MQ=255)                                                tgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATccc                                                                                                               >  1:868184/1‑133 (MQ=255)                                                        aCGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGcc                                                                                      <  1:217838/150‑1 (MQ=255)                                                         cGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCg                                                                                     <  1:784290/150‑1 (MQ=255)                                                            gCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCaaa                                                                                                                        >  1:243058/1‑112 (MQ=255)                                                            gCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCaaa                                                                                                                        <  2:243058/112‑1 (MQ=255)                                                                     tgctACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCAAC‑ATTTTCCTGGGCTGCTGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGcccc                                                                         >  1:477910/1‑150 (MQ=255)                                                                       ttgcGTGCCACGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTAAAGCCGCCTTGGCAGCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCag                                                                       >  1:1119233/4‑150 (MQ=25)                                                                       ctACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCag                                                                       >  1:703123/1‑150 (MQ=255)                                                                               cGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAgg                                                               <  1:631284/150‑1 (MQ=255)                                                                               cGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAgg                                                               <  2:776757/150‑1 (MQ=255)                                                                                   gCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTc                                                           >  2:911249/1‑150 (MQ=255)                                                                                          aCGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTgg                                                    <  1:510257/150‑1 (MQ=255)                                                                                                cacaggctgatgccaaggccgctgtaGCCCAG‑GAAAATCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGACAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCGCCAGAGCCACGGCTTCATGCTGGTAGGca                                              <  1:185449‑M1/124‑1 (MQ=255)                                                                                                  tACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGcaca                                            <  1:598459/150‑1 (MQ=255)                                                                                                  tACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGcaca                                            >  1:671598/1‑150 (MQ=255)                                                                                                   acacGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCacac                                           >  2:1256811/1‑150 (MQ=255)                                                                                                      cGCCGTTCTTGCTGACCCTTGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCacac                                           <  2:806382/147‑1 (MQ=255)                                                                                                      cGCCGTTCTTGCTGACCCTTGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCacac                                           >  1:806382/1‑147 (MQ=255)                                                                                                       gcagTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGtt                                       >  1:1282655/4‑150 (MQ=255)                                                                                                           ttCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATc                                   <  2:1282655/150‑1 (MQ=255)                                                                                                              aaggccgctgtaGCCCAGGAAAATC‑TGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCag                                                                       >  2:1059728‑M1/13‑111 (MQ=255)                                                                                                              aaggccgctgtaGCCCAGGAAAATC‑TGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCag                                                                       <  1:1059728‑M1/99‑1 (MQ=255)                                                                                                                gCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGcc                              <  2:586796/150‑1 (MQ=255)                                                                                                                     cccTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATc                                                                                               <  1:1123700/80‑1 (MQ=255)                                                                                                                     cccTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATc                                                                                               >  2:1123700/1‑80 (MQ=255)                                                                                                                      ccTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTc                        >  2:714903/1‑150 (MQ=255)                                                                                                                            CCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATc                                   >  2:401536‑M1/1‑133 (MQ=255)                                                                                                                            CCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATc                                   <  1:401536‑M1/133‑1 (MQ=255)                                                                                                                            CCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTCGCTTgg                  >  1:714903‑M1/1‑150 (MQ=255)                                                                                                                                      ccTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTCGCTTGGCTGATCCGa         <  2:671598/150‑1 (MQ=255)                                                                                                                                          ggcTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTCGCTTGGCTGATCCGACTGt     <  2:925707‑M2/147‑1 (MQ=255)                                                                                                                                            cTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATACTGCCCAGTTCGCTTGGCTGATCCGACTGTTc   <  2:703123‑M2/149‑1 (MQ=255)                                                                                                                                             tACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTCGCTTGGCTGATCCGACTGTTCa  <  1:1256811/150‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                      GTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTCGCTTGGCTGATCCGACTGTTCA  >  NC_002947/3776085‑3776373

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.