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

TGGCCTACCCGCAAATCGCCGCCCGCTGGTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTC  >  NC_002947/3776057‑3776351                                                                                                                                                      |                                                                                                                                                   tGGCCTACCCGCAAATCGCCGCCCGCTGGTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTgg                                                                                                                                                    <  1:1032596/150‑1 (MQ=255) gaacagtcggatcagccaagcgaactgggcagtatgaacagtgtgcctaccagcatgaagccttggctctggggcggcgctgcggcttcccagatgctgatcgacggcgggatgatgtttggccacaggctgatgccaaggccgctgtag                                                                                                                                                    <  2:703123‑M1/1‑1 (MQ=255)   acagtcggatcagccaagcgaactgggcaggatgaacagtgtgcctaccagcatgaagccttggctctggggcggcgctgcggcttcccagatgctgatcgacggcgggatgatgtttggccacaggctgatgccaaggccgctgtaGcc                                                                                                                                                  <  2:925707‑M1/3‑1 (MQ=255)         ccGCAAATCGCCGCCCGCTGGTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑Att                                                                                                                                           >  1:776757/1‑150 (MQ=255)              aaTCGCCGCCCGCTGGTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCt                                                                                                                                      <  1:1144984/150‑1 (MQ=255)               aTCGCCGCCCGCTGGTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTg                                                                                                                                     <  1:152228/150‑1 (MQ=255)                tCGCCGCCCGCTGGTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTAAATCTGGCCCAG‑ATTTTCCTgg                                                                                                                                    >  1:65667/1‑150 (MQ=255)                             gTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCt                                                                                                                       <  1:812443/150‑1 (MQ=255)                              ttCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCtt                                                                                                                      >  2:784290/1‑150 (MQ=255)                              ttCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCtt                                                                                                                      <  2:1050546/150‑1 (MQ=255)                              tgcAGCATGCACAACCTGCTCTAGTTCATGGCGGTGCCGATCCTGGGGCTGGTGACGTGCTACGGGCTGCTACGGGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCtt                                                                                                                      <  1:925652/148‑1 (MQ=255)                                  gCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCt                                                                                                                                      >  2:1178544/1‑130 (MQ=255)                                  gCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCt                                                                                                                                      <  1:1178544/130‑1 (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)                                             cTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTgg                                                                                                       <  1:717029/150‑1 (MQ=255)                                                ctctGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCa                                                                                                    >  1:586796/1‑150 (MQ=255)                                                     gTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAAcat                                                                                               <  1:300198/150‑1 (MQ=255)                                                      ttCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGc                                                                                                                                  <  1:1183687/114‑1 (MQ=255)                                                      ttCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGc                                                                                                                                  >  2:1183687/1‑114 (MQ=255)                                                         aTGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACatcatc                                                                                           <  2:251116/150‑1 (MQ=255)                                                         aTGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACatcatc                                                                                           <  2:798028/150‑1 (MQ=255)                                                                         tggtgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGc                                                                                                                   >  2:276931/1‑110 (MQ=255)                                                                         tggtgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGc                                                                                                                   <  1:276931/110‑1 (MQ=255)                                                                            tgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATccc                                                                                         >  1:868184/1‑133 (MQ=255)                                                                            tgctggtgACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATccc                                                                                         <  2:868184/133‑1 (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                                         <  2:776757/150‑1 (MQ=255)                                                                                                           cGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAgg                                         <  1:631284/150‑1 (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                      >  1:671598/1‑150 (MQ=255)                                                                                                                              tACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGcaca                      <  1:598459/150‑1 (MQ=255)                                                                                                                               acacGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCacac                     >  2:1256811/1‑150 (MQ=255)                                                                                                                                  cGCCGTTCTTGCTGACCCTTGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCacac                     >  1:806382/1‑147 (MQ=255)                                                                                                                                  cGCCGTTCTTGCTGACCCTTGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCacac                     <  2:806382/147‑1 (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                                                                         >  2:1123700/1‑80 (MQ=255)                                                                                                                                                 cccTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATc                                                                         <  1:1123700/80‑1 (MQ=255)                                                                                                                                                  ccTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTc  >  2:714903/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                   TGGCCTACCCGCAAATCGCCGCCCGCTGGTTCAGCATGCACAACCTGCTCTGGTTCATGCCGGTGCCGATCCTGGTGCTGGTGACGTGCTACGGGCTGCTACGTGCCGTGGCACGCAACGCGCACTACACGCCGTTCTTGCTGACCCTGGCCCAG‑ATTTTCCTGGGCTACAGCGGCCTTGGCATCAGCCTGTGGCCAAACATCATCCCGCCGTCGATCAGCATCTGGGAAGCCGCAGCGCCGCCCCAGAGCCAAGGCTTCATGCTGGTAGGCACACTGTTCATCCTGCCCAGTTC  >  NC_002947/3776057‑3776351

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.