New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 6098913	50 (0.950)	3 (0.060)	3/228	NT	6.3%	coding (232/867 nt)	PP_5350	RpiR family transcriptional regulator
	?	NC_002947	= 6098932	43 (0.880)					coding (213/867 nt)	PP_5350	RpiR family transcriptional regulator

GCAGCGCCTGCGGATCAAGGTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCATGACGGCAGCCGGGTCGAGCAGCACGTGGTCG  >  NC_002947/6098790‑6099079                                                                                                                                               |                                                                                                                                                     gCAGCGCCTGCGGATCAAGGTGCTCGCGCACTTCCATCAGGGTGTGAAGGGGGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCgccagct                                                                                                                                               <  1:329819‑M2/150‑8 (MQ=255)      gcCTGCGGATCAAGGTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCgccag                                                                                                                                                 >  1:276916‑M2/1‑138 (MQ=255)      gcCTGCGGATCAAGGTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCgccag                                                                                                                                                 <  2:276916‑M2/143‑6 (MQ=255)          gCGGATCAAGGTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAgcttcagcttca                                                                                                                                      <  1:383778/150‑1 (MQ=255)            ggATCAAGGTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAgg                                                                                                                                    <  2:783324/150‑1 (MQ=255)                   ggTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTgg                                                                                                                              <  2:1335274/149‑1 (MQ=255)                   ggTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTgg                                                                                                                              >  1:1335274/1‑149 (MQ=255)                    gTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGaa                                                                                                                            <  1:146855/150‑1 (MQ=255)                          gcgcACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGa                                                                                                                      <  2:437908/150‑1 (MQ=255)                                    agcAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGCACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATg                                                                                                           >  1:634033/3‑150 (MQ=255)                                    aTCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCagcttcagcttc                                                                                                                                       >  1:1245902/1‑123 (MQ=255)                                    aTCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCagcttcagcttc                                                                                                                                       <  2:1245902/123‑1 (MQ=255)                                     tCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCgc                                                                                                                                                    <  2:896426‑M2/109‑3 (MQ=255)                                     tCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCgc                                                                                                                                                    >  1:896426‑M2/1‑107 (MQ=255)                                     tCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATgg                                                                                                          <  1:803946/150‑1 (MQ=255)                                        gggTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGccc                                                                                                       <  1:569856/150‑1 (MQ=255)                                         ggTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCg                                                                                                      <  1:989002/150‑1 (MQ=255)                                              gCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTACGTCATCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGa                                                                                                 >  1:1021823/1‑150 (MQ=255)                                               cAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGa                                                                                                                      <  2:206297/129‑1 (MQ=255)                                               cAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGa                                                                                                                      >  1:206297/1‑129 (MQ=255)                                                      gtgtCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACg                                                                                         >  2:883036/1‑150 (MQ=255)                                                         tCGAAGAACTTCAGGCTGTAGTCGGCGCCCGAATCGTATTCGTGAATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGCAACCCGAGCA‑GCAAATGGCCCGACAGAAACGCCCGATg                                                                                      >  2:648865/1‑150 (MQ=255)                                                           gAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGt                                                                                    >  2:966737/1‑150 (MQ=255)                                                            aaGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAACTTCGCGTTGCAGAAGCCCGAGTG‑GCCAATGGCCCGGCAGAAACGCACGATGGTc                                                                                   <  1:218876/150‑1 (MQ=255)                                                              gATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATgg                                                                                                          <  1:257333/125‑1 (MQ=255)                                                              gATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATgg                                                                                                          >  2:257333/1‑125 (MQ=255)                                                               aTCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGc                                                                                >  1:920045/1‑150 (MQ=255)                                                                  ttCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCcagcttca                                                                                                                                            >  2:649361/1‑88 (MQ=255)                                                                  ttCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCcagcttca                                                                                                                                            <  1:649361/88‑1 (MQ=255)                                                                  ttCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCa                                                                             >  1:414901/1‑150 (MQ=255)                                                                    cAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACt                                                                           <  1:817341/150‑1 (MQ=255)                                                                      ggCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGa                                                                         >  2:835333/1‑150 (MQ=255)                                                                       gCTGTAGTCGGTGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCTGGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGGCGGCTCACTGAt                                                                        >  1:865611/1‑150 (MQ=255)                                                                       gCTGTAGTCGGCGACCGAATCGTCTTGGTGGATGGCGACCTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTCCGCCAGCTTCAGCTTCAGGCCCTGGAAGCCCGAGCA‑GCAAACGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGAt                                                                        >  1:475281/1‑150 (MQ=255)                                                                       gCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCa                                                                                           >  1:1178174/1‑131 (MQ=255)                                                                       gCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCa                                                                                           <  2:1178174/131‑1 (MQ=255)                                                                       gCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGAt                                                                        >  2:981317/1‑150 (MQ=255)                                                                         tGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCACAGCGAT‑GCCCGGCAGAAACGCACGATGGTCGGCTCACTGATAc                                                                      >  1:727336/1‑150 (MQ=255)                                                                           tAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATAccc                                                                    >  2:1388463/1‑150 (MQ=255)                                                                            aGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCa                                                                   <  2:926642/150‑1 (MQ=255)                                                                                        aaTCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCgcc                                                                                                                                                   >  2:460201‑M2/1‑56 (MQ=255)                                                                                        aaTCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCgcc                                                                                                                                                   <  1:460201‑M2/59‑4 (MQ=255)                                                                                                   tGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATg                                            <  2:861279/150‑1 (MQ=255)                                                                                                        ggCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCt                                       <  1:981317/150‑1 (MQ=255)                                                                                                           gAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCtgtg                                    >  2:595012/1‑150 (MQ=255)                                                                                                             aCTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCa                                  >  1:663502/1‑150 (MQ=255)                                                                                                                  ccGAAGCTGGCCCCGGCAGCCAGGCTTTGCgccagcttcggtcagttcgccatccacgaagacgattcggtcgccgactacagcctgaagatcttcgacaccaccctgcacaccctgatggaagtgcgcgagcaccttgatccgcaggcg                              <  1:534124‑M2/150‑121 (MQ=255)                                                                                                                   cGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTgc                                                           <  2:469496/119‑1 (MQ=255)                                                                                                                   cGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTgc                                                           >  1:469496/1‑119 (MQ=255)                                                                                                                    gAAGCTGGCCCCGGCAGCCAGGCTTTGCgccagcttcggtcagttcgccatccacgaagacgattcggtcgccgactacagcctgaagatcttcgacaccaccctgcacaccc                                                                 >  2:1423845‑M2/1‑28 (MQ=255)                                                                                                                    gAAGCTGGCCCCGGCAGCCAGGCTTTGCgccagcttcggtcagttcgccatccacgaagacgattcggtcgccgactacagcctgaagatcttcgacaccaccctgcacaccc                                                                 <  1:1423845‑M2/113‑86 (MQ=255)                                                                                                                     aaGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCATGACGGCa                          <  2:663502/150‑1 (MQ=255)                                                                                                                           gCCCCGGCAGCCAGGCTTTACGTTAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCATGACGGCAGCCggg                    <  2:329819/150‑1 (MQ=255)                                                                                                                                      cAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATCATCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCATGACGACAGCGGGGTCGaggagcgc         >  2:65956/1‑148 (MQ=255)                                                                                                                                       aGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCATGACGGCAGCCGGGTCGAGCAGCACg        >  1:1069446/1‑150 (MQ=255)                                                                                                                                           tttGCGCCAGCTTCAGCTTCAGGTAGTGGAAGCCCGAGCA‑GCCAATGGTCCTGCAGAAACGCACGCTGGCCAGCTCACTGCTAAGCTCGGTGGGCGCCAAATCGGCCATGGAGCTGTGCATGACGGCAGCCGGCTCGAGCAACACGTGGt    >  1:1169515/1‑150 (MQ=255)                                                                                                                                             tGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCATGACGGCAGCCGGGTCGAGCAGCACGTGGTCg  <  1:966737/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                     GCAGCGCCTGCGGATCAAGGTGCTCGCGCACTTCCATCAGGGTGTGCAGGGTGGTGTCGAAGATCTTCAGGCTGTAGTCGGCGACCGAATCGTCTTCGTGGATGGCGAACTGACCGAAGCTGGCCCCGGCAGCCAGGCTTTGCGCCAGCTTCAGCTTCAGGTCCTGGAAGCCCGAGCA‑GCCAATGGCCCGGCAGAAACGCACGATGGTCGGCTCACTGATACCCACGCTGTGCGCCAAATCGGCCATGGAGCTGTGCATGACGGCAGCCGGGTCGAGCAGCACGTGGTCG  >  NC_002947/6098790‑6099079

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.