New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4253409	43 (1.020)	3 (0.070)	3/246	NT	6.5%	coding (270/1407 nt)	rocE	amino acid permease RocE
	?	NC_002947	= 4253453	45 (1.120)					coding (226/1407 nt)	rocE	amino acid permease RocE

CGAACAGCACCACCACGAACAGCGCCGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGATCGCGCCCACCGGCCCGCCCTGA  >  NC_002947/4253261‑4253556                                                                                                                                                     |                                                                                                                                                    cGAACAGCACCCCCACGAACAGCGCCGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGCACCCGGTG                                                                                                                                                     >  5:57208‑M1/1‑149 (MQ=255)        caccaccacGAACAGAGCCGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGc                                                                                                                                              >  8:173050/1‑149 (MQ=255)           caccacGAACAGCGCCGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCaa                                                                                                                                           >  4:94019/1‑149 (MQ=255)                 gAACAGCGCCGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCgg                                                                                                                                                <  1:101478/138‑1 (MQ=255)                 gAACAGCGCCGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCgg                                                                                                                                                >  2:101478/1‑138 (MQ=255)                          cGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGt                                                                                                                            <  3:94019/149‑1 (MQ=255)                           gACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAAt                                                                                                                                          <  3:261776/134‑1 (MQ=255)                           gACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAAt                                                                                                                                          >  4:261776/1‑134 (MQ=255)                                     aGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAAACCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAAc                                                                                                                 >  5:169022/1‑149 (MQ=255)                                        tCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGtccggttcgtttcaggcccacgccaccaaatacattggc                                                                                                              >  2:5369‑M1/1‑110 (MQ=255)                                         cGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAAc                                                                                                             >  6:234734/1‑149 (MQ=255)                                               cTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCCGGCCAATGTATTTGGTGGCGTGGGCCTGAAAAGAACCGGAca                                                                                                       <  1:210998‑M2/149‑3 (MQ=255)                                                  cGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGtccggttcgtttcaggcccacgccaccaaatacattggcccggccaccg                                                                                                    <  1:5369‑M1/149‑50 (MQ=255)                                                  cGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGtccggttcgtttcaggcccacgccaccaaatacattggcccggccacc                                                                                                     <  1:82287‑M1/148‑49 (MQ=255)                                                  cGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGaaa                                                                                                                  >  6:13614/1‑135 (MQ=255)                                                  cGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGaaa                                                                                                                  <  5:13614/135‑1 (MQ=255)                                                         cAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTg                                                                                             >  2:151933/1‑149 (MQ=255)                                                          aGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGc                                                                                            <  7:173050/149‑1 (MQ=255)                                                           gCGGGTCATCAACAAGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCa                                                                                           >  1:155554/1‑149 (MQ=255)                                                            cGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCAc                                                                                          <  7:96858/149‑1 (MQ=255)                                                                tcatcaACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGaaa                                                                                                                  <  1:73447/121‑1 (MQ=255)                                                                tcatcaACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGaaa                                                                                                                  >  2:73447/1‑121 (MQ=255)                                                                tcatcaACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGCTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGAc                                                                                      <  5:234734/149‑1 (MQ=255)                                                                            cGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGGCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAgg                                                                          <  2:155554/149‑1 (MQ=255)                                                                            cGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAgg                                                                          >  4:206124/1‑149 (MQ=255)                                                                                          tCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAg                                                            >  1:105560/1‑149 (MQ=255)                                                                                          tCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAg                                                            >  6:175132/1‑149 (MQ=255)                                                                                          tCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAg                                                            >  6:179050/1‑149 (MQ=255)                                                                                          tCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGAACCGACAGCTCGCCCAgg                                                                          >  1:136486/1‑135 (MQ=255)                                                                                          tCCAGGCCTACGGTGGGGGCCCAGCTCATCCAGTCCACCCAGCCTATCATGAACCGGGGGGCCGGGCCAATGTATTTGGGGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCCgg                                                                          <  2:136486/135‑1 (MQ=255)                                                                                            cAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAgg                                                           >  7:37833/1‑148 (MQ=255)                                                                                             aGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTa                                                         >  5:99761/1‑149 (MQ=255)                                                                                                ccTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCTGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACAt                                                      <  6:99761/149‑1 (MQ=255)                                                                                                  tACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGAc                                                                                      >  8:10013/1‑115 (MQ=255)                                                                                                    cGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAg                                                   <  3:206124/148‑1 (MQ=255)                                                                                                            gCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGTCCATCACCAGGTACATCAGCAAGCCTGc                                          <  1:151933/149‑1 (MQ=255)                                                                                                            gCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGc                                          >  3:221190/1‑149 (MQ=255)                                                                                                              ccAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGa                                        >  1:210252/1‑149 (MQ=255)                                                                                                                  cTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAg                                    <  5:175132/149‑1 (MQ=255)                                                                                                                  cTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAg                                    <  5:179050/149‑1 (MQ=255)                                                                                                                    cATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAgg                                   >  5:255881/1‑148 (MQ=255)                                                                                                                     aTCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAg                                    <  6:169022/146‑1 (MQ=255)                                                                                                                     aTCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGt                                  >  1:227011/1‑148 (MQ=255)                                                                                                                       ccAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAg                               >  3:226686/1‑149 (MQ=255)                                                                                                                              acCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGAt                        >  8:2863/1‑149 (MQ=255)                                                                                                                                ccAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGATcg                      >  4:58809/1‑149 (MQ=255)                                                                                                                                  aGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGATcgcg                    <  4:226686/149‑1 (MQ=255)                                                                                                                                      gATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGATCGCGCCCa                >  1:147037/1‑149 (MQ=255)                                                                                                                                             aaCCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGATCGCGCCCACCGgccc         <  6:255881/149‑1 (MQ=255)                                                                                                                                               cccGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGATCGCGCCCACCGgcccgc       >  1:139319/1‑149 (MQ=255)                                                                                                                                                 cGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGAcaccgggttcatgatcggctgggtgtactggatgagctgggccaccaccgtaggcctggagttcaccgctgccggcatgttgatgacccgctggttcccg     <  1:5369‑M2/149‑101 (MQ=255)                                                                                                                                                  ggTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGAcaccgggttcatgatcggctgggtgtactggatgagctgggccaccaccgtaggcctggagttcaccgctgccggcatgttgatgacccgctggttcccg     <  1:82287‑M2/148‑101 (MQ=255)                                                                                                                                                    tgtccggttcttttcaggcccacgccaccaaatacattggccgggccaccgggttcatgatcggctgggtgtactggatgagctgggccaccaccgtaggcctggagttcaccgctgccggcatgttgatgacccgctggttcccggag  <  1:210998‑M1/149‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CGAACAGCACCACCACGAACAGCGCCGACCAGTACCAGATCGGCACCTCCGGGAACCAGCGGGTCATCAACATGCCGGCAGCGGTGAACTCCAGGCCTACGGTGGTGGCCCAGCTCATCCAGTACACCCAGCCGATCATGAACCCGGTGGCCGGGCCAATGTATTTGGTGGCGTGGGCCTGAAACGAACCGGACACCGGCATCTGCACCGACAGCTCGCCCAGGCAGACCATCACCAGGTACATCAGCAAGCCTGCGACCAGGTAAGCCAGGATCGCGCCCACCGGCCCGCCCTGA  >  NC_002947/4253261‑4253556

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.