New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5331738	42 (0.860)	3 (0.060)	3/240	NT	6.4%	intergenic (‑130/‑81)	PP_4692/dksA	aspartate/tyrosine/aromatic aminotransferase/RNA polymerase‑binding transcription factor DksA
	?	NC_002947	= 5331762	48 (1.020)					intergenic (‑154/‑57)	PP_4692/dksA	aspartate/tyrosine/aromatic aminotransferase/RNA polymerase‑binding transcription factor DksA

TCAAATGGGTCTAAACTGGAGATTCTACCTCTGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAGGGTGAGGAGTACATGGGTGAGC  >  NC_002947/5331618‑5331909                                                                                                                                                 |                                                                                                                                                     tcAAATGGGTCTAAACTGGAGATTCTACCTCTGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTcgccg                                                                                                                                                 >  1:491998‑M2/1‑145 (MQ=255)         gTCTAAACTGGAGATTCTACCTCTGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGa                                                                                                                                         >  1:112763/1‑150 (MQ=255)             aaaCTGGAGATTCTACCTCTGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCAt                                                                                                                                     >  1:231622/1‑150 (MQ=255)                  ggAGATTCTACCTCTGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTgc                                                                                                                               <  1:1148214/150‑1 (MQ=255)                         cTACCTCTGCACACCACCGAACGTACCGCTCAGGCCGGCGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTgg                                                                                                                        >  2:443183/1‑150 (MQ=255)                           aCCTCTGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGAt                                                                                                                      >  2:448218/1‑150 (MQ=255)                             ctctGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTg                                                                                                                         <  1:1271932/145‑1 (MQ=255)                             ctctGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTg                                                                                                                         >  2:1271932/1‑145 (MQ=255)                               ctGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTgcg                                                                                                                              <  1:1139692/138‑1 (MQ=255)                               ctGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTgcg                                                                                                                              >  2:1139692/1‑138 (MQ=255)                                   acacCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCa                                                                                                                    <  1:999833/144‑1 (MQ=255)                                   acacCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCa                                                                                                                    >  2:999833/1‑144 (MQ=255)                                       caccGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGAtgagtgag                                                                                                          >  2:597688/1‑150 (MQ=255)                                       caccGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGAtgagtgag                                                                                                          >  2:1096264/1‑150 (MQ=255)                                              cGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGt                                                                                                   <  2:112763/150‑1 (MQ=255)                                                  ccGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTAt                                                                                               <  2:144345/150‑1 (MQ=255)                                                   cGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTAtt                                                                                              <  2:994162/150‑1 (MQ=255)                                                   cGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTAtt                                                                                              >  2:804013/1‑150 (MQ=255)                                                   cGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTAtt                                                                                              <  1:597688/150‑1 (MQ=255)                                                        aGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGt                                                                                         <  1:448218/150‑1 (MQ=255)                                                         ggCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTc                                                                                        <  1:1088635/150‑1 (MQ=255)                                                           ccGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCa                                                                                      <  1:1169735/150‑1 (MQ=255)                                                              gtgtCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCAccc                                                                                   >  1:942263/1‑150 (MQ=255)                                                                 tCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAg                                                                                <  1:443183/150‑1 (MQ=255)                                                                             aTCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAATGAGAGGCGGGCTATTCATGTCCACCCTAGAAGAGCAAAAAg                                                                    >  2:8481/1‑150 (MQ=255)                                                                                                ccccGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCAtt                                                                                                                          >  1:224141/1‑77 (MQ=255)                                                                                                ccccGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCAtt                                                                                                                          <  2:224141/77‑1 (MQ=255)                                                                                                 cccGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTcgccg                                                                                                                                                 >  1:960115‑M2/1‑49 (MQ=255)                                                                                                 cccGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTcgccg                                                                                                                                                 <  2:960115‑M2/54‑6 (MQ=255)                                                                                                 cccGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGCCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATggg                                                <  1:804013/150‑1 (MQ=255)                                                                                                  ccGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATgggg                                               >  1:794172/1‑150 (MQ=255)                                                                                                        tatctGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCAc                                         <  2:1134367/150‑1 (MQ=255)                                                                                                         atctGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGCTAG‑CCACCGCGGCGCATTGGGTCAGAGGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCAcc                                        >  1:1121272/1‑150 (MQ=255)                                                                                                            tGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTa                                     >  2:325654/1‑150 (MQ=255)                                                                                                             ggTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGaaaa                                                                            <  2:853515/110‑1 (MQ=255)                                                                                                             ggTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGaaaa                                                                            >  1:853515/1‑110 (MQ=255)                                                                                                               tAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCa                                                             >  1:870010/1‑123 (MQ=255)                                                                                                               tAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCa                                                             <  2:870010/123‑1 (MQ=255)                                                                                                                  gTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTcgccgaacttaccagatagatcgggggtgcgctaccccgcccgatcctgctaattgacaccggcctgagcggtacgttcggtggtgtgcagaggtagaatctccagtttagacccatt                                <  2:931690‑M2/150‑119 (MQ=255)                                                                                                                  gTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGga                               >  1:715664/1‑150 (MQ=255)                                                                                                                   ttCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGCGAGGCGGTCGATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGgag                              >  1:477322/1‑150 (MQ=255)                                                                                                                   ttCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGgag                              >  2:545227/1‑150 (MQ=255)                                                                                                                        cggcTCGCAGTCGCAGGGCCGGCGGTcgccgaacttaccagatagatcgggggtgcgctaccccgcccgatcctgctaattgacaccggcctgagcggtacgtt                                                                        >  2:883717‑M2/1‑26 (MQ=255)                                                                                                                        cggcTCGCAGTCGCAGGGCCGGCGGTcgccgaacttaccagatagatcgggggtgcgctaccccgcccgatcctgctaattgacaccggcctgagcggtacgtt                                                                        <  1:883717‑M2/104‑79 (MQ=255)                                                                                                                         ggcTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAg                        <  1:1096264/150‑1 (MQ=255)                                                                                                                          gcTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCaaaa                                                                      >  2:387290/1‑103 (MQ=255)                                                                                                                          gcTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCaaaa                                                                      <  1:387290/103‑1 (MQ=255)                                                                                                                            tcgcagtcgcagGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGt                                                                                         <  2:700781/82‑1 (MQ=255)                                                                                                                            tcgcagtcgcagGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGt                                                                                         >  1:700781/1‑82 (MQ=255)                                                                                                                              gcagtcgcagGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCAcc                                        <  1:431035/129‑1 (MQ=255)                                                                                                                              gcagtcgcagGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCAcc                                        >  2:431035/1‑129 (MQ=255)                                                                                                                               cagtcgcagGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAGGGTgag                  <  2:1121272/150‑1 (MQ=255)                                                                                                                                 gacgcagGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTAGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAGGGTgagga                <  2:466765/148‑1 (MQ=255)                                                                                                                                    gcagGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAGGGTGAGGAGTa             <  1:545227/150‑1 (MQ=255)                                                                                                                                             gcggTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAGGGTGAGGAGTACATGGGTGa    <  2:231622/150‑1 (MQ=255)                                                                                                                                               ggTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAGGGTGAGGAGTACATGGGTGAGc  <  1:690688/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     TCAAATGGGTCTAAACTGGAGATTCTACCTCTGCACACCACCGAACGTACCGCTCAGGCCGGTGTCAATTAGCAGGATCGGGCGGGGTAGCGCACCCCCGATCTATCTGGTAAGTTCGGCGGCTCGCAGTCGCAGGGCCGGCGGTCGCCGGAGATGGAGCATC‑CTGCGCATTGGATCAGATGAGTGAGAGGCGGTCTATTCATGTCCACCCTAGAAAAGCAAAAAGCCAACCAGAATCTTTATGGGGTTGCACCCTATCAGGAGACCAAGGGTGAGGAGTACATGGGTGAGC  >  NC_002947/5331618‑5331909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.