New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4466973	36 (0.650)	3 (0.060)	3/246	NT	7.4%	coding (716/1362 nt)	nhaA‑II	Na(+)/H(+) antiporter NhaA
	?	NC_002947	= 4466996	40 (0.750)					coding (739/1362 nt)	nhaA‑II	Na(+)/H(+) antiporter NhaA

CTTGATTACACCGGCTTCGGCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGATGCCAGCGACCTCATG  >  NC_002947/4466834‑4467121                                                                                                                                             |                                                                                                                                                     cTTGATTACACCGGCTTCGGCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCt                                                                                                                                             >  5:362739/1‑149 (MQ=255)    gATTACCCCGGCTTCGGCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTc                                                                                                                                            <  4:273584/147‑1 (MQ=255)        acacCGGCTTCGGCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAgg                                                                                                                                       <  6:362739/148‑1 (MQ=255)         cacCGGCTTAGGCGTTGCAGTGATCGGACTGCTAATGCTGATCGGGCTTAAGAAGATCGGAGTGGGTTCAGCCTACGCCAATGTAATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCTCACACCCGAAACACGCAggag                                                                                                                                     >  5:55900/1‑147 (MQ=255)          acCGGCTTCGGCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGCCCCTCGCAGGcgt                                                                                                                                    >  2:89386/1‑149 (MQ=255)                ttCGGCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCt                                                                                                                              <  3:172740‑M2/149‑2 (MQ=255)                    gCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCtgggc                                                                                                                          >  8:279298‑M2/1‑144 (MQ=255)                         gCAGTGATCGGCCTGCTATTGGCGATCGGGCGTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCAgcacgacgcctgcgagggtcgggtgggcgccg                                                                                                                      <  4:245268‑M1/148‑33 (MQ=255)                          cAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCtgatg                                                                                                                    <  3:98990/149‑1 (MQ=255)                           aGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCtgatga                                                                                                                   <  4:172740/149‑1 (MQ=255)                            gTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCAgcacgacgcctgcgagggtcgggtgggcgccggtc                                                                                                                   <  7:263371‑M1/148‑36 (MQ=255)                            gTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCAgcacgacgcctgcgagggtcgggtgggcgccggtc                                                                                                                   >  8:263371‑M1/1‑113 (MQ=255)                               aTCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTGCTTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGaca                                                                                                                 <  1:89386/148‑1 (MQ=255)                                        cTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACGGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCAcct                                                                                                       <  6:55900/148‑2 (MQ=255)                                          aaTGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGacac                                                                                                                >  3:215685/1‑137 (MQ=255)                                          aaTGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGacac                                                                                                                <  4:215685/137‑1 (MQ=255)                                           aTGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAAt                                                                                                   >  5:302489/1‑149 (MQ=255)                                                gATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGa                                                                                              >  5:218294/1‑149 (MQ=255)                                                               gaTCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCAc                                                                               >  1:248833/1‑149 (MQ=255)                                                                  cGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTg                                                                             >  7:310026/1‑148 (MQ=255)                                                                    gAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGAc                                                                          <  2:248833/149‑1 (MQ=255)                                                                    gAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGAc                                                                          >  1:317217/1‑149 (MQ=255)                                                                         ggTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCAt                                                                     >  3:320731/1‑149 (MQ=255)                                                                           ttCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGacac                                                                                                                >  6:161041/1‑104 (MQ=255)                                                                           ttCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGacac                                                                                                                <  5:161041/104‑1 (MQ=255)                                                                                ccTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGGTGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGc                                                              >  5:100998/1‑149 (MQ=255)                                                                                            tCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTAcc                                                                 <  3:300528/134‑1 (MQ=255)                                                                                            tCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCAACTGGACGCCATTAcc                                                                 >  4:300528/1‑134 (MQ=255)                                                                                              aTTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAAtt                                                <  6:218294/149‑1 (MQ=255)                                                                                                tCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGc                                              >  8:282596/1‑149 (MQ=255)                                                                                                  ccGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCt                                             <  5:235206/148‑1 (MQ=255)                                                                                                   cGGTGCGATCGTCTGGCTGGGCATCGTG‑TTGACCGGCGGCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTgg                                           <  3:125828/149‑1 (MQ=255)                                                                                                           tCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCGGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGgcgcgc                                    >  2:264329/1‑148 (MQ=255)                                                                                                                  gctggGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCg                                                               <  8:294633/114‑1 (MQ=255)                                                                                                                  gctggGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCg                                                               >  7:294633/1‑114 (MQ=255)                                                                                                                    tggGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCt                          >  8:125087/1‑149 (MQ=255)                                                                                                                      ggCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGa                        <  3:178574/149‑1 (MQ=255)                                                                                                                         aTCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGc                      >  3:111692/1‑148 (MQ=255)                                                                                                                              g‑ttgACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGGTGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGGCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAg                   <  6:100998/146‑1 (MQ=255)                                                                                                                              g‑ttgACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCTCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGAt                 <  4:320731/148‑1 (MQ=255)                                                                                                                                  gACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCtgggcgccggtcaacaagatgcccagccagacgatcgcaccgggaatgacataggcgtaggctgaacccactccgatcttctgaagcccgatcaccattagcaggccgatcac              >  8:263371‑M2/1‑35 (MQ=255)                                                                                                                                  gACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCtgggcgccggtcaacaagatgcccagccagacgatcgcaccgggaatgacataggcgtaggctgaacccactccgatcttctgaagcccgatcaccattagcaggccgatcac              <  7:263371‑M2/148‑114 (MQ=255)                                                                                                                                     cGGCGCCCACCCGACCCTCGCAGGCGTCGTGCtgggcgccggtcaacaagatgcccagccagacgatcgcaccgggaatgacataggcgtaggctgaacccactccgatcttctgacgcccgatcgccaatagcaggccgatcactgc           <  4:245268‑M2/148‑117 (MQ=255)                                                                                                                                      ggCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGATGCCAGCGa         <  8:310026/149‑1 (MQ=255)                                                                                                                                         gcCCAgcacgacgcctgcgagggtcgggtgggcgccggtcaacaagatgcccagccagacgatcgcaccgggaatgacataggcgtaggctgaacccactccgatcttctgaagcccgatcaccattagcaggccgatcactgcaacgc      >  8:279298‑M1/1‑5 (MQ=255)                                                                                                                                         gcCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGa                        >  6:134163/1‑131 (MQ=255)                                                                                                                                         gcCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGa                        <  5:134163/131‑1 (MQ=255)                                                                                                                                         gcCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGATGCCAGCGACCt      >  2:229006/1‑149 (MQ=255)                                                                                                                                           ccACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGATGCCAGCGACCTCa    >  5:82373/1‑149 (MQ=255)                                                                                                                                           ccACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGATGCCAGCGACCTCa    >  1:139890/1‑149 (MQ=255)                                                                                                                                            cACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGATGCCAGCGACCTCAt   <  6:302489/149‑1 (MQ=255)                                                                                                                                             agcacgacgcctgcgagggtcgggtgggcgccggtcaacaagatgcccagccagacgatcgcaccgggaatgacataggcgtaggctgaacccactccgatcttctgaagcccgatcaccattagcaggccgatcactgcaacgccgaa  <  3:172740‑M1/149‑149 (MQ=255)                                                                                                                                             |                                                                                                                                                     CTTGATTACACCGGCTTCGGCGTTGCAGTGATCGGCCTGCTAATGGTGATCGGGCTTCAGAAGATCGGAGTGGGTTCAGCCTACGCCTATGTCATTCCCGGTGCGATCGTCTGGCTGGGCATCTTG‑TTGACCGGCGCCCACCCGACCCTCGCAGGCGTCGTGCTGGGCCTGATGACACCTGTCACCGCAATGCCGATGCGTGAGCGCCCACTGGACGCCATTACCCGCTTCACCGGCGAATTGCTGGGGCGCGCCAAAGCGCCTGAGCAAGATGCCAGCGACCTCATG  >  NC_002947/4466834‑4467121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.