New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 = 218584555 (0.240)34 (0.150) 20/194 23.8 0.42 intergenic (+118/‑387) mtlK/RCAP_rcc02028 mannitol 2‑dehydrogenase/FeoA family protein
?NC_014034 2330182 = 37 (0.160)intergenic (+157/+155) RCAP_rcc02161/mrcA hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

CCGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.G.CCCCGCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGAACCG.CCCCTTTCACCT  >  NC_014034/2185746‑2185942
                                                                                                     |                                                                                                  
ccGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.G.ccccc                                                                                                   <  1:3782910/101‑2 (MQ=255)
    gaCAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.G.cccccgcac                                                                                               <  2:1765710/100‑6 (MQ=255)
      cAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCAccc                                                                                              <  1:3252886/101‑1 (MQ=255)
        ggcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCAccccc                                                                                            <  2:1784012/101‑1 (MQ=255)
        ggcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCAccccc                                                                                            <  2:2176261/101‑1 (MQ=255)
           ggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCAcccccggc                                                                                         <  1:2363493/101‑4 (MQ=255)
            gcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCAcccccggcg                                                                                        <  1:601575/101‑5 (MQ=255)
            gcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCACCCCCCgcg                                                                                        >  1:519227/1‑99 (MQ=255)
              cccGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTa                                                                                     <  2:3271817/101‑1 (MQ=255)
               ccGCTCCCGCCCGGGCGGGGCGGCCGGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGCCCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTAt                                                                                    <  1:152806/101‑1 (MQ=25)
               ccGCTCCCCCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTAt                                                                                    <  1:4456021/101‑1 (MQ=37)
                cGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTTtt                                                                                   <  1:1749015/101‑1 (MQ=37)
                cGCCCCCCCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTAtt                                                                                   <  1:1749016/101‑1 (MQ=25)
                 gCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCACCCCCCgcggattt                                                                                   >  1:3177367/1‑94 (MQ=37)
                     cctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATcc                                                                              >  2:4238734/1‑101 (MQ=255)
                        ccggggcgggGCCGCCCGATGGGCAAAGCGTTTGCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCaa                                                                           <  2:607047/98‑1 (MQ=21)
                        cccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCaa                                                                           <  1:1778061/101‑1 (MQ=255)
                           gggcgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGaa                                                                        <  2:3924496/101‑1 (MQ=255)
                              cgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGaaaaa                                                                     <  1:814826/101‑1 (MQ=255)
                               ggggCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAag                                                                    <  1:544237/101‑1 (MQ=255)
                               ggggCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAag                                                                    <  2:3119799/101‑1 (MQ=255)
                                     gccTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGGGCC.G.CCCCCCCCCCCCCCGCGGGTTTTTCCCCAAaaaaaaaaacgg                                                              >  2:2859695/1‑94 (MQ=255)
                                      ccTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGc                                                             >  2:2119210/1‑101 (MQ=255)
                                       cTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCt                                                            <  1:3265158/101‑1 (MQ=255)
                                        tGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCtt                                                           <  2:856432/101‑1 (MQ=255)
                                         gATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTg                                                          >  1:2347984/1‑101 (MQ=255)
                                         gATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCCCC.G.CCCCCGCCCCCCCCGCGTATTTATCCCAAGAAAAAGCAGCGGCttt                                                          >  2:1732477/1‑100 (MQ=255)
                                              gCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCg                                                     <  1:428203/101‑1 (MQ=255)
                                                aaaGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGaa                                                   <  2:1744444/101‑1 (MQ=255)
                                                 aaGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGCAg                                                  >  2:4396335/1‑101 (MQ=37)
                                                 aaGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAg                                                  <  2:2127560/101‑1 (MQ=255)
                                                  aGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGGTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGcccccgaag                                                 >  1:978463/1‑96 (MQ=37)
                                                      gTTTCGCCTCGGCGGTGCCGAGGCGCCCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCtt                                             <  1:210947/101‑1 (MQ=37)
                                                      gTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCtt                                             <  1:1470529/101‑1 (MQ=255)
                                                      gTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCtt                                             <  1:918315/101‑1 (MQ=255)
                                                       tttCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTg                                            <  1:3781134/101‑1 (MQ=255)
                                                       tttCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTg                                            <  2:171009/101‑1 (MQ=255)
                                                        ttCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGt                                           <  2:472515/101‑1 (MQ=255)
                                                        ttCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGt                                           <  2:4219766/101‑1 (MQ=255)
                                                          cGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGttt                                         <  1:2149102/101‑1 (MQ=255)
                                                          cGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGttt                                         <  1:4268351/101‑1 (MQ=255)
                                                             cTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGttttga                                      <  1:2028005/101‑3 (MQ=37)
                                                             cTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGttttga                                      <  1:2260589/101‑3 (MQ=37)
                                                               cggcggTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGttttgatg                                    <  1:1782658/101‑5 (MQ=37)
                                                                 gcggTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGc                                 <  1:2152105/101‑1 (MQ=37)
                                                                  cggTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGca                                <  2:1512858/101‑1 (MQ=37)
                                                                   ggTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGccc                               >  1:1352495/1‑99 (MQ=25)
                                                                   ggTGCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGcac                               <  1:827531/101‑1 (MQ=37)
                                                                      gCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAg                            <  2:2841915/101‑1 (MQ=37)
                                                                      gCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAg                            <  2:1030814/101‑1 (MQ=37)
                                                                      gCCGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAg                            <  1:2725082/101‑1 (MQ=37)
                                                                       ccGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGa                           <  2:3397668/101‑1 (MQ=37)
                                                                        cGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGaa                          <  2:4425561/101‑1 (MQ=37)
                                                                        cGAGGCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGaa                          <  1:641860/101‑1 (MQ=37)
                                                                           ggCGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACg                       <  2:2131358/101‑1 (MQ=37)
                                                                             cGACCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGcc                     <  2:2606674/101‑1 (MQ=37)
                                                                               aCCCTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGa                   <  1:3408880/101‑1 (MQ=37)
                                                                                cccTGCGGGGGCTCCAC.CCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGaa                  <  1:1087045/101‑1 (MQ=37)
                                                                                 ccTGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAAc                 <  2:1203007/101‑1 (MQ=37)
                                                                                   tGCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCg               <  2:1605340/101‑1 (MQ=37)
                                                                                    gCGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCCAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.c             >  2:3681964/1‑101 (MQ=25)
                                                                                     cGGGGGCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.cc            >  1:1677143/1‑101 (MQ=37)
                                                                                       ggggCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACCAGAAACGCCGAACCC.cccc          >  1:1312641/1‑101 (MQ=25)
                                                                                       ggggCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.cccc          <  1:2813353/101‑1 (MQ=37)
                                                                                          gCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.CCCCctt       <  1:2590385/101‑1 (MQ=37)
                                                                                          gCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.CCCCctt       <  1:1843519/101‑1 (MQ=37)
                                                                                          gCTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.CCCCctt       <  2:502260/101‑1 (MQ=37)
                                                                                           cTCC.GCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.CCCCcttt      <  1:1488086/101‑2 (MQ=37)
                                                                                             tccgcccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.CCCCctttc     >  1:2330710/6‑99 (MQ=37)
                                                                                              ccgcccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCa     <  2:2213473/97‑1 (MQ=37)
                                                                                              ccgcccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.CCCCctttcc    >  1:1797228/5‑98 (MQ=38)
                                                                                                gcccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCAcc   <  1:4220803/99‑1 (MQ=38)
                                                                                                 cccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCACCt  <  2:3119675/100‑1 (MQ=38)
                                                                                                 cccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCACCt  <  2:4541455/100‑1 (MQ=38)
                                                                                                     |                                                                                                  
CCGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCGGGGGCTCC.G.CCCCGCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGAACCG.CCCCTTTCACCT  >  NC_014034/2185746‑2185942

Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG