New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 392436 =45 (0.240)33 (0.180) 24/174 15.7 0.46 intergenic (‑84/+59) RCAP_rcc00363/trmD hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
?NC_014034 = 2330277 32 (0.150)intergenic (+252/+60) RCAP_rcc02161/mrcA hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

GATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCGGCCGCCGGTC  >  NC_014034/392336‑392533
                                                                                                     |                                                                                                      
gATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAata                                                                                                        >  2:1618732/1‑101 (MQ=255)
gATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAata                                                                                                        <  2:3787410/101‑1 (MQ=255)
gATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAata                                                                                                        <  1:656939/101‑1 (MQ=255)
 aTCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAatat                                                                                                       <  2:2010353/101‑1 (MQ=255)
 aTCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAatat                                                                                                       >  1:2512484/1‑101 (MQ=255)
 aTCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAatat                                                                                                       <  2:3631484/101‑1 (MQ=255)
  tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATc                                                                                                      <  2:2655884/101‑1 (MQ=255)
  tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATc                                                                                                      <  1:579124/101‑1 (MQ=255)
  tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATc                                                                                                      <  1:976865/101‑1 (MQ=255)
  tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATc                                                                                                      <  2:364959/101‑1 (MQ=255)
  tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATc                                                                                                      >  1:2753752/1‑101 (MQ=255)
   ccGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATcc                                                                                                     <  2:626536/101‑1 (MQ=255)
   ccGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATcc                                                                                                     <  1:771119/101‑1 (MQ=255)
    cGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATccc                                                                                                    >  2:4030578/1‑101 (MQ=255)
    cGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATccc                                                                                                    >  2:2904013/1‑101 (MQ=255)
     ggggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCg                                                                                                   >  1:2736524/1‑101 (MQ=255)
     ggggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCg                                                                                                   <  2:3673870/101‑1 (MQ=255)
      gggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCgg                                                                                                  <  2:4097172/101‑1 (MQ=255)
      gggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCgg                                                                                                  <  2:213243/101‑1 (MQ=255)
       ggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCggg                                                                                                 <  2:2289419/101‑1 (MQ=255)
         aCGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCggggg                                                                                               >  1:2540407/1‑101 (MQ=255)
          cGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCgggggg                                                                                              >  2:2915092/1‑100 (MQ=255)
          cGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGt                                                                                              <  2:639960/101‑1 (MQ=255)
          cGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGt                                                                                              <  2:3276306/101‑1 (MQ=255)
          cGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGt                                                                                              <  1:2325717/101‑1 (MQ=255)
            gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTc.c                                                                                           <  2:2805464/101‑1 (MQ=255)
            gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTc.c                                                                                           <  2:813908/101‑1 (MQ=255)
             ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cg                                                                                          <  2:3766840/101‑1 (MQ=255)
             ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cg                                                                                          <  2:2793156/101‑1 (MQ=255)
             ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cg                                                                                          <  1:1610610/101‑1 (MQ=255)
               aTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cggg                                                                                        <  1:2849769/101‑1 (MQ=255)
               aTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cggg                                                                                        >  1:1568017/1‑101 (MQ=255)
               aTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cggg                                                                                        <  1:3954191/101‑1 (MQ=255)
                tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGTGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                       <  1:1962671/101‑1 (MQ=255)
                tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                       >  1:3147335/1‑101 (MQ=255)
                tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                       <  1:1176040/101‑1 (MQ=255)
                tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                       <  2:1545299/101‑1 (MQ=255)
                tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                       <  1:4030839/101‑1 (MQ=255)
                 cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTACCTCAAATATCCCGGGGGTC.Cggggg                                                                                      >  1:2547077/1‑101 (MQ=255)
                    aaaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCgg                                                                                   <  1:4125650/101‑1 (MQ=255)
                     aaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGa                                                                                  >  2:2659420/1‑101 (MQ=255)
                      aTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAg                                                                                 <  1:3480705/101‑1 (MQ=255)
                       tCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGc                                                                                <  1:3156965/101‑1 (MQ=255)
                       tCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CCGGGGCGGacc                                                                                >  1:4195807/1‑99 (MQ=255)
                        cccTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcc                                                                               <  2:25883/101‑1 (MQ=255)
                        cccTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcc                                                                               >  2:845307/1‑101 (MQ=255)
                          ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcccc                                                                             <  1:1054498/101‑1 (MQ=255)
                          ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcccc                                                                             >  1:3105347/1‑101 (MQ=255)
                          ctccgTGTTACCCCGCTACACTACGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATAGCCCGGGGGTC.GCGGGGCGGAGcccc                                                                             <  2:1202450/101‑1 (MQ=25)
                             ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc...gg                                                                       >  2:769280/1‑101 (MQ=255)
                             ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc...gg                                                                       >  1:1704039/1‑101 (MQ=255)
                             ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc...gg                                                                       >  1:2471801/1‑101 (MQ=255)
                             ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc...gg                                                                       >  1:736046/1‑101 (MQ=255)
                              ttGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc...ggc                                                                      >  2:1240050/1‑101 (MQ=255)
                               tGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc...ggcg                                                                     >  1:2642247/1‑101 (MQ=255)
                                gTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc...ggcgg                                                                    >  1:3517381/1‑101 (MQ=255)
                                   aCCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCggggg                                                                 >  2:1959911/1‑99 (MQ=255)
                                       cgcAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCgggggggcc                                                             >  2:156752/1‑95 (MQ=255)
                                        gcAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCggggggccgc                                                            >  1:3166499/1‑94 (MQ=255)
                                        gcAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCggggggccgc                                                            >  2:2277071/1‑94 (MQ=255)
                                          aaGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCgggggggcgcgg                                                          >  2:570466/1‑92 (MQ=255)
                                             acctgtggggccAAACCGGGAGGGAAATGGGCGGGCCTTTTCATTTTCCCTAAAATACCCGGGGGGCC.CGGGGGCGGACCCCCC...GGCGGGTCGCCTCGgcg                                                        <  2:2779980/91‑1 (MQ=12)
                                                      cccAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGGGGGCCCGgcgcgccgcgggg                                              >  2:4065/1‑92 (MQ=18)
                                                       caaaccc.GGAGGAAAAAGGGCAGCCCTTTTCATCTTGCCTAAAATACCCGGGGGGCC.GGGGGGCGGACCCCCC...GGCGGGTCGCCTCGGCGCAGCCGAGGCg                                             <  2:2736318/96‑1 (MQ=16)
                                                                gAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGGGGCCCCGGCGCGGCCGGgggggaaaaaac                                     >  1:2240591/1‑91 (MQ=18)
                                                                 aGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGGGGCCCCGGCGCGGCCCCGGCGgaaaacaac                                    >  2:2111482/1‑95 (MQ=18)
                                                                            cAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGGGGCGCCGGCGCCGCCGCGGCGGGAACAACTGCCGAACCtc.t                        >  2:15990/1‑101 (MQ=14)
                                                                                      cATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGGCGGCCCGGGGGCGCCCGGGGGGAAACACCTGGCCAACCTC.Tcccccccacc              >  1:3145008/1‑94 (MQ=2)
                                                                                         cTTGCCCCAAAAGCCCCGGGGGGCGGGGGGGGGGCCCCCCC...GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCg            <  1:1251340/101‑1 (MQ=21)
                                                                                         attctcgcAAAAATCCCGGGGGGG.GGGGGGGGGCGCCCCCCCGGGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATc              <  1:1960037/94‑1 (MQ=16)
                                                                                                 aaaTATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGGCGCCCCGGGGCCGCCGAGGGGGAAAAAACTGCCGGACTTC.TCCCCCCAAACCCgccccccgc   >  1:4106576/1‑98 (MQ=9)
                                                                                                   atatCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGGCGGCCCGGCGCCGGCGGGGGGGAAACACCTTCCGCACTTCTTCCCCCAAACCAGCCCCCCggcc  >  2:3848414/1‑99 (MQ=2)
                                                                                                     |                                                                                                      
GATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC...GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCGGCCGCCGGTC  >  NC_014034/392336‑392533

Base quality scores:  ATCG  < 3 ≤  ATCG  < 26 ≤  ATCG  < 32 ≤  ATCG  < 35 ≤  ATCG  < 41 ≤  ATCG