New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 1397234 =164 (1.050)56 (0.360) 11/132 22.0 0.27 coding (1116/1578 nt) RCAP_rcc01307 hypothetical protein
?NC_014034 = 1397936 144 (0.610)intergenic (+240/+1658) RCAP_rcc01307/RCAP_rcc01309 hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

GCGCGTGCGCGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC...............................................................................  <  NC_014034/1397278‑1397234
...............................................................................GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAGA  <  NC_014034/1397936‑1397892
                                             ||||||||||||||||||||||||||||||||||                                             
tgcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:3209574/11‑101 (MQ=0)
tgcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:999628/11‑101 (MQ=0)
tgcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:1578890/11‑101 (MQ=0)
 gcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCG                        >  1:948913/10‑101 (MQ=0)
  gggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       <  1:2768590/93‑1 (MQ=0)
  cggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  1:1029870/9‑101 (MQ=0)
  cggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  1:3249901/9‑101 (MQ=0)
  cggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  2:1868317/9‑101 (MQ=0)
   ggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGG                      <  2:1878752/94‑1 (MQ=0)
     cgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGG                    <  1:1403224/96‑1 (MQ=1)
     cgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGG                    >  1:3368537/6‑101 (MQ=1)
      gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:2698902/97‑1 (MQ=1)
      gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:2781279/97‑1 (MQ=1)
      gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:3881684/97‑1 (MQ=1)
      gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  1:4333310/97‑1 (MQ=1)
      gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   >  1:4104686/5‑101 (MQ=1)
       ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCCCCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  2:4592278/98‑1 (MQ=0)
       ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCTATCCACGCCCCCGCGGGGGGA                  <  1:2642608/98‑1 (MQ=0)
       ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  2:129795/98‑1 (MQ=1)
       ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  1:732437/98‑1 (MQ=1)
        cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGgg                 >  2:3285940/3‑99 (MQ=1)
        cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGgg                 >  2:3645967/3‑99 (MQ=1)
        cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  2:2501011/99‑1 (MQ=1)
        cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 >  1:4326623/3‑101 (MQ=1)
        cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  1:4012192/99‑1 (MQ=1)
        cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  1:1627564/99‑1 (MQ=1)
         gGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:416133/100‑1 (MQ=1)
         gGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:535910/100‑1 (MQ=1)
          ggtcgTTCGATCCACGCCCCCGGGGGGGGAGCGACCACCGGCCTGACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:3131705/96‑1 (MQ=0)
          GGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGTCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:566111/101‑1 (MQ=1)
          GGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:3511552/101‑1 (MQ=1)
          GGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:2890673/101‑1 (MQ=1)
           GTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA              >  1:3443481/1‑101 (MQ=1)
           GTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA              >  2:394976/1‑101 (MQ=1)
            TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC             >  2:708896/1‑101 (MQ=1)
            TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC             >  2:1076338/1‑101 (MQ=1)
             GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACT            <  2:2796313/101‑1 (MQ=32)
             GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGANCNACT            >  1:1314756/1‑101 (MQ=1)
              ttcCGATCCACGCCCCCGGGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCTATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           <  2:760971/98‑1 (MQ=0)
              TTTCGATCCACGCCCCCGCGGGGGGAGCGACCCCCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           <  1:1503479/101‑1 (MQ=1)
              TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           >  1:2800545/1‑101 (MQ=1)
              TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           <  1:4535998/101‑1 (MQ=1)
               TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          <  1:1929326/101‑2 (MQ=1)
               TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          >  1:1535494/1‑100 (MQ=1)
               TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          >  2:439538/1‑100 (MQ=1)
               TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          <  1:3856527/101‑2 (MQ=1)
                TCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaa         <  1:2635635/101‑3 (MQ=1)
                TCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaa         <  1:2222085/101‑3 (MQ=1)
                 CGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaat        >  1:3400467/1‑98 (MQ=1)
                    TCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatctt     <  2:4072194/101‑7 (MQ=1)
                     CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  1:2860000/1‑94 (MQ=1)
                     CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  2:3194019/1‑94 (MQ=1)
                     CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  1:3209641/1‑94 (MQ=1)
                      CACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttga   <  2:605887/101‑9 (MQ=1)
                       cCGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttgac  <  1:3519410/100‑10 (MQ=1)
                       ACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttgac  <  1:4369775/101‑10 (MQ=1)
                                             ||||||||||||||||||||||||||||||||||                                             
GCGCGTGCGCGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC...............................................................................  <  NC_014034/1397278‑1397234
...............................................................................GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAGA  <  NC_014034/1397936‑1397892

Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG