New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 1396903 =180 (1.150)59 (0.380) 8/132 24.4 0.27 coding (785/1578 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.

CGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC...............................................................................  <  NC_014034/1396948‑1396903
................................................................................GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAGA  <  NC_014034/1397936‑1397892
                                              ||||||||||||||||||||||||||||||||||                                             
ctgcgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCG                          <  1:3608683/96‑1 (MQ=0)
ctgcgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCG                          <  2:1073579/96‑1 (MQ=0)
ctgcgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCG                          >  1:2166188/6‑101 (MQ=0)
 tgcgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:999628/5‑101 (MQ=0)
 tgcgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:1578890/5‑101 (MQ=0)
 tgcgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:3209574/5‑101 (MQ=0)
  gcgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCG                        >  1:948913/4‑101 (MQ=0)
   ggGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       <  1:2768590/99‑1 (MQ=0)
   cgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  1:3249901/3‑101 (MQ=0)
   cgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  2:1868317/3‑101 (MQ=0)
   cgGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  1:1029870/3‑101 (MQ=0)
    gGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGG                      <  2:1878752/100‑1 (MQ=0)
      CGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGG                    <  1:1403224/101‑1 (MQ=1)
      CGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGG                    >  1:3368537/1‑101 (MQ=1)
       gccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   >  1:4104686/7‑101 (MQ=1)
       gccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  1:4333310/95‑1 (MQ=1)
       gccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:3881684/95‑1 (MQ=1)
       gccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:2781279/95‑1 (MQ=1)
       gccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:2698902/95‑1 (MQ=1)
        ccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCCCCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  2:4592278/96‑1 (MQ=0)
        ccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCTATCCACGCCCCCGCGGGGGGA                  <  1:2642608/96‑1 (MQ=0)
        ccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  2:129795/96‑1 (MQ=1)
        ccgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  1:732437/96‑1 (MQ=1)
         cgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGgg                 >  2:3645967/5‑99 (MQ=1)
         cgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGgg                 >  2:3285940/5‑99 (MQ=1)
         cgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  1:1627564/97‑1 (MQ=1)
         cgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  2:2501011/97‑1 (MQ=1)
         cgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  1:4012192/97‑1 (MQ=1)
         cgggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 >  1:4326623/5‑101 (MQ=1)
          gggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:535910/98‑1 (MQ=1)
          gggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:416133/98‑1 (MQ=1)
           ggtcgTTCGATCCACGCCCCCGGGGGGGGAGCGACCACCGGCCTGACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:3131705/96‑1 (MQ=0)
           ggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGTCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:566111/99‑1 (MQ=1)
           ggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:3511552/99‑1 (MQ=1)
           ggTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:2890673/99‑1 (MQ=1)
            gTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA              >  2:394976/2‑101 (MQ=1)
            gTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA              >  1:3443481/2‑101 (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           <  1:4535998/101‑1 (MQ=1)
               TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           >  1:2800545/1‑101 (MQ=1)
                TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          <  1:3856527/101‑2 (MQ=1)
                TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          >  2:439538/1‑100 (MQ=1)
                TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          >  1:1535494/1‑100 (MQ=1)
                TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          <  1:1929326/101‑2 (MQ=1)
                 TCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaa         <  1:2222085/101‑3 (MQ=1)
                 TCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaa         <  1:2635635/101‑3 (MQ=1)
                  CGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaat        >  1:3400467/1‑98 (MQ=1)
                     TCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatctt     <  2:4072194/101‑7 (MQ=1)
                      CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  2:3194019/1‑94 (MQ=1)
                      CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  1:2860000/1‑94 (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)
                                              ||||||||||||||||||||||||||||||||||                                             
CGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC...............................................................................  <  NC_014034/1396948‑1396903
................................................................................GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAGA  <  NC_014034/1397936‑1397892

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