New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 1397632 =200 (1.020)44 (0.230) 9/134 28.0 0.18 coding (1514/1578 nt) RCAP_rcc01307 hypothetical protein
?NC_014034 = 1397934 188 (0.650)intergenic (+238/+1660) RCAP_rcc01307/RCAP_rcc01309 hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

ACCGGAACTCTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC..........................................................................  <  NC_014034/1397678‑1397632
................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGA  <  NC_014034/1397934‑1397894
                                               |||||||||||||||||||||||||||||||||                                         
agagccccggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCG                      >  1:1361164/11‑101 (MQ=0)
  agcccctgTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGG                    <  1:935169/93‑1 (MQ=0)
    ccccggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGG                  >  1:2181086/7‑101 (MQ=0)
    ccccggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGG                  >  2:1110004/7‑101 (MQ=0)
     cccggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGG                 <  2:3011021/96‑1 (MQ=1)
     cccggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATACACGCCCCCGCGGGGGG                 >  2:5192638/6‑101 (MQ=0)
      ccggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGg                >  2:4852853/5‑100 (MQ=1)
      ccggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGA                <  1:4078220/97‑1 (MQ=1)
      caggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGg                >  1:4776734/5‑100 (MQ=1)
       cggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAG               <  2:5706767/98‑1 (MQ=1)
       cggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAG               >  2:2829983/4‑101 (MQ=1)
       cggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAG               <  1:3513749/98‑1 (MQ=1)
        ggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGC              <  2:5157848/99‑1 (MQ=1)
        ggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGC              <  2:2760915/99‑1 (MQ=1)
        ggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGC              <  2:2338114/99‑1 (MQ=1)
        ggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGC              >  1:1320285/3‑101 (MQ=1)
        ggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGC              >  1:1938260/3‑101 (MQ=1)
        ggTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGC              >  1:4114767/3‑101 (MQ=1)
         gTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCG             <  2:4646957/100‑1 (MQ=1)
         gTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCG             >  2:461384/2‑101 (MQ=1)
         gTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCG             <  2:2277579/100‑1 (MQ=1)
          TGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGGGCGA            >  2:1286268/1‑101 (MQ=1)
          TGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA            >  2:5540432/1‑101 (MQ=1)
           GTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC           >  1:2642265/1‑101 (MQ=1)
           GTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC           <  1:3485296/101‑1 (MQ=1)
            TAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc          <  2:902527/101‑2 (MQ=1)
             AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcg         <  1:8645/101‑3 (MQ=1)
             AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcg         >  2:3559995/1‑99 (MQ=1)
             AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcg         <  2:3475397/101‑3 (MQ=1)
              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcgg        <  1:2873016/101‑4 (MQ=1)
               TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggg       >  2:4361005/1‑97 (MQ=1)
               TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggg       <  1:4257652/101‑5 (MQ=1)
                TTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcgggg      <  1:4669965/101‑6 (MQ=1)
                TTCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGGTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcgggg      <  1:1842902/101‑6 (MQ=0)
                 TCGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggc     >  1:5074197/1‑95 (MQ=1)
                  CGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggcc    <  1:3719194/101‑8 (MQ=0)
                  CGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggcc    >  1:5312254/1‑94 (MQ=0)
                  CGATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggcc    >  2:5557210/1‑94 (MQ=0)
                  CGATCCACGCCCCCGCGGGGGGAGCGACCACGTCAAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGgggcc    >  1:3268649/1‑96 (MQ=0)
                   GATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggcca   <  2:5744647/101‑9 (MQ=0)
                   GATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggcca   >  2:952884/1‑93 (MQ=0)
                   GATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggcca   <  1:3697366/101‑9 (MQ=0)
                    ATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggccaa  <  2:4653207/101‑10 (MQ=0)
                    ATCCACGCCCCCGCGGGGGGAGCGACCACGTCCAGCGCATAGGCCGTTGCCGGGTCAGTTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggggccaa  >  1:4372076/1‑92 (MQ=0)
                                               |||||||||||||||||||||||||||||||||                                         
ACCGGAACTCTGTAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC..........................................................................  <  NC_014034/1397678‑1397632
................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGA  <  NC_014034/1397934‑1397894

Base quality scores:  ATCG  < 3 ≤  ATCG  < 21 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG